Simulation of Heterogeneous Atom Probe Tip Shapes Evolution during Field Evaporation Using a Level Set Method and Different Evaporation Models

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

Xu, Zhijie; Li, Dongsheng; Xu, Wei

2015-04-01

In atom probe tomography (APT), accurate reconstruction of the spatial positions of field evaporated ions from measured detector patterns depends upon a correct understanding of the dynamic tip shape evolution and evaporation laws of component atoms. Artifacts in APT reconstructions of heterogeneous materials can be attributed to the assumption of homogeneous evaporation of all the elements in the material in addition to the assumption of a steady state hemispherical dynamic tip shape evolution. A level set method based specimen shape evolution model is developed in this study to simulate the evaporation of synthetic layered-structured APT tips. The simulation results ofmore » the shape evolution by the level set model qualitatively agree with the finite element method and the literature data using the finite difference method. The asymmetric evolving shape predicted by the level set model demonstrates the complex evaporation behavior of heterogeneous tip and the interface curvature can potentially lead to the artifacts in the APT reconstruction of such materials. Compared with other APT simulation methods, the new method provides smoother interface representation with the aid of the intrinsic sub-grid accuracy. Two evaporation models (linear and exponential evaporation laws) are implemented in the level set simulations and the effect of evaporation laws on the tip shape evolution is also presented.« less

An electrophysiological signature for proactive interference resolution in working memory.

PubMed

Du, Yingchun; Xiao, Zhuangwei; Song, Yan; Fan, Silu; Wu, Renhua; Zhang, John X

2008-08-01

We used event-related potentials (ERPs) to study the temporal dynamics of proactive interference in working memory. Participants performed a Sternberg item-recognition task to determine whether a probe was in a target memory set. Familiar negative probes were found to be more difficult to reject than less familiar ones. A fronto-central N2 component peaking around 300 ms post-probe-onset differentiated among target probes, familiar and less familiar non-target probes. The study identifies N2 as the ERP signature for proactive interference resolution. It also indicates that the resolution process occurs in the same time window as target/non-target discrimination and provides the first piece of electrophysiological evidence supporting a recent interference resolution model based on localization data [Jonides, J., Nee, D.E., 2006. Brain mechanisms of proactive interference in working memory. Neuroscience 139, 181-193].

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

PubMed Central

Greuter, Daniel; Loy, Alexander; Horn, Matthias; Rattei, Thomas

2016-01-01

probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase. PMID:26586809

SigReannot-mart: a query environment for expression microarray probe re-annotations.

PubMed

Moreews, François; Rauffet, Gaelle; Dehais, Patrice; Klopp, Christophe

2011-01-01

Expression microarrays are commonly used to study transcriptomes. Most of the arrays are now based on oligo-nucleotide probes. Probe design being a tedious task, it often takes place once at the beginning of the project. The oligo set is then used for several years. During this time period, the knowledge gathered by the community on the genome and the transcriptome increases and gets more precise. Therefore re-annotating the set is essential to supply the biologists with up-to-date annotations. SigReannot-mart is a query environment populated with regularly updated annotations for different oligo sets. It stores the results of the SigReannot pipeline that has mainly been used on farm and aquaculture species. It permits easy extraction in different formats using filters. It is used to compare probe sets on different criteria, to choose the set for a given experiment to mix probe sets in order to create a new one.

Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest.

PubMed

Saka, Ernur; Harrison, Benjamin J; West, Kirk; Petruska, Jeffrey C; Rouchka, Eric C

2017-12-06

Since the introduction of microarrays in 1995, researchers world-wide have used both commercial and custom-designed microarrays for understanding differential expression of transcribed genes. Public databases such as ArrayExpress and the Gene Expression Omnibus (GEO) have made millions of samples readily available. One main drawback to microarray data analysis involves the selection of probes to represent a specific transcript of interest, particularly in light of the fact that transcript-specific knowledge (notably alternative splicing) is dynamic in nature. We therefore developed a framework for reannotating and reassigning probe groups for Affymetrix® GeneChip® technology based on functional regions of interest. This framework addresses three issues of Affymetrix® GeneChip® data analyses: removing nonspecific probes, updating probe target mapping based on the latest genome knowledge and grouping probes into gene, transcript and region-based (UTR, individual exon, CDS) probe sets. Updated gene and transcript probe sets provide more specific analysis results based on current genomic and transcriptomic knowledge. The framework selects unique probes, aligns them to gene annotations and generates a custom Chip Description File (CDF). The analysis reveals only 87% of the Affymetrix® GeneChip® HG-U133 Plus 2 probes uniquely align to the current hg38 human assembly without mismatches. We also tested new mappings on the publicly available data series using rat and human data from GSE48611 and GSE72551 obtained from GEO, and illustrate that functional grouping allows for the subtle detection of regions of interest likely to have phenotypical consequences. Through reanalysis of the publicly available data series GSE48611 and GSE72551, we profiled the contribution of UTR and CDS regions to the gene expression levels globally. The comparison between region and gene based results indicated that the detected expressed genes by gene-based and region-based CDFs show high consistency and regions based results allows us to detection of changes in transcript formation.

Fine and Gross Motor Task Performance When Using Computer-Based Video Models by Students with Autism and Moderate Intellectual Disability

ERIC Educational Resources Information Center

Mechling, Linda C.; Swindle, Catherine O.

2013-01-01

This investigation examined the effects of video modeling on the fine and gross motor task performance by three students with a diagnosis of moderate intellectual disability (Group 1) and by three students with a diagnosis of autism spectrum disorder (Group 2). Using a multiple probe design across three sets of tasks, the study examined the…

Performance Comparison of High-Speed Dual-Pneumatic Vitrectomy Cutters during Simulated Vitrectomy with Balanced Salt Solution.

PubMed

Abulon, Dina Joy K; Buboltz, David C

2015-02-01

To measure flow rate of balanced salt solution and IOP during simulated vitrectomy using two sets of high-speed dual-pneumatic probes. A closed-model eye system measured IOP and flow rate of a balanced salt solution through infusion cannula. The Constellation Vision System was tested with two sets of high-speed dual-pneumatic probes (UltraVit 23-gauge and enhanced 25+-gauge 5000-cpm probes; UltraVit 23-gauge and enhanced 25+-gauge 7500-cpm probes; n = 6 each) under different vacuum levels and cut rates in three duty cycle modes. In both probe sets, flow rates were dependent on cut rate with the biased open and biased closed duty cycles. Flow rates were highest with the biased open duty cycle, lower with the 50/50 duty cycle, and lowest with the biased closed duty cycle. IOP, as expected, was inversely associated with flow rate using both probe sets. The 7500-cpm probes offer greater control and customization compared with 5000-cpm probes under certain experimental conditions. At maximum cut rates, performance of 7500-cpm probes was similar to that of 5000-cpm probes, suggesting that 7500-cpm probes may be used without sacrifice of flow rate and IOP stability. Customization of vitrectomy parameters allows greater surgeon control during vitrectomy and may expand the usefulness of vitrectomy probes.

Probing the toxicity of nanoparticles: a unified in silico machine learning model based on perturbation theory.

PubMed

Concu, Riccardo; Kleandrova, Valeria V; Speck-Planche, Alejandro; Cordeiro, M Natália D S

2017-09-01

Nanoparticles (NPs) are part of our daily life, having a wide range of applications in engineering, physics, chemistry, and biomedicine. However, there are serious concerns regarding the harmful effects that NPs can cause to the different biological systems and their ecosystems. Toxicity testing is an essential step for assessing the potential risks of the NPs, but the experimental assays are often very expensive and usually too slow to flag the number of NPs that may cause adverse effects. In silico models centered on quantitative structure-activity/toxicity relationships (QSAR/QSTR) are alternative tools that have become valuable supports to risk assessment, rationalizing the search for safer NPs. In this work, we develop a unified QSTR-perturbation model based on artificial neural networks, aimed at simultaneously predicting general toxicity profiles of NPs under diverse experimental conditions. The model is derived from 54,371 NP-NP pair cases generated by applying the perturbation theory to a set of 260 unique NPs, and showed an accuracy higher than 97% in both training and validation sets. Physicochemical interpretation of the different descriptors in the model are additionally provided. The QSTR-perturbation model is then employed to predict the toxic effects of several NPs not included in the original dataset. The theoretical results obtained for this independent set are strongly consistent with the experimental evidence found in the literature, suggesting that the present QSTR-perturbation model can be viewed as a promising and reliable computational tool for probing the toxicity of NPs.

[Research progress of probe design software of oligonucleotide microarrays].

PubMed

Chen, Xi; Wu, Zaoquan; Liu, Zhengchun

2014-02-01

DNA microarray has become an essential medical genetic diagnostic tool for its high-throughput, miniaturization and automation. The design and selection of oligonucleotide probes are critical for preparing gene chips with high quality. Several sets of probe design software have been developed and are available to perform this work now. Every set of the software aims to different target sequences and shows different advantages and limitations. In this article, the research and development of these sets of software are reviewed in line with three main criteria, including specificity, sensitivity and melting temperature (Tm). In addition, based on the experimental results from literatures, these sets of software are classified according to their applications. This review will be helpful for users to choose an appropriate probe-design software. It will also reduce the costs of microarrays, improve the application efficiency of microarrays, and promote both the research and development (R&D) and commercialization of high-performance probe design software.

Phase I Experimental Testing of a Generic Submarine Model in the DSTO Low Speed Wind Tunnel

DTIC Science & Technology

2012-07-01

used during the tests , along with the test methodology . A sub-set of the data gathered is also presented and briefly discussed. Overall, the force...total pressure probe when positioned close to the model. 4. Results Selected results from the testing of the generic submarine model in the...Appendix B summaries the test conditions. 4.3.1 Smoke Generator and Probe An Aerotech smoke generator and probe were used for visualisation of

A new digitized reverse correction method for hypoid gears based on a one-dimensional probe

NASA Astrophysics Data System (ADS)

Li, Tianxing; Li, Jubo; Deng, Xiaozhong; Yang, Jianjun; Li, Genggeng; Ma, Wensuo

2017-12-01

In order to improve the tooth surface geometric accuracy and transmission quality of hypoid gears, a new digitized reverse correction method is proposed based on the measurement data from a one-dimensional probe. The minimization of tooth surface geometrical deviations is realized from the perspective of mathematical analysis and reverse engineering. Combining the analysis of complex tooth surface generation principles and the measurement mechanism of one-dimensional probes, the mathematical relationship between the theoretical designed tooth surface, the actual machined tooth surface and the deviation tooth surface is established, the mapping relation between machine-tool settings and tooth surface deviations is derived, and the essential connection between the accurate calculation of tooth surface deviations and the reverse correction method of machine-tool settings is revealed. Furthermore, a reverse correction model of machine-tool settings is built, a reverse correction strategy is planned, and the minimization of tooth surface deviations is achieved by means of the method of numerical iterative reverse solution. On this basis, a digitized reverse correction system for hypoid gears is developed by the organic combination of numerical control generation, accurate measurement, computer numerical processing, and digitized correction. Finally, the correctness and practicability of the digitized reverse correction method are proved through a reverse correction experiment. The experimental results show that the tooth surface geometric deviations meet the engineering requirements after two trial cuts and one correction.

Where do pulse oximeter probes break?

PubMed

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.

A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays

PubMed Central

2012-01-01

Background DNA microarrays are used both for research and for diagnostics. In research, Affymetrix arrays are commonly used for genome wide association studies, resequencing, and for gene expression analysis. These arrays provide large amounts of data. This data is analyzed using statistical methods that quite often discard a large portion of the information. Most of the information that is lost comes from probes that systematically fail across chips and from batch effects. The aim of this study was to develop a comprehensive model for hybridization that predicts probe intensities for Affymetrix arrays and that could provide a basis for improved microarray analysis and probe development. The first part of the model calculates probe binding affinities to all the possible targets in the hybridization solution using the Langmuir isotherm. In the second part of the model we integrate details that are specific to each experiment and contribute to the differences between hybridization in solution and on the microarray. These details include fragmentation, wash stringency, temperature, salt concentration, and scanner settings. Furthermore, the model fits probe synthesis efficiency and target concentration parameters directly to the data. All the parameters used in the model have a well-established physical origin. Results For the 302 chips that were analyzed the mean correlation between expected and observed probe intensities was 0.701 with a range of 0.88 to 0.55. All available chips were included in the analysis regardless of the data quality. Our results show that batch effects arise from differences in probe synthesis, scanner settings, wash strength, and target fragmentation. We also show that probe synthesis efficiencies for different nucleotides are not uniform. Conclusions To date this is the most complete model for binding on microarrays. This is the first model that includes both probe synthesis efficiency and hybridization kinetics/cross-hybridization. These two factors are sequence dependent and have a large impact on probe intensity. The results presented here provide novel insight into the effect of probe synthesis errors on Affymetrix microarrays; furthermore, the algorithms developed in this work provide useful tools for the analysis of cross-hybridization, probe synthesis efficiency, fragmentation, wash stringency, temperature, and salt concentration on microarray intensities. PMID:23270536

Probing flavor models with ^{ {76}}Ge-based experiments on neutrinoless double-β decay

NASA Astrophysics Data System (ADS)

Agostini, Matteo; Merle, Alexander; Zuber, Kai

2016-04-01

The physics impact of a staged approach for double-β decay experiments based on ^{ {76}}Ge is studied. The scenario considered relies on realistic time schedules envisioned by the Gerda and the Majorana collaborations, which are jointly working towards the realization of a future larger scale ^{ {76}}Ge experiment. Intermediate stages of the experiments are conceived to perform quasi background-free measurements, and different data sets can be reliably combined to maximize the physics outcome. The sensitivity for such a global analysis is presented, with focus on how neutrino flavor models can be probed already with preliminary phases of the experiments. The synergy between theory and experiment yields strong benefits for both sides: the model predictions can be used to sensibly plan the experimental stages, and results from intermediate stages can be used to constrain whole groups of theoretical scenarios. This strategy clearly generates added value to the experimental efforts, while at the same time it allows to achieve valuable physics results as early as possible.

Simulation and training of ultrasound supported anaesthesia: a low-cost approach

NASA Astrophysics Data System (ADS)

Schaaf, T.; Lamontain, M.; Hilpert, J.; Schilling, F.; Tolxdorff, T.

2010-03-01

The use of ultrasound imaging technology during techniques of peripheral nerve blockade offers several clinical benefits. Here we report on a new method to educate residents in ultrasound-guided regional anesthesia. The daily challenge for the anesthesiologists is the 3D angle-depending handling of the stimulation needle and the ultrasound probe while watching the 2D ultrasound image on the monitor. Purpose: Our approach describes how a computer-aided simulation and training set for ultrasound-guided regional anesthesia could be built based on wireless low-cost devices and an interactive simulation of a 2D ultrasound image. For training purposes the injection needle and the ultrasound probe are replaced by wireless Bluetooth-connected 3D tracking devices, which are embedded in WII-mote controllers (Nintendo-Brand). In correlation to the tracked 3D positions of the needle and transducer models the visibility and position of the needle should be simulated in the 2D generated ultrasound image. Conclusion: In future, this tracking and visualization software module could be integrated in a more complex training set, where complex injection paths could be trained based on a 3D segmented model and the training results could be part of a curricular e-learning module.

Probing Quark-Gluon-Plasma properties with a Bayesian model-to-data comparison

NASA Astrophysics Data System (ADS)

Cai, Tianji; Bernhard, Jonah; Ke, Weiyao; Bass, Steffen; Duke QCD Group Team

2016-09-01

Experiments at RHIC and LHC study a special state of matter called the Quark Gluon Plasma (QGP), where quarks and gluons roam freely, by colliding relativistic heavy-ions. Given the transitory nature of the QGP, its properties can only be explored by comparing computational models of its formation and evolution to experimental data. The models fall, roughly speaking, under two categories-those solely using relativistic viscous hydrodynamics (pure hydro model) and those that in addition couple to a microscopic Boltzmann transport for the later evolution of the hadronic decay products (hybrid model). Each of these models has multiple parameters that encode the physical properties we want to probe and that need to be calibrated to experimental data, a task which is computationally expensive, but necessary for the knowledge extraction and determination of the models' quality. Our group has developed an analysis technique based on Bayesian Statistics to perform the model calibration and to extract probability distributions for each model parameter. Following the previous work that applies the technique to the hybrid model, we now perform a similar analysis on a pure-hydro model and display the posterior distributions for the same set of model parameters. We also develop a set of criteria to assess the quality of the two models with respect to their ability to describe current experimental data. Funded by Duke University Goldman Sachs Research Fellowship.

Comparing student performance on paper- and computer-based math curriculum-based measures.

PubMed

Hensley, Kiersten; Rankin, Angelica; Hosp, John

2017-01-01

As the number of computerized curriculum-based measurement (CBM) tools increases, it is necessary to examine whether or not student performance can generalize across a variety of test administration modes (i.e., paper or computer). The purpose of this study is to compare math fact fluency on paper versus computer for 197 upper elementary students. Students completed identical sets of probes on paper and on the computer, which were then scored for digits correct, problems correct, and accuracy. Results showed a significant difference in performance between the two sets of probes, with higher fluency rates on the paper probes. Because decisions about levels of student support and interventions often rely on measures such as these, more research in this area is needed to examine the potential differences in student performance between paper-based and computer-based CBMs.

A novel dicyanoisophorone based red-emitting fluorescent probe with a large Stokes shift for detection of hydrazine in solution and living cells

NASA Astrophysics Data System (ADS)

Lv, Hongshui; Sun, Haiyan; Wang, Shoujuan; Kong, Fangong

2018-05-01

A novel dicyanoisophorone based fluorescent probe HP was developed to detect hydrazine. Upon the addition of hydrazine, probe HP displayed turn-on fluorescence in the red region with a large Stokes shift (180 nm). This probe exhibited high selectivity and high sensitivity to hydrazine in solution. The detection limit of HP was found to be 3.26 ppb, which was lower than the threshold limit value set by USEPA (10 ppb). Moreover, the probe was successfully applied to detect hydrazine in different water samples and living cells.

Luminescent probes for optical in vivo imaging

NASA Astrophysics Data System (ADS)

Texier, Isabelle; Josserand, Veronique; Garanger, Elisabeth; Razkin, Jesus; Jin, Zhaohui; Dumy, Pascal; Favrot, Marie; Boturyn, Didier; Coll, Jean-Luc

2005-04-01

Going along with instrumental development for small animal fluorescence in vivo imaging, we are developing molecular fluorescent probes, especially for tumor targeting. Several criteria have to be taken into account for the optimization of the luminescent label. It should be adapted to the in vivo imaging optical conditions : red-shifted absorption and emission, limited overlap between absorption and emission for a good signal filtering, optimized luminescence quantum yield, limited photo-bleaching. Moreover, the whole probe should fulfill the biological requirements for in vivo labeling : adapted blood-time circulation, biological conditions compatibility, low toxicity. We here demonstrate the ability of the imaging fluorescence set-up developed in LETI to image the bio-distribution of molecular probes on short times after injection. Targeting with Cy5 labeled holo-transferrin of subcutaneous TS/Apc (angiogenic murine breast carcinoma model) or IGROV1 (human ovarian cancer) tumors was achieved. Differences in the kinetics of the protein uptake by the tumors were evidenced. IGROV1 internal metastatic nodes implanted in the peritoneal cavity could be detected in nude mice. However, targeted metastatic nodes in lung cancer could only be imaged after dissection of the mouse. These results validate our fluorescence imaging set-up and the use of Cy5 as a luminescent label. New fluorescent probes based on this dye and a molecular delivery template (the RAFT molecule) can thus be envisioned.

The Visual Geophysical Exploration Environment: A Multi-dimensional Scientific Visualization

NASA Astrophysics Data System (ADS)

Pandya, R. E.; Domenico, B.; Murray, D.; Marlino, M. R.

2003-12-01

The Visual Geophysical Exploration Environment (VGEE) is an online learning environment designed to help undergraduate students understand fundamental Earth system science concepts. The guiding principle of the VGEE is the importance of hands-on interaction with scientific visualization and data. The VGEE consists of four elements: 1) an online, inquiry-based curriculum for guiding student exploration; 2) a suite of El Nino-related data sets adapted for student use; 3) a learner-centered interface to a scientific visualization tool; and 4) a set of concept models (interactive tools that help students understand fundamental scientific concepts). There are two key innovations featured in this interactive poster session. One is the integration of concept models and the visualization tool. Concept models are simple, interactive, Java-based illustrations of fundamental physical principles. We developed eight concept models and integrated them into the visualization tool to enable students to probe data. The ability to probe data using a concept model addresses the common problem of transfer: the difficulty students have in applying theoretical knowledge to everyday phenomenon. The other innovation is a visualization environment and data that are discoverable in digital libraries, and installed, configured, and used for investigations over the web. By collaborating with the Integrated Data Viewer developers, we were able to embed a web-launchable visualization tool and access to distributed data sets into the online curricula. The Thematic Real-time Environmental Data Distributed Services (THREDDS) project is working to provide catalogs of datasets that can be used in new VGEE curricula under development. By cataloging this curricula in the Digital Library for Earth System Education (DLESE), learners and educators can discover the data and visualization tool within a framework that guides their use.

DNA detection and single nucleotide mutation identification using SERS for molecular diagnostics and global health

NASA Astrophysics Data System (ADS)

Ngo, Hoan T.; Gandra, Naveen; Fales, Andrew M.; Taylor, Steve M.; Vo-Dinh, Tuan

2017-02-01

Nucleic acid-based molecular diagnostics at the point-of-care (POC) and in resource-limited settings is still a challenge. We present a sensitive yet simple DNA detection method with single nucleotide polymorphism (SNP) identification capability. The detection scheme involves sandwich hybridization of magnetic beads conjugated with capture probes, target sequences, and ultrabright surface-enhanced Raman Scattering (SERS) nanorattles conjugated with reporter probes. Upon hybridization, the sandwich probes are concentrated at the detection focus controlled by a magnetic system for SERS measurements. The ultrabright SERS nanorattles, consisting of a core and a shell with resonance Raman reporters loaded in the gap space between the core and the shell, serve as SERS tags for ultrasensitive signal detection. Specific DNA sequences of the malaria parasite Plasmodium falciparum and dengue virus 1 (DENV1) were used as the model marker system. Detection limit of approximately 100 attomoles was achieved. Single nucleotide polymorphism (SNP) discrimination of wild type malaria DNA and mutant malaria DNA, which confers resistance to artemisinin drugs, was also demonstrated. The results demonstrate the molecular diagnostic potential of the nanorattle-based method to both detect and genotype infectious pathogens. The method's simplicity makes it a suitable candidate for molecular diagnosis at the POC and in resource-limited settings.

Towards Open-World Person Re-Identification by One-Shot Group-Based Verification.

PubMed

Zheng, Wei-Shi; Gong, Shaogang; Xiang, Tao

2016-03-01

Solving the problem of matching people across non-overlapping multi-camera views, known as person re-identification (re-id), has received increasing interests in computer vision. In a real-world application scenario, a watch-list (gallery set) of a handful of known target people are provided with very few (in many cases only a single) image(s) (shots) per target. Existing re-id methods are largely unsuitable to address this open-world re-id challenge because they are designed for (1) a closed-world scenario where the gallery and probe sets are assumed to contain exactly the same people, (2) person-wise identification whereby the model attempts to verify exhaustively against each individual in the gallery set, and (3) learning a matching model using multi-shots. In this paper, a novel transfer local relative distance comparison (t-LRDC) model is formulated to address the open-world person re-identification problem by one-shot group-based verification. The model is designed to mine and transfer useful information from a labelled open-world non-target dataset. Extensive experiments demonstrate that the proposed approach outperforms both non-transfer learning and existing transfer learning based re-id methods.

PCR Amplicon Prediction from Multiplex Degenerate Primer and Probe Sets

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

Gardner, S. N.

2013-08-08

Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. Code is described to predict potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons.

GeneChip{sup {trademark}} screening assay for cystic fibrosis mutations

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

Cronn, M.T.; Miyada, C.G.; Fucini, R.V.

1994-09-01

GeneChip{sup {trademark}} assays are based on high density, carefully designed arrays of short oligonucleotide probes (13-16 bases) built directly on derivatized silica substrates. DNA target sequence analysis is achieved by hybridizing fluorescently labeled amplification products to these arrays. Fluorescent hybridization signals located within the probe array are translated into target sequence information using the known probe sequence at each array feature. The mutation screening assay for cystic fibrosis includes sets of oligonucleotide probes designed to detect numerous different mutations that have been described in 14 exons and one intron of the CFTR gene. Each mutation site is addressed by amore » sub-array of at least 40 probe sequences, half designed to detect the wild type gene sequence and half designed to detect the reported mutant sequence. Hybridization with homozygous mutant, homozygous wild type or heterozygous targets results in distinctive hybridization patterns within a sub-array, permitting specific discrimination of each mutation. The GeneChip probe arrays are very small (approximately 1 cm{sup 2}). There miniature size coupled with their high information content make GeneChip probe arrays a useful and practical means for providing CF mutation analysis in a clinical setting.« less

Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria.

PubMed

Jansen, G J; Wildeboer-Veloo, A C; Tonk, R H; Franks, A H; Welling, G W

1999-09-01

An automated microscopy-based method using fluorescently labelled 16S rRNA-targeted oligonucleotide probes directed against the predominant groups of intestinal bacteria was developed and validated. The method makes use of the Leica 600HR image analysis system, a Kodak MegaPlus camera model 1.4 and a servo-controlled Leica DM/RXA ultra-violet microscope. Software for automated image acquisition and analysis was developed and tested. The performance of the method was validated using a set of four fluorescent oligonucleotide probes: a universal probe for the detection of all bacterial species, one probe specific for Bifidobacterium spp., a digenus-probe specific for Bacteroides spp. and Prevotella spp. and a trigenus-probe specific for Ruminococcus spp., Clostridium spp. and Eubacterium spp. A nucleic acid stain, 4',6-diamidino-2-phenylindole (DAPI), was also included in the validation. In order to quantify the assay-error, one faecal sample was measured 20 times using each separate probe. Thereafter faecal samples of 20 different volunteers were measured following the same procedure in order to quantify the error due to individual-related differences in gut flora composition. It was concluded that the combination of automated microscopy and fluorescent whole-cell hybridisation enables distinction in gut flora-composition between volunteers at a significant level. With this method it is possible to process 48 faecal samples overnight, with coefficients of variation ranging from 0.07 to 0.30.

Loss and source mechanisms of Jupiter's radiation belts near the inner boundary of trapping regions

NASA Astrophysics Data System (ADS)

Santos-Costa, Daniel; Bolton, Scott J.; Becker, Heidi N.; Clark, George; Kollmann, Peter; Paranicas, Chris; Mauk, Barry; Joergensen, John L.; Adriani, Alberto; Thorne, Richard M.; Bagenal, Fran; Janssen, Mike A.; Levin, Steve M.; Oyafuso, Fabiano A.; Williamson, Ross; Adumitroaie, Virgil; Ingersoll, Andrew P.; Kurth, Bill; Connerney, John E. P.

2017-04-01

We have merged a set of physics-based and empirical models to investigate the energy and spatial distributions of Jupiter's electron and proton populations in the inner and middle magnetospheric regions. Beyond the main source of plasma (> 5 Rj) where interchange instability is believed to drive the radial transport of charged particles, the method originally developed by Divine and Garrett [J. Geophys. Res., 88, 6889-6903, 1983] has been adapted. Closer to the planet where field fluctuations control the radial transport, a diffusion theory approach is used. Our results for the equatorial and mid-latitude regions are compared with Pioneer and Galileo Probe measurements. Data collected along Juno's polar orbit allow us to examine the features of Jupiter's radiation environment near the inner boundary of trapping regions. Significant discrepancies between Juno (JEDI keV energy particles and high energy radiation environment measurements made by Juno's SRU and ASC star cameras and the JIRAM infrared imager) and Galileo Probe data sets and models are observed close to the planet. Our simulations of Juno MWR observations of Jupiter's electron-belt emission confirm the limitation of our model to realistically depict the energy and spatial distributions of the ultra-energetic electrons. In this paper, we present our modeling approach, the data sets and resulting data-model comparisons for Juno's first science orbits. We describe our effort to improve our models of electron and proton belts. To gain a physical understanding of the dissimilarities with observations, we revisit the magnetic environment and the mechanisms of loss and source in our models.

Mechanism-based biomarker gene sets for glutathione depletion-related hepatotoxicity in rats

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

Gao Weihua; Mizukawa, Yumiko; Nakatsu, Noriyuki

Chemical-induced glutathione depletion is thought to be caused by two types of toxicological mechanisms: PHO-type glutathione depletion [glutathione conjugated with chemicals such as phorone (PHO) or diethyl maleate (DEM)], and BSO-type glutathione depletion [i.e., glutathione synthesis inhibited by chemicals such as L-buthionine-sulfoximine (BSO)]. In order to identify mechanism-based biomarker gene sets for glutathione depletion in rat liver, male SD rats were treated with various chemicals including PHO (40, 120 and 400 mg/kg), DEM (80, 240 and 800 mg/kg), BSO (150, 450 and 1500 mg/kg), and bromobenzene (BBZ, 10, 100 and 300 mg/kg). Liver samples were taken 3, 6, 9 andmore » 24 h after administration and examined for hepatic glutathione content, physiological and pathological changes, and gene expression changes using Affymetrix GeneChip Arrays. To identify differentially expressed probe sets in response to glutathione depletion, we focused on the following two courses of events for the two types of mechanisms of glutathione depletion: a) gene expression changes occurring simultaneously in response to glutathione depletion, and b) gene expression changes after glutathione was depleted. The gene expression profiles of the identified probe sets for the two types of glutathione depletion differed markedly at times during and after glutathione depletion, whereas Srxn1 was markedly increased for both types as glutathione was depleted, suggesting that Srxn1 is a key molecule in oxidative stress related to glutathione. The extracted probe sets were refined and verified using various compounds including 13 additional positive or negative compounds, and they established two useful marker sets. One contained three probe sets (Akr7a3, Trib3 and Gstp1) that could detect conjugation-type glutathione depletors any time within 24 h after dosing, and the other contained 14 probe sets that could detect glutathione depletors by any mechanism. These two sets, with appropriate scoring systems, could be promising biomarkers for preclinical examination of hepatotoxicity.« less

Comparative mRNA analysis of behavioral and genetic mouse models of aggression.

PubMed

Malki, Karim; Tosto, Maria G; Pain, Oliver; Sluyter, Frans; Mineur, Yann S; Crusio, Wim E; de Boer, Sietse; Sandnabba, Kenneth N; Kesserwani, Jad; Robinson, Edward; Schalkwyk, Leonard C; Asherson, Philip

2016-04-01

Mouse models of aggression have traditionally compared strains, most notably BALB/cJ and C57BL/6. However, these strains were not designed to study aggression despite differences in aggression-related traits and distinct reactivity to stress. This study evaluated expression of genes differentially regulated in a stress (behavioral) mouse model of aggression with those from a recent genetic mouse model aggression. The study used a discovery-replication design using two independent mRNA studies from mouse brain tissue. The discovery study identified strain (BALB/cJ and C57BL/6J) × stress (chronic mild stress or control) interactions. Probe sets differentially regulated in the discovery set were intersected with those uncovered in the replication study, which evaluated differences between high and low aggressive animals from three strains specifically bred to study aggression. Network analysis was conducted on overlapping genes uncovered across both studies. A significant overlap was found with the genetic mouse study sharing 1,916 probe sets with the stress model. Fifty-one probe sets were found to be strongly dysregulated across both studies mapping to 50 known genes. Network analysis revealed two plausible pathways including one centered on the UBC gene hub which encodes ubiquitin, a protein well-known for protein degradation, and another on P38 MAPK. Findings from this study support the stress model of aggression, which showed remarkable molecular overlap with a genetic model. The study uncovered a set of candidate genes including the Erg2 gene, which has previously been implicated in different psychopathologies. The gene networks uncovered points at a Redox pathway as potentially being implicated in aggressive related behaviors. © 2016 Wiley Periodicals, Inc.

Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry

PubMed Central

Walker, Peter

2017-01-01

Abstract The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. PMID:28108663

The Use of Cell Phones to Address Safety Skills for Students with a Moderate ID in Community-Based Settings

ERIC Educational Resources Information Center

Bassette, Laura A.; Taber-Doughty, Teresa; Gama, Roberto I.; Alberto, Paul; Yakubova, Gulnoza; Cihak, David

2018-01-01

The purpose of this study was to examine the impact of a video modeling (VM) intervention in conjunction with a system of least prompts (SLP) to teach safety skills using cell phones to students with a moderate intellectual disability. A multiple-probe design across three participants was used to assess student acquisition in taking and sending a…

Search for direct production of supersymmetric partners of the top quark in the all-jets final state in proton-proton collisions at √{s}=13 TeV

NASA Astrophysics Data System (ADS)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Ambrogi, F.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Grossmann, J.; Hrubec, J.; Jeitler, M.; König, A.; Krammer, N.; Krätschmer, I.; Liko, D.; Madlener, T.; Mikulec, I.; Pree, E.; Rabady, D.; Rad, N.; Rohringer, H.; Schieck, J.; Schöfbeck, R.; Spanring, M.; Spitzbart, D.; Strauss, J.; Waltenberger, W.; Wittmann, J.; Wulz, C.-E.; Zarucki, M.; Chekhovsky, V.; Mossolov, V.; Suarez Gonzalez, J.; De Wolf, E. A.; Di Croce, D.; Janssen, X.; Lauwers, J.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; De Bruyn, I.; De Clercq, J.; Deroover, K.; Flouris, G.; Lontkovskyi, D.; Lowette, S.; Moortgat, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Skovpen, K.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Brun, H.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Luetic, J.; Maerschalk, T.; Marinov, A.; Randle-conde, A.; Seva, T.; Vander Velde, C.; Vanlaer, P.; Vannerom, D.; Yonamine, R.; Zenoni, F.; Zhang, F.; Cimmino, A.; Cornelis, T.; Dobur, D.; Fagot, A.; Gul, M.; Khvastunov, I.; Poyraz, D.; Roskas, C.; Salva, S.; Tytgat, M.; Verbeke, W.; Zaganidis, N.; Bakhshiansohi, H.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; De Visscher, S.; Delaere, C.; Delcourt, M.; Francois, B.; Giammanco, A.; Jafari, A.; Komm, M.; Krintiras, G.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Piotrzkowski, K.; Quertenmont, L.; Vidal Marono, M.; Wertz, S.; Beliy, N.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; Fonseca De Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Melo De Almeida, M.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Torres Da Silva De Araujo, F.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Misheva, M.; Rodozov, M.; Shopova, M.; Stoykova, S.; Sultanov, G.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Fang, W.; Gao, X.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Chen, Y.; Jiang, C. H.; Leggat, D.; Liao, H.; Liu, Z.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Yazgan, E.; Zhang, H.; Zhao, J.; Ban, Y.; Chen, G.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; González Hernández, C. F.; Ruiz Alvarez, J. D.; Courbon, B.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Sculac, T.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Ferencek, D.; Kadija, K.; Mesic, B.; Starodumov, A.; Susa, T.; Ather, M. W.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Finger, M.; Finger, M.; Carrera Jarrin, E.; El-khateeb, E.; Elgammal, S.; Mohamed, A.; Dewanjee, R. K.; Kadastik, M.; Perrini, L.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Faure, J. L.; Ferri, F.; Ganjour, S.; Ghosh, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Kucher, I.; Locci, E.; Machet, M.; Malcles, J.; Negro, G.; Rander, J.; Rosowsky, A.; Sahin, M. Ö.; Titov, M.; Abdulsalam, A.; Antropov, I.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Charlot, C.; Granier de Cassagnac, R.; Jo, M.; Lisniak, S.; Lobanov, A.; Martin Blanco, J.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Pigard, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Stahl Leiton, A. G.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Coubez, X.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Jansová, M.; Le Bihan, A.-C.; Tonon, N.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Bernet, C.; Boudoul, G.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fay, J.; Finco, L.; Gascon, S.; Gouzevitch, M.; Grenier, G.; Ille, B.; Lagarde, F.; Laktineh, I. B.; Lethuillier, M.; Mirabito, L.; Pequegnot, A. L.; Perries, S.; Popov, A.; Sordini, V.; Vander Donckt, M.; Viret, S.; Khvedelidze, A.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Feld, L.; Kiesel, M. K.; Klein, K.; Lipinski, M.; Preuten, M.; Schomakers, C.; Schulz, J.; Verlage, T.; Albert, A.; Dietz-Laursonn, E.; Duchardt, D.; Endres, M.; Erdmann, M.; Erdweg, S.; Esch, T.; Fischer, R.; Güth, A.; Hamer, M.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Knutzen, S.; Merschmeyer, M.; Meyer, A.; Millet, P.; Mukherjee, S.; Olschewski, M.; Padeken, K.; Pook, T.; Radziej, M.; Reithler, H.; Rieger, M.; Scheuch, F.; Teyssier, D.; Thüer, S.; Flügge, G.; Kargoll, B.; Kress, T.; Künsken, A.; Lingemann, J.; Müller, T.; Nehrkorn, A.; Nowack, A.; Pistone, C.; Pooth, O.; Stahl, A.; Aldaya Martin, M.; Arndt, T.; Asawatangtrakuldee, C.; Beernaert, K.; Behnke, O.; Behrens, U.; Bermúdez Martínez, A.; Bin Anuar, A. A.; Borras, K.; Botta, V.; Campbell, A.; Connor, P.; Contreras-Campana, C.; Costanza, F.; Diez Pardos, C.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Eren, E.; Gallo, E.; Garay Garcia, J.; Geiser, A.; Gizhko, A.; Grados Luyando, J. M.; Grohsjean, A.; Gunnellini, P.; Harb, A.; Hauk, J.; Hempel, M.; Jung, H.; Kalogeropoulos, A.; Kasemann, M.; Keaveney, J.; Kleinwort, C.; Korol, I.; Krücker, D.; Lange, W.; Lelek, A.; Lenz, T.; Leonard, J.; Lipka, K.; Lohmann, W.; Mankel, R.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Ntomari, E.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Roland, B.; Savitskyi, M.; Saxena, P.; Shevchenko, R.; Spannagel, S.; Stefaniuk, N.; Van Onsem, G. P.; Walsh, R.; Wen, Y.; Wichmann, K.; Wissing, C.; Zenaiev, O.; Bein, S.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Dreyer, T.; Garutti, E.; Gonzalez, D.; Haller, J.; Hinzmann, A.; Hoffmann, M.; Karavdina, A.; Klanner, R.; Kogler, R.; Kovalchuk, N.; Kurz, S.; Lapsien, T.; Marchesini, I.; Marconi, D.; Meyer, M.; Niedziela, M.; Nowatschin, D.; Pantaleo, F.; Peiffer, T.; Perieanu, A.; Scharf, C.; Schleper, P.; Schmidt, A.; Schumann, S.; Schwandt, J.; Sonneveld, J.; Stadie, H.; Steinbrück, G.; Stober, F. M.; Stöver, M.; Tholen, H.; Troendle, D.; Usai, E.; Vanelderen, L.; Vanhoefer, A.; Vormwald, B.; Akbiyik, M.; Barth, C.; Baur, S.; Butz, E.; Caspart, R.; Chwalek, T.; Colombo, F.; De Boer, W.; Dierlamm, A.; Freund, B.; Friese, R.; Giffels, M.; Gilbert, A.; Haitz, D.; Hartmann, F.; Heindl, S. M.; Husemann, U.; Kassel, F.; Kudella, S.; Mildner, H.; Mozer, M. U.; Müller, Th.; Plagge, M.; Quast, G.; Rabbertz, K.; Schröder, M.; Shvetsov, I.; Sieber, G.; Simonis, H. J.; Ulrich, R.; Wayand, S.; Weber, M.; Weiler, T.; Williamson, S.; Wöhrmann, C.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Topsis-Giotis, I.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Evangelou, I.; Foudas, C.; Kokkas, P.; Mallios, S.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Strologas, J.; Triantis, F. A.; Csanad, M.; Filipovic, N.; Pasztor, G.; Bencze, G.; Hajdu, C.; Horvath, D.; Hunyadi, Á.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Makovec, A.; Molnar, J.; Szillasi, Z.; Bartók, M.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Choudhury, S.; Komaragiri, J. R.; Bahinipati, S.; Bhowmik, S.; Mal, P.; Mandal, K.; Nayak, A.; Sahoo, D. K.; Sahoo, N.; Swain, S. K.; Bansal, S.; Beri, S. B.; Bhatnagar, V.; Bhawandeep, U.; Chawla, R.; Dhingra, N.; Kalsi, A. K.; Kaur, A.; Kaur, M.; Kumar, R.; Kumari, P.; Mehta, A.; Singh, J. B.; Walia, G.; Kumar, Ashok; Shah, Aashaq; Bhardwaj, A.; Chauhan, S.; Choudhary, B. C.; Garg, R. B.; Keshri, S.; Kumar, A.; Malhotra, S.; Naimuddin, M.; Ranjan, K.; Sharma, R.; Sharma, V.; Bhardwaj, R.; Bhattacharya, R.; Bhattacharya, S.; Dey, S.; Dutt, S.; Dutta, S.; Ghosh, S.; Majumdar, N.; Modak, A.; Mondal, K.; Mukhopadhyay, S.; Nandan, S.; Purohit, A.; Roy, A.; Roy, D.; Roy Chowdhury, S.; Sarkar, S.; Sharan, M.; Thakur, S.; Behera, P. K.; Chudasama, R.; Dutta, D.; Jha, V.; Kumar, V.; Mohanty, A. K.; Netrakanti, P. K.; Pant, L. M.; Shukla, P.; Topkar, A.; Aziz, T.; Dugad, S.; Mahakud, B.; Mitra, S.; Mohanty, G. B.; Parida, B.; Sur, N.; Sutar, B.; Banerjee, S.; Bhattacharya, S.; Chatterjee, S.; Das, P.; Guchait, M.; Jain, Sa.; Kumar, S.; Maity, M.; Majumder, G.; Mazumdar, K.; Sarkar, T.; Wickramage, N.; Chauhan, S.; Dube, S.; Hegde, V.; Kapoor, A.; Kothekar, K.; Pandey, S.; Rane, A.; Sharma, S.; Chenarani, S.; Eskandari Tadavani, E.; Etesami, S. M.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Calabria, C.; Caputo, C.; Colaleo, A.; Creanza, D.; Cristella, L.; De Filippis, N.; De Palma, M.; Errico, F.; Fiore, L.; Iaselli, G.; Lezki, S.; Maggi, G.; Maggi, M.; Miniello, G.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Ranieri, A.; Selvaggi, G.; Sharma, A.; Silvestris, L.; Venditti, R.; Verwilligen, P.; Abbiendi, G.; Battilana, C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Chhibra, S. S.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Rossi, A. M.; Rovelli, T.; Siroli, G. P.; Tosi, N.; Albergo, S.; Costa, S.; Di Mattia, A.; Giordano, F.; Potenza, R.; Tricomi, A.; Tuve, C.; Barbagli, G.; Chatterjee, K.; Ciulli, V.; Civinini, C.; D'Alessandro, R.; Focardi, E.; Lenzi, P.; Meschini, M.; Paoletti, S.; Russo, L.; Sguazzoni, G.; Strom, D.; Viliani, L.; Benussi, L.; Bianco, S.; Fabbri, F.; Piccolo, D.; Primavera, F.; Calvelli, V.; Ferro, F.; Robutti, E.; Tosi, S.; Brianza, L.; Brivio, F.; Ciriolo, V.; Dinardo, M. E.; Fiorendi, S.; Gennai, S.; Ghezzi, A.; Govoni, P.; Malberti, M.; Malvezzi, S.; Manzoni, R. A.; Menasce, D.; Moroni, L.; Paganoni, M.; Pauwels, K.; Pedrini, D.; Pigazzini, S.; Ragazzi, S.; Tabarelli de Fatis, T.; Buontempo, S.; Cavallo, N.; Di Guida, S.; Esposito, M.; Fabozzi, F.; Fienga, F.; Iorio, A. O. M.; Khan, W. A.; Lanza, G.; Lista, L.; Meola, S.; Paolucci, P.; Sciacca, C.; Thyssen, F.; Azzi, P.; Bacchetta, N.; Benato, L.; Bisello, D.; Boletti, A.; Carlin, R.; Carvalho Antunes De Oliveira, A.; Checchia, P.; Dall'Osso, M.; De Castro Manzano, P.; Dorigo, T.; Dosselli, U.; Gasparini, F.; Gozzelino, A.; Lacaprara, S.; Margoni, M.; Maron, G.; Meneguzzo, A. T.; Michelotto, M.; Montecassiano, F.; Pozzobon, N.; Ronchese, P.; Rossin, R.; Torassa, E.; Zanetti, M.; Zotto, P.; Braghieri, A.; Fallavollita, F.; Magnani, A.; Montagna, P.; Ratti, S. P.; Re, V.; Ressegotti, M.; Riccardi, C.; Salvini, P.; Vai, I.; Vitulo, P.; Alunni Solestizi, L.; Biasini, M.; Bilei, G. M.; Cecchi, C.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Leonardi, R.; Manoni, E.; Mantovani, G.; Mariani, V.; Menichelli, M.; Rossi, A.; Santocchia, A.; Spiga, D.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Borrello, L.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Fedi, G.; Giannini, L.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Manca, E.; Mandorli, G.; Martini, L.; Messineo, A.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Spagnolo, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; Cipriani, M.; Del Re, D.; Diemoz, M.; Gelli, S.; Longo, E.; Margaroli, F.; Marzocchi, B.; Meridiani, P.; Organtini, G.; Paramatti, R.; Preiato, F.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bartosik, N.; Bellan, R.; Biino, C.; Cartiglia, N.; Cenna, F.; Costa, M.; Covarelli, R.; Degano, A.; Demaria, N.; Kiani, B.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Monteil, E.; Monteno, M.; Obertino, M. M.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Ravera, F.; Romero, A.; Ruspa, M.; Sacchi, R.; Shchelina, K.; Sola, V.; Solano, A.; Staiano, A.; Traczyk, P.; Belforte, S.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Zanetti, A.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Lee, J.; Lee, S.; Lee, S. W.; Moon, C. S.; Oh, Y. D.; Sekmen, S.; Son, D. C.; Yang, Y. C.; Lee, A.; Kim, H.; Moon, D. H.; Oh, G.; Brochero Cifuentes, J. A.; Goh, J.; Kim, T. J.; Cho, S.; Choi, S.; Go, Y.; Gyun, D.; Ha, S.; Hong, B.; Jo, Y.; Kim, Y.; Lee, K.; Lee, K. S.; Lee, S.; Lim, J.; Park, S. K.; Roh, Y.; Almond, J.; Kim, J.; Kim, J. S.; Lee, H.; Lee, K.; Nam, K.; Oh, S. B.; Radburn-Smith, B. C.; Seo, S. h.; Yang, U. K.; Yoo, H. D.; Yu, G. B.; Choi, M.; Kim, H.; Kim, J. H.; Lee, J. S. H.; Park, I. C.; Ryu, G.; Choi, Y.; Hwang, C.; Lee, J.; Yu, I.; Dudenas, V.; Juodagalvis, A.; Vaitkus, J.; Ahmed, I.; Ibrahim, Z. A.; Ali, M. A. B. Md; Mohamad Idris, F.; Wan Abdullah, W. A. T.; Yusli, M. N.; Zolkapli, Z.; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-De La Cruz, I.; Lopez-Fernandez, R.; Mejia Guisao, J.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Oropeza Barrera, C.; Vazquez Valencia, F.; Pedraza, I.; Salazar Ibarguen, H. A.; Uribe Estrada, C.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Saddique, A.; Shah, M. A.; Shoaib, M.; Waqas, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Bunkowski, K.; Byszuk, A.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Pyskir, A.; Walczak, M.; Bargassa, P.; Beirão Da Cruz E Silva, C.; Calpas, B.; Di Francesco, A.; Faccioli, P.; Gallinaro, M.; Hollar, J.; Leonardo, N.; Lloret Iglesias, L.; Nemallapudi, M. 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D.; Wang, Q.; Ivanov, A.; Kaadze, K.; Maravin, Y.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Toda, S.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Calvert, B.; Eno, S. C.; Ferraioli, C.; Hadley, N. J.; Jabeen, S.; Jeng, G. Y.; Kellogg, R. G.; Kunkle, J.; Mignerey, A. C.; Ricci-Tam, F.; Shin, Y. H.; Skuja, A.; Tonwar, S. C.; Abercrombie, D.; Allen, B.; Azzolini, V.; Barbieri, R.; Baty, A.; Bi, R.; Brandt, S.; Busza, W.; Cali, I. A.; D'Alfonso, M.; Demiragli, Z.; Gomez Ceballos, G.; Goncharov, M.; Hsu, D.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Maier, B.; Marini, A. C.; Mcginn, C.; Mironov, C.; Narayanan, S.; Niu, X.; Paus, C.; Roland, C.; Roland, G.; Salfeld-Nebgen, J.; Stephans, G. S. F.; Tatar, K.; Velicanu, D.; Wang, J.; Wang, T. W.; Wyslouch, B.; Benvenuti, A. C.; Chatterjee, R. 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2017-10-01

A search for direct production of top squark pairs in events with jets and large transverse momentum imbalance is presented. The data are based on proton-proton collisions at a center-of-mass energy of 13 TeV, collected with the CMS detector in 2016 at the CERN LHC, and correspond to an integrated luminosity of 35.9 fb-1. The search considers a variety of R-parity conserving supersymmetric models, including ones for which the top squark and neutralino masses are nearly degenerate. Specialized jet reconstruction tools are developed to exploit the unique characteristics of the signal topologies. With no significant excess of events observed above the standard model expectations, upper limits are set on the direct top squark pair production cross section in the context of simplified supersymmetric models for various decay hypotheses. Models with larger differences in mass between the top squark and neutralino are probed for masses up to 1040 and 500 GeV, respectively, whereas models with a more compressed mass hierarchy are probed up to 660 and 610 GeV, respectively. The smallest mass difference probed is for masses near to 550 and 540 GeV, respectively. [Figure not available: see fulltext.

High-sensitivity detection and monitoring of microcirculation using cutaneous and catheter probes for Doppler optical coherence tomography

NASA Astrophysics Data System (ADS)

Yang, Victor X.; Gordon, M. L.; Qi, B.; Yue, E. Seng; Tang, S.; Bisland, Stuart K.; Pekar, J.; Lo, S.; Marcon, Norman E.; Wilson, B.; Vitkin, Alex

2003-07-01

Background: Currently clinical Doppler ultrasound cannot detect microvascular blood flow and it is difficult to provide depth discrimination using laser Doppler flowmetry. Doppler optical coherence tomography (DOCT) is a novel technique for noninvasive subsurface imaging of microcirculation and tissue structure. Aims: To design handheld and catheter-based DOCT probes for clinical cutaneous and endoscopic imaging. To develop signal processing techniques for real-time detection and quantification of microvascular blood flow. Methods: A DOCT system, with interchangeable cutaneous and catheter probes, was developed. The axial spatial resolution was 10 μm, and the velocity resolution was 20 μm/s, using a 1300 nm broadband infrared light. The system achieved real-time imaging with frame rates up to 32 Hz at 512 x 256 pixels per frame. We used the system to detect microcirculation in human skin and rat esophagus, and to monitor microvascular responses to photodynamic therapy (PDT) in a rat tumor model. Results: We present experimental results from in vivo DOCT imaging of microcirculation in human skin arterio-venous malformations (AVM), normal rat esophagus, and a rat gliosarcoma PDT model. In the PDT model, we followed microvascular responses to PDT and observed differences in the microcirculation during and after therapy, which can have important implications for PDT dosimetry and treatment optimization. Conclusions: To our knowledge, this is the first demonstration of endoscopic catheter-based DOCT detection of microcirculation in vivo. In addition, AVM can be detected using handheld cutaneous DOCT probes under clinical settings. DOCT may serve as a real-time monitoring tool for PDT dosimetry, especially for vascular targeting photosensitizers.

Integrated cosmological probes: concordance quantified

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

Nicola, Andrina; Amara, Adam; Refregier, Alexandre, E-mail: andrina.nicola@phys.ethz.ch, E-mail: adam.amara@phys.ethz.ch, E-mail: alexandre.refregier@phys.ethz.ch

2017-10-01

Assessing the consistency of parameter constraints derived from different cosmological probes is an important way to test the validity of the underlying cosmological model. In an earlier work [1], we computed constraints on cosmological parameters for ΛCDM from an integrated analysis of CMB temperature anisotropies and CMB lensing from Planck, galaxy clustering and weak lensing from SDSS, weak lensing from DES SV as well as Type Ia supernovae and Hubble parameter measurements. In this work, we extend this analysis and quantify the concordance between the derived constraints and those derived by the Planck Collaboration as well as WMAP9, SPT andmore » ACT. As a measure for consistency, we use the Surprise statistic [2], which is based on the relative entropy. In the framework of a flat ΛCDM cosmological model, we find all data sets to be consistent with one another at a level of less than 1σ. We highlight that the relative entropy is sensitive to inconsistencies in the models that are used in different parts of the analysis. In particular, inconsistent assumptions for the neutrino mass break its invariance on the parameter choice. When consistent model assumptions are used, the data sets considered in this work all agree with each other and ΛCDM, without evidence for tensions.« less

A novel multisensor traffic state assessment system based on incomplete data.

PubMed

Zeng, Yiliang; Lan, Jinhui; Ran, Bin; Jiang, Yaoliang

2014-01-01

A novel multisensor system with incomplete data is presented for traffic state assessment. The system comprises probe vehicle detection sensors, fixed detection sensors, and traffic state assessment algorithm. First of all, the validity checking of the traffic flow data is taken as preprocessing of this method. And then a new method based on the history data information is proposed to fuse and recover the incomplete data. According to the characteristics of space complementary of data based on the probe vehicle detector and fixed detector, a fusion model of space matching is presented to estimate the mean travel speed of the road. Finally, the traffic flow data include flow, speed and, occupancy rate, which are detected between Beijing Deshengmen bridge and Drum Tower bridge, are fused to assess the traffic state of the road by using the fusion decision model of rough sets and cloud. The accuracy of experiment result can reach more than 98%, and the result is in accordance with the actual road traffic state. This system is effective to assess traffic state, and it is suitable for the urban intelligent transportation system.

A Novel Multisensor Traffic State Assessment System Based on Incomplete Data

PubMed Central

Zeng, Yiliang; Lan, Jinhui; Ran, Bin; Jiang, Yaoliang

2014-01-01

A novel multisensor system with incomplete data is presented for traffic state assessment. The system comprises probe vehicle detection sensors, fixed detection sensors, and traffic state assessment algorithm. First of all, the validity checking of the traffic flow data is taken as preprocessing of this method. And then a new method based on the history data information is proposed to fuse and recover the incomplete data. According to the characteristics of space complementary of data based on the probe vehicle detector and fixed detector, a fusion model of space matching is presented to estimate the mean travel speed of the road. Finally, the traffic flow data include flow, speed and, occupancy rate, which are detected between Beijing Deshengmen bridge and Drum Tower bridge, are fused to assess the traffic state of the road by using the fusion decision model of rough sets and cloud. The accuracy of experiment result can reach more than 98%, and the result is in accordance with the actual road traffic state. This system is effective to assess traffic state, and it is suitable for the urban intelligent transportation system. PMID:25162055

Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

DOEpatents

Chee, Mark; Gingeras, Thomas R.; Fodor, Stephen P. A.; Hubble, Earl A.; Morris, MacDonald S.

1999-01-19

The invention provides an array of oligonucleotide probes immobilized on a solid support for analysis of a target sequence from a human immunodeficiency virus. The array comprises at least four sets of oligonucleotide probes 9 to 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus. A probe is related to its corresponding nucleotide by being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that is occupied by a complementary nucleotide to the corresponding nucleotide. The three additional probe sets each have a corresponding probe for each probe in the first probe set. Thus, for each nucleotide in the reference sequence, there are four corresponding probes, one from each of the probe sets. The three corresponding probes in the three additional probe sets are identical to the corresponding probe from the first probe or a subsequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes.

Optimization of Designs for Nanotube-based Scanning Probes

NASA Technical Reports Server (NTRS)

Harik, V. M.; Gates, T. S.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

Optimization of designs for nanotube-based scanning probes, which may be used for high-resolution characterization of nanostructured materials, is examined. Continuum models to analyze the nanotube deformations are proposed to help guide selection of the optimum probe. The limitations on the use of these models that must be accounted for before applying to any design problem are presented. These limitations stem from the underlying assumptions and the expected range of nanotube loading, end conditions, and geometry. Once the limitations are accounted for, the key model parameters along with the appropriate classification of nanotube structures may serve as a basis for the design optimization of nanotube-based probe tips.

Investigating dye performance and crosstalk in fluorescence enabled bioimaging using a model system

PubMed Central

Arppe, Riikka; Carro-Temboury, Miguel R.; Hempel, Casper; Vosch, Tom

2017-01-01

Detailed imaging of biological structures, often smaller than the diffraction limit, is possible in fluorescence microscopy due to the molecular size and photophysical properties of fluorescent probes. Advances in hardware and multiple providers of high-end bioimaging makes comparing images between studies and between research groups very difficult. Therefore, we suggest a model system to benchmark instrumentation, methods and staining procedures. The system we introduce is based on doped zeolites in stained polyvinyl alcohol (PVA) films: a highly accessible model system which has the properties needed to act as a benchmark in bioimaging experiments. Rather than comparing molecular probes and imaging methods in complicated biological systems, we demonstrate that the model system can emulate this complexity and can be used to probe the effect of concentration, brightness, and cross-talk of fluorophores on the detected fluorescence signal. The described model system comprises of lanthanide (III) ion doped Linde Type A zeolites dispersed in a PVA film stained with fluorophores. We tested: F18, MitoTracker Red and ATTO647N. This model system allowed comparing performance of the fluorophores in experimental conditions. Importantly, we here report considerable cross-talk of the dyes when exchanging excitation and emission settings. Additionally, bleaching was quantified. The proposed model makes it possible to test and benchmark staining procedures before these dyes are applied to more complex biological systems. PMID:29176775

Fusion set selection with surrogate metric in multi-atlas based image segmentation

NASA Astrophysics Data System (ADS)

Zhao, Tingting; Ruan, Dan

2016-02-01

Multi-atlas based image segmentation sees unprecedented opportunities but also demanding challenges in the big data era. Relevant atlas selection before label fusion plays a crucial role in reducing potential performance loss from heterogeneous data quality and high computation cost from extensive data. This paper starts with investigating the image similarity metric (termed ‘surrogate’), an alternative to the inaccessible geometric agreement metric (termed ‘oracle’) in atlas relevance assessment, and probes into the problem of how to select the ‘most-relevant’ atlases and how many such atlases to incorporate. We propose an inference model to relate the surrogates and the oracle geometric agreement metrics. Based on this model, we quantify the behavior of the surrogates in mimicking oracle metrics for atlas relevance ordering. Finally, analytical insights on the choice of fusion set size are presented from a probabilistic perspective, with the integrated goal of including the most relevant atlases and excluding the irrelevant ones. Empirical evidence and performance assessment are provided based on prostate and corpus callosum segmentation.

Absorption systems at z ˜ 2 as a probe of the circum galactic medium: a probabilistic approach

NASA Astrophysics Data System (ADS)

Mongardi, C.; Viel, M.; D'Odorico, V.; Kim, T.-S.; Barai, P.; Murante, G.; Monaco, P.

2018-05-01

We characterize the properties of the intergalactic medium (IGM) around a sample of galaxies extracted from state-of-the-art hydrodynamical simulations of structure formation in a cosmological volume of 25 Mpc comoving at z ˜ 2. The simulations are based on two different sub-resolution schemes for star formation and supernova feedback: the MUlti-Phase Particle Integrator (MUPPI) scheme and the Effective Model. We develop a quantitative and probabilistic analysis based on the apparent optical depth method of the properties of the absorbers as a function of impact parameter from their nearby galaxies: in such a way we probe different environments from circumgalactic medium (CGM) to low density filaments. Absorbers' properties are then compared with a spectroscopic observational data set obtained from high resolution quasar spectra. Our main focus is on the NCIV - NHI relation around simulated galaxies: the results obtained with MUPPI and the Effective model are remarkably similar, with small differences only confined to regions at impact parameters b = [1 - 3] × rvir. Using {C IV} as a tracer of the metallicity, we obtain evidence that the observed metal absorption systems have the highest probability to be confined in a region of 150-400 kpc around galaxies. Near-filament environments have instead metallicities too low to be probed by present-day telescopes, but could be probed by future spectroscopical studies. Finally we compute {C IV} covering fractions which are in agreement with observational data.

Segmentation of vessels cluttered with cells using a physics based model.

PubMed

Schmugge, Stephen J; Keller, Steve; Nguyen, Nhat; Souvenir, Richard; Huynh, Toan; Clemens, Mark; Shin, Min C

2008-01-01

Segmentation of vessels in biomedical images is important as it can provide insight into analysis of vascular morphology, topology and is required for kinetic analysis of flow velocity and vessel permeability. Intravital microscopy is a powerful tool as it enables in vivo imaging of both vasculature and circulating cells. However, the analysis of vasculature in those images is difficult due to the presence of cells and their image gradient. In this paper, we provide a novel method of segmenting vessels with a high level of cell related clutter. A set of virtual point pairs ("vessel probes") are moved reacting to forces including Vessel Vector Flow (VVF) and Vessel Boundary Vector Flow (VBVF) forces. Incorporating the cell detection, the VVF force attracts the probes toward the vessel, while the VBVF force attracts the virtual points of the probes to localize the vessel boundary without being distracted by the image features of the cells. The vessel probes are moved according to Newtonian Physics reacting to the net of forces applied on them. We demonstrate the results on a set of five real in vivo images of liver vasculature cluttered by white blood cells. When compared against the ground truth prepared by the technician, the Root Mean Squared Error (RMSE) of segmentation with VVF and VBVF was 55% lower than the method without VVF and VBVF.

Search for direct production of supersymmetric partners of the top quark in the all-jets final state in proton-proton collisions at $$ \\sqrt{s}=13 $$ TeV

DOE PAGES

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; ...

2017-10-02

A search for direct production of top squark pairs in events with jets and large transverse momentum imbalance is presented. The data are based on proton-proton collisions at a center-of-mass energy of 13 TeV, collected in 2016 at the CERN LHC, and correspond to an integrated luminosity of 35.9 fb –1. The search considers a variety of R-parity conserving supersymmetric models, including ones for which the top squark and neutralino masses are nearly degenerate. Specialized jet reconstruction tools are developed to exploit the unique characteristics of the signal topologies. With no significant excess of events observed above the standard modelmore » expectations, upper limits are set on the direct top squark pair production cross section in the context of simplified supersymmetric models for various decay hypotheses. Moreover, models with larger differences in mass between the top squark and neutralino are probed for masses up to 1040 and 500 GeV, respectively, whereas models with a more compressed mass hierarchy are probed up to 660 and 610 GeV, respectively. The smallest mass difference probed is for masses near to 550 and 540 GeV, respectively.« less

Numerical modelling as a cost-reduction tool for probability of detection of bolt hole eddy current testing

NASA Astrophysics Data System (ADS)

Mandache, C.; Khan, M.; Fahr, A.; Yanishevsky, M.

2011-03-01

Probability of detection (PoD) studies are broadly used to determine the reliability of specific nondestructive inspection procedures, as well as to provide data for damage tolerance life estimations and calculation of inspection intervals for critical components. They require inspections on a large set of samples, a fact that makes these statistical assessments time- and cost-consuming. Physics-based numerical simulations of nondestructive testing inspections could be used as a cost-effective alternative to empirical investigations. They realistically predict the inspection outputs as functions of the input characteristics related to the test piece, transducer and instrument settings, which are subsequently used to partially substitute and/or complement inspection data in PoD analysis. This work focuses on the numerical modelling aspects of eddy current testing for the bolt hole inspections of wing box structures typical of the Lockheed Martin C-130 Hercules and P-3 Orion aircraft, found in the air force inventory of many countries. Boundary element-based numerical modelling software was employed to predict the eddy current signal responses when varying inspection parameters related to probe characteristics, crack geometry and test piece properties. Two demonstrator exercises were used for eddy current signal prediction when lowering the driver probe frequency and changing the material's electrical conductivity, followed by subsequent discussions and examination of the implications on using simulated data in the PoD analysis. Despite some simplifying assumptions, the modelled eddy current signals were found to provide similar results to the actual inspections. It is concluded that physics-based numerical simulations have the potential to partially substitute or complement inspection data required for PoD studies, reducing the cost, time, effort and resources necessary for a full empirical PoD assessment.

Improvements to direct quantitative analysis of multiple microRNAs facilitating faster analysis.

PubMed

Ghasemi, Farhad; Wegman, David W; Kanoatov, Mirzo; Yang, Burton B; Liu, Stanley K; Yousef, George M; Krylov, Sergey N

2013-11-05

Studies suggest that patterns of deregulation in sets of microRNA (miRNA) can be used as cancer diagnostic and prognostic biomarkers. Establishing a "miRNA fingerprint"-based diagnostic technique requires a suitable miRNA quantitation method. The appropriate method must be direct, sensitive, capable of simultaneous analysis of multiple miRNAs, rapid, and robust. Direct quantitative analysis of multiple microRNAs (DQAMmiR) is a recently introduced capillary electrophoresis-based hybridization assay that satisfies most of these criteria. Previous implementations of the method suffered, however, from slow analysis time and required lengthy and stringent purification of hybridization probes. Here, we introduce a set of critical improvements to DQAMmiR that address these technical limitations. First, we have devised an efficient purification procedure that achieves the required purity of the hybridization probe in a fast and simple fashion. Second, we have optimized the concentrations of the DNA probe to decrease the hybridization time to 10 min. Lastly, we have demonstrated that the increased probe concentrations and decreased incubation time removed the need for masking DNA, further simplifying the method and increasing its robustness. The presented improvements bring DQAMmiR closer to use in a clinical setting.

Development of a group-specific 16S rRNA-targeted probe set for the identification of Marinobacter by fluorescence in situ hybridization

NASA Astrophysics Data System (ADS)

McKay, Luke J.; Gutierrez, Tony; Teske, Andreas P.

2016-07-01

Members of the Marinobacter genus play an important role in hydrocarbon degradation in the ocean - a topic of special significance in light of the recent Deepwater Horizon oil spill of 2010. The Marinobacter group has thus far lacked a genus level phylogenetic probe that would allow in situ identification of representative members. Here, we developed two new 16S rRNA-targeted oligonucleotide probes (Mrb-0625-a and Mrb-0625-b) to enumerate Marinobacter species by fluorescence in situ hybridization (FISH). In silico analysis of this probe set demonstrated 80% coverage of the Marinobacter genus. A competitor probe was developed to block hybridization by Mrb-0625-a to six Halomonas species with which it shared a one base pair mismatch. The probe set was optimized using pure cultures, and then used in an enrichment experiment with a deep sea oil plume water sample collected from the Deepwater Horizon oil spill. Marinobacter cells rapidly increased as a significant fraction of total microbial abundance in all incubations of original contaminated seawater as well as those amended with n-hexadecane, suggesting this group may be among the first microbial responders to oil pollution in the marine environment. The new probe set will provide a reliable tool for quantifying Marinobacter in the marine environment, particularly at contaminated sites where these organisms can play an important role in the biodegradation of oil pollutants.

Probing 6D operators at future e - e + colliders

NASA Astrophysics Data System (ADS)

Chiu, Wen Han; Leung, Sze Ching; Liu, Tao; Lyu, Kun-Feng; Wang, Lian-Tao

2018-05-01

We explore the sensitivities at future e - e + colliders to probe a set of six-dimensional operators which can modify the SM predictions on Higgs physics and electroweak precision measurements. We consider the case in which the operators are turned on simultaneously. Such an analysis yields a "conservative" interpretation on the collider sensitivities, complementary to the "optimistic" scenario where the operators are individually probed. After a detail analysis at CEPC in both "conservative" and "optimistic" scenarios, we also considered the sensitivities for FCC-ee and ILC. As an illustration of the potential of constraining new physics models, we applied sensitivity analysis to two benchmarks: holographic composite Higgs model and littlest Higgs model.

Characterization and global modelling of low-pressure hydrogen-based RF plasmas suitable for surface cleaning processes

NASA Astrophysics Data System (ADS)

Škoro, Nikola; Puač, Nevena; Lazović, Saša; Cvelbar, Uroš; Kokkoris, George; Gogolides, Evangelos

2013-11-01

In this paper we present results of measurements and global modelling of low-pressure inductively coupled H2 plasma which is suitable for surface cleaning applications. The plasma is ignited at 1 Pa in a helicon-type reactor and is characterized using optical emission measurements (optical actinometry) and electrical measurements, namely Langmuir and catalytic probe. By comparing catalytic probe data obtained at the centre of the chamber with optical actinometry results, an approximate calibration of the actinometry method as a semi-quantititative measure of H density was achieved. Coefficients for conversion of actinometric ratios to H densities are tabulated and provided. The approximate validity region of the simple actinometry formula for low-pressure H2 plasma is discussed in the online supplementary data (stacks.iop.org/JPhysD/46/475206/mmedia). Best agreement with catalytic probe results was obtained for (Hβ, Ar750) and (Hβ, Ar811) actinometric line pairs. Additionally, concentrations of electrons and ions as well as plasma potential, electron temperature and ion fluxes were measured in the chamber centre at different plasma powers using a Langmuir probe. Moreover, a global model of an inductively coupled plasma was formulated using a compiled reaction set for H2/Ar gas mixture. The model results compared reasonably well with the results on H atom and charge particle densities and a sensitivity analysis of important input parameters was conducted. The influence of the surface recombination, ionization, and dissociation coefficients, and the ion-neutral collision cross-section on model results was demonstrated.

A novel surgical marking system for small peripheral lung nodules based on radio frequency identification technology: Feasibility study in a canine model.

PubMed

Kojima, Fumitsugu; Sato, Toshihiko; Takahata, Hiromi; Okada, Minoru; Sugiura, Tadao; Oshiro, Osamu; Date, Hiroshi; Nakamura, Tatsuo

2014-04-01

We investigated the feasibility and accuracy of a novel surgical marking system based on radiofrequency identification (RFID) technology for the localization of small peripheral lung nodules (SPLNs) in a canine model. The system consists of 4 components: (1) micro RFID tags (13.56 MHz, 1.0 × 1.0 × 0.8 mm), (2) a tag delivery system with a bronchoscope, (3) a wand-shaped locating probe (10-mm diameter), and (4) a signal processing unit with audio interface. Before the operation, pseudolesions mimicking SPLNs were prepared in 7 dogs by injecting colored collagen. By use of a computed tomographic (CT) guide, an RFID tag was placed via a bronchoscope close to each target lesion. This was then followed by scanning with the locating probe, and wedge resection was performed when possible. Operators can locate the tag by following the sound emitted by the system, which exhibits tone changes according to the tag-probe distance. The primary outcome measure was the rate of wedge resection with good margins. A total of 10 pseudolesions imitating SPLNs were selected as targets. During thoracoscopic procedures, 9 of 10 tags were detected by the system within a median of 27 seconds. Wedge resections were performed for these 9 lesions with a median margin of 11 mm. The single failure was caused by tag dislocation to the central airway. Successful localization and wedge resection of pseudolesions with appropriate margins were accomplished in an experimental setting. Our RFID marking system has future applications for accurately locating SPLNs in a clinical setting. Copyright © 2014 The American Association for Thoracic Surgery. Published by Mosby, Inc. All rights reserved.

Vertical structure of the near-surface expanding ionosphere of comet 67P probed by Rosetta

NASA Astrophysics Data System (ADS)

Heritier, K. L.; Henri, P.; Vallières, X.; Galand, M.; Odelstad, E.; Eriksson, A. I.; Johansson, F. L.; Altwegg, K.; Behar, E.; Beth, A.; Broiles, T. W.; Burch, J. L.; Carr, C. M.; Cupido, E.; Nilsson, H.; Rubin, M.; Vigren, E.

2017-07-01

The plasma environment has been measured for the first time near the surface of a comet. This unique data set has been acquired at 67P/Churyumov-Gerasimenko during ESA/Rosetta spacecraft's final descent on 2016 September 30. The heliocentric distance was 3.8 au and the comet was weakly outgassing. Electron density was continuously measured with Rosetta Plasma Consortium (RPC)-Mutual Impedance Probe (MIP) and RPC-LAngmuir Probe (LAP) during the descent from a cometocentric distance of 20 km down to the surface. Data set from both instruments have been cross-calibrated for redundancy and accuracy. To analyse this data set, we have developed a model driven by Rosetta Orbiter Spectrometer for Ion and Neutral Analysis-COmetary Pressure Sensor total neutral density. The two ionization sources considered are solar extreme ultraviolet radiation and energetic electrons. The latter are estimated from the RPC-Ion and Electron Sensor (IES) and corrected for the spacecraft potential probed by RPC-LAP. We have compared the results of the model to the electron densities measured by RPC-MIP and RPC-LAP at the location of the spacecraft. We find good agreement between observed and modelled electron densities. The energetic electrons have access to the surface of the nucleus and contribute as the main ionization source. As predicted, the measurements exhibit a peak in the ionospheric density close to the surface. The location and magnitude of the peak are estimated analytically. The measured ionospheric densities cannot be explained with a constant outflow velocity model. The use of a neutral model with an expanding outflow is critical to explain the plasma observations.

Electrophysiological correlates of proactive interference in the 'Recent Probes' verbal working memory task.

PubMed

Zhang, John X; Wu, Renhua; Kong, Lingyue; Weng, Xuchu; Du, Yingchun

2010-06-01

Using event-related potentials (ERPs), the present study examined the temporal dynamics of proactive interference in working memory using a recent probes task. Participants memorized and retained a target set of four letters over a short retention interval. They then responded to a recognition probe by judging whether it was from the memory set. ERP waveforms elicited by positive probes compared to those from negative probes showed positive shifts in a fronto-central early N2 component and a parietal late positive component (LPC). The LPC was identified as the electrophysiological signature of proactive interference, as it differentiated between two types of negative probes defined based on whether they were recently encountered. These results indicate that the proactive interference we observed arises from a mismatch between familiarity and contextual information during recognition memory. When considered together with related studies in the literature, the results also suggest that there are different forms of proactive interference associated with different neural correlates. Copyright 2010 Elsevier Ltd. All rights reserved.

Two-Phase flow instrumentation for nuclear accidents simulation

NASA Astrophysics Data System (ADS)

Monni, G.; De Salve, M.; Panella, B.

2014-11-01

The paper presents the research work performed at the Energy Department of the Politecnico di Torino, concerning the development of two-phase flow instrumentation and of models, based on the analysis of experimental data, that are able to interpret the measurement signals. The study has been performed with particular reference to the design of power plants, such as nuclear water reactors, where the two-phase flow thermal fluid dynamics must be accurately modeled and predicted. In two-phase flow typically a set of different measurement instruments (Spool Piece - SP) must be installed in order to evaluate the mass flow rate of the phases in a large range of flow conditions (flow patterns, pressures and temperatures); moreover, an interpretative model of the SP need to be developed and experimentally verified. The investigated meters are: Turbine, Venturi, Impedance Probes, Concave sensors, Wire mesh sensor, Electrical Capacitance Probe. Different instrument combinations have been tested, and the performance of each one has been analyzed.

Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks

PubMed Central

2013-01-01

Background The usefulness of the data from Affymetrix microarray analysis depends largely on the reliability of the files describing the correspondence between probe sets, genes and transcripts. Particularly, when a gene is targeted by several probe sets, these files should give information about the similarity of each alternative probe set pair. Transcriptional networks integrate the multiple correlations that exist between all probe sets and supply much more information than a simple correlation coefficient calculated for two series of signals. In this study, we used the PSAWN (Probe Set Assignment With Networks) programme we developed to investigate whether similarity of alternative probe sets resulted in some specific properties. Findings PSAWNpy delivered a full textual description of each probe set and information on the number and properties of secondary targets. PSAWNml calculated the similarity of each alternative probe set pair and allowed finding relationships between similarity and localisation of probes in common transcripts or exons. Similar alternative probe sets had very low negative correlation, high positive correlation and similar neighbourhood overlap. Using these properties, we devised a test that allowed grouping similar probe sets in a given network. By considering several networks, additional information concerning the similarity reproducibility was obtained, which allowed defining the actual similarity of alternative probe set pairs. In particular, we calculated the common localisation of probes in exons and in known transcripts and we showed that similarity was correctly correlated with them. The information collected on all pairs of alternative probe sets in the most popular 3’ IVT Affymetrix chips is available in tabular form at http://bns.crbm.cnrs.fr/download.html. Conclusions These processed data can be used to obtain a finer interpretation when comparing microarray data between biological conditions. They are particularly well adapted for searching 3’ alternative poly-adenylation events and can be also useful for studying the structure of transcriptional networks. The PSAWNpy, (in Python) and PSAWNml (in Matlab) programmes are freely available and can be downloaded at http://code.google.com/p/arraymatic. Tutorials and reference manuals are available at BMC Research Notes online (Additional file 1) or from http://bns.crbm.cnrs.fr/softwares.html. PMID:23517579

Personalized Medicine in Veterans with Traumatic Brain Injuries

DTIC Science & Technology

2012-05-01

UPGMA ) based on cosine correlation of row mean centered log2 signal values; this was the top 50%-tile, 3) In the DA top 50%-tile, selected probe sets...GeneMaths XT following row mean centering of log2 trans- formed MAS5.0 signal values; probe set cluster- ing was performed by the UPGMA method using...hierarchical clustering analysis using the UPGMA algorithm with cosine correlation as the similarity metric. Results are presented as a heat map (left

Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.

PubMed

Shi, Xuesong; Walker, Peter; Harbury, Pehr B; Herschlag, Daniel

2017-05-05

The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures. We show that the XSI-based model of the TAR RNA ensemble closely resembles an independent model derived from NMR-RDC data. Further, we show how the TAR RNA ensemble changes shape at different salt concentrations. Finally, we demonstrate that a single hybrid model of the TAR RNA ensemble simultaneously fits both the XSI and NMR-RDC data set and show that XSI can be combined with NMR-RDC to further improve the quality of the determined ensemble. The results suggest that XSI-RNA will be a powerful approach for characterizing the solution conformational ensembles of RNAs and RNA-protein complexes under diverse solution conditions. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Use of Attribute Driven Incremental Discretization and Logic Learning Machine to build a prognostic classifier for neuroblastoma patients.

PubMed

Cangelosi, Davide; Muselli, Marco; Parodi, Stefano; Blengio, Fabiola; Becherini, Pamela; Versteeg, Rogier; Conte, Massimo; Varesio, Luigi

2014-01-01

Cancer patient's outcome is written, in part, in the gene expression profile of the tumor. We previously identified a 62-probe sets signature (NB-hypo) to identify tissue hypoxia in neuroblastoma tumors and showed that NB-hypo stratified neuroblastoma patients in good and poor outcome 1. It was important to develop a prognostic classifier to cluster patients into risk groups benefiting of defined therapeutic approaches. Novel classification and data discretization approaches can be instrumental for the generation of accurate predictors and robust tools for clinical decision support. We explored the application to gene expression data of Rulex, a novel software suite including the Attribute Driven Incremental Discretization technique for transforming continuous variables into simplified discrete ones and the Logic Learning Machine model for intelligible rule generation. We applied Rulex components to the problem of predicting the outcome of neuroblastoma patients on the bases of 62 probe sets NB-hypo gene expression signature. The resulting classifier consisted in 9 rules utilizing mainly two conditions of the relative expression of 11 probe sets. These rules were very effective predictors, as shown in an independent validation set, demonstrating the validity of the LLM algorithm applied to microarray data and patients' classification. The LLM performed as efficiently as Prediction Analysis of Microarray and Support Vector Machine, and outperformed other learning algorithms such as C4.5. Rulex carried out a feature selection by selecting a new signature (NB-hypo-II) of 11 probe sets that turned out to be the most relevant in predicting outcome among the 62 of the NB-hypo signature. Rules are easily interpretable as they involve only few conditions. Our findings provided evidence that the application of Rulex to the expression values of NB-hypo signature created a set of accurate, high quality, consistent and interpretable rules for the prediction of neuroblastoma patients' outcome. We identified the Rulex weighted classification as a flexible tool that can support clinical decisions. For these reasons, we consider Rulex to be a useful tool for cancer classification from microarray gene expression data.

An analytical model for floating probes in AC plasma and its application to double probes for high density, high power RF discharges

NASA Astrophysics Data System (ADS)

Caneses, Juan Francisco; Blackwell, Boyd; Plasma Research Laboratory Team

2013-10-01

In this work we provide an analytical model that allows one to quantitatively assess the RF compensation performance and suitability of the double probe technique for use in RF generated plasma. The model is based in the theory of the self-bias effect as described in Braithwaite's work, which we extend to include the time resolved behavior of floating probes. We provide experimental verification for this model and show that the theory of transient RF self-bias probes and harmonic current detection probes are limiting cases of this extended model. Furthermore, the model shows that the RF compensation is solely dependent on the sheath impedance, the probe's stray capacitance to ground and RF frequency. In addition, we use these results to implement a double probe system for use in high density helicon plasma where heat loads could potentially damage the intricate components in an RF compensating circuit. Finally we use this model to (1) recommend ways to extend the operational regime of double probes where the plasma conditions would render them unsuitable and to (2) comment on the use of this model to aid design of RF compensated Langmuir probes.

Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer

USGS Publications Warehouse

Thiem, S.M.; Krumme, M.L.; Smith, R.L.; Tiedje, J.M.

1994-01-01

A PCR primer set and an internal probe that are specific for Pseudomonas sp. strain B13, a 3-chlorobenzoate-metabolizing strain, were developed. Using this primer set and probe, we were able to detect Pseudomonas sp. strain B13 DNA sequences in DNA extracted from aquifer samples 14.5 months after Pseudomonas sp. strain B13 had been injected into a sand and gravel aquifer. This primer set and probe were also used to analyze isolates from 3-chlorobenzoate enrichments of the aquifer samples by Southern blot analysis. Hybridization of Southern blots with the Pseudomonas sp. strain B13-specific probe and a catabolic probe in conjunction with restriction fragment length polymorphism (RFLP) analysis of ribosome genes was used to determine that viable Pseudomonas sp. strain B13 persisted in this environment. We isolated a new 3-chlorobenzoate-degrading strain from one of these enrichment cultures. The B13-specific probe does not hybridize to DNA from this isolate. The new strain could be the result of gene exchange between Pseudomonas sp. strain B13 and an indigenous bacterium. This speculation is based on an RFLP pattern of ribosome genes that differs from that of Pseudomonas sp. strain B13, the fact that identically sized restriction fragments hybridized to the catabolic gene probe, and the absence of any enrichable 3-chlorobenzoate-degrading strains in the aquifer prior to inoculation.

Students' models in some topics of electricity and magnetism

NASA Astrophysics Data System (ADS)

Warnakulasooriya, Rasil

Model-based learning have been emphasized by many researchers. Furthermore, many theories have been put forward by researchers on how students reason. However, how the theories of reasoning are manifested within the context of electricity and magnetism and how to implement a model-based learning environment within such a context has not been the object of research. In this dissertation, we address the above two concerns. We probe students' reasoning, through a model-based diagnostic instrument. The instrument consists of a set of related multiple-choice questions that can be categorized as belonging to the same conceptual domain. The contextual features of a set are also kept to a minimum. We find that students' responses are tied to the models they have constructed or construct on the spot when faced with novel situations. We find that the concepts such as electric fields and electric potentials exist as mere "definitions" and do not contribute to forming a set of working models, and as such the need for the use of such concepts cannot be easily recognized. We also find that students function within a set of procedural rules. Whether these rules are extended directly from familiar situations through analogies or lead to constructing a set of new rules is constrained by the underlying models and the context of the questions. Models also either exist or are constructed in ways that lead students to overlook the common sense reality of physical phenomena. We also find that the way questions are perceived and interpreted are dependent on the underlying models and that different models exist without conflicting with each other. Based on the above findings, we argue that students' reasoning is context specific and is sensitive to the way the learning has taken place. Thus, we suggest a recontexualization process as a specific model-based learning environment to help students learn electricity and magnetism. The step-by-step guidance through a series of such related questions would then elucidate the context within which concepts are introduced, the limitations of particular representations and the ontological demands required by the subject.

Intrusion detection using rough set classification.

PubMed

Zhang, Lian-hua; Zhang, Guan-hua; Zhang, Jie; Bai, Ying-cai

2004-09-01

Recently machine learning-based intrusion detection approaches have been subjected to extensive researches because they can detect both misuse and anomaly. In this paper, rough set classification (RSC), a modern learning algorithm, is used to rank the features extracted for detecting intrusions and generate intrusion detection models. Feature ranking is a very critical step when building the model. RSC performs feature ranking before generating rules, and converts the feature ranking to minimal hitting set problem addressed by using genetic algorithm (GA). This is done in classical approaches using Support Vector Machine (SVM) by executing many iterations, each of which removes one useless feature. Compared with those methods, our method can avoid many iterations. In addition, a hybrid genetic algorithm is proposed to increase the convergence speed and decrease the training time of RSC. The models generated by RSC take the form of "IF-THEN" rules, which have the advantage of explication. Tests and comparison of RSC with SVM on DARPA benchmark data showed that for Probe and DoS attacks both RSC and SVM yielded highly accurate results (greater than 99% accuracy on testing set).

Probing Reliability of Transport Phenomena Based Heat Transfer and Fluid Flow Analysis in Autogeneous Fusion Welding Process

NASA Astrophysics Data System (ADS)

Bag, S.; de, A.

2010-09-01

The transport phenomena based heat transfer and fluid flow calculations in weld pool require a number of input parameters. Arc efficiency, effective thermal conductivity, and viscosity in weld pool are some of these parameters, values of which are rarely known and difficult to assign a priori based on the scientific principles alone. The present work reports a bi-directional three-dimensional (3-D) heat transfer and fluid flow model, which is integrated with a real number based genetic algorithm. The bi-directional feature of the integrated model allows the identification of the values of a required set of uncertain model input parameters and, next, the design of process parameters to achieve a target weld pool dimension. The computed values are validated with measured results in linear gas-tungsten-arc (GTA) weld samples. Furthermore, a novel methodology to estimate the overall reliability of the computed solutions is also presented.

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

Bernal, José Luis; Cuesta, Antonio J.; Verde, Licia, E-mail: joseluis.bernal@icc.ub.edu, E-mail: liciaverde@icc.ub.edu, E-mail: ajcuesta@icc.ub.edu

We perform an empirical consistency test of General Relativity/dark energy by disentangling expansion history and growth of structure constraints. We replace each late-universe parameter that describes the behavior of dark energy with two meta-parameters: one describing geometrical information in cosmological probes, and the other controlling the growth of structure. If the underlying model (a standard wCDM cosmology with General Relativity) is correct, that is under the null hypothesis, the two meta-parameters coincide. If they do not, it could indicate a failure of the model or systematics in the data. We present a global analysis using state-of-the-art cosmological data sets whichmore » points in the direction that cosmic structures prefer a weaker growth than that inferred by background probes. This result could signify inconsistencies of the model, the necessity of extensions to it or the presence of systematic errors in the data. We examine all these possibilities. The fact that the result is mostly driven by a specific sub-set of galaxy clusters abundance data, points to the need of a better understanding of this probe.« less

Developing a Dynamic Pharmacophore Model for HIV-1 Integrase

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

Carlson, Heather A.; Masukawa, Keven M.; Rubins, Kathleen

2000-05-11

We present the first receptor-based pharmacophore model for HIV-1 integrase. The development of ''dynamic'' pharmacophore models is a new method that accounts for the inherent flexibility of the active site and aims to reduce the entropic penalties associated with binding a ligand. Furthermore, this new drug discovery method overcomes the limitation of an incomplete crystal structure of the target protein. A molecular dynamics (MD) simulation describes the flexibility of the uncomplexed protein. Many conformational models of the protein are saved from the MD simulations and used in a series of multi-unit search for interacting conformers (MUSIC) simulations. MUSIC is amore » multiple-copy minimization method, available in the BOSS program; it is used to determine binding regions for probe molecules containing functional groups that complement the active site. All protein conformations from the MD are overlaid, and conserved binding regions for the probe molecules are identified. Those conserved binding regions define the dynamic pharmacophore model. Here, the dynamic model is compared to known inhibitors of the integrase as well as a three-point, ligand-based pharmacophore model from the literature. Also, a ''static'' pharmacophore model was determined in the standard fashion, using a single crystal structure. Inhibitors thought to bind in the active site of HIV-1 integrase fit the dynamic model but not the static model. Finally, we have identified a set of compounds from the Available Chemicals Directory that fit the dynamic pharmacophore model, and experimental testing of the compounds has confirmed several new inhibitors.« less

Evaluation of a duplex reverse-transcription real-time PCR assay for the detection of encephalomyocarditis virus.

PubMed

Qin, Shaomin; Underwood, Darren; Driver, Luke; Kistler, Carol; Diallo, Ibrahim; Kirkland, Peter D

2018-06-01

We evaluated a fluorogenic probe-based assay for the detection of encephalomyocarditis virus (EMCV) by comparing a set of published primers and probe to a new set of primers and probe. The published reagents failed to amplify a range of Australian isolates and an Italian reference strain of EMCV. In contrast, an assay based on 2 new sets of primers and probes that were run in a duplex reverse-transcription real-time PCR (RT-rtPCR) worked well, with high amplification efficiency. The analytical sensitivity was ~100-fold higher than virus isolation in cell culture. The intra-assay variation was 0.21-4.90%. No cross-reactivity was observed with a range of other porcine viruses. One hundred and twenty-two clinical specimens were tested simultaneously by RT-rtPCR and virus isolation in cell culture; 72 specimens gave positive results by RT-rtPCR, and 63 of these were also positive by virus isolation. Of 245 archived cell culture isolates of EMCV that were tested in the RT-rtPCR, 242 samples were positive. The new duplex RT-rtPCR assay is a reliable tool for the detection of EMCV in clinical specimens and for use in epidemiologic investigations.

Minimum probe length for unique identification of all open reading frames in a microbial genome

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

Sokhansanj, B A; Ng, J; Fitch, J P

2000-03-05

In this paper, we determine the minimum hybridization probe length to uniquely identify at least 95% of the open reading frame (ORF) in an organism. We analyze the whole genome sequences of 17 species, 11 bacteria, 4 archaea, and 2 eukaryotes. We also present a mathematical model for minimum probe length based on assuming that all ORFs are random, of constant length, and contain an equal distribution of bases. The model accurately predicts the minimum probe length for all species, but it incorrectly predicts that all ORFs may be uniquely identified. However, a probe length of just 9 bases ismore » adequate to identify over 95% of the ORFs for all 15 prokaryotic species we studied. Using a minimum probe length, while accepting that some ORFs may not be identified and that data will be lost due to hybridization error, may result in significant savings in microarray and oligonucleotide probe design.« less

Real-time PCR detection of Vibrio vulnificus in oysters: comparison of oligonucleotide primers and probes targeting vvhA.

PubMed

Panicker, Gitika; Bej, Asim K

2005-10-01

We compared three sets of oligonucleotide primers and two probes designed for Vibrio vulnificus hemolysin A gene (vvhA) for TaqMan-based real-time PCR method enabling specific detection of Vibrio vulnificus in oysters. Two of three sets of primers with a probe were specific for the detection of all 81 V. vulnificus isolates by TaqMan PCR. The 25 nonvibrio and 12 other vibrio isolates tested were negative. However, the third set of primers, F-vvh1059 and R-vvh1159, with the P-vvh1109 probe, although positive for all V. vulnificus isolates, also exhibited positive cycle threshold (C(T)) values for other Vibrio spp. Optimization of the TaqMan PCR assay using F-vvh785/R-vvh990 or F-vvh731/R-vvh1113 primers and the P-vvh874 probe detected 1 pg of purified DNA and 10(3) V. vulnificus CFU/ml in pure cultures. The enriched oyster tissue homogenate did not exhibit detectable inhibition to the TaqMan PCR amplification of vvhA. Detection of 3 x 10(3) CFU V. vulnificus, resulting from a 5-h enrichment of an initial inoculum of 1 CFU/g of oyster tissue homogenate, was achieved with F-vvh785/R-vvh990 or F-vvh731/R-vvh1113 primers and P-vvh875 probe. The application of the TaqMan PCR using these primers and probe, exhibited detection of V. vulnificus on 5-h-enriched natural oysters harvested from the Gulf of Mexico. Selection of appropriate primers and a probe on vvhA for TaqMan-PCR-based detection of V. vulnificus in post-harvest-treated oysters would help avoid false-positive results, thus ensuring a steady supply of safe oysters to consumers and reducing V. vulnificus-related illnesses and deaths.

The effectiveness of three sets of school-based instructional materials and community training on the acquisition and generalization of community laundry skills by students with severe handicaps.

PubMed

Morrow, S A; Bates, P E

1987-01-01

This study examined the effectiveness of three sets of school-based instructional materials and community training on acquisition and generalization of a community laundry skill by nine students with severe handicaps. School-based instruction involved artificial materials (pictures), simulated materials (cardboard replica of a community washing machine), and natural materials (modified home model washing machine). Generalization assessments were conducted at two different community laundromats, on two machines represented fully by the school-based instructional materials and two machines not represented fully by these materials. After three phases of school-based instruction, the students were provided ten community training trials in one laundromat setting and a final assessment was conducted in both the trained and untrained community settings. A multiple probe design across students was used to evaluate the effectiveness of the three types of school instruction and community training. After systematic training, most of the students increased their laundry performance with all three sets of school-based materials; however, generalization of these acquired skills was limited in the two community settings. Direct training in one of the community settings resulted in more efficient acquisition of the laundry skills and enhanced generalization to the untrained laundromat setting for most of the students. Results of this study are discussed in regard to the issue of school versus community-based instruction and recommendations are made for future research in this area.

Competitive hybridization models

NASA Astrophysics Data System (ADS)

Cherepinsky, Vera; Hashmi, Ghazala; Mishra, Bud

2010-11-01

Microarray technology, in its simplest form, allows one to gather abundance data for target DNA molecules, associated with genomes or gene-expressions, and relies on hybridizing the target to many short probe oligonucleotides arrayed on a surface. While for such multiplexed reactions conditions are optimized to make the most of each individual probe-target interaction, subsequent analysis of these experiments is based on the implicit assumption that a given experiment yields the same result regardless of whether it was conducted in isolation or in parallel with many others. It has been discussed in the literature that this assumption is frequently false, and its validity depends on the types of probes and their interactions with each other. We present a detailed physical model of hybridization as a means of understanding probe interactions in a multiplexed reaction. Ultimately, the model can be derived from a system of ordinary differential equations (ODE’s) describing kinetic mass action with conservation-of-mass equations completing the system. We examine pairwise probe interactions in detail and present a model of “competition” between the probes for the target—especially, when the target is effectively in short supply. These effects are shown to be predictable from the affinity constants for each of the four probe sequences involved, namely, the match and mismatch sequences for both probes. These affinity constants are calculated from the thermodynamic parameters such as the free energy of hybridization, which are in turn computed according to the nearest neighbor (NN) model for each probe and target sequence. Simulations based on the competitive hybridization model explain the observed variability in the signal of a given probe when measured in parallel with different groupings of other probes or individually. The results of the simulations can be used for experiment design and pooling strategies, based on which probes have been shown to have a strong effect on each other’s signal in the in silico experiment. These results are aimed at better design of multiplexed reactions on arrays used in genotyping (e.g., HLA typing, SNP, or CNV detection, etc.) and mutation analysis (e.g., cystic fibrosis, cancer, autism, etc.).

Predicting vehicle fuel consumption patterns using floating vehicle data.

PubMed

Du, Yiman; Wu, Jianping; Yang, Senyan; Zhou, Liutong

2017-09-01

The status of energy consumption and air pollution in China is serious. It is important to analyze and predict the different fuel consumption of various types of vehicles under different influence factors. In order to fully describe the relationship between fuel consumption and the impact factors, massive amounts of floating vehicle data were used. The fuel consumption pattern and congestion pattern based on large samples of historical floating vehicle data were explored, drivers' information and vehicles' parameters from different group classification were probed, and the average velocity and average fuel consumption in the temporal dimension and spatial dimension were analyzed respectively. The fuel consumption forecasting model was established by using a Back Propagation Neural Network. Part of the sample set was used to train the forecasting model and the remaining part of the sample set was used as input to the forecasting model. Copyright © 2017. Published by Elsevier B.V.

Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing.

PubMed

O'Flaherty, Brigid M; Li, Yan; Tao, Ying; Paden, Clinton R; Queen, Krista; Zhang, Jing; Dinwiddie, Darrell L; Gross, Stephen M; Schroth, Gary P; Tong, Suxiang

2018-06-01

Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%-99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology. © 2018 O'Flaherty et al.; Published by Cold Spring Harbor Laboratory Press.

Activity-based probes for the ubiquitin conjugation-deconjugation machinery: new chemistries, new tools, and new insights.

PubMed

Hewings, David S; Flygare, John A; Bogyo, Matthew; Wertz, Ingrid E

2017-05-01

The reversible post-translational modification of proteins by ubiquitin and ubiquitin-like proteins regulates almost all cellular processes, by affecting protein degradation, localization, and complex formation. Deubiquitinases (DUBs) are proteases that remove ubiquitin modifications or cleave ubiquitin chains. Most DUBs are cysteine proteases, which makes them well suited for study by activity-based probes. These DUB probes report on deubiquitinase activity by reacting covalently with the active site in an enzyme-catalyzed manner. They have proven to be important tools to study DUB selectivity and proteolytic activity in different settings, to identify novel DUBs, and to characterize deubiquitinase inhibitors. Inspired by the efficacy of activity-based probes for DUBs, several groups have recently reported probes for the ubiquitin conjugation machinery (E1, E2, and E3 enzymes). Many of these enzymes, while not proteases, also posses active site cysteine residues and can be targeted by covalent probes. In this review, we will discuss how features of the probe (cysteine-reactive group, recognition element, and reporter tag) affect reactivity and suitability for certain experimental applications. We will also review the diverse applications of the current probes, and discuss the need for new probe types to study emerging aspects of ubiquitin biology. © 2017 Federation of European Biochemical Societies.

Identification of genes and gene pathways associated with major depressive disorder by integrative brain analysis of rat and human prefrontal cortex transcriptomes

PubMed Central

Malki, K; Pain, O; Tosto, M G; Du Rietz, E; Carboni, L; Schalkwyk, L C

2015-01-01

Despite moderate heritability estimates, progress in uncovering the molecular substrate underpinning major depressive disorder (MDD) has been slow. In this study, we used prefrontal cortex (PFC) gene expression from a genetic rat model of MDD to inform probe set prioritization in PFC in a human post-mortem study to uncover genes and gene pathways associated with MDD. Gene expression differences between Flinders sensitive (FSL) and Flinders resistant (FRL) rat lines were statistically evaluated using the RankProd, non-parametric algorithm. Top ranking probe sets in the rat study were subsequently used to prioritize orthologous selection in a human PFC in a case–control post-mortem study on MDD from the Stanley Brain Consortium. Candidate genes in the human post-mortem study were then tested against a matched control sample using the RankProd method. A total of 1767 probe sets were differentially expressed in the PFC between FSL and FRL rat lines at (q⩽0.001). A total of 898 orthologous probe sets was found on Affymetrix's HG-U95A chip used in the human study. Correcting for the number of multiple, non-independent tests, 20 probe sets were found to be significantly dysregulated between human cases and controls at q⩽0.05. These probe sets tagged the expression profile of 18 human genes (11 upregulated and seven downregulated). Using an integrative rat–human study, a number of convergent genes that may have a role in pathogenesis of MDD were uncovered. Eighty percent of these genes were functionally associated with a key stress response signalling cascade, involving NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells), AP-1 (activator protein 1) and ERK/MAPK, which has been systematically associated with MDD, neuroplasticity and neurogenesis. PMID:25734512

Early Probe and Drug Discovery in Academia: A Minireview.

PubMed

Roy, Anuradha

2018-02-09

Drug discovery encompasses processes ranging from target selection and validation to the selection of a development candidate. While comprehensive drug discovery work flows are implemented predominantly in the big pharma domain, early discovery focus in academia serves to identify probe molecules that can serve as tools to study targets or pathways. Despite differences in the ultimate goals of the private and academic sectors, the same basic principles define the best practices in early discovery research. A successful early discovery program is built on strong target definition and validation using a diverse set of biochemical and cell-based assays with functional relevance to the biological system being studied. The chemicals identified as hits undergo extensive scaffold optimization and are characterized for their target specificity and off-target effects in in vitro and in animal models. While the active compounds from screening campaigns pass through highly stringent chemical and Absorption, Distribution, Metabolism, and Excretion (ADME) filters for lead identification, the probe discovery involves limited medicinal chemistry optimization. The goal of probe discovery is identification of a compound with sub-µM activity and reasonable selectivity in the context of the target being studied. The compounds identified from probe discovery can also serve as starting scaffolds for lead optimization studies.

In vivo quantitative bioluminescence tomography using heterogeneous and homogeneous mouse models.

PubMed

Liu, Junting; Wang, Yabin; Qu, Xiaochao; Li, Xiangsi; Ma, Xiaopeng; Han, Runqiang; Hu, Zhenhua; Chen, Xueli; Sun, Dongdong; Zhang, Rongqing; Chen, Duofang; Chen, Dan; Chen, Xiaoyuan; Liang, Jimin; Cao, Feng; Tian, Jie

2010-06-07

Bioluminescence tomography (BLT) is a new optical molecular imaging modality, which can monitor both physiological and pathological processes by using bioluminescent light-emitting probes in small living animal. Especially, this technology possesses great potential in drug development, early detection, and therapy monitoring in preclinical settings. In the present study, we developed a dual modality BLT prototype system with Micro-computed tomography (MicroCT) registration approach, and improved the quantitative reconstruction algorithm based on adaptive hp finite element method (hp-FEM). Detailed comparisons of source reconstruction between the heterogeneous and homogeneous mouse models were performed. The models include mice with implanted luminescence source and tumor-bearing mice with firefly luciferase report gene. Our data suggest that the reconstruction based on heterogeneous mouse model is more accurate in localization and quantification than the homogeneous mouse model with appropriate optical parameters and that BLT allows super-early tumor detection in vivo based on tomographic reconstruction of heterogeneous mouse model signal.

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

NASA Astrophysics Data System (ADS)

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 reproduce time-resolved data far above probe resonant frequency.

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression.

PubMed

Lemieux, Sébastien

2006-08-25

The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear Model) method implements a linear model applied on the probe-level data to directly estimate the treatment effect. A finite mixture of Gaussian components is then used to identify DEGs using the coefficients estimated by the linear model. This approach can readily be applied to experimental design with or without replication. On a wholly defined dataset, the PL-LM method was able to identify 75% of the differentially expressed genes within 10% of false positives. This accuracy was achieved both using the three replicates per conditions available in the dataset and using only one replicate per condition. The method achieves, on this dataset, a higher accuracy than the best set of tools identified by the authors of the dataset, and does so using only one replicate per condition.

Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

NASA Technical Reports Server (NTRS)

Urakawa, Hidetoshi; El Fantroussi, Said; Smidt, Hauke; Smoot, James C.; Tribou, Erik H.; Kelly, John J.; Noble, Peter A.; Stahl, David A.

2003-01-01

The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

Expert system for neurosurgical treatment planning

NASA Astrophysics Data System (ADS)

Cheng, Andrew Y. S.; Chung, Sally S. Y.; Kwok, John C. K.

1996-04-01

A specially designed expert system is in development for neurosurgical treatment planning. The knowledge base contains knowledge and experiences on neurosurgical treatment planning from neurosurgeon consultants, who also determine the risks of different regions in human brains. When completed, the system can simulate the decision making process of neurosurgeons to determine the safest probing path for operation. The Computed Tomography (CT) or Magnetic Resonance Imaging (MRI) scan images for each patient are grabbed as the input. The system also allows neurosurgeons to include for any particular patient the additional information, such as how the tumor affects its neighboring functional regions, which is also important for calculating the safest probing path. It can then consider all the relevant information and find the most suitable probing path on the patient's brain. A 3D brain model is constructed for each set of the CT/MRI scan images and is displayed real-time together with the possible probing paths found. The precise risk value of each path is shown as a number between 0 and 1, together with its possible damages in text. Neurosurgeons can view more than one possible path simultaneously, and make the final decision on the selected path for operation.

High-throughput flow alignment of barcoded hydrogel microparticles†

PubMed Central

Chapin, Stephen C.; Pregibon, Daniel C.

2010-01-01

Suspension (particle-based) arrays offer several advantages over conventional planar arrays in the detection and quantification of biomolecules, including the use of smaller sample volumes, more favorable probe-target binding kinetics, and rapid probe-set modification. We present a microfluidic system for the rapid alignment of multifunctional hydrogel microparticles designed to bear one or several biomolecule probe regions, as well as a graphical code to identify the embedded probes. Using high-speed imaging, we have developed and optimized a flow-through system that (1) allows for a high particle throughput, (2) ensures proper particle alignment for decoding and target quantification, and (3) can be reliably operated continuously without clogging. A tapered channel flanked by side focusing streams is used to orient the flexible, tablet-shaped particles into a well-ordered flow in the center of the channel. The effects of channel geometry, particle geometry, particle composition, particle loading density, and barcode design are explored to determine the best combination for eventual use in biological assays. Particles in the optimized system move at velocities of ~50 cm s−1 and with throughputs of ~40 particles s−1. Simple physical models and CFD simulations have been used to investigate flow behavior in the device. PMID:19823726

Measurement and analysis of electron-neutral collision frequency in the calibrated cutoff probe

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

You, K. H.; Seo, B. H.; Kim, J. H.

2016-03-15

As collisions between electrons and neutral particles constitute one of the most representative physical phenomena in weakly ionized plasma, the electron-neutral (e-n) collision frequency is a very important plasma parameter as regards understanding the physics of this material. In this paper, we measured the e-n collision frequency in the plasma using a calibrated cutoff-probe. A highly accurate reactance spectrum of the plasma/cutoff-probe system, which is expected based on previous cutoff-probe circuit simulations [Kim et al., Appl. Phys. Lett. 99, 131502 (2011)], is obtained using the calibrated cutoff-probe method, and the e-n collision frequency is calculated based on the cutoff-probe circuitmore » model together with the high-frequency conductance model. The measured e-n collision frequency (by the calibrated cutoff-probe method) is compared and analyzed with that obtained using a Langmuir probe, with the latter being calculated from the measured electron-energy distribution functions, in wide range of gas pressure.« less

Measurement of Flow Pattern Within a Rotating Stall Cell in an Axial Compressor

NASA Technical Reports Server (NTRS)

Lepicovsky, Jan; Braunscheidel, Edward P.

2006-01-01

Effective active control of rotating stall in axial compressors requires detailed understanding of flow instabilities associated with this compressor regime. Newly designed miniature high frequency response total and static pressure probes as well as commercial thermoanemometric probes are suitable tools for this task. However, during the rotating stall cycle the probes are subjected to flow direction changes that are far larger than the range of probe incidence acceptance, and therefore probe data without a proper correction would misrepresent unsteady variations of flow parameters. A methodology, based on ensemble averaging, is proposed to circumvent this problem. In this approach the ensemble averaged signals acquired for various probe setting angles are segmented, and only the sections for probe setting angles close to the actual flow angle are used for signal recombination. The methodology was verified by excellent agreement between velocity distributions obtained from pressure probe data, and data measured with thermoanemometric probes. Vector plots of unsteady flow behavior during the rotating stall regime indicate reversed flow within the rotating stall cell that spreads over to adjacent rotor blade channels. Results of this study confirmed that the NASA Low Speed Axial Compressor (LSAC) while in a rotating stall regime at rotor design speed exhibits one stall cell that rotates at a speed equal to 50.6 percent of the rotor shaft speed.

pathChirp: Efficient Available Bandwidth Estimation for Network Paths

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

Cottrell, Les

2003-04-30

This paper presents pathChirp, a new active probing tool for estimating the available bandwidth on a communication network path. Based on the concept of ''self-induced congestion,'' pathChirp features an exponential flight pattern of probes we call a chirp. Packet chips offer several significant advantages over current probing schemes based on packet pairs or packet trains. By rapidly increasing the probing rate within each chirp, pathChirp obtains a rich set of information from which to dynamically estimate the available bandwidth. Since it uses only packet interarrival times for estimation, pathChirp does not require synchronous nor highly stable clocks at the sendermore » and receiver. We test pathChirp with simulations and Internet experiments and find that it provides good estimates of the available bandwidth while using only a fraction of the number of probe bytes that current state-of-the-art techniques use.« less

Five-Hole Flow Angle Probe Calibration for the NASA Glenn Icing Research Tunnel

NASA Technical Reports Server (NTRS)

Gonsalez, Jose C.; Arrington, E. Allen

1999-01-01

A spring 1997 test section calibration program is scheduled for the NASA Glenn Research Center Icing Research Tunnel following the installation of new water injecting spray bars. A set of new five-hole flow angle pressure probes was fabricated to properly calibrate the test section for total pressure, static pressure, and flow angle. The probes have nine pressure ports: five total pressure ports on a hemispherical head and four static pressure ports located 14.7 diameters downstream of the head. The probes were calibrated in the NASA Glenn 3.5-in.-diameter free-jet calibration facility. After completing calibration data acquisition for two probes, two data prediction models were evaluated. Prediction errors from a linear discrete model proved to be no worse than those from a full third-order multiple regression model. The linear discrete model only required calibration data acquisition according to an abridged test matrix, thus saving considerable time and financial resources over the multiple regression model that required calibration data acquisition according to a more extensive test matrix. Uncertainties in calibration coefficients and predicted values of flow angle, total pressure, static pressure. Mach number. and velocity were examined. These uncertainties consider the instrumentation that will be available in the Icing Research Tunnel for future test section calibration testing.

Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging

PubMed Central

Dempsey, Graham T.; Vaughan, Joshua C.; Chen, Kok Hao; Bates, Mark; Zhuang, Xiaowei

2011-01-01

One approach to super-resolution fluorescence imaging uses sequential activation and localization of individual fluorophores to achieve high spatial resolution. Essential to this technique is the choice of fluorescent probes — the properties of the probes, including photons per switching event, on/off duty cycle, photostability, and number of switching cycles, largely dictate the quality of super-resolution images. While many probes have been reported, a systematic characterization of the properties of these probes and their impact on super-resolution image quality has been described in only a few cases. Here, we quantitatively characterized the switching properties of 26 organic dyes and directly related these properties to the quality of super-resolution images. This analysis provides a set of guidelines for characterization of super-resolution probes and a resource for selecting probes based on performance. Our evaluation identified several photoswitchable dyes with good to excellent performance in four independent spectral ranges, with which we demonstrated low crosstalk, four-color super-resolution imaging. PMID:22056676

A dynamic model of reasoning and memory.

PubMed

Hawkins, Guy E; Hayes, Brett K; Heit, Evan

2016-02-01

Previous models of category-based induction have neglected how the process of induction unfolds over time. We conceive of induction as a dynamic process and provide the first fine-grained examination of the distribution of response times observed in inductive reasoning. We used these data to develop and empirically test the first major quantitative modeling scheme that simultaneously accounts for inductive decisions and their time course. The model assumes that knowledge of similarity relations among novel test probes and items stored in memory drive an accumulation-to-bound sequential sampling process: Test probes with high similarity to studied exemplars are more likely to trigger a generalization response, and more rapidly, than items with low exemplar similarity. We contrast data and model predictions for inductive decisions with a recognition memory task using a common stimulus set. Hierarchical Bayesian analyses across 2 experiments demonstrated that inductive reasoning and recognition memory primarily differ in the threshold to trigger a decision: Observers required less evidence to make a property generalization judgment (induction) than an identity statement about a previously studied item (recognition). Experiment 1 and a condition emphasizing decision speed in Experiment 2 also found evidence that inductive decisions use lower quality similarity-based information than recognition. The findings suggest that induction might represent a less cautious form of recognition. We conclude that sequential sampling models grounded in exemplar-based similarity, combined with hierarchical Bayesian analysis, provide a more fine-grained and informative analysis of the processes involved in inductive reasoning than is possible solely through examination of choice data. PsycINFO Database Record (c) 2016 APA, all rights reserved.

A peptide-based positron emission tomography probe for in vivo detection of caspase activity in apoptotic cells.

PubMed

Hight, Matthew R; Cheung, Yiu-Yin; Nickels, Michael L; Dawson, Eric S; Zhao, Ping; Saleh, Samir; Buck, Jason R; Tang, Dewei; Washington, M Kay; Coffey, Robert J; Manning, H Charles

2014-04-15

Apoptosis, or programmed cell death, can be leveraged as a surrogate measure of response to therapeutic interventions in medicine. Cysteine aspartic acid-specific proteases, or caspases, are essential determinants of apoptosis signaling cascades and represent promising targets for molecular imaging. Here, we report development and in vivo validation of [(18)F]4-fluorobenzylcarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone ([(18)F]FB-VAD-FMK), a novel peptide-based molecular probe suitable for quantification of caspase activity in vivo using positron emission tomography (PET). Supported by molecular modeling studies and subsequent in vitro assays suggesting probe feasibility, the labeled pan-caspase inhibitory peptide, [(18)F]FB-VAD-FMK, was produced in high radiochemical yield and purity using a simple two-step, radiofluorination. The biodistribution of [(18)F]FB-VAD-FMK in normal tissue and its efficacy to predict response to molecularly targeted therapy in tumors was evaluated using microPET imaging of mouse models of human colorectal cancer. Accumulation of [(18)F]FB-VAD-FMK was found to agree with elevated caspase-3 activity in response to Aurora B kinase inhibition as well as a multidrug regimen that combined an inhibitor of mutant BRAF and a dual PI3K/mTOR inhibitor in (V600E)BRAF colon cancer. In the latter setting, [(18)F]FB-VAD-FMK PET was also elevated in the tumors of cohorts that exhibited reduction in size. These studies illuminate [(18)F]FB-VAD-FMK as a promising PET imaging probe to detect apoptosis in tumors and as a novel, potentially translatable biomarker for predicting response to personalized medicine. ©2014 AACR.

Model development and validation of geometrically complex eddy current coils using finite element methods

NASA Astrophysics Data System (ADS)

Brown, Alexander; Eviston, Connor

2017-02-01

Multiple FEM models of complex eddy current coil geometries were created and validated to calculate the change of impedance due to the presence of a notch. Capable realistic simulations of eddy current inspections are required for model assisted probability of detection (MAPOD) studies, inversion algorithms, experimental verification, and tailored probe design for NDE applications. An FEM solver was chosen to model complex real world situations including varying probe dimensions and orientations along with complex probe geometries. This will also enable creation of a probe model library database with variable parameters. Verification and validation was performed using other commercially available eddy current modeling software as well as experimentally collected benchmark data. Data analysis and comparison showed that the created models were able to correctly model the probe and conductor interactions and accurately calculate the change in impedance of several experimental scenarios with acceptable error. The promising results of the models enabled the start of an eddy current probe model library to give experimenters easy access to powerful parameter based eddy current models for alternate project applications.

Using video modeling to teach reciprocal pretend play to children with autism.

PubMed

MacDonald, Rebecca; Sacramone, Shelly; Mansfield, Renee; Wiltz, Kristine; Ahearn, William H

2009-01-01

The purpose of the present study was to use video modeling to teach children with autism to engage in reciprocal pretend play with typically developing peers. Scripted play scenarios involving various verbalizations and play actions with adults as models were videotaped. Two children with autism were each paired with a typically developing child, and a multiple-probe design across three play sets was used to evaluate the effects of the video modeling procedure. Results indicated that both children with autism and the typically developing peers acquired the sequences of scripted verbalizations and play actions quickly and maintained this performance during follow-up probes. In addition, probes indicated an increase in the mean number of unscripted verbalizations as well as reciprocal verbal interactions and cooperative play. These findings are discussed as they relate to the development of reciprocal pretend-play repertoires in young children with autism.

Using Video Modeling to Teach Reciprocal Pretend Play to Children with Autism

PubMed Central

MacDonald, Rebecca; Sacramone, Shelly; Mansfield, Renee; Wiltz, Kristine; Ahearn, William H

2009-01-01

The purpose of the present study was to use video modeling to teach children with autism to engage in reciprocal pretend play with typically developing peers. Scripted play scenarios involving various verbalizations and play actions with adults as models were videotaped. Two children with autism were each paired with a typically developing child, and a multiple-probe design across three play sets was used to evaluate the effects of the video modeling procedure. Results indicated that both children with autism and the typically developing peers acquired the sequences of scripted verbalizations and play actions quickly and maintained this performance during follow-up probes. In addition, probes indicated an increase in the mean number of unscripted verbalizations as well as reciprocal verbal interactions and cooperative play. These findings are discussed as they relate to the development of reciprocal pretend-play repertoires in young children with autism. PMID:19721729

Wideband THz Time Domain Spectroscopy based on Optical Rectification and Electro-Optic Sampling

PubMed Central

Tomasino, A.; Parisi, A.; Stivala, S.; Livreri, P.; Cino, A. C.; Busacca, A. C.; Peccianti, M.; Morandotti, R.

2013-01-01

We present an analytical model describing the full electromagnetic propagation in a THz time-domain spectroscopy (THz-TDS) system, from the THz pulses via Optical Rectification to the detection via Electro Optic-Sampling. While several investigations deal singularly with the many elements that constitute a THz-TDS, in our work we pay particular attention to the modelling of the time-frequency behaviour of all the stages which compose the experimental set-up. Therefore, our model considers the following main aspects: (i) pump beam focusing into the generation crystal; (ii) phase-matching inside both the generation and detection crystals; (iii) chromatic dispersion and absorption inside the crystals; (iv) Fabry-Perot effect; (v) diffraction outside, i.e. along the propagation, (vi) focalization and overlapping between THz and probe beams, (vii) electro-optic sampling. In order to validate our model, we report on the comparison between the simulations and the experimental data obtained from the same set-up, showing their good agreement. PMID:24173583

Van Allen Probes Science Gateway: Single-Point Access to Long-Term Radiation Belt Measurements and Space Weather Nowcasting

NASA Astrophysics Data System (ADS)

Romeo, G.; Barnes, R. J.; Ukhorskiy, A. Y.; Sotirelis, T.; Stephens, G.

2017-12-01

The Science Gateway gives single-point access to over 4.5 years of comprehensive wave and particle measurements from the Van Allen Probes NASA twin-spacecraft mission. The Gateway provides a set of visualization and data analysis tools including: HTML5-based interactive visualization of high-level data products from all instrument teams in the form of: line plots, orbital content plots, dynamical energy spectra, L-shell context plots (including two-spacecraft plotting), FFT spectra of wave data, solar wind and geomagnetic indices data, etc.; download custom multi-instrument CDF data files of selected data products; publication quality plots of digital data; combined orbit predicts for mission planning and coordination including: Van Allen Probes, MMS, THEMIS, Arase (ERG), Cluster, GOES, Geotail, FIREBIRD; magnetic footpoint calculator for coordination with LEO and ground-based assets; real-time computation and processing of empirical magnetic field models - computation of magnetic ephemeris, computation of adiabatic invariants. Van Allen Probes is the first spacecraft mission to provide a nowcast of the radiation environment in the heart of the radiation belts, where the radiation levels are the highest and most dangerous for spacecraft operations. For this purpose, all instruments continuously broadcast a subset of their science data in real time. Van Allen Probes partners with four foreign institutions who operate ground stations that receive the broadcast: Korea (KASI), the Czech republic (CAS), Argentina (CONAE), and Brazil (INPE). The SpWx broadcast is then collected at APL and delivered to the community via the Science Gateway.

Minimally invasive photopolymerization in intervertebral disc tissue cavities

NASA Astrophysics Data System (ADS)

Schmocker, Andreas M.; Khoushabi, Azadeh; Gantenbein-Ritter, Benjamin; Chan, Samantha; Bonél, Harald Marcel; Bourban, Pierre-Etienne; Mânson, Jan Anders; Schizas, Constantin; Pioletti, Dominique; Moser, Christophe

2014-03-01

Photopolymerized hydrogels are commonly used for a broad range of biomedical applications. As long as the polymer volume is accessible, gels can easily be hardened using light illumination. However, in clinics, especially for minimally invasive surgery, it becomes highly challenging to control photopolymerization. The ratios between polymerizationvolume and radiating-surface-area are several orders of magnitude higher than for ex-vivo settings. Also tissue scattering occurs and influences the reaction. We developed a Monte Carlo model for photopolymerization, which takes into account the solid/liquid phase changes, moving solid/liquid-boundaries and refraction on these boundaries as well as tissue scattering in arbitrarily designable tissue cavities. The model provides a tool to tailor both the light probe and the scattering/absorption properties of the photopolymer for applications such as medical implants or tissue replacements. Based on the simulations, we have previously shown that by adding scattering additives to the liquid monomer, the photopolymerized volume was considerably increased. In this study, we have used bovine intervertebral disc cavities, as a model for spinal degeneration, to study photopolymerization in-vitro. The cavity is created by enzyme digestion. Using a custom designed probe, hydrogels were injected and photopolymerized. Magnetic resonance imaging (MRI) and visual inspection tools were employed to investigate the successful photopolymerization outcomes. The results provide insights for the development of novel endoscopic light-scattering polymerization probes paving the way for a new generation of implantable hydrogels.

Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set.

PubMed

Kawahara, Akito Y; Breinholt, Jesse W; Espeland, Marianne; Storer, Caroline; Plotkin, David; Dexter, Kelly M; Toussaint, Emmanuel F A; St Laurent, Ryan A; Brehm, Gunnar; Vargas, Sergio; Forero, Dimitri; Pierce, Naomi E; Lohman, David J

2018-06-11

The Neotropical moth-like butterflies (Hedylidae) are perhaps the most unusual butterfly family. In addition to being species-poor, this family is predominantly nocturnal and has anti-bat ultrasound hearing organs. Evolutionary relationships among the 36 described species are largely unexplored. A new, target capture, anchored hybrid enrichment probe set ('BUTTERFLY2.0') was developed to infer relationships of hedylids and some of their butterfly relatives. The probe set includes 13 genes that have historically been used in butterfly phylogenetics. Our dataset comprised of up to 10,898 aligned base pairs from 22 hedylid species and 19 outgroups. Eleven of the thirteen loci were successfully captured from all samples, and the remaining loci were captured from ≥94% of samples. The inferred phylogeny was consistent with recent molecular studies by placing Hedylidae sister to Hesperiidae, and the tree had robust support for 80% of nodes. Our results are also consistent with morphological studies, with Macrosoma tipulata as the sister species to all remaining hedylids, followed by M. semiermis sister to the remaining species in the genus. We tested the hypothesis that nocturnality evolved once from diurnality in Hedylidae, and demonstrate that the ancestral condition was likely diurnal, with a shift to nocturnality early in the diversification of this family. The BUTTERFLY2.0 probe set includes standard butterfly phylogenetics markers, captures sequences from decades-old museum specimens, and is a cost-effective technique to infer phylogenetic relationships of the butterfly tree of life. Copyright © 2018 Elsevier Inc. All rights reserved.

Characterization of Biofilm Community Structure by Ribosomal RNA sequences

DTIC Science & Technology

1989-12-01

for strains of Fibrobacter, 2) Desulfobacter genus-specific probe, 3) Desulfosarcina genus-specific probe, 4) archaebacterial kingdom -specific probes...and 5) eubacterial kingdom -specific probes 5) eukaryote kingdom -specific probe and 6) a general probe encompassing all characterized sulfate-reducing...sets have been fabricated. The group-specific primer sets selectively amplify either sulfate-reducing bacteria or archaebacteria . The SRB-specific

Reactive underwater object inspection based on artificial electric sense.

PubMed

Lebastard, Vincent; Boyer, Frédéric; Lanneau, Sylvain

2016-07-26

Weakly electric fish can perform complex cognitive tasks based on extracting information from blurry electric images projected from their immediate environment onto their electro-sensitive skin. In particular they can be trained to recognize the intrinsic properties of objects such as their shape, size and electric nature. They do this by means of novel perceptual strategies that exploit the relations between the physics of a self-generated electric field, their body morphology and the ability to perform specific movement termed probing motor acts (PMAs). In this article we artificially reproduce and combine these PMAs to build an autonomous control strategy that allows an artificial electric sensor to find electrically contrasted objects, and to orbit around them based on a minimum set of measurements and simple reactive feedback control laws of the probe's motion. The approach does not require any simulation models and could be implemented on an autonomous underwater vehicle (AUV) equipped with artificial electric sense. The AUV has only to satisfy certain simple geometric properties, such as bi-laterally (left/right) symmetrical electrodes and possess a reasonably high aspect (length/width) ratio.

The role of curvature in the slowing down acceleration scenario

NASA Astrophysics Data System (ADS)

Cárdenas, Víctor H.; Rivera, Marco

2012-04-01

We introduce the curvature Ωk as a new free parameter in the Bayesian analysis using SNIa, BAO and CMB data, in a model with variable equation of state parameter w(z). We compare the results using both the Constitution and Union 2 data sets, and also study possible low redshift transitions in the deceleration parameter q(z). We found that, incorporating Ωk in the analysis, it is possible to make all the three observational probes consistent using both SNIa data sets. Our results support dark energy evolution at small redshift, and show that the tension between small and large redshift probes is ameliorated. However, although the tension decreases, it is still not possible to find a consensus set of parameters that fit all the three data set using the Chevalier-Polarski-Linder CPL parametrization.

[Application of characteristic NIR variables selection in portable detection of soluble solids content of apple by near infrared spectroscopy].

PubMed

Fan, Shu-Xiang; Huang, Wen-Qian; Li, Jiang-Bo; Guo, Zhi-Ming; Zhaq, Chun-Jiang

2014-10-01

In order to detect the soluble solids content(SSC)of apple conveniently and rapidly, a ring fiber probe and a portable spectrometer were applied to obtain the spectroscopy of apple. Different wavelength variable selection methods, including unin- formative variable elimination (UVE), competitive adaptive reweighted sampling (CARS) and genetic algorithm (GA) were pro- posed to select effective wavelength variables of the NIR spectroscopy of the SSC in apple based on PLS. The back interval LS- SVM (BiLS-SVM) and GA were used to select effective wavelength variables based on LS-SVM. Selected wavelength variables and full wavelength range were set as input variables of PLS model and LS-SVM model, respectively. The results indicated that PLS model built using GA-CARS on 50 characteristic variables selected from full-spectrum which had 1512 wavelengths achieved the optimal performance. The correlation coefficient (Rp) and root mean square error of prediction (RMSEP) for prediction sets were 0.962, 0.403°Brix respectively for SSC. The proposed method of GA-CARS could effectively simplify the portable detection model of SSC in apple based on near infrared spectroscopy and enhance the predictive precision. The study can provide a reference for the development of portable apple soluble solids content spectrometer.

Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms

PubMed Central

Pacheco, Maria P.; Pfau, Thomas; Sauter, Thomas

2016-01-01

Recent progress in high-throughput data acquisition has shifted the focus from data generation to processing and understanding of how to integrate collected information. Context specific reconstruction based on generic genome scale models like ReconX or HMR has the potential to become a diagnostic and treatment tool tailored to the analysis of specific individuals. The respective computational algorithms require a high level of predictive power, robustness and sensitivity. Although multiple context specific reconstruction algorithms were published in the last 10 years, only a fraction of them is suitable for model building based on human high-throughput data. Beside other reasons, this might be due to problems arising from the limitation to only one metabolic target function or arbitrary thresholding. This review describes and analyses common validation methods used for testing model building algorithms. Two major methods can be distinguished: consistency testing and comparison based testing. The first is concerned with robustness against noise, e.g., missing data due to the impossibility to distinguish between the signal and the background of non-specific binding of probes in a microarray experiment, and whether distinct sets of input expressed genes corresponding to i.e., different tissues yield distinct models. The latter covers methods comparing sets of functionalities, comparison with existing networks or additional databases. We test those methods on several available algorithms and deduce properties of these algorithms that can be compared with future developments. The set of tests performed, can therefore serve as a benchmarking procedure for future algorithms. PMID:26834640

Method for determining thermal conductivity and thermal capacity per unit volume of earth in situ

DOEpatents

Poppendiek, Heinz F.

1982-01-01

A method for determining the thermal conductivity of the earth in situ is based upon a cylindrical probe (10) having a thermopile (16) for measuring the temperature gradient between sets of thermocouple junctions (18 and 20) of the probe after it has been positioned in a borehole and has reached thermal equilibrium with its surroundings, and having means (14) for heating one set of thermocouple junctions (20) of the probe at a constant rate while the temperature gradient of the probe is recorded as a rise in temperature over several hours (more than about 3 hours). A fluid annulus thermally couples the probe to the surrounding earth. The recorded temperature curves are related to the earth's thermal conductivity, k.sub..infin., and to the thermal capacity per unit volume, (.gamma.c.sub.p).sub..infin., by comparison with calculated curves using estimates of k.sub..infin. and (.gamma.c.sub.p).sub..infin. in an equation which relates these parameters to a rise in the earth's temperature for a known and constant heating rate.

A method for automatically extracting infectious disease-related primers and probes from the literature

PubMed Central

2010-01-01

Background Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1) convert each document into a tree of paper sections, (2) detect the candidate sequences using a set of finite state machine-based recognizers, (3) refine problem sequences using a rule-based expert system, and (4) annotate the extracted sequences with their related organism/gene information. Results We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. Conclusions We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch. PMID:20682041

Wake flowfields for Jovian probe

NASA Technical Reports Server (NTRS)

Engel, C. D.; Hair, L. M.

1980-01-01

The wake flow field developed by the Galileo probe as it enters the Jovian atmosphere was modeled. The wake produced by the probe is highly energetic, yielding both convective and radiative heat inputs to the base of the probe. A component mathematical model for the inviscid near and far wake, the viscous near and far wake, and near wake recirculation zone was developed. Equilibrium thermodynamics were used for both the ablation and atmospheric species. Flow fields for three entry conditions were calculated. The near viscous wave was found to exhibit a variable axial pressure distribution with the neck pressure approximately three times the base pressure. Peak wake flow field temperatures were found to be in proportion to forebody post shock temperatures.

Single-Cell Resolution Imaging of Retinal Ganglion Cell Apoptosis In Vivo Using a Cell-Penetrating Caspase-Activatable Peptide Probe

PubMed Central

Qiu, Xudong; Johnson, James R.; Wilson, Bradley S.; Gammon, Seth T.; Piwnica-Worms, David; Barnett, Edward M.

2014-01-01

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 vivo imaging standard for functional evaluation of future probe analogues and provides a basis for extending this strategy into glaucoma-specific animal models. PMID:24586415

Review: Modelling chemical kinetics and convective heating in giant planet entries

NASA Astrophysics Data System (ADS)

Reynier, Philippe; D'Ammando, Giuliano; Bruno, Domenico

2018-01-01

A review of the existing chemical kinetics models for H2 / He mixtures and related transport and thermodynamic properties is presented as a pre-requisite towards the development of innovative models based on the state-to-state approach. A survey of the available results obtained during the mission preparation and post-flight analyses of the Galileo mission has been undertaken and a computational matrix has been derived. Different chemical kinetics schemes for hydrogen/helium mixtures have been applied to numerical simulations of the selected points along the entry trajectory. First, a reacting scheme, based on literature data, has been set up for computing the flow-field around the probe at high altitude and comparisons with existing numerical predictions are performed. Then, a macroscopic model derived from a state-to-state model has been constructed and incorporated into a CFD code. Comparisons with existing numerical results from the literature have been performed as well as cross-check comparisons between the predictions provided by the different models in order to evaluate the potential of innovative chemical kinetics models based on the state-to-state approach.

Rapid real-time diagnostic PCR for Trichophyton rubrum and Trichophyton mentagrophytes in patients with tinea unguium and tinea pedis using specific fluorescent probes.

PubMed

Miyajima, Yoshiharu; Satoh, Kazuo; Uchida, Takao; Yamada, Tsuyoshi; Abe, Michiko; Watanabe, Shin-ichi; Makimura, Miho; Makimura, Koichi

2013-03-01

Trichophyton rubrum and Trichophyton mentagrophytes human-type (synonym, Trichophyton interdigitale (anthropophilic)) are major causative pathogens of tinea unguium. For suitable diagnosis and treatment, rapid and accurate identification of etiologic agents in clinical samples using reliable molecular based method is required. For identification of organisms causing tinea unguium, we developed a new real-time polymerase chain reaction (PCR) with a pan-fungal primer set and probe, as well as specific primer sets and probes for T. rubrum and T. mentagrophytes human-type. We designed two sets of primers from the internal transcribed spacer 1 (ITS1) region of fungal ribosomal DNA (rDNA) and three quadruple fluorescent probes, one for detection wide range pathogenic fungi and two for classification of T. rubrum and T. mentagrophytes by specific binding to different sites in the ITS1 region. We investigated the specificity of these primer sets and probes using fungal genomic DNA, and also examined 42 clinical specimens with our real-time PCR. The primers and probes specifically detected T. rubrum, T. mentagrophytes, and a wide range of pathogenic fungi. The causative pathogens were identified in 42 nail and skin samples from 32 patients. The total time required for identification of fungal species in each clinical specimen was about 3h. The copy number of each fungal DNA in the clinical specimens was estimated from the intensity of fluorescence simultaneously. This PCR system is one of the most rapid and sensitive methods available for diagnosing dermatophytosis, including tinea unguium and tinea pedis. Copyright © 2012 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.

Partition coefficients of organic compounds between water and imidazolium-, pyridinium-, and phosphonium-based ionic liquids.

PubMed

Padró, Juan M; Pellegrino Vidal, Rocío B; Reta, Mario

2014-12-01

The partition coefficients, P IL/w, of several compounds, some of them of biological and pharmacological interest, between water and room-temperature ionic liquids based on the imidazolium, pyridinium, and phosphonium cations, namely 1-octyl-3-methylimidazolium hexafluorophosphate, N-octylpyridinium tetrafluorophosphate, trihexyl(tetradecyl)phosphonium chloride, trihexyl(tetradecyl)phosphonium bromide, trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl)imide, and trihexyl(tetradecyl)phosphonium dicyanamide, were accurately measured. In this way, we extended our database of partition coefficients in room-temperature ionic liquids previously reported. We employed the solvation parameter model with different probe molecules (the training set) to elucidate the chemical interactions involved in the partition process and discussed the most relevant differences among the three types of ionic liquids. The multiparametric equations obtained with the aforementioned model were used to predict the partition coefficients for compounds (the test set) not present in the training set, most being of biological and pharmacological interest. An excellent agreement between calculated and experimental log P IL/w values was obtained. Thus, the obtained equations can be used to predict, a priori, the extraction efficiency for any compound using these ionic liquids as extraction solvents in liquid-liquid extractions.

Outer planet probe cost estimates: First impressions

NASA Technical Reports Server (NTRS)

Niehoff, J.

1974-01-01

An examination was made of early estimates of outer planetary atmospheric probe cost by comparing the estimates with past planetary projects. Of particular interest is identification of project elements which are likely cost drivers for future probe missions. Data are divided into two parts: first, the description of a cost model developed by SAI for the Planetary Programs Office of NASA, and second, use of this model and its data base to evaluate estimates of probe costs. Several observations are offered in conclusion regarding the credibility of current estimates and specific areas of the outer planet probe concept most vulnerable to cost escalation.

Setting up a probe based, closed tube real-time PCR assay for focused detection of variable sequence alterations.

PubMed

Becságh, Péter; Szakács, Orsolya

2014-10-01

During diagnostic workflow when detecting sequence alterations, sometimes it is important to design an algorithm that includes screening and direct tests in combination. Normally the use of direct test, which is mainly sequencing, is limited. There is an increased need for effective screening tests, with "closed tube" during the whole process and therefore decreasing the risk of PCR product contamination. The aim of this study was to design such a closed tube, detection probe based screening assay to detect different kind of sequence alterations in the exon 11 of the human c-kit gene region. Inside this region there are variable possible deletions and single nucleotide changes. During assay setup, more probe chemistry formats were screened and tested. After some optimization steps the taqman probe format was selected.

An expression database for roots of the model legume Medicago truncatula under salt stress

PubMed Central

2009-01-01

Background Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. Description The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. Conclusion MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/. PMID:19906315

An expression database for roots of the model legume Medicago truncatula under salt stress.

PubMed

Li, Daofeng; Su, Zhen; Dong, Jiangli; Wang, Tao

2009-11-11

Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/.

Quasi-optical antenna-mixer-array design for terahertz frequencies

NASA Technical Reports Server (NTRS)

Guo, Yong; Potter, Kent A.; Rutledge, David B.

1992-01-01

A new quasi-optical antenna-mixer-array design for terahertz frequencies is presented. In the design, antenna and mixer are combined into an entity, based on the technology in which millimeter-wave horn antenna arrays have been fabricated in silicon wafers. It consists of a set of forward- and backward-looking horns made with a set of silicon wafers. The front side is used to receive incoming signal, and the back side is used to feed local oscillator signal. Intermediate frequency is led out from the side of the array. Signal received by the horn array is picked up by antenna probes suspended on thin silicon-oxynitride membranes inside the horns. Mixer diodes will be located on the membranes inside the horns. Modeling of such an antenna-mixer-array design is done on a scaled model at microwave frequencies. The impedance matching, RF and LO isolation, and patterns of the array have been tested and analyzed.

Versatile robotic probe calibration for position tracking in ultrasound imaging.

PubMed

Bø, Lars Eirik; Hofstad, Erlend Fagertun; Lindseth, Frank; Hernes, Toril A N

2015-05-07

Within the field of ultrasound-guided procedures, there are a number of methods for ultrasound probe calibration. While these methods are usually developed for a specific probe, they are in principle easily adapted to other probes. In practice, however, the adaptation often proves tedious and this is impractical in a research setting, where new probes are tested regularly. Therefore, we developed a method which can be applied to a large variety of probes without adaptation. The method used a robot arm to move a plastic sphere submerged in water through the ultrasound image plane, providing a slow and precise movement. The sphere was then segmented from the recorded ultrasound images using a MATLAB programme and the calibration matrix was computed based on this segmentation in combination with tracking information. The method was tested on three very different probes demonstrating both great versatility and high accuracy.

Versatile robotic probe calibration for position tracking in ultrasound imaging

NASA Astrophysics Data System (ADS)

Eirik Bø, Lars; Fagertun Hofstad, Erlend; Lindseth, Frank; Hernes, Toril A. N.

2015-05-01

Within the field of ultrasound-guided procedures, there are a number of methods for ultrasound probe calibration. While these methods are usually developed for a specific probe, they are in principle easily adapted to other probes. In practice, however, the adaptation often proves tedious and this is impractical in a research setting, where new probes are tested regularly. Therefore, we developed a method which can be applied to a large variety of probes without adaptation. The method used a robot arm to move a plastic sphere submerged in water through the ultrasound image plane, providing a slow and precise movement. The sphere was then segmented from the recorded ultrasound images using a MATLAB programme and the calibration matrix was computed based on this segmentation in combination with tracking information. The method was tested on three very different probes demonstrating both great versatility and high accuracy.

3D deformable organ model based liver motion tracking in ultrasound videos

NASA Astrophysics Data System (ADS)

Kim, Jung-Bae; Hwang, Youngkyoo; Oh, Young-Taek; Bang, Won-Chul; Lee, Heesae; Kim, James D. K.; Kim, Chang Yeong

2013-03-01

This paper presents a novel method of using 2D ultrasound (US) cine images during image-guided therapy to accurately track the 3D position of a tumor even when the organ of interest is in motion due to patient respiration. Tracking is possible thanks to a 3D deformable organ model we have developed. The method consists of three processes in succession. The first process is organ modeling where we generate a personalized 3D organ model from high quality 3D CT or MR data sets captured during three different respiratory phases. The model includes the organ surface, vessel and tumor, which can all deform and move in accord with patient respiration. The second process is registration of the organ model to 3D US images. From 133 respiratory phase candidates generated from the deformable organ model, we resolve the candidate that best matches the 3D US images according to vessel centerline and surface. As a result, we can determine the position of the US probe. The final process is real-time tracking using 2D US cine images captured by the US probe. We determine the respiratory phase by tracking the diaphragm on the image. The 3D model is then deformed according to respiration phase and is fitted to the image by considering the positions of the vessels. The tumor's 3D positions are then inferred based on respiration phase. Testing our method on real patient data, we have found the accuracy of 3D position is within 3.79mm and processing time is 5.4ms during tracking.

A Fiber Optic Probe for the Detection of Cataracts

NASA Technical Reports Server (NTRS)

Ansari, Rafat R.; Dhadwal, Harbans S.

1993-01-01

A compact fiber optic probe developed for on-orbit science experiments was used to detect the onset of cataracts, a capability that could eliminate physicians' guesswork and result in new drugs to 'dissolve' or slow down the cataract formation before surgery is necessary. The probe is based upon dynamic light scattering (DLS) principles. It has no moving parts, no apertures, and requires no optical alignment. It is flexible and easy to use. Results are presented for excised but intact human eye lenses. In a clinical setting, the device can be easily incorporated into a slit-lamp apparatus (ophthalmoscope) for complete eye diagnostics. In this set-up, the integrated fiber optic probe, the size of a pencil, delivers a low power cone of laser light into the eye of a patient and guides the light which is backscattered by the protein molecules of the lens through a receiving optical fiber to a photo detector. The non-invasive DLS measurements provide rapid determination of protein crystalline size and its size distribution in the eye lens.

Optimization of pressure probe placement and data analysis of engine-inlet distortion

NASA Astrophysics Data System (ADS)

Walter, S. F.

The purpose of this research is to examine methods by which quantification of inlet flow distortion may be improved upon. Specifically, this research investigates how data interpolation effects results, optimizing sampling locations of the flow, and determining the sensitivity related to how many sample locations there are. The main parameters that are indicative of a "good" design are total pressure recovery, mass flow capture, and distortion. This work focuses on the total pressure distortion, which describes the amount of non-uniformity that exists in the flow as it enters the engine. All engines must tolerate some level of distortion, however too much distortion can cause the engine to stall or the inlet to unstart. Flow distortion is measured at the interface between the inlet and the engine. To determine inlet flow distortion, a combination of computational and experimental pressure data is generated and then collapsed into an index that indicates the amount of distortion. Computational simulations generate continuous contour maps, but experimental data is discrete. Researchers require continuous contour maps to evaluate the overall distortion pattern. There is no guidance on how to best manipulate discrete points into a continuous pattern. Using one experimental, 320 probe data set and one, 320 point computational data set with three test runs each, this work compares the pressure results obtained using all 320 points of data from the original sets, both quantitatively and qualitatively, with results derived from selecting 40 grid point subsets and interpolating to 320 grid points. Each of the two, 40 point sets were interpolated to 320 grid points using four different interpolation methods in an attempt to establish the best method for interpolating small sets of data into an accurate, continuous contour map. Interpolation methods investigated are bilinear, spline, and Kriging in Cartesian space, as well as angular in polar space. Spline interpolation methods should be used as they result in the most accurate, precise, and visually correct predictions when compared results achieved from the full data sets. Researchers were interested if fewer than the recommended 40 probes could be used - especially when placed in areas of high interest - but still obtain equivalent or better results. For this investigation, the computational results from a two-dimensional inlet and experimental results of an axisymmetric inlet were used. To find the areas of interest, a uniform sampling of all possible locations was run through a Monte Carlo simulation with a varying number of probes. A probability density function of the resultant distortion index was plotted. Certain probes are required to come within the desired accuracy level of the distortion index based on the full data set. For the experimental results, all three test cases could be characterized with 20 probes. For the axisymmetric inlet, placing 40 probes in select locations could get the results for parameters of interest within less than 10% of the exact solution for almost all cases. For the two dimensional inlet, the results were not as clear. 80 probes were required to get within 10% of the exact solution for all run numbers, although this is largely due to the small value of the exact result. The sensitivity of each probe added to the experiment was analyzed. Instead of looking at the overall pattern established by optimizing probe placements, the focus is on varying the number of sampled probes from 20 to 40. The number of points falling within a 1% tolerance band of the exact solution were counted as good points. The results were normalized for each data set and a general sensitivity function was found to determine the sensitivity of the results. A linear regression was used to generalize the results for all data sets used in this work. However, they can be used by directly comparing the number of good points obtained with various numbers of probes as well. The sensitivity in the results is higher when fewer probes are used and gradually tapers off near 40 probes. There is a bigger gain in good points when the number of probes is increased from 20 to 21 probes than from 39 to 40 probes.

Restoring the lattice of Si-based atom probe reconstructions for enhanced information on dopant positioning.

PubMed

Breen, Andrew J; Moody, Michael P; Ceguerra, Anna V; Gault, Baptiste; Araullo-Peters, Vicente J; Ringer, Simon P

2015-12-01

The following manuscript presents a novel approach for creating lattice based models of Sb-doped Si directly from atom probe reconstructions for the purposes of improving information on dopant positioning and directly informing quantum mechanics based materials modeling approaches. Sophisticated crystallographic analysis techniques are used to detect latent crystal structure within the atom probe reconstructions with unprecedented accuracy. A distortion correction algorithm is then developed to precisely calibrate the detected crystal structure to the theoretically known diamond cubic lattice. The reconstructed atoms are then positioned on their most likely lattice positions. Simulations are then used to determine the accuracy of such an approach and show that improvements to short-range order measurements are possible for noise levels and detector efficiencies comparable with experimentally collected atom probe data. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative ptychographic reconstruction by applying a probe constraint

NASA Astrophysics Data System (ADS)

Reinhardt, J.; Schroer, C. G.

2018-04-01

The coherent scanning technique X-ray ptychography has become a routine tool for high-resolution imaging and nanoanalysis in various fields of research such as chemistry, biology or materials science. Often the ptychographic reconstruction results are analysed in order to yield absolute quantitative values for the object transmission and illuminating probe function. In this work, we address a common ambiguity encountered in scaling the object transmission and probe intensity via the application of an additional constraint to the reconstruction algorithm. A ptychographic measurement of a model sample containing nanoparticles is used as a test data set against which to benchmark in the reconstruction results depending on the type of constraint used. Achieving quantitative absolute values for the reconstructed object transmission is essential for advanced investigation of samples that are changing over time, e.g., during in-situ experiments or in general when different data sets are compared.

Evaluation of Finite-Rate Gas/Surface Interaction Models for a Carbon Based Ablator

NASA Technical Reports Server (NTRS)

Chen, Yih-Kanq; Goekcen, Tahir

2015-01-01

Two sets of finite-rate gas-surface interaction model between air and the carbon surface are studied. The first set is an engineering model with one-way chemical reactions, and the second set is a more detailed model with two-way chemical reactions. These two proposed models intend to cover the carbon surface ablation conditions including the low temperature rate-controlled oxidation, the mid-temperature diffusion-controlled oxidation, and the high temperature sublimation. The prediction of carbon surface recession is achieved by coupling a material thermal response code and a Navier-Stokes flow code. The material thermal response code used in this study is the Two-dimensional Implicit Thermal-response and Ablation Program, which predicts charring material thermal response and shape change on hypersonic space vehicles. The flow code solves the reacting full Navier-Stokes equations using Data Parallel Line Relaxation method. Recession analyses of stagnation tests conducted in NASA Ames Research Center arc-jet facilities with heat fluxes ranging from 45 to 1100 wcm2 are performed and compared with data for model validation. The ablating material used in these arc-jet tests is Phenolic Impregnated Carbon Ablator. Additionally, computational predictions of surface recession and shape change are in good agreement with measurement for arc-jet conditions of Small Probe Reentry Investigation for Thermal Protection System Engineering.

TARGETED PRINCIPLE COMPONENT ANALYSIS: A NEW MOTION ARTIFACT CORRECTION APPROACH FOR NEAR-INFRARED SPECTROSCOPY

PubMed Central

YÜCEL, MERYEM A.; SELB, JULIETTE; COOPER, ROBERT J.; BOAS, DAVID A.

2014-01-01

As near-infrared spectroscopy (NIRS) broadens its application area to different age and disease groups, motion artifacts in the NIRS signal due to subject movement is becoming an important challenge. Motion artifacts generally produce signal fluctuations that are larger than physiological NIRS signals, thus it is crucial to correct for them before obtaining an estimate of stimulus evoked hemodynamic responses. There are various methods for correction such as principle component analysis (PCA), wavelet-based filtering and spline interpolation. Here, we introduce a new approach to motion artifact correction, targeted principle component analysis (tPCA), which incorporates a PCA filter only on the segments of data identified as motion artifacts. It is expected that this will overcome the issues of filtering desired signals that plagues standard PCA filtering of entire data sets. We compared the new approach with the most effective motion artifact correction algorithms on a set of data acquired simultaneously with a collodion-fixed probe (low motion artifact content) and a standard Velcro probe (high motion artifact content). Our results show that tPCA gives statistically better results in recovering hemodynamic response function (HRF) as compared to wavelet-based filtering and spline interpolation for the Velcro probe. It results in a significant reduction in mean-squared error (MSE) and significant enhancement in Pearson’s correlation coefficient to the true HRF. The collodion-fixed fiber probe with no motion correction performed better than the Velcro probe corrected for motion artifacts in terms of MSE and Pearson’s correlation coefficient. Thus, if the experimental study permits, the use of a collodion-fixed fiber probe may be desirable. If the use of a collodion-fixed probe is not feasible, then we suggest the use of tPCA in the processing of motion artifact contaminated data. PMID:25360181

Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods

NASA Astrophysics Data System (ADS)

Sippl, Wolfgang

2000-08-01

One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient ( r 2 = 0.617, q 2 LOO = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained ( r 2 = 0.991, q 2 LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment ( r 2 = 0.951, q 2 LOO = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model.

Supporting Collaborative Health Tracking in the Hospital: Patients’ Perspectives

PubMed Central

Mishra, Sonali R.; Miller, Andrew D.; Haldar, Shefali; Khelifi, Maher; Eschler, Jordan; Elera, Rashmi G.; Pollack, Ari H; Pratt, Wanda

2018-01-01

The hospital setting creates a high-stakes environment where patients’ lives depend on accurate tracking of health data. Despite recent work emphasizing the importance of patients’ engagement in their own health care, less is known about how patients track their health and care in the hospital. Through interviews and design probes, we investigated hospitalized patients’ tracking activity and analyzed our results using the stage-based personal informatics model. We used this model to understand how to support the tracking needs of hospitalized patients at each stage. In this paper, we discuss hospitalized patients’ needs for collaboratively tracking their health with their care team. We suggest future extensions of the stage-based model to accommodate collaborative tracking situations, such as hospitals, where data is collected, analyzed, and acted on by multiple people. Our findings uncover new directions for HCI research and highlight ways to support patients in tracking their care and improving patient safety. PMID:29721554

Illustration of Step-Wise Latent Class Modeling With Covariates and Taxometric Analysis in Research Probing Children's Mental Models in Learning Sciences

PubMed Central

Stamovlasis, Dimitrios; Papageorgiou, George; Tsitsipis, Georgios; Tsikalas, Themistoklis; Vaiopoulou, Julie

2018-01-01

This paper illustrates two psychometric methods, latent class analysis (LCA) and taxometric analysis (TA) using empirical data from research probing children's mental representation in science learning. LCA is used to obtain a typology based on observed variables and to further investigate how the encountered classes might be related to external variables, where the effectiveness of classification process and the unbiased estimations of parameters become the main concern. In the step-wise LCA, the class membership is assigned and subsequently its relationship with covariates is established. This leading-edge modeling approach suffers from severe downward-biased estimations. The illustration of LCA is focused on alternative bias correction approaches and demonstrates the effect of modal and proportional class-membership assignment along with BCH and ML correction procedures. The illustration of LCA is presented with three covariates, which are psychometric variables operationalizing formal reasoning, divergent thinking and field dependence-independence, respectively. Moreover, taxometric analysis, a method designed to detect the type of the latent structural model, categorical or dimensional, is introduced, along with the relevant basic concepts and tools. TA was applied complementarily in the same data sets to answer the fundamental hypothesis about children's naïve knowledge on the matters under study and it comprises an additional asset in building theory which is fundamental for educational practices. Taxometric analysis provided results that were ambiguous as far as the type of the latent structure. This finding initiates further discussion and sets a problematization within this framework rethinking fundamental assumptions and epistemological issues. PMID:29713300

Development of the polymerase chain reaction for diagnosis of chancroid.

PubMed Central

Chui, L; Albritton, W; Paster, B; Maclean, I; Marusyk, R

1993-01-01

The published nucleotide sequences of the 16S rRNA gene of Haemophilus ducreyi were used to develop primer sets and probes for the diagnosis of chancroid by polymerase chain reaction (PCR) DNA amplification. One set of broad specificity primers yielded a 303-bp PCR product from all bacteria tested. Two 16-base probes internal to this sequence were species specific for H. ducreyi when tested with 12 species of the families Pasteurellaceae and Enterobacteriaceae. The two probes in combination with the broad specificity primers were 100% sensitive with 51 strains of H. ducreyi isolated from six continents over a 15-year period. The direct detection of H. ducreyi from 100 clinical specimens by PCR showed a sensitivity of 83 to 98% and a specificity of 51 to 67%, depending on the number of amplification cycles. Images PMID:8458959

Stellar Occultation Probe of Triton's Atmosphere

NASA Technical Reports Server (NTRS)

Elliot, James L.

1998-01-01

The goals of this research were (i) to better characterize Triton's atmospheric structure by probing a region not well investigated by Voyager and (ii) to begin acquiring baseline data for an investigation of the time evolution of the atmosphere which will set limits on the thermal conductivity of the surface and the total mass of N2 in the atmosphere. Our approach was to use observations (with the Kuiper Airborne Observatory) of a stellar occultation by Triton that was predicted to occur on 1993 July 10. As described in the attached reprint, we achieved these objectives through observation of this occultation and a subsequent one with the KAO in 1995. We found new results about Triton's atmospheric structure from the analysis of the two occultations observed with the KAO and ground-based data. These stellar occultation observations made both in the visible and infrared, have good spatial coverage of Triton including the first Triton central-flash observations, and are the first data to probe the 20-100 km altitude level on Triton. The small-planet light curve model of Elliot and Young (AJ 103, 991-1015) was generalized to include stellar flux refracted by the far limb, and then fitted to the data. Values of the pressure, derived from separate immersion and emersion chords, show no significant trends with latitude indicating that Triton's atmosphere is spherically symmetric at approximately 50 km altitude to within the error of the measurements. However, asymmetry observed in the central flash indicates the atmosphere is not homogeneous at the lowest levels probed (approximately 20 km altitude). From the average of the 1995 occultation data, the equivalent-isothermal temperature of the atmosphere is 47 +/- 1 K and the atmospheric pressure at 1400 km radius (approximately 50 km altitude) is 1.4 +/- 0.1 microbar. Both of these are not consistent with a model based on Voyager UVS and RSS observations in 1989 (Strobel et al, Icarus 120, 266-289). The atmospheric temperature from the occultation is 5 K colder than that predicted by the model and the observed pressure is a factor of 1.8 greater than the model.

Space Flight Plasma Data Analysis

NASA Technical Reports Server (NTRS)

Wright, Kenneth H.; Minow, Joseph I.

2009-01-01

This slide presentation reviews a method to analyze the plasma data that is reported on board the International Space station (ISS). The Floating Potential Measurement Unit (FPMU), the role of which is to obtain floating potential and ionosphere plasma measurements for validation of the ISS charging model, assess photo voltaic array variability and interpreting IRI predictions, is composed of four probes: Floating Potential Probe (FPP), Wide-sweep Langmuir Probe (WLP), Narrow-sweep Langmuir Probe (NLP) and the Plasma Impedance Probe (PIP). This gives redundant measurements of each parameter. There are also many 'boxes' that the data must pass through before being captured by the ground station, which leads to telemetry noise. Methods of analysis for the various signals from the different sets are reviewed. There is also a brief discussion of LP analysis of Low Earth Orbit plasma simulation source.

Effects of Computer-Assisted Instruction on Students' Knowledge of the Self-Determined Learning Model of Instruction and Disruptive Behavior

ERIC Educational Resources Information Center

Mazzotti, Valerie L.; Wood, Charles L.; Test, David W.; Fowler, Catherine H.

2012-01-01

Instruction about goal setting can increase students' self-determination and reduce problem behavior. Computer-assisted instruction could offer teachers another format for teaching goal setting and self-determination. This study used a multiple probes across participants design to examine the effects of computer-assisted instruction on students'…

Accuracy, reproducibility, and uncertainty analysis of thyroid-probe-based activity measurements for determination of dose calibrator settings.

PubMed

Esquinas, Pedro L; Tanguay, Jesse; Gonzalez, Marjorie; Vuckovic, Milan; Rodríguez-Rodríguez, Cristina; Häfeli, Urs O; Celler, Anna

2016-12-01

In the nuclear medicine department, the activity of radiopharmaceuticals is measured using dose calibrators (DCs) prior to patient injection. The DC consists of an ionization chamber that measures current generated by ionizing radiation (emitted from the radiotracer). In order to obtain an activity reading, the current is converted into units of activity by applying an appropriate calibration factor (also referred to as DC dial setting). Accurate determination of DC dial settings is crucial to ensure that patients receive the appropriate dose in diagnostic scans or radionuclide therapies. The goals of this study were (1) to describe a practical method to experimentally determine dose calibrator settings using a thyroid-probe (TP) and (2) to investigate the accuracy, reproducibility, and uncertainties of the method. As an illustration, the TP method was applied to determine 188 Re dial settings for two dose calibrator models: Atomlab 100plus and Capintec CRC-55tR. Using the TP to determine dose calibrator settings involved three measurements. First, the energy-dependent efficiency of the TP was determined from energy spectra measurements of two calibration sources ( 152 Eu and 22 Na). Second, the gamma emissions from the investigated isotope ( 188 Re) were measured using the TP and its activity was determined using γ-ray spectroscopy methods. Ambient background, scatter, and source-geometry corrections were applied during the efficiency and activity determination steps. Third, the TP-based 188 Re activity was used to determine the dose calibrator settings following the calibration curve method [B. E. Zimmerman et al., J. Nucl. Med. 40, 1508-1516 (1999)]. The interobserver reproducibility of TP measurements was determined by the coefficient of variation (COV) and uncertainties associated to each step of the measuring process were estimated. The accuracy of activity measurements using the proposed method was evaluated by comparing the TP activity estimates of 99m Tc, 188 Re, 131 I, and 57 Co samples to high purity Ge (HPGe) γ-ray spectroscopy measurements. The experimental 188 Re dial settings determined with the TP were 76.5 ± 4.8 and 646 ± 43 for Atomlab 100plus and Capintec CRC-55tR, respectively. In the case of Atomlab 100plus, the TP-based dial settings improved the accuracy of 188 Re activity measurements (confirmed by HPGe measurements) as compared to manufacturer-recommended settings. For Capintec CRC-55tR, the TP-based settings were in agreement with previous results [B. E. Zimmerman et al., J. Nucl. Med. 40, 1508-1516 (1999)] which demonstrated that manufacturer-recommended settings overestimate 188 Re activity by more than 20%. The largest source of uncertainty in the experimentally determined dial settings was due to the application of a geometry correction factor, followed by the uncertainty of the scatter-corrected photopeak counts and the uncertainty of the TP efficiency calibration experiment. When using the most intense photopeak of the sample's emissions, the TP method yielded accurate (within 5% errors) and reproducible (COV = 2%) measurements of sample's activity. The relative uncertainties associated with such measurements ranged from 6% to 8% (expanded uncertainty at 95% confidence interval, k = 2). Accurate determination/verification of dose calibrator dial settings can be performed using a thyroid-probe in the nuclear medicine department.

To bind or not to bind, that's the wrong question: Features and objects coexist in visual short-term memory.

PubMed

Geigerman, Shriradha; Verhaeghen, Paul; Cerella, John

2016-06-01

In three experiments, we investigated whether features and whole-objects can be represented simultaneously in visual short-term memory (VSTM). Participants were presented with a memory set of colored shapes; we probed either for the constituent features or for the whole object, and analyzed retrieval dynamics (cumulative response time distributions). In our first experiment, we used whole-object probes that recombined features from the memory display; we found that subjects' data conformed to a kitchen-line model, showing that they used whole-object representations for the matching process. In the second experiment, we encouraged independent-feature representations by using probes that used features not present in the memory display; subjects' data conformed to the race-model inequality, showing that they used independent-feature representations for the matching process. In a final experiment, we used both types of probes; subjects now used both types of representations, depending on the nature of the probe. Combined, our three experiments suggest that both feature and whole-object representations can coexist in VSTM. Copyright © 2016 Elsevier B.V. All rights reserved.

Visual attention is required for multiple object tracking.

PubMed

Tran, Annie; Hoffman, James E

2016-12-01

In the multiple object tracking task, participants attempt to keep track of a moving set of target objects embedded in an identical set of moving distractors. Depending on several display parameters, observers are usually only able to accurately track 3 to 4 objects. Various proposals attribute this limit to a fixed number of discrete indexes (Pylyshyn, 1989), limits in visual attention (Cavanagh & Alvarez, 2005), or "architectural limits" in visual cortical areas (Franconeri, 2013). The present set of experiments examined the specific role of visual attention in tracking using a dual-task methodology in which participants tracked objects while identifying letter probes appearing on the tracked objects and distractors. As predicted by the visual attention model, probe identification was faster and/or more accurate when probes appeared on tracked objects. This was the case even when probes were more than twice as likely to appear on distractors suggesting that some minimum amount of attention is required to maintain accurate tracking performance. When the need to protect tracking accuracy was relaxed, participants were able to allocate more attention to distractors when probes were likely to appear there but only at the expense of large reductions in tracking accuracy. A final experiment showed that people attend to tracked objects even when letters appearing on them are task-irrelevant, suggesting that allocation of attention to tracked objects is an obligatory process. These results support the claim that visual attention is required for tracking objects. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization

PubMed Central

Okamura, Yukio; Kondo, Satoshi; Sase, Ichiro; Suga, Takayuki; Mise, Kazuyuki; Furusawa, Iwao; Kawakami, Shigeki; Watanabe, Yuichiro

2000-01-01

A set of fluorescently-labeled DNA probes that hybridize with the target RNA and produce fluorescence resonance energy transfer (FRET) signals can be utilized for the detection of specific RNA. We have developed probe sets to detect and discriminate single-strand RNA molecules of plant viral genome, and sought a method to improve the FRET signals to handle in vivo applications. Consequently, we found that a double-labeled donor probe labeled with Bodipy dye yielded a remarkable increase in fluorescence intensity compared to a single-labeled donor probe used in an ordinary FRET. This double-labeled donor system can be easily applied to improve various FRET probes since the dependence upon sequence and label position in enhancement is not as strict. Furthermore this method could be applied to other nucleic acid substances, such as oligo RNA and phosphorothioate oligonucleotides (S-oligos) to enhance FRET signal. Although the double-labeled donor probes labeled with a variety of fluorophores had unexpected properties (strange UV-visible absorption spectra, decrease of intensity and decay of donor fluorescence) compared with single-labeled ones, they had no relation to FRET enhancement. This signal amplification mechanism cannot be explained simply based on our current results and knowledge of FRET. Yet it is possible to utilize this double-labeled donor system in various applications of FRET as a simple signal-enhancement method. PMID:11121494

Sensitive DNA detection and SNP discrimination using ultrabright SERS nanorattles and magnetic beads for malaria diagnostics.

PubMed

Ngo, Hoan T; Gandra, Naveen; Fales, Andrew M; Taylor, Steve M; Vo-Dinh, Tuan

2016-07-15

One of the major obstacles to implement nucleic acid-based molecular diagnostics at the point-of-care (POC) and in resource-limited settings is the lack of sensitive and practical DNA detection methods that can be seamlessly integrated into portable platforms. Herein we present a sensitive yet simple DNA detection method using a surface-enhanced Raman scattering (SERS) nanoplatform: the ultrabright SERS nanorattle. The method, referred to as the nanorattle-based method, involves sandwich hybridization of magnetic beads that are loaded with capture probes, target sequences, and ultrabright SERS nanorattles that are loaded with reporter probes. Upon hybridization, a magnet was applied to concentrate the hybridization sandwiches at a detection spot for SERS measurements. The ultrabright SERS nanorattles, composed of a core and a shell with resonance Raman reporters loaded in the gap space between the core and the shell, serve as SERS tags for signal detection. Using this method, a specific DNA sequence of the malaria parasite Plasmodium falciparum could be detected with a detection limit of approximately 100 attomoles. Single nucleotide polymorphism (SNP) discrimination of wild type malaria DNA and mutant malaria DNA, which confers resistance to artemisinin drugs, was also demonstrated. These test models demonstrate the molecular diagnostic potential of the nanorattle-based method to both detect and genotype infectious pathogens. Furthermore, the method's simplicity makes it a suitable candidate for integration into portable platforms for POC and in resource-limited settings applications. Copyright © 2016. Published by Elsevier B.V.

Evanescent wave absorbance based fiber optic biosensor for label-free detection of E. coli at 280 nm wavelength.

PubMed

Bharadwaj, Reshma; Sai, V V R; Thakare, Kamini; Dhawangale, Arvind; Kundu, Tapanendu; Titus, Susan; Verma, Pradeep Kumar; Mukherji, Soumyo

2011-03-15

A novel label-free technique for the detection of pathogens based on evanescent wave absorbance (EWA) changes at 280 nm from a U-bent optical fiber sensor is demonstrated. Bending a decladded fiber into a U-shaped structure enhances the penetration depth of evanescent waves and hence sensitivity of the probe. We show that the enhanced EWA response from such U-bent probes, caused by the inherent optical absorbance properties of bacterial cells or biomolecules specifically bound to the sensor surface, can be exploited for the detection of pathogens. A portable optical set-up with a UV light emitting diode, a spectrometer and U-bent fiber optic probe of 200 μm core diameter, 0.75 mm bend radius and effective probe length of 1cm demonstrated an ability to detect less than 1000 cfu/ml. Copyright © 2011. Published by Elsevier B.V.

Prospective comparison of virtual fluoroscopy to fluoroscopy and plain radiographs for placement of lumbar pedicle screws.

PubMed

Resnick, Daniel K

2003-06-01

Fluoroscopy-based frameless stereotactic systems provide feedback to the surgeon using virtual fluoroscopic images. The real-life accuracy of these virtual images has not been compared with traditional fluoroscopy in a clinical setting. We prospectively studied 23 consecutive cases. In two cases, registration errors precluded the use of virtual fluoroscopy. Pedicle probes placed with virtual fluoroscopic imaging were imaged with traditional fluoroscopy in the remaining 21 cases. Position of the probes was judged to be ideal, acceptable but not ideal, or not acceptable based on the traditional fluoroscopic images. Virtual fluoroscopy was used to place probes in for 97 pedicles from L1 to the sacrum. Eighty-eight probes were judged to be in ideal position, eight were judged to be acceptable but not ideal, and one probe was judged to be in an unacceptable position. This probe was angled toward an adjacent disc space. Therefore, 96 of 97 probes placed using virtual fluoroscopy were found to be in an acceptable position. The positive predictive value for acceptable screw placement with virtual fluoroscopy compared with traditional fluoroscopy was 99%. A probe placed with virtual fluoroscopic guidance will be judged to be in an acceptable position when imaged with traditional fluoroscopy 99% of the time.

OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture.

PubMed

Gasc, Cyrielle; Constantin, Antony; Jaziri, Faouzi; Peyret, Pierre

2017-01-01

The detection and identification of bacterial pathogens involved in acts of bio- and agroterrorism are essential to avoid pathogen dispersal in the environment and propagation within the population. Conventional molecular methods, such as PCR amplification, DNA microarrays or shotgun sequencing, are subject to various limitations when assessing environmental samples, which can lead to inaccurate findings. We developed a hybridization capture strategy that uses a set of oligonucleotide probes to target and enrich biomarkers of interest in environmental samples. Here, we present Oligonucleotide Capture Probes for Pathogen Identification Database (OCaPPI-Db), an online capture probe database containing a set of 1,685 oligonucleotide probes allowing for the detection and identification of 30 biothreat agents up to the species level. This probe set can be used in its entirety as a comprehensive diagnostic tool or can be restricted to a set of probes targeting a specific pathogen or virulence factor according to the user's needs. : http://ocappidb.uca.works. © The Author(s) 2017. Published by Oxford University Press.

Automated data selection method to improve robustness of diffuse optical tomography for breast cancer imaging

PubMed Central

Vavadi, Hamed; Zhu, Quing

2016-01-01

Imaging-guided near infrared diffuse optical tomography (DOT) has demonstrated a great potential as an adjunct modality for differentiation of malignant and benign breast lesions and for monitoring treatment response of breast cancers. However, diffused light measurements are sensitive to artifacts caused by outliers and errors in measurements due to probe-tissue coupling, patient and probe motions, and tissue heterogeneity. In general, pre-processing of the measurements is needed by experienced users to manually remove these outliers and therefore reduce imaging artifacts. An automated method of outlier removal, data selection, and filtering for diffuse optical tomography is introduced in this manuscript. This method consists of multiple steps to first combine several data sets collected from the same patient at contralateral normal breast and form a single robust reference data set using statistical tests and linear fitting of the measurements. The second step improves the perturbation measurements by filtering out outliers from the lesion site measurements using model based analysis. The results of 20 malignant and benign cases show similar performance between manual data processing and automated processing and improvement in tissue characterization of malignant to benign ratio by about 27%. PMID:27867711

Gemi: PCR Primers Prediction from Multiple Alignments

PubMed Central

Sobhy, Haitham; Colson, Philippe

2012-01-01

Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size. PMID:23316117

A revised design for microarray experiments to account for experimental noise and uncertainty of probe response.

PubMed

Pozhitkov, Alex E; Noble, Peter A; Bryk, Jarosław; Tautz, Diethard

2014-01-01

Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal response was fitted to an adsorption model. We found that significant variance of the signal could be controlled by averaging across probes and removing probes that are nonresponsive or poorly responsive in the calibration experiment. Taking this into account, one can obtain a more reliable signal with the added option of obtaining absolute rather than relative measurements. The assessment of technical variance within the experiments, combined with the calibration of probes allows to remove poorly responding probes and yields more reliable signals for the remaining ones. Once an array is properly calibrated, absolute quantification of signals becomes straight forward, alleviating the need for normalization and reference hybridizations.

Nanospot soldering polystyrene nanoparticles with an optical fiber probe laser irradiating a metallic AFM probe based on the near-field enhancement effect.

PubMed

Cui, Jianlei; Yang, Lijun; Wang, Yang; Mei, Xuesong; Wang, Wenjun; Hou, Chaojian

2015-02-04

With the development of nanoscience and nanotechnology for the bottom-up nanofabrication of nanostructures formed from polystyrene nanoparticles, joining technology is an essential step in the manufacturing and assembly of nanodevices and nanostructures in order to provide mechanical integration and connection. To study the nanospot welding of polystyrene nanoparticles, we propose a new nanospot-soldering method using the near-field enhancement effect of a metallic atomic force microscope (AFM) probe tip that is irradiated by an optical fiber probe laser. On the basis of our theoretical analysis of the near-field enhancement effect, we set up an experimental system for nanospot soldering; this approach is carried out by using an optical fiber probe laser to irradiate the AFM probe tip to sinter the nanoparticles, providing a promising technical approach for the application of nanosoldering in nanoscience and nanotechnology.

NMR based solvent exchange experiments to understand the conformational preference of intrinsically disordered proteins using FG-nucleoporin peptide as a model

PubMed Central

Heisel, Kurt A.; Krishnan, V. V.

2014-01-01

The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex (NPC) is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on 13Cα, 1Hα, and 1HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water). PMID:24037535

Subject-specific and pose-oriented facial features for face recognition across poses.

PubMed

Lee, Ping-Han; Hsu, Gee-Sern; Wang, Yun-Wen; Hung, Yi-Ping

2012-10-01

Most face recognition scenarios assume that frontal faces or mug shots are available for enrollment to the database, faces of other poses are collected in the probe set. Given a face from the probe set, one needs to determine whether a match in the database exists. This is under the assumption that in forensic applications, most suspects have their mug shots available in the database, and face recognition aims at recognizing the suspects when their faces of various poses are captured by a surveillance camera. This paper considers a different scenario: given a face with multiple poses available, which may or may not include a mug shot, develop a method to recognize the face with poses different from those captured. That is, given two disjoint sets of poses of a face, one for enrollment and the other for recognition, this paper reports a method best for handling such cases. The proposed method includes feature extraction and classification. For feature extraction, we first cluster the poses of each subject's face in the enrollment set into a few pose classes and then decompose the appearance of the face in each pose class using Embedded Hidden Markov Model, which allows us to define a set of subject-specific and pose-priented (SSPO) facial components for each subject. For classification, an Adaboost weighting scheme is used to fuse the component classifiers with SSPO component features. The proposed method is proven to outperform other approaches, including a component-based classifier with local facial features cropped manually, in an extensive performance evaluation study.

EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments.

PubMed

Milewski, Marek C; Kamel, Karol; Kurzynska-Kokorniak, Anna; Chmielewski, Marcin K; Figlerowicz, Marek

2017-10-01

Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. The software applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions. To provide optimal solutions, the evolutionary algorithm sorts oligonucleotides into sets, preserves preselected parts of the oligonucleotides, and shapes their remaining parts. In addition, the oligonucleotide sets can be designed and grouped based on their melting temperatures. For the user's convenience, EvOligo is provided with a user-friendly graphical interface. EvOligo was used to design individual oligonucleotides, oligonucleotide pairs, and groups of oligonucleotide pairs that are characterized by the following parameters: (1) weaker cross-interactions between the non-complementary oligonucleotides and (2) more uniform ranges of the oligonucleotide pair melting temperatures than other available software products. In addition, in contrast to other grouping algorithms, EvOligo offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user.

Development of coaxial ultrasonic probe for fatty liver diagnostic system using ultrasonic velocity change

NASA Astrophysics Data System (ADS)

Hori, Makoto; Yokota, Daiki; Aotani, Yuhei; Kumagai, Yuta; Wada, Kenji; Matsunaka, Toshiyuki; Morikawa, Hiroyasu; Horinaka, Hiromichi

2017-07-01

A diagnostic system for fatty liver at an early stage is needed because fatty liver is linked to metabolic syndrome. We have already proposed a fatty liver diagnosis method based on the temperature coefficient of ultrasonic velocity. In this study, we fabricated a coaxial ultrasonic probe by integrating two kinds of transducers for warming and signal detection. The diagnosis system equipped with the coaxial probe was applied to tissue-mimicking phantoms including the fat area. The fat content rates corresponding to the set rates of the phantoms were estimated by the ultrasonic velocity-change method.

Determination of plasma density from data on the ion current to cylindrical and planar probes

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

Voloshin, D. G., E-mail: dvoloshin@mics.msu.su; Vasil’eva, A. N.; Kovalev, A. S.

2016-12-15

To improve probe methods of plasma diagnostics, special probe measurements were performed and numerical models describing ion transport to a probe with allowance for collisions were developed. The current–voltage characteristics of cylindrical and planar probes were measured in an RF capacitive discharge in argon at a frequency of 81 MHz and plasma densities of 10{sup 10}–10{sup 11} cm{sup –3}, typical of modern RF reactors. 1D and 2D numerical models based on the particle-in-cell method with Monte Carlo collisions for simulating ion motion and the Boltzmann equilibrium for electrons are developed to describe current collection by a probe. The models weremore » used to find the plasma density from the ion part of the current–voltage characteristic, study the effect of ion collisions, and verify simplified approaches to determining the plasma density. A 1D hydrodynamic model of the ion current to a cylindrical probe with allowance for ion collisions is proposed. For a planar probe, a method to determine the plasma density from the averaged numerical results is developed. A comparative analysis of different approaches to calculating the plasma density from the ion current to a probe is performed.« less

X-ray fluorescence microscopy artefacts in elemental maps of topologically complex samples: Analytical observations, simulation and a map correction method

NASA Astrophysics Data System (ADS)

Billè, Fulvio; Kourousias, George; Luchinat, Enrico; Kiskinova, Maya; Gianoncelli, Alessandra

2016-08-01

XRF spectroscopy is among the most widely used non-destructive techniques for elemental analysis. Despite the known angular dependence of X-ray fluorescence (XRF), topological artefacts remain an unresolved issue when using X-ray micro- or nano-probes. In this work we investigate the origin of the artefacts in XRF imaging of topologically complex samples, which are unresolved problems in studies of organic matter due to the limited travel distances of low energy XRF emission from the light elements. In particular we mapped Human Embryonic Kidney (HEK293T) cells. The exemplary results with biological samples, obtained with a soft X-ray scanning microscope installed at a synchrotron facility were used for testing a mathematical model based on detector response simulations, and for proposing an artefact correction method based on directional derivatives. Despite the peculiar and specific application, the methodology can be easily extended to hard X-rays and to set-ups with multi-array detector systems when the dimensions of surface reliefs are in the order of the probing beam size.

Teaching adolescents with severe disabilities to use the public telephone.

PubMed

Test, D W; Spooner, F; Keul, P K; Grossi, T

1990-04-01

Two adolescents with severe disabilities served as participants in a study conducted to train in the use of the public telephone to call home. Participants were trained to complete a 17-step task analysis using a training package which consisted of total task presentation in conjunction with a four-level prompting procedure (i.e., independent, verbal, verbal + gesture, verbal + guidance). All instruction took place in a public setting (e.g., a shopping mall) with generalization probes taken in two alternative settings (e.g., a movie theater and a convenience store). A multiple probe across individuals design demonstrated the training package was successful in teaching participants to use the telephone to call home. In addition, newly acquired skills generalized to the two untrained settings. Implications for community-based training are discussed.

Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization

PubMed Central

Ullrich, Thomas; Ermantraut, Eugen; Schulz, Torsten; Steinmetzer, Katrin

2012-01-01

Background State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. Methodology and Principal Findings The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. Conclusions and Significance The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a single assay and to perform the assay on simple and robust instrumentation is a prerequisite for the development of novel molecular point of care tests. PMID:22539973

The precedence of topological change over top-down attention in masked priming.

PubMed

Huang, Yan; Zhou, Tiangang; Chen, Lin

2011-10-14

Recent data indicate that unconscious masked priming can be mediated by top-down attentional set, so that priming effects of congruence between a masked prime and a subsequent probe vanish when the congruence ceases to be task relevant. Here, we show that, while the attentional set determines masked priming for color and orientation features, it does not fully determine priming based on the topological properties of stimuli. Specifically, across a series of different choice-RT tasks, we find that topological congruence between prime and probe stimuli affects RTs for the probes even when other stimulus information (e.g., color or orientation) is required for the response, whereas congruence priming effects of color or orientation occur only when these features are response relevant. Our results suggest that changes in topological properties take precedence over task-directed top-down attentional modulation in masked priming.

Statistical prediction of dynamic distortion of inlet flow using minimum dynamic measurement. An application to the Melick statistical method and inlet flow dynamic distortion prediction without RMS measurements

NASA Technical Reports Server (NTRS)

Schweikhard, W. G.; Chen, Y. S.

1986-01-01

The Melick method of inlet flow dynamic distortion prediction by statistical means is outlined. A hypothetic vortex model is used as the basis for the mathematical formulations. The main variables are identified by matching the theoretical total pressure rms ratio with the measured total pressure rms ratio. Data comparisons, using the HiMAT inlet test data set, indicate satisfactory prediction of the dynamic peak distortion for cases with boundary layer control device vortex generators. A method for the dynamic probe selection was developed. Validity of the probe selection criteria is demonstrated by comparing the reduced-probe predictions with the 40-probe predictions. It is indicated that the the number of dynamic probes can be reduced to as few as two and still retain good accuracy.

PROBING THE EXPANSION HISTORY OF THE UNIVERSE BY MODEL-INDEPENDENT RECONSTRUCTION FROM SUPERNOVAE AND GAMMA-RAY BURST MEASUREMENTS

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

Feng, Chao-Jun; Li, Xin-Zhou, E-mail: fengcj@shnu.edu.cn, E-mail: kychz@shnu.edu.cn

To probe the late evolution history of the universe, we adopt two kinds of optimal basis systems. One of them is constructed by performing the principle component analysis, and the other is built by taking the multidimensional scaling approach. Cosmological observables such as the luminosity distance can be decomposed into these basis systems. These basis systems are optimized for different kinds of cosmological models that are based on different physical assumptions, even for a mixture model of them. Therefore, the so-called feature space that is projected from the basis systems is cosmological model independent, and it provides a parameterization for studying and reconstructing themore » Hubble expansion rate from the supernova luminosity distance and even gamma-ray burst (GRB) data with self-calibration. The circular problem when using GRBs as cosmological candles is naturally eliminated in this procedure. By using the Levenberg–Marquardt technique and the Markov Chain Monte Carlo method, we perform an observational constraint on this kind of parameterization. The data we used include the “joint light-curve analysis” data set that consists of 740 Type Ia supernovae and 109 long GRBs with the well-known Amati relation.« less

Two Variations of Video Modeling Interventions for Teaching Play Skills to Children with Autism

ERIC Educational Resources Information Center

Sancho, Kimberly; Sidener, Tina M.; Reeve, Sharon A.; Sidener, David W.

2010-01-01

The current study employed an adapted alternating treatments design with reversal and multiple probe across participants components to compare the effects of traditional video priming and simultaneous video modeling on the acquisition of play skills in two children diagnosed with autism. Generalization was programmed across play sets, instructors,…

Asymmetric rotor-like probes to polarized fluorescence study of the macroscopically oriented uniaxial media: Model parameters recognition

NASA Astrophysics Data System (ADS)

Buczkowski, M.; Fisz, J. J.

2008-07-01

In this paper the possibility of the numerical data modelling in the case of angle- and time-resolved fluorescence spectroscopy is investigated. The asymmetric fluorescence probes are assumed to undergo the restricted rotational diffusion in a hosting medium. This process is described quantitatively by the diffusion tensor and the aligning potential. The evolution of the system is expressed in terms of the Smoluchowski equation with an appropriate time-developing operator. A matrix representation of this operator is calculated, then symmetrized and diagonalized. The resulting propagator is used to generate the synthetic noisy data set that imitates results of experimental measurements. The data set serves as a groundwork to the χ2 optimization, performed by the genetic algorithm followed by the gradient search, in order to recover model parameters, which are diagonal elements of the diffusion tensor, aligning potential expansion coefficients and directions of the electronic dipole moments. This whole procedure properly identifies model parameters, showing that the outlined formalism should be taken in the account in the case of analysing real experimental data.

Orientational Dynamics of a Functionalized Alkyl Planar Monolayer Probed by Polarization-Selective Angle-Resolved Infrared Pump-Probe Spectroscopy.

PubMed

Nishida, Jun; Yan, Chang; Fayer, Michael D

2016-10-12

Polarization-selective angle-resolved infrared pump-probe spectroscopy was developed and used to study the orientational dynamics of a planar alkylsiloxane monolayer functionalized with a rhenium metal carbonyl headgroup on an SiO 2 surface. The technique, together with a time-averaged infrared linear dichroism measurement, characterized picosecond orientational relaxation of the headgroup occurring at the monolayer-air interface by employing several sets of incident angles of the infrared pulses relative to the sample surface. By application of this method and using a recently developed theory, it was possible to extract both the out-of-plane and "mainly"-in-plane orientational correlation functions in a model-independent manner. The observed correlation functions were compared with theoretically derived correlation functions based on several dynamical models. The out-of-plane correlation function reveals the highly restricted out-of-plane motions of the head groups and also suggests that the angular distribution of the transition dipole moments is bimodal. The mainly-in-plane correlation function, for the sample studied here with the strongly restricted out-of-plane motions, essentially arises from the purely in-plane dynamics. In contrast to the out-of-plane dynamics, significant in-plane motions occurring over various time scales were observed including an inertial motion, a restricted wobbling motion of ∼3 ps, and complete randomization occurring in ∼25 ps.

A novel constant-force scanning probe incorporating mechanical-magnetic coupled structures.

PubMed

Wang, Hongxi; Zhao, Jian; Gao, Renjing; Yang, Yintang

2011-07-01

A one-dimensional scanning probe with constant measuring force is designed and fabricated by utilizing the negative stiffness of the magnetic coupled structure, which mainly consists of the magnetic structure, the parallel guidance mechanism, and the pre-stressed spring. Based on the theory of material mechanics and the equivalent surface current model for computing the magnetic force, the analytical model of the scanning probe subjected to multi-forces is established, and the nonlinear relationship between the measuring force and the probe displacement is obtained. The practicability of introducing magnetic coupled structure in the constant-force probe is validated by the consistency of the results in numerical simulation and experiments.

Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4.

PubMed

Lee, Tong Geon; Lee, Yong Jin; Kim, Dae Yeon; Seo, Yong Weon

2010-12-01

Physical maps of chromosomes provide a framework for organizing and integrating diverse genetic information. DNA microarrays are a valuable technique for physical mapping and can also be used to facilitate the discovery of single feature polymorphisms (SFPs). Wheat chromosome arm 2BL was physically mapped using a Wheat Genome Array onto near-isogenic lines (NILs) with the aid of wheat-rice synteny and mapped wheat EST information. Using high variance probe set (HVP) analysis, 314 HVPs constituting genes present on 2BL were identified. The 314 HVPs were grouped into 3 categories: HVPs that match only rice chromosome 4 (298 HVPs), those that match only wheat ESTs mapped on 2BL (1), and those that match both rice chromosome 4 and wheat ESTs mapped on 2BL (15). All HVPs were converted into gene sets, which represented either unique rice gene models or mapped wheat ESTs that matched identified HVPs. Comparative physical maps were constructed for 16 wheat gene sets and 271 rice gene sets. Of the 271 rice gene sets, 257 were mapped to the 18-35 Mb regions on rice chromosome 4. Based on HVP analysis and sequence similarity between the gene models in the rice chromosomes and mapped wheat ESTs, the outermost rice gene model that limits the translocation breakpoint to orthologous regions was identified.

DNA sequence analysis with droplet-based microfluidics

PubMed Central

Abate, Adam R.; Hung, Tony; Sperling, Ralph A.; Mary, Pascaline; Rotem, Assaf; Agresti, Jeremy J.; Weiner, Michael A.; Weitz, David A.

2014-01-01

Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based assay. Using probes of different sequences, we interrogate a target DNA molecule for polymorphisms. With a larger probe set, additional polymorphisms can be interrogated as well as targets of arbitrary sequence. PMID:24185402

Development and evaluation of probe based real time loop mediated isothermal amplification for Salmonella: A new tool for DNA quantification.

PubMed

Mashooq, Mohmad; Kumar, Deepak; Niranjan, Ankush Kiran; Agarwal, Rajesh Kumar; Rathore, Rajesh

2016-07-01

A one step, single tube, accelerated probe based real time loop mediated isothermal amplification (RT LAMP) assay was developed for detecting the invasion gene (InvA) of Salmonella. The probe based RT LAMP is a novel method of gene amplification that amplifies nucleic acid with high specificity and rapidity under isothermal conditions with a set of six primers. The whole procedure is very simple and rapid, and amplification can be obtained in 20min. Detection of gene amplification was accomplished by amplification curve, turbidity and addition of DNA binding dye at the end of the reaction results in colour difference and can be visualized under normal day light and in UV. The sensitivity of developed assay was found 10 fold higher than taqman based qPCR. The specificity of the RT LAMP assay was validated by the absence of any cross reaction with other members of enterobacteriaceae family and other gram negative bacteria. These results indicate that the probe based RT LAMP assay is extremely rapid, cost effective, highly specific and sensitivity and has potential usefulness for rapid Salmonella surveillance. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Solar-wind predictions for the Parker Solar Probe orbit. Near-Sun extrapolations derived from an empirical solar-wind model based on Helios and OMNI observations

NASA Astrophysics Data System (ADS)

Venzmer, M. S.; Bothmer, V.

2018-03-01

Context. The Parker Solar Probe (PSP; formerly Solar Probe Plus) mission will be humanitys first in situ exploration of the solar corona with closest perihelia at 9.86 solar radii (R⊙) distance to the Sun. It will help answer hitherto unresolved questions on the heating of the solar corona and the source and acceleration of the solar wind and solar energetic particles. The scope of this study is to model the solar-wind environment for PSPs unprecedented distances in its prime mission phase during the years 2018 to 2025. The study is performed within the Coronagraphic German And US SolarProbePlus Survey (CGAUSS) which is the German contribution to the PSP mission as part of the Wide-field Imager for Solar PRobe. Aim. We present an empirical solar-wind model for the inner heliosphere which is derived from OMNI and Helios data. The German-US space probes Helios 1 and Helios 2 flew in the 1970s and observed solar wind in the ecliptic within heliocentric distances of 0.29 au to 0.98 au. The OMNI database consists of multi-spacecraft intercalibrated in situ data obtained near 1 au over more than five solar cycles. The international sunspot number (SSN) and its predictions are used to derive dependencies of the major solar-wind parameters on solar activity and to forecast their properties for the PSP mission. Methods: The frequency distributions for the solar-wind key parameters, magnetic field strength, proton velocity, density, and temperature, are represented by lognormal functions. In addition, we consider the velocity distributions bi-componental shape, consisting of a slower and a faster part. Functional relations to solar activity are compiled with use of the OMNI data by correlating and fitting the frequency distributions with the SSN. Further, based on the combined data set from both Helios probes, the parameters frequency distributions are fitted with respect to solar distance to obtain power law dependencies. Thus an empirical solar-wind model for the inner heliosphere confined to the ecliptic region is derived, accounting for solar activity and for solar distance through adequate shifts of the lognormal distributions. Finally, the inclusion of SSN predictions and the extrapolation down to PSPs perihelion region enables us to estimate the solar-wind environment for PSPs planned trajectory during its mission duration. Results: The CGAUSS empirical solar-wind model for PSP yields dependencies on solar activity and solar distance for the solar-wind parameters' frequency distributions. The estimated solar-wind median values for PSPs first perihelion in 2018 at a solar distance of 0.16 au are 87 nT, 340 km s-1, 214 cm-3, and 503 000 K. The estimates for PSPs first closest perihelion, occurring in 2024 at 0.046 au (9.86 R⊙), are 943 nT, 290 km s-1, 2951 cm-3, and 1 930 000 K. Since the modeled velocity and temperature values below approximately 20 R⊙appear overestimated in comparison with existing observations, this suggests that PSP will directly measure solar-wind acceleration and heating processes below 20 R⊙ as planned.

Design and characterization of planar capacitive imaging probe based on the measurement sensitivity distribution

NASA Astrophysics Data System (ADS)

Yin, X.; Chen, G.; Li, W.; Huthchins, D. A.

2013-01-01

Previous work indicated that the capacitive imaging (CI) technique is a useful NDE tool which can be used on a wide range of materials, including metals, glass/carbon fibre composite materials and concrete. The imaging performance of the CI technique for a given application is determined by design parameters and characteristics of the CI probe. In this paper, a rapid method for calculating the whole probe sensitivity distribution based on the finite element model (FEM) is presented to provide a direct view of the imaging capabilities of the planar CI probe. Sensitivity distributions of CI probes with different geometries were obtained. Influencing factors on sensitivity distribution were studied. Comparisons between CI probes with point-to-point triangular electrode pair and back-to-back triangular electrode pair were made based on the analysis of the corresponding sensitivity distributions. The results indicated that the sensitivity distribution could be useful for optimising the probe design parameters and predicting the imaging performance.

Dimensionality of Data Matrices with Applications to Gene Expression Profiles

ERIC Educational Resources Information Center

Feng, Xingdong

2009-01-01

Probe-level microarray data are usually stored in matrices. Take a given probe set (gene), for example, each row of the matrix corresponds to an array, and each column corresponds to a probe. Often, people summarize each array by the gene expression level. Is one number sufficient to summarize a whole probe set for a specific gene in an array?…

Monte Carlo modeling of ultrasound probes for image guided radiotherapy

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

Bazalova-Carter, Magdalena, E-mail: bazalova@uvic.ca; Schlosser, Jeffrey; Chen, Josephine

2015-10-15

Purpose: To build Monte Carlo (MC) models of two ultrasound (US) probes and to quantify the effect of beam attenuation due to the US probes for radiation therapy delivered under real-time US image guidance. Methods: MC models of two Philips US probes, an X6-1 matrix-array transducer and a C5-2 curved-array transducer, were built based on their megavoltage (MV) CT images acquired in a Tomotherapy machine with a 3.5 MV beam in the EGSnrc, BEAMnrc, and DOSXYZnrc codes. Mass densities in the probes were assigned based on an electron density calibration phantom consisting of cylinders with mass densities between 0.2 andmore » 8.0 g/cm{sup 3}. Beam attenuation due to the US probes in horizontal (for both probes) and vertical (for the X6-1 probe) orientation was measured in a solid water phantom for 6 and 15 MV (15 × 15) cm{sup 2} beams with a 2D ionization chamber array and radiographic films at 5 cm depth. The MC models of the US probes were validated by comparison of the measured dose distributions and dose distributions predicted by MC. Attenuation of depth dose in the (15 × 15) cm{sup 2} beams and small circular beams due to the presence of the probes was assessed by means of MC simulations. Results: The 3.5 MV CT number to mass density calibration curve was found to be linear with R{sup 2} > 0.99. The maximum mass densities in the X6-1 and C5-2 probes were found to be 4.8 and 5.2 g/cm{sup 3}, respectively. Dose profile differences between MC simulations and measurements of less than 3% for US probes in horizontal orientation were found, with the exception of the penumbra region. The largest 6% dose difference was observed in dose profiles of the X6-1 probe placed in vertical orientation, which was attributed to inadequate modeling of the probe cable. Gamma analysis of the simulated and measured doses showed that over 96% of measurement points passed the 3%/3 mm criteria for both probes placed in horizontal orientation and for the X6-1 probe in vertical orientation. The X6-1 probe in vertical orientation caused the highest attenuation of the 6 and 15 MV beams, which at 10 cm depth accounted for 33% and 43% decrease compared to the respective (15 × 15) cm{sup 2} open fields. The C5-2 probe in horizontal orientation, on the other hand, caused a dose increase of 10% and 53% for the 6 and 15 MV beams, respectively, in the buildup region at 0.5 cm depth. For the X6-1 probe in vertical orientation, the dose at 5 cm depth for the 3-cm diameter 6 MV and 5-cm diameter 15 MV beams was attenuated compared to the corresponding open fields to a greater degree by 65% and 43%, respectively. Conclusions: MC models of two US probes used for real-time image guidance during radiotherapy have been built. Due to the high beam attenuation of the US probes, the authors generally recommend avoiding delivery of treatment beams that intersect the probe. However, the presented MC models can be effectively integrated into US-guided radiotherapy treatment planning in cases for which beam avoidance is not practical due to anatomy geometry.« less

The eigenmode perspective of NMR spin relaxation in proteins

NASA Astrophysics Data System (ADS)

Shapiro, Yury E.; Meirovitch, Eva

2013-12-01

We developed in recent years the two-body (protein and probe) coupled-rotator slowly relaxing local structure (SRLS) approach for elucidating protein dynamics from NMR spin relaxation. So far we used as descriptors the set of physical parameters that enter the SRLS model. They include the global (protein-related) diffusion tensor, D1, the local (probe-related) diffusion tensor, D2, and the local coupling/ordering potential, u. As common in analyzes based on mesoscopic dynamic models, these parameters have been determined with data-fitting techniques. In this study, we describe structural dynamics in terms of the eigenmodes comprising the SRLS time correlation functions (TCFs) generated by using the best-fit parameters as input to the Smoluchowski equation. An eigenmode is a weighted exponential with decay constant given by an eigenvalue of the Smoluchowski operator, and weighting factor determined by the corresponding eigenvector. Obviously, both quantities depend on the SRLS parameters as determined by the SRLS model. Unlike the set of best-fit parameters, the eigenmodes represent patterns of motion of the probe-protein system. The following new information is obtained for the typical probe, the 15N-1H bond. Two eigenmodes, associated with the protein and the probe, dominate when the time scale separation is large (i.e., D2 ≫ D1), the tensorial properties are simple, and the local potential is either very strong or very weak. When the potential exceeds these limits while the remaining conditions are preserved, new eigenmodes arise. The multi-exponentiality of the TCFs is associated in this case with the restricted nature of the local motion. When the time scale separation is no longer large, the rotational degrees of freedom of the protein and the probe become statistically dependent (coupled dynamically). The multi-exponentiality of the TCFs is associated in this case with the restricted nature of both the local and the global motion. The effects of local diffusion axiality, potential strength, and extent of mode-coupling on the eigenmode setup are investigated. We detect largely global motional or largely local motional eigenmodes. In addition, we detect mixed eigenmodes associated with correlated/prograde or anti-correlated/retrograde rotations of the global (D1) and local (D2) motional modes. The eigenmode paradigm is applied to N-H bond dynamics in the β-sheet residue K19, and the α-helix residue A34, of the third immunoglobulin-binding domain of streptococcal protein G. The largest contribution to the SRLS TCFs is made by mixed anti-correlated D1 and D2 eigenmodes. The next largest contribution is made by D1-dominated eigenmodes. Eigenmodes dominated by the local motion contribute appreciably to A34 and marginally to K19. Correlated D1 and D2 eigenmodes contribute exclusively to K19 and do not contribute above 1% to A34. The differences between K19 and A34 are delineated and rationalized in terms of the best-fit SRLS parameters and mode-mixing. It may be concluded that eigenmode analysis is complementary and supplementary to data-fitting-based analysis.

Kinetic Description of the Impedance Probe

NASA Astrophysics Data System (ADS)

Oberrath, Jens; Lapke, Martin; Mussenbrock, Thomas; Brinkmann, Ralf

2011-10-01

Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. The authors acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG) via the Ruhr University Research School and the Federal Ministry of Education and Research in frame of the PluTO project.

Teaching the handicapped to eat in public places: acquisition, generalization and maintenance of restaurant skills.

PubMed Central

van den Pol, R A; Iwata, B A; Ivancic, M T; Page, T J; Neef, N A; Whitley, F P

1981-01-01

This study examined classroom-based instruction in restaurant skills for handicapped persons. Three male students were taught each of four skill components in sequential order: locating, ordering, paying, and eating and exiting. Training was implemented in a multiple baseline design across subjects and consisted of modeling and role playing in conjunction with photo slide sequences and a simulated ordering counter. The use of a menu containing general item classes and a finger matching procedure for identifying errors in the delivery of change greatly reduced the reading and math skills necessary to enter and complete the program. Periodic probes were conducted in a McDonald's restaurant prior to, during, and up to one-year following the termination of training. In addition, two probes (overt and covert observation) were conducted in a Burger King restaurant to assess further generalization to a location different from the one depicted throughout training. Results showed that students' performance on restaurant probes improved as a result of training, generalized to novel settings, maintained over an extended period of time, and was comparable to that of a normative sample of nonretarded persons. PMID:6452436

Application of spatial time domain reflectometry measurements in heterogeneous, rocky substrates

NASA Astrophysics Data System (ADS)

Gonzales, C.; Scheuermann, A.; Arnold, S.; Baumgartl, T.

2016-10-01

Measurement of soil moisture across depths using sensors is currently limited to point measurements or remote sensing technologies. Point measurements have limitations on spatial resolution, while the latter, although covering large areas may not represent real-time hydrologic processes, especially near the surface. The objective of the study was to determine the efficacy of elongated soil moisture probes—spatial time domain reflectometry (STDR)—and to describe transient soil moisture dynamics of unconsolidated mine waste rock materials. The probes were calibrated under controlled conditions in the glasshouse. Transient soil moisture content was measured using the gravimetric method and STDR. Volumetric soil moisture content derived from weighing was compared with values generated from a numerical model simulating the drying process. A calibration function was generated and applied to STDR field data sets. The use of elongated probes effectively assists in the real-time determination of the spatial distribution of soil moisture. It also allows hydrologic processes to be uncovered in the unsaturated zone, especially for water balance calculations that are commonly based on point measurements. The elongated soil moisture probes can potentially describe transient substrate processes and delineate heterogeneity in terms of the pore size distribution in a seasonally wet but otherwise arid environment.

Development of Prevotella intermedia-specific PCR primers based on the nucleotide sequences of a DNA probe Pig27.

PubMed

Kim, Min Jung; Hwang, Kyung Hwan; Lee, Young-Seok; Park, Jae-Yoon; Kook, Joong-Ki

2011-03-01

The aim of this study was to develop Prevotella intermedia-specific PCR primers based on the P. intermedia-specific DNA probe. The P. intermedia-specific DNA probe was screened by inverted dot blot hybridization and confirmed by Southern blot hybridization. The nucleotide sequences of the species-specific DNA probes were determined using a chain termination method. Southern blot analysis showed that the DNA probe, Pig27, detected only the genomic DNA of P. intermedia strains. PCR showed that the PCR primers, Pin-F1/Pin-R1, had species-specificity for P. intermedia. The detection limits of the PCR primer sets were 0.4pg of the purified genomic DNA of P. intermedia ATCC 49046. These results suggest that the PCR primers, Pin-F1/Pin-R1, could be useful in the detection of P. intermedia as well as in the development of a PCR kit in epidemiological studies related to periodontal diseases. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

Optical imaging probes in oncology

PubMed Central

Martelli, Cristina; Dico, Alessia Lo; Diceglie, Cecilia; Lucignani, Giovanni; Ottobrini, Luisa

2016-01-01

Cancer is a complex disease, characterized by alteration of different physiological molecular processes and cellular features. Keeping this in mind, the possibility of early identification and detection of specific tumor biomarkers by non-invasive approaches could improve early diagnosis and patient management. Different molecular imaging procedures provide powerful tools for detection and non-invasive characterization of oncological lesions. Clinical studies are mainly based on the use of computed tomography, nuclear-based imaging techniques and magnetic resonance imaging. Preclinical imaging in small animal models entails the use of dedicated instruments, and beyond the already cited imaging techniques, it includes also optical imaging studies. Optical imaging strategies are based on the use of luminescent or fluorescent reporter genes or injectable fluorescent or luminescent probes that provide the possibility to study tumor features even by means of fluorescence and luminescence imaging. Currently, most of these probes are used only in animal models, but the possibility of applying some of them also in the clinics is under evaluation. The importance of tumor imaging, the ease of use of optical imaging instruments, the commercial availability of a wide range of probes as well as the continuous description of newly developed probes, demonstrate the significance of these applications. The aim of this review is providing a complete description of the possible optical imaging procedures available for the non-invasive assessment of tumor features in oncological murine models. In particular, the characteristics of both commercially available and newly developed probes will be outlined and discussed. PMID:27145373

Mass Spec Studio for Integrative Structural Biology

PubMed Central

Rey, Martial; Sarpe, Vladimir; Burns, Kyle; Buse, Joshua; Baker, Charles A.H.; van Dijk, Marc; Wordeman, Linda; Bonvin, Alexandre M.J.J.; Schriemer, David C.

2015-01-01

SUMMARY The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/ deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-tandem MS (MS2) and data-independent HX-MS2. The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions. PMID:25242457

A Transport Model for Non-Local Heating of Electrons in ICP Reactors

NASA Technical Reports Server (NTRS)

Chang, C. H.; Bose, Deepak; Arnold, James O. (Technical Monitor)

1998-01-01

A new model has been developed for non-local heating of electrons in ICP reactors, based on a hydrodynamic approach. The model has been derived using the electron momentum conservation in azimuthal direction with electromagnetic and frictional forces respectively as driving force and damper of harmonic oscillatory motion of electrons. The resulting transport equations include the convection of azimuthal electron momentum in radial and axial directions, thereby accounting for the non-local effects. The azimuthal velocity of electrons and the resulting electrical current are coupled to the Maxwell's relations, thus forming a self-consistent model for non-local heating. This model is being implemented along with a set of Navier-Stokes equations for plasma dynamics and gas flow to simulate low-pressure (few mTorr's) ICP discharges. Characteristics of nitrogen plasma in a TCP 300mm etch reactor is being studied. The results will be compared against the available Langmuir probe measurements.

Aeroacoustic effects of reduced aft tip speed at constant thrust for a model counterrotation turboprop at takeoff conditions

NASA Technical Reports Server (NTRS)

Woodward, Richard P.; Hughes, Christopher E.

1990-01-01

A model high-speed, advanced counterrotation propeller, F7/A7, was tested in the NASA Lewis Research Center's 9- by 15-foot anechoic wind tunnel at simulated takeoff and approach conditions of Mach 0.2. The propeller was operated in a baseline configuration with the forward and aft rotor blade setting angles (36.2deg and 35.4 deg) and forward and aft rotational speeds essentially equal. Two additional configurations were tested with the aft rotor at increased blade setting angles and the rotational speed reduced to achieve overall performance similar to that of the baseline configuration. The aft rotor blade angles were adjusted such that the thrust and power absorption for each rotor remained the same as for the baseline configuration. Acoustic data were taken with an axially translating microphone probe that was attached to the tunnel floor. Concurrent aerodynamic data were taken to define propeller operating conditions. The aft rotor fundamental tone was about 6 dB lower with the 36.2 deg and 38.4 deg blade setting angles, and about 9 dB lower with the 36.2 and 41.4 deg blade setting angles. Predicted noise reductions based on tip speed considerations were 5 and 9.5 dB, respectively, for the two altered blade setting angles.

Genotyping by alkaline dehybridization using graphically encoded particles.

PubMed

Zhang, Huaibin; DeConinck, Adam J; Slimmer, Scott C; Doyle, Patrick S; Lewis, Jennifer A; Nuzzo, Ralph G

2011-03-01

This work describes a nonenzymatic, isothermal genotyping method based on the kinetic differences exhibited in the dehybridization of perfectly matched (PM) and single-base mismatched (MM) DNA duplexes in an alkaline solution. Multifunctional encoded hydrogel particles incorporating allele-specific oligonucleotide (ASO) probes in two distinct regions were fabricated by using microfluidic-based stop-flow lithography. Each particle contained two distinct ASO probe sequences differing at a single base position, and thus each particle was capable of simultaneously probing two distinct target alleles. Fluorescently labeled target alleles were annealed to both probe regions of a particle, and the rate of duplex dehybridization was monitored by using fluorescence microscopy. Duplex dehybridization was achieved through an alkaline stimulus using either a pH step function or a temporal pH gradient. When a single target probe sequence was used, the rate of mismatch duplex dehybridization could be discriminated from the rate of perfect match duplex dehybridization. In a more demanding application in which two distinct probe sequences were used, we found that the rate profiles provided a means to discriminate probe dehybridizations from both of the two mismatched duplexes as well as to distinguish at high certainty the dehybridization of the two perfectly matched duplexes. These results demonstrate an ability of alkaline dehybridization to correctly discriminate the rank hierarchy of thermodynamic stability among four sets of perfect match and single-base mismatch duplexes. We further demonstrate that these rate profiles are strongly temperature dependent and illustrate how the sensitivity can be compensated beneficially by the use of an actuating gradient pH field. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Signal amplification of padlock probes by rolling circle replication.

PubMed Central

Banér, J; Nilsson, M; Mendel-Hartvig, M; Landegren, U

1998-01-01

Circularizing oligonucleotide probes (padlock probes) have the potential to detect sets of gene sequences with high specificity and excellent selectivity for sequence variants, but sensitivity of detection has been limiting. By using a rolling circle replication (RCR) mechanism, circularized but not unreacted probes can yield a powerful signal amplification. We demonstrate here that in order for the reaction to proceed efficiently, the probes must be released from the topological link that forms with target molecules upon hybridization and ligation. If the target strand has a nearby free 3' end, then the probe-target hybrids can be displaced by the polymerase used for replication. The displaced probe can then slip off the targetstrand and a rolling circle amplification is initiated. Alternatively, the target sequence itself can prime an RCR after its non-base paired 3' end has been removed by exonucleolytic activity. We found the Phi29 DNA polymerase to be superior to the Klenow fragment in displacing the target DNA strand, and it maintained the polymerization reaction for at least 12 h, yielding an extension product that represents several thousand-fold the length of the padlock probe. PMID:9801302

HINTW, a W-chromosome HINT gene in chick, is expressed ubiquitously and is a robust female cell marker applicable in intraspecific chimera studies.

PubMed

Nagai, Hiroki; Sezaki, Maiko; Bertocchini, Federica; Fukuda, Kimiko; Sheng, Guojun

2014-05-01

Grafting and transplantation experiments in embryology require proper distinction between host and donor tissues. For the avian model this has traditionally been achieved by using two closely related species (e.g., chick and quail) followed by species-specific antibody staining. Here, we show that an in situ hybridization probe against the HINTW gene is a robust and reliable marker for female-derived chicken cells. At all pre-circulation stages tested, all cells in female embryos, independently confirmed by PCR analysis, were strongly positive for HINTW, whereas all male embryos were negative. This probe is broadly applicable in intra-specific chick/chick chimera studies, and as a proof of principle, we utilized this probe to detect female cells in three experimental settings: (1) to mark female donor cells in a node transplantation assay; (2) to distinguish female cells in male/female twins generated by the Cornish pasty culture; and (3) to detect female half of the embryo in artificially generated bilateral gynandromorphs. A rapid, PCR based pre-screening step increases the efficiency of obtaining desired donor/host sex combination from 25% to 100%. For most avian chimera studies, this female-specific in situ probe is a low cost alternative to the commonly used QCPN antibody and to ubiquitous-GFP chicken strains which are not widely available to the research community. © 2014 Wiley Periodicals, Inc.

Monte Carlo simulations within avalanche rescue

NASA Astrophysics Data System (ADS)

Reiweger, Ingrid; Genswein, Manuel; Schweizer, Jürg

2016-04-01

Refining concepts for avalanche rescue involves calculating suitable settings for rescue strategies such as an adequate probing depth for probe line searches or an optimal time for performing resuscitation for a recovered avalanche victim in case of additional burials. In the latter case, treatment decisions have to be made in the context of triage. However, given the low number of incidents it is rarely possible to derive quantitative criteria based on historical statistics in the context of evidence-based medicine. For these rare, but complex rescue scenarios, most of the associated concepts, theories, and processes involve a number of unknown "random" parameters which have to be estimated in order to calculate anything quantitatively. An obvious approach for incorporating a number of random variables and their distributions into a calculation is to perform a Monte Carlo (MC) simulation. We here present Monte Carlo simulations for calculating the most suitable probing depth for probe line searches depending on search area and an optimal resuscitation time in case of multiple avalanche burials. The MC approach reveals, e.g., new optimized values for the duration of resuscitation that differ from previous, mainly case-based assumptions.

Fast Open-World Person Re-Identification.

PubMed

Zhu, Xiatian; Wu, Botong; Huang, Dongcheng; Zheng, Wei-Shi

2018-05-01

Existing person re-identification (re-id) methods typically assume that: 1) any probe person is guaranteed to appear in the gallery target population during deployment (i.e., closed-world) and 2) the probe set contains only a limited number of people (i.e., small search scale). Both assumptions are artificial and breached in real-world applications, since the probe population in target people search can be extremely vast in practice due to the ambiguity of probe search space boundary. Therefore, it is unrealistic that any probe person is assumed as one target people, and a large-scale search in person images is inherently demanded. In this paper, we introduce a new person re-id search setting, called large scale open-world (LSOW) re-id, characterized by huge size probe images and open person population in search thus more close to practical deployments. Under LSOW, the under-studied problem of person re-id efficiency is essential in addition to that of commonly studied re-id accuracy. We, therefore, develop a novel fast person re-id method, called Cross-view Identity Correlation and vErification (X-ICE) hashing, for joint learning of cross-view identity representation binarisation and discrimination in a unified manner. Extensive comparative experiments on three large-scale benchmarks have been conducted to validate the superiority and advantages of the proposed X-ICE method over a wide range of the state-of-the-art hashing models, person re-id methods, and their combinations.

Use of the Genomic Subtractive Hybridization Technique To Develop a Real-Time PCR Assay for Quantitative Detection of Prevotella spp. in Oral Biofilm Samples

PubMed Central

Nagashima, Shiori; Yoshida, Akihiro; Suzuki, Nao; Ansai, Toshihiro; Takehara, Tadamichi

2005-01-01

Genomic subtractive hybridization was used to design Prevotella nigrescens-specific primers and TaqMan probes. Based on this technique, a TaqMan real-time PCR assay was developed for quantifying four oral black-pigmented Prevotella species. The combination of real-time PCR and genomic subtractive hybridization is useful for preparing species-specific primer-probe sets for closely related species. PMID:15956428

Ensemble kalman filtering to perform data assimilation with soil water content probes and pedotransfer functions in modeling water flow in variably saturated soils

USDA-ARS?s Scientific Manuscript database

Data from modern soil water contents probes can be used for data assimilation in soil water flow modeling, i.e. continual correction of the flow model performance based on observations. The ensemble Kalman filter appears to be an appropriate method for that. The method requires estimates of the unce...

PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei

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

Müller, Patrick; Rößler, Jens; Schwarz-Finsterle, Jutta

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 atmore » 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.« less

The design and application of fluorophore–gold nanoparticle activatable probes

PubMed Central

Swierczewska, Magdalena; Lee, Seulki; Chen, Xiaoyuan

2013-01-01

Fluorescence-based assays and detection techniques are among the most highly sensitive and popular biological tests for researchers. To match the needs of research and the clinic, detection limits and specificities need to improve, however. One mechanism is to decrease non-specific background signals, which is most efficiently done by increasing fluorescence quenching abilities. Reports in the literature of theoretical and experimental work have shown that metallic gold surfaces and nanoparticles are ultra-efficient fluorescence quenchers. Based on these findings, subsequent reports have described gold nanoparticle fluorescence-based activatable probes that were designed to increase fluorescence intensity based on a range of stimuli. In this way, these probes can detect and signify assorted biomarkers and changes in environmental conditions. In this review, we explore the various factors and theoretical models that affect gold nanoparticle fluorescence quenching, explore current uses of activatable probes, and propose an engineering approach for future development of fluorescence based gold nanoparticle activatable probes. PMID:21380462

Learning through ferroelectric domain dynamics in solid-state synapses

NASA Astrophysics Data System (ADS)

Boyn, Sören; Grollier, Julie; Lecerf, Gwendal; Xu, Bin; Locatelli, Nicolas; Fusil, Stéphane; Girod, Stéphanie; Carrétéro, Cécile; Garcia, Karin; Xavier, Stéphane; Tomas, Jean; Bellaiche, Laurent; Bibes, Manuel; Barthélémy, Agnès; Saïghi, Sylvain; Garcia, Vincent

2017-04-01

In the brain, learning is achieved through the ability of synapses to reconfigure the strength by which they connect neurons (synaptic plasticity). In promising solid-state synapses called memristors, conductance can be finely tuned by voltage pulses and set to evolve according to a biological learning rule called spike-timing-dependent plasticity (STDP). Future neuromorphic architectures will comprise billions of such nanosynapses, which require a clear understanding of the physical mechanisms responsible for plasticity. Here we report on synapses based on ferroelectric tunnel junctions and show that STDP can be harnessed from inhomogeneous polarization switching. Through combined scanning probe imaging, electrical transport and atomic-scale molecular dynamics, we demonstrate that conductance variations can be modelled by the nucleation-dominated reversal of domains. Based on this physical model, our simulations show that arrays of ferroelectric nanosynapses can autonomously learn to recognize patterns in a predictable way, opening the path towards unsupervised learning in spiking neural networks.

Probing the Small-scale Structure in Strongly Lensed Systems via Transdimensional Inference

NASA Astrophysics Data System (ADS)

Daylan, Tansu; Cyr-Racine, Francis-Yan; Diaz Rivero, Ana; Dvorkin, Cora; Finkbeiner, Douglas P.

2018-02-01

Strong lensing is a sensitive probe of the small-scale density fluctuations in the Universe. We implement a pipeline to model strongly lensed systems using probabilistic cataloging, which is a transdimensional, hierarchical, and Bayesian framework to sample from a metamodel (union of models with different dimensionality) consistent with observed photon count maps. Probabilistic cataloging allows one to robustly characterize modeling covariances within and across lens models with different numbers of subhalos. Unlike traditional cataloging of subhalos, it does not require model subhalos to improve the goodness of fit above the detection threshold. Instead, it allows the exploitation of all information contained in the photon count maps—for instance, when constraining the subhalo mass function. We further show that, by not including these small subhalos in the lens model, fixed-dimensional inference methods can significantly mismodel the data. Using a simulated Hubble Space Telescope data set, we show that the subhalo mass function can be probed even when many subhalos in the sample catalogs are individually below the detection threshold and would be absent in a traditional catalog. The implemented software, Probabilistic Cataloger (PCAT) is made publicly available at https://github.com/tdaylan/pcat.

The Sagittarius Stream: Probing the Outer Halo Potential

NASA Astrophysics Data System (ADS)

Fardal, Mark; HSTPROMO

2018-01-01

The Sagittarius Stream should be the premier probe of the outer Milky Way halo potential. Instead it has generated a series of puzzles that have frustrated modelers and prevented us from measuring the halo forces. The latest such puzzle is the factor of two difference between leading and trailing apocenter distances, seen most clearly in a recent sample of RR Lyraes from PS1. Using a set of dynamical models, we explain how to match this feature. The key element are that the debris at apocenter should dynamically young, originating from the last two pericentric passages only. We also explain the important roles played by the mass profile of the halo, dynamical friction, and departures from sphericity. The models show that the separate components already visible in the PS1 data should separate clearly once velocities are obtained, and the youngest component should probe the potential even beyond the observed distances of >~ 100 kpc. We explain what observations would be useful to eliminate remaining degeneracies in the models and fulfill the promise of the stream for understanding the Milky Way.

Rational Design of in Vivo Tau Tangle-Selective Near-Infrared Fluorophores: Expanding the BODIPY Universe.

PubMed

Verwilst, Peter; Kim, Hye-Ri; Seo, Jinho; Sohn, Nak-Won; Cha, Seung-Yun; Kim, Yeongmin; Maeng, Sungho; Shin, Jung-Won; Kwak, Jong Hwan; Kang, Chulhun; Kim, Jong Seung

2017-09-27

The elucidation of the cause of Alzheimer's disease remains one of the greatest questions in neurodegenerative research. The lack of highly reliable low-cost sensors to study the structural changes in key proteins during the progression of the disease is a contributing factor to this lack of insight. In the current work, we describe the rational design and synthesis of two fluorescent BODIPY-based probes, named Tau 1 and Tau 2. The probes were evaluated on the molecular surface formed by a fibril of the PHF6 ( 306 VQIVYK 311 ) tau fragment using molecular docking studies to provide a potential molecular model to rationalize the selectivity of the new probes as compared to a homologous Aβ-selective probe. The probes were synthesized in a few steps from commercially available starting products and could thus prove to be highly cost-effective. We demonstrated the excellent photophysical properties of the dyes, such as a large Stokes shift and emission in the near-infrared window of the electromagnetic spectrum. The probes demonstrated a high selectivity for self-assembled microtubule-associated protein tau (Tau protein), in both solution and cell-based experiments. Moreover, the administration to an acute murine model of tauopathy clearly revealed the staining of self-assembled hyperphosphorylated tau protein in pathologically relevant hippocampal brain regions. Tau 1 demonstrated efficient blood-brain barrier penetrability and demonstrated a clear selectivity for tau tangles over Aβ plaques, as well as the capacity for in vivo imaging in a transgenic mouse model. The current work could open up avenues for the cost-effective monitoring of the tau protein aggregation state in animal models as well as tissue staining. Furthermore, these fluorophores could serve as the basis for the development of clinically relevant sensors, for example based on PET imaging.

Apparent Anomalous Diffusion in the Cytoplasm of Human Cells: The Effect of Probes' Polydispersity.

PubMed

Kalwarczyk, Tomasz; Kwapiszewska, Karina; Szczepanski, Krzysztof; Sozanski, Krzysztof; Szymanski, Jedrzej; Michalska, Bernadeta; Patalas-Krawczyk, Paulina; Duszynski, Jerzy; Holyst, Robert

2017-10-26

This work, based on in vivo and in vitro measurements, as well as in silico simulations, provides a consistent analysis of diffusion of polydisperse nanoparticles in the cytoplasm of living cells. Using the example of fluorescence correlation spectroscopy (FCS), we show the effect of polydispersity of probes on the experimental results. Although individual probes undergo normal diffusion, in the ensemble of probes, an effective broadening of the distribution of diffusion times occurs-similar to anomalous diffusion. We introduced fluorescently labeled dextrans into the cytoplasm of HeLa cells and found that cytoplasmic hydrodynamic drag, exponentially dependent on probe size, extraordinarily broadens the distribution of diffusion times across the focal volume. As a result, the in vivo FCS data were effectively fitted with the anomalous subdiffusion model while for a monodisperse probe the normal diffusion model was most suitable. Diffusion time obtained from the anomalous diffusion model corresponds to a probe whose size is determined by the weight-average molecular weight of the polymer. The apparent anomaly exponent decreases with increasing polydispersity of the probes. Our results and methodology can be applied in intracellular studies of the mobility of nanoparticles, polymers, or oligomerizing proteins.

Ubiquitin C-terminal electrophiles are activity-based probes for identification and mechanistic study of ubiquitin conjugating machinery.

PubMed

Love, Kerry Routenberg; Pandya, Renuka K; Spooner, Eric; Ploegh, Hidde L

2009-04-17

Protein modification by ubiquitin (Ub) and ubiquitin-like modifiers (Ubl) requires the action of activating (E1), conjugating (E2), and ligating (E3) enzymes and is a key step in the specific destruction of proteins. Deubiquitinating enzymes (DUBs) deconjugate substrates modified with Ub/Ubl's and recycle Ub inside the cell. Genome mining based on sequence homology to proteins with known function has assigned many enzymes to this pathway without confirmation of either conjugating or DUB activity. Function-dependent methodologies are still the most useful for rapid identification or assessment of biological activity of expressed proteins from cells. Activity-based protein profiling uses chemical probes that are active-site-directed for the classification of protein activities in complex mixtures. Here we show that the design and use of an expanded set of Ub-based electrophilic probes allowed us to recover and identify members of each enzyme class in the ubiquitin-proteasome system, including E3 ligases and DUBs with previously unverified activity. We show that epitope-tagged Ub-electrophilic probes can be used as activity-based probes for E3 ligase identification by in vitro labeling and activity studies of purified enzymes identified from complex mixtures in cell lysate. Furthermore, the reactivity of our probe with the HECT domain of the E3 Ub ligase ARF-BP1 suggests that multiple cysteines may be in the vicinity of the E2-binding site and are capable of the transfer of Ub to self or to a substrate protein.

Are mind wandering rates an artifact of the probe-caught method? Using self-caught mind wandering in the classroom to test, and reject, this possibility.

PubMed

Varao-Sousa, Trish L; Kingstone, Alan

2018-06-26

Mind wandering (MW) reports often rely on individuals responding to specific external thought probes. Researchers have used this probe-caught method almost exclusively, due to its reliability across a wide range of testing situations. However, it remains an open question whether the probe-caught MW rates in more complex settings converge with those for simpler tasks, because of the rather artificial and controlled nature of the probe-caught methodology itself, which is shared across the different settings. To address this issue, we measured MW in a real-world lecture, during which students indicated whether they were mind wandering by simply catching themselves (as one would normally do in real life) or by catching themselves and responding to thought probes. Across three separate lectures, self-caught MW reports were stable and unaffected by the inclusion of MW probes. That the probe rates were similar to those found in prior classroom research and did not affect the self-caught MW rates strongly suggests that the past consistency of probe-caught MW rates across a range of different settings is not an artifact of the thought-probe method. Our study also indicates that the self-caught MW methodology is a reliable way to acquire MW data. The extension of measurement techniques to include students' self-caught reports provides valuable information about how to successfully and naturalistically monitor MW in lecture settings, outside the laboratory.

MgF2 prism/rhodium/graphene: efficient refractive index sensing structure in optical domain

NASA Astrophysics Data System (ADS)

Mishra, Akhilesh Kumar; Mishra, Satyendra Kumar

2017-04-01

A theoretical study of a noble surface plasmon resonance (SPR) based sensing probe has been carried out. The sensing probe consists of a magnesium fluoride (MgF2) prism with its base coated with rarely used noble metal rhodium (Rh) and a bio-compatible layer of graphene. The refractive indices (RIs) of the sensing medium vary from 1.33 to 1.36 refractive index unit (RIU). The thickness of Rh and the number of graphene layers have been optimized for maximum sensitivity in a constraint set by the detection accuracy (DA). For the operating wavelength of 632 nm, the optimized sensing probe Rh (12 nm)/graphene (single layer) demonstrates sensitivity of ~259 degree/RIU with corresponding DA of ~0.32 degree-1 while for 532 nm of excitation, the optimized sensing probe Rh (12 nm)/graphene (three layer) exhibits sensitivity of ~240 degree/RIU and DA of ~0.27 degree-1.

MgF2 prism/rhodium/graphene: efficient refractive index sensing structure in optical domain.

PubMed

Mishra, Akhilesh Kumar; Mishra, Satyendra Kumar

2017-04-12

A theoretical study of a noble surface plasmon resonance (SPR) based sensing probe has been carried out. The sensing probe consists of a magnesium fluoride (MgF 2 ) prism with its base coated with rarely used noble metal rhodium (Rh) and a bio-compatible layer of graphene. The refractive indices (RIs) of the sensing medium vary from 1.33 to 1.36 refractive index unit (RIU). The thickness of Rh and the number of graphene layers have been optimized for maximum sensitivity in a constraint set by the detection accuracy (DA). For the operating wavelength of 632 nm, the optimized sensing probe Rh (12 nm)/graphene (single layer) demonstrates sensitivity of ~259 degree/RIU with corresponding DA of ~0.32 degree -1 while for 532 nm of excitation, the optimized sensing probe Rh (12 nm)/graphene (three layer) exhibits sensitivity of ~240 degree/RIU and DA of ~0.27 degree -1 .

Pump-probe experiments at the TEMPO beamline using the low-α operation mode of Synchrotron SOLEIL.

PubMed

Silly, Mathieu G; Ferté, Tom; Tordeux, Marie Agnes; Pierucci, Debora; Beaulieu, Nathan; Chauvet, Christian; Pressacco, Federico; Sirotti, Fausto; Popescu, Horia; Lopez-Flores, Victor; Tortarolo, Marina; Sacchi, Maurizio; Jaouen, Nicolas; Hollander, Philippe; Ricaud, Jean Paul; Bergeard, Nicolas; Boeglin, Christine; Tudu, Bharati; Delaunay, Renaud; Luning, Jan; Malinowski, Gregory; Hehn, Michel; Baumier, Cédric; Fortuna, Franck; Krizmancic, Damjan; Stebel, Luigi; Sergo, Rudi; Cautero, Giuseppe

2017-07-01

The SOLEIL synchrotron radiation source is regularly operated in special filling modes dedicated to pump-probe experiments. Among others, the low-α mode operation is characterized by shorter pulse duration and represents the natural bridge between 50 ps synchrotron pulses and femtosecond experiments. Here, the capabilities in low-α mode of the experimental set-ups developed at the TEMPO beamline to perform pump-probe experiments with soft X-rays based on photoelectron or photon detection are presented. A 282 kHz repetition-rate femtosecond laser is synchronized with the synchrotron radiation time structure to induce fast electronic and/or magnetic excitations. Detection is performed using a two-dimensional space resolution plus time resolution detector based on microchannel plates equipped with a delay line. Results of time-resolved photoelectron spectroscopy, circular dichroism and magnetic scattering experiments are reported, and their respective advantages and limitations in the framework of high-time-resolution pump-probe experiments compared and discussed.

Comparison of optical localization techniques for optical coherence tomography of the hand for multi-fraction orthovoltage radiotherapy or photodynamic therapy: white light vs. optical surface imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Jakubovic, Raphael; Bains, Amitpal; Ramjist, Joel; Babic, Steve; Chin, Lee; Barnes, Elizabeth; Yang, Victor X. D.

2017-02-01

Non-melanoma skin cancer (NMSC) is considered the most commonly diagnosed cancer in the United States and Canada. Treatment options include radiotherapy, surgical excision, radiotherapy, topical therapies, electrocautery, and cryotherapy. For patients undergoing fractionated orthovoltage radiation therapy or photodynamic therapy (PDT), the lesions are typically delineated by clinical markup prior to treatment without providing any information about the underlying tissue thus increasing the risk of geographic miss. The development of biomarkers for response in NMSC is imperative considering the current treatment paradigm is based on clinical examination and biopsy confirmation. Therefore, a non-invasive image-based evaluation of skin structure would allow for faster and potentially more comprehensive microscopic evaluation of the treated region at the point of care. To address this, our group is investigating the use of optical coherence tomography (OCT) for pre- and post- treatment evaluation of NMSC lesions during radiation therapy and PDT. Localization of the OCT probe for follow-up is complex, especially in the context of treatment response where the lesion is not present, precluding accurate delineation of the planning treatment area. Further, comparison to standard white light pre-treatment images is limited by the scale of the OCT probe (6 mm X 6 mm) relative to target region. In this study we compare the set-up accuracy of a typical OCT probe to detect a theoretical lesion on a patient's hand. White light images, optical surface imaging (OSI) and OCT will be obtained at baseline and used for probe set up on subsequent scans. Set-up error will be quantified using advanced image processing techniques.

Laser transit anemometer and Pitot probe comparative measurements in a sharp cone boundary layer at Mach 4

NASA Technical Reports Server (NTRS)

Hunter, W. W., Jr.; Ocheltree, S. L.; Russ, C. E., Jr.

1991-01-01

Laser transit anemometer (LTA) measurements of a 7 degree sharp cone boundary layer were conducted in the Air Force/AEDC Supersonic Tunnel A Mach 4 flow field. These measurements are compared with Pitot probe measurements and tricone theory provided by AEDC staff. Measurements were made both in laminar and turbulent boundary layers of the model. Comparison of LTA measurements with theory showed agreement to better than 1 percent for the laminar boundary layer cases. This level of agreement was obtained after small position corrections, 0.01 to 0.6 mm, were applied to the experimental data sets. Pitot probe data when compared with theory also showed small positioning errors. The Pitot data value was also limited due to probe interference with the flow near the model. The LTA turbulent boundary layer data indicated a power law dependence of 6.3 to 6.9. The LTA data was analyzed in the time (Tau) domain in which it was obtained and in the velocity domain. No significant differences were noted between Tau and velocity domain results except in one turbulent boundary layer case.

Method And Apparatus For Two Dimensional Surface Property Analysis Based On Boundary Measurement

DOEpatents

Richardson, John G.

2005-11-15

An apparatus and method for determining properties of a conductive film is disclosed. A plurality of probe locations selected around a periphery of the conductive film define a plurality of measurement lines between each probe location and all other probe locations. Electrical resistance may be measured along each of the measurement lines. A lumped parameter model may be developed based on the measured values of electrical resistance. The lumped parameter model may be used to estimate resistivity at one or more selected locations encompassed by the plurality of probe locations. The resistivity may be extrapolated to other physical properties if the conductive film includes a correlation between resistivity and the other physical properties. A profile of the conductive film may be developed by determining resistivity at a plurality of locations. The conductive film may be applied to a structure such that resistivity may be estimated and profiled for the structure's surface.

Comparison of the Predictive Accuracy of DNA Array-Based Multigene Classifiers across cDNA Arrays and Affymetrix GeneChips

PubMed Central

Stec, James; Wang, Jing; Coombes, Kevin; Ayers, Mark; Hoersch, Sebastian; Gold, David L.; Ross, Jeffrey S; Hess, Kenneth R.; Tirrell, Stephen; Linette, Gerald; Hortobagyi, Gabriel N.; Symmans, W. Fraser; Pusztai, Lajos

2005-01-01

We examined how well differentially expressed genes and multigene outcome classifiers retain their class-discriminating values when tested on data generated by different transcriptional profiling platforms. RNA from 33 stage I-III breast cancers was hybridized to both Affymetrix GeneChip and Millennium Pharmaceuticals cDNA arrays. Only 30% of all corresponding gene expression measurements on the two platforms had Pearson correlation coefficient r ≥ 0.7 when UniGene was used to match probes. There was substantial variation in correlation between different Affymetrix probe sets matched to the same cDNA probe. When cDNA and Affymetrix probes were matched by basic local alignment tool (BLAST) sequence identity, the correlation increased substantially. We identified 182 genes in the Affymetrix and 45 in the cDNA data (including 17 common genes) that accurately separated 91% of cases in supervised hierarchical clustering in each data set. Cross-platform testing of these informative genes resulted in lower clustering accuracy of 45 and 79%, respectively. Several sets of accurate five-gene classifiers were developed on each platform using linear discriminant analysis. The best 100 classifiers showed average misclassification error rate of 2% on the original data that rose to 19.5% when tested on data from the other platform. Random five-gene classifiers showed misclassification error rate of 33%. We conclude that multigene predictors optimized for one platform lose accuracy when applied to data from another platform due to missing genes and sequence differences in probes that result in differing measurements for the same gene. PMID:16049308

Development and validation of an in-line NIR spectroscopic method for continuous blend potency determination in the feed frame of a tablet press.

PubMed

De Leersnyder, Fien; Peeters, Elisabeth; Djalabi, Hasna; Vanhoorne, Valérie; Van Snick, Bernd; Hong, Ke; Hammond, Stephen; Liu, Angela Yang; Ziemons, Eric; Vervaet, Chris; De Beer, Thomas

2018-03-20

A calibration model for in-line API quantification based on near infrared (NIR) spectra collection during tableting in the tablet press feed frame was developed and validated. First, the measurement set-up was optimised and the effect of filling degree of the feed frame on the NIR spectra was investigated. Secondly, a predictive API quantification model was developed and validated by calculating the accuracy profile based on the analysis results of validation experiments. Furthermore, based on the data of the accuracy profile, the measurement uncertainty was determined. Finally, the robustness of the API quantification model was evaluated. An NIR probe (SentroPAT FO) was implemented into the feed frame of a rotary tablet press (Modul™ P) to monitor physical mixtures of a model API (sodium saccharine) and excipients with two different API target concentrations: 5 and 20% (w/w). Cutting notches into the paddle wheel fingers did avoid disturbances of the NIR signal caused by the rotating paddle wheel fingers and hence allowed better and more complete feed frame monitoring. The effect of the design of the notched paddle wheel fingers was also investigated and elucidated that straight paddle wheel fingers did cause less variation in NIR signal compared to curved paddle wheel fingers. The filling degree of the feed frame was reflected in the raw NIR spectra. Several different calibration models for the prediction of the API content were developed, based on the use of single spectra or averaged spectra, and using partial least squares (PLS) regression or ratio models. These predictive models were then evaluated and validated by processing physical mixtures with different API concentrations not used in the calibration models (validation set). The β-expectation tolerance intervals were calculated for each model and for each of the validated API concentration levels (β was set at 95%). PLS models showed the best predictive performance. For each examined saccharine concentration range (i.e., between 4.5 and 6.5% and between 15 and 25%), at least 95% of future measurements will not deviate more than 15% from the true value. Copyright © 2018 Elsevier B.V. All rights reserved.

Probing gravity at cosmological scales by measurements which test the relationship between gravitational lensing and matter overdensity.

PubMed

Zhang, Pengjie; Liguori, Michele; Bean, Rachel; Dodelson, Scott

2007-10-05

The standard cosmology is based on general relativity (GR) and includes dark matter and dark energy and predicts a fixed relationship between the gravitational potentials responsible for gravitational lensing and the matter overdensity. Alternative theories of gravity often make different predictions. We propose a set of measurements which can test this relationship, thereby distinguishing between dark energy or matter models and models in which gravity differs from GR. Planned surveys will be able to measure E(G), an observational quantity whose expectation value is equal to the ratio of the Laplacian of the Newtonian potentials to the peculiar velocity divergence, to percent accuracy. This will easily separate alternatives such as the cold dark matter model with a cosmological constant, Dvali-Gabadadze-Porrati, TeVeS, and f(R) gravity.

Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain.

PubMed

Guo, Yahui; Cheng, Junjie; Wang, Jine; Zhou, Xiaodong; Hu, Jiming; Pei, Renjun

2014-09-01

A simple, versatile, and label-free DNA computing strategy was designed by using toehold-mediated strand displacement and stem-loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two-layer logic cascade were constructed. The probes contain a G-quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light-up fluorescent signal of G-quadruplex/NMM complex was used as the output readout. The inputs are the disease-specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label-free and modular strategy might be adapted in multi-target diagnosis through DNA hybridization and aptamer-target interaction. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analyzing Planck and low redshift data sets with advanced statistical methods

NASA Astrophysics Data System (ADS)

Eifler, Tim

The recent ESA/NASA Planck mission has provided a key data set to constrain cosmology that is most sensitive to physics of the early Universe, such as inflation and primordial NonGaussianity (Planck 2015 results XIII). In combination with cosmological probes of the LargeScale Structure (LSS), the Planck data set is a powerful source of information to investigate late time phenomena (Planck 2015 results XIV), e.g. the accelerated expansion of the Universe, the impact of baryonic physics on the growth of structure, and the alignment of galaxies in their dark matter halos. It is the main objective of this proposal to re-analyze the archival Planck data, 1) with different, more recently developed statistical methods for cosmological parameter inference, and 2) to combine Planck and ground-based observations in an innovative way. We will make the corresponding analysis framework publicly available and believe that it will set a new standard for future CMB-LSS analyses. Advanced statistical methods, such as the Gibbs sampler (Jewell et al 2004, Wandelt et al 2004) have been critical in the analysis of Planck data. More recently, Approximate Bayesian Computation (ABC, see Weyant et al 2012, Akeret et al 2015, Ishida et al 2015, for cosmological applications) has matured to an interesting tool in cosmological likelihood analyses. It circumvents several assumptions that enter the standard Planck (and most LSS) likelihood analyses, most importantly, the assumption that the functional form of the likelihood of the CMB observables is a multivariate Gaussian. Beyond applying new statistical methods to Planck data in order to cross-check and validate existing constraints, we plan to combine Planck and DES data in a new and innovative way and run multi-probe likelihood analyses of CMB and LSS observables. The complexity of multiprobe likelihood analyses scale (non-linearly) with the level of correlations amongst the individual probes that are included. For the multi-probe analysis proposed here we will use the existing CosmoLike software, a computationally efficient analysis framework that is unique in its integrated ansatz of jointly analyzing probes of large-scale structure (LSS) of the Universe. We plan to combine CosmoLike with publicly available CMB analysis software (Camb, CLASS) to include modeling capabilities of CMB temperature, polarization, and lensing measurements. The resulting analysis framework will be capable to independently and jointly analyze data from the CMB and from various probes of the LSS of the Universe. After completion we will utilize this framework to check for consistency amongst the individual probes and subsequently run a joint likelihood analysis of probes that are not in tension. The inclusion of Planck information in a joint likelihood analysis substantially reduces DES uncertainties in cosmological parameters, and allows for unprecedented constraints on parameters that describe astrophysics. In their recent review Observational Probes of Cosmic Acceleration (Weinberg et al 2013) the authors emphasize the value of a balanced program that employs several of the most powerful methods in combination, both to cross-check systematic uncertainties and to take advantage of complementary information. The work we propose follows exactly this idea: 1) cross-checking existing Planck results with alternative methods in the data analysis, 2) checking for consistency of Planck and DES data, and 3) running a joint analysis to constrain cosmology and astrophysics. It is now expedient to develop and refine multi-probe analysis strategies that allow the comparison and inclusion of information from disparate probes to optimally obtain cosmology and astrophysics. Analyzing Planck and DES data poses an ideal opportunity for this purpose and corresponding lessons will be of great value for the science preparation of Euclid and WFIRST.

Finite element simulation of thunderstorm electrodynamics in the proximity of the storm

NASA Technical Reports Server (NTRS)

Baginski, Michael Edward

1988-01-01

Observations of electric fields, Maxwell current density, and air conductivity over thunderstorms were presented. The measurements were obtained using electric field mils and conductivity probes installed on a U2 aircraft as the aircraft passed approximately directly over an active thunderstorm at an altitude of 18 to 20 km. Accurate electrical observations of this type are rare and provide important information to those involved in numerically modeling a thunderstorm. A preliminary set of computer simulations based on this data were conducted and are described. The simulations show good agreement with measurements and are used to infer the thundercloud's charging current and amount of charge exchanged per flash.

Three-dimensional ophthalmic optical coherence tomography with a refraction correction algorithm

NASA Astrophysics Data System (ADS)

Zawadzki, Robert J.; Leisser, Christoph; Leitgeb, Rainer; Pircher, Michael; Fercher, Adolf F.

2003-10-01

We built an optical coherence tomography (OCT) system with a rapid scanning optical delay (RSOD) line, which allows probing full axial eye length. The system produces Three-dimensional (3D) data sets that are used to generate 3D tomograms of the model eye. The raw tomographic data were processed by an algorithm, which is based on Snell"s law to correct the interface positions. The Zernike polynomials representation of the interfaces allows quantitative wave aberration measurements. 3D images of our results are presented to illustrate the capabilities of the system and the algorithm performance. The system allows us to measure intra-ocular distances.

Discovery of Highly Selective and Nanomolar Carbamate-Based Butyrylcholinesterase Inhibitors by Rational Investigation into Their Inhibition Mode.

PubMed

Sawatzky, Edgar; Wehle, Sarah; Kling, Beata; Wendrich, Jan; Bringmann, Gerhard; Sotriffer, Christoph A; Heilmann, Jörg; Decker, Michael

2016-03-10

Butyrylcholinesterase (BChE) is a promising target for the treatment of later stage cognitive decline in Alzheimer's disease. A set of pseudo-irreversible BChE inhibitors with high selectivity over hAChE was synthesized based on carbamates attached to tetrahydroquinazoline scaffolds with the 2-thiophenyl compound 2p as the most potent inhibitor of eqBChE (KC = 14.3 nM) and also of hBChE (KC = 19.7 nM). The inhibitors transfer the carbamate moiety onto the active site under release of the phenolic tetrahydroquinazoline scaffolds that themselves act as neuroprotectants. By combination of kinetic data with molecular docking studies, a plausible binding model was probed describing how the tetrahydroquinazoline scaffold guides the carbamate into a close position to the active site. The model explains the influence of the carrier scaffold onto the affinity of an inhibitor just before carbamate transfer. This strategy can be used to utilize the binding mode of other carbamate-based inhibitors.

Array magnetics modal analysis for the DIII-D tokamak based on localized time-series modelling

DOE PAGES

Olofsson, K. Erik J.; Hanson, Jeremy M.; Shiraki, Daisuke; ...

2014-07-14

Here, time-series analysis of magnetics data in tokamaks is typically done using block-based fast Fourier transform methods. This work presents the development and deployment of a new set of algorithms for magnetic probe array analysis. The method is based on an estimation technique known as stochastic subspace identification (SSI). Compared with the standard coherence approach or the direct singular value decomposition approach, the new technique exhibits several beneficial properties. For example, the SSI method does not require that frequencies are orthogonal with respect to the timeframe used in the analysis. Frequencies are obtained directly as parameters of localized time-series models.more » The parameters are extracted by solving small-scale eigenvalue problems. Applications include maximum-likelihood regularized eigenmode pattern estimation, detection of neoclassical tearing modes, including locked mode precursors, and automatic clustering of modes, and magnetics-pattern characterization of sawtooth pre- and postcursors, edge harmonic oscillations and fishbones.« less

Leaving out control groups: an internal contrast analysis of gene expression profiles in atrial fibrillation patients--a systems biology approach to clinical categorization.

PubMed

Vanhoutte, Kurt; de Asmundis, Carlo; Francesconi, Anna; Figysl, Jurgen; Steurs, Griet; Boussy, Tim; Roos, Markus; Mueller, Andreas; Massimo, Lucio; Paparella, Gaetano; Van Caelenberg, Kristien; Chierchia, Gian Battista; Sarkozy, Andrea; Terradellas, Pedro Brugada Y; Zizi, Martin

2009-01-01

Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical focus on potential entry pathways into the disease. We used a RMA (Robust Multichip Average) normalized Affymetrix micro-array data set from 10 AF patients (geo_accession #GSE2240). Four series of probes were selected based on physiopathogenic links with AF entryways: apoptosis (remodeling), MAP kinase (cell remodeling), OXPHOS (ability to sustain hemodynamic workload) and glycolysis (ischemia). Annotated probe lists were polled with Bioconductor packages in R (version 2.7.1). Genetic profile contrasts were analysed with hierarchical clustering and principal component analysis. The analysis revealed distinct patient groups for all probe sets. A substantial part (54% till 67%) of the variance is explained in the first 2 principal components. Genes in PC1/2 with high discriminatory value were selected and analyzed in detail. We aim for reliable molecular stratification of AF. We show that stratification is possible based on physiologically relevant gene sets. Genes with high contrast value are likely to give pathophysiological insight into permanent AF subtypes.

Spatial dispersion effects upon local excitation of extrinsic plasmons in a graphene micro-disk

NASA Astrophysics Data System (ADS)

Mencarelli, D.; Bellucci, S.; Sindona, A.; Pierantoni, L.

2015-11-01

Excitation of surface plasmon waves in extrinsic graphene is studied using a full-wave electromagnetic field solver as analysis engine. Particular emphasis is placed on the role played by spatial dispersion due to the finite size of the two-dimensional material at the micro-scale. A simple instructive set up is considered where the near field of a wire antenna is held at sub-micrometric distance from a disk-shaped graphene patch. The key-input of the simulation is the graphene conductivity tensor at terahertz frequencies, being modeled by the Boltzmann transport equation for the valence and conduction electrons at the Dirac points (where a linear wave-vector dependence of the band energies is assumed). The conductivity equation is worked out in different levels of approximations, based on the relaxation time ansatz with an additional constraint for particle number conservation. Both drift and diffusion currents are shown to significantly contribute to the spatially dispersive anisotropic features of micro-scale graphene. More generally, spatial dispersion effects are predicted to influence not only plasmon propagation free of external sources, but also typical scanning probe microscopy configurations. The paper sets the focus on plasmon excitation phenomena induced by near field probes, being a central issue for the design of optical devices and photonic circuits.

Improved mathematical and computational tools for modeling photon propagation in tissue

NASA Astrophysics Data System (ADS)

Calabro, Katherine Weaver

Light interacts with biological tissue through two predominant mechanisms: scattering and absorption, which are sensitive to the size and density of cellular organelles, and to biochemical composition (ex. hemoglobin), respectively. During the progression of disease, tissues undergo a predictable set of changes in cell morphology and vascularization, which directly affect their scattering and absorption properties. Hence, quantification of these optical property differences can be used to identify the physiological biomarkers of disease with interest often focused on cancer. Diffuse reflectance spectroscopy is a diagnostic tool, wherein broadband visible light is transmitted through a fiber optic probe into a turbid medium, and after propagating through the sample, a fraction of the light is collected at the surface as reflectance. The measured reflectance spectrum can be analyzed with appropriate mathematical models to extract the optical properties of the tissue, and from these, a set of physiological properties. A number of models have been developed for this purpose using a variety of approaches -- from diffusion theory, to computational simulations, and empirical observations. However, these models are generally limited to narrow ranges of tissue and probe geometries. In this thesis, reflectance models were developed for a much wider range of measurement parameters, and influences such as the scattering phase function and probe design were investigated rigorously for the first time. The results provide a comprehensive understanding of the factors that influence reflectance, with novel insights that, in some cases, challenge current assumptions in the field. An improved Monte Carlo simulation program, designed to run on a graphics processing unit (GPU), was built to simulate the data used in the development of the reflectance models. Rigorous error analysis was performed to identify how inaccuracies in modeling assumptions can be expected to affect the accuracy of extracted optical property values from experimentally-acquired reflectance spectra. From this analysis, probe geometries that offer the best robustness against error in estimation of physiological properties from tissue, are presented. Finally, several in vivo studies demonstrating the use of reflectance spectroscopy for both research and clinical applications are presented.

Manual Skill Acquisition During Transesophageal Echocardiography Simulator Training of Cardiology Fellows: A Kinematic Assessment.

PubMed

Matyal, Robina; Montealegre-Gallegos, Mario; Mitchell, John D; Kim, Han; Bergman, Remco; Hawthorne, Katie M; O'Halloran, David; Wong, Vanessa; Hess, Phillip E; Mahmood, Feroze

2015-12-01

To investigate whether a transesophageal echocardiography (TEE) simulator with motion analysis can be used to impart proficiency in TEE in an integrated curriculum-based model. A prospective cohort study. A tertiary-care university hospital. TEE-naïve cardiology fellows. Participants underwent an 8-session multimodal TEE training program. Manual skills were assessed at the end of sessions 2 and 8 using motion analysis of the TEE simulator's probe. At the end of the course, participants performed an intraoperative TEE; their examinations were video captured, and a blinded investigator evaluated the total time and image transitions needed for each view. Results are reported as mean±standard deviation, or median (interquartile range) where appropriate. Eleven fellows completed the knowledge and kinematic portions of the study. Five participants were excluded from the evaluation in the clinical setting because of interim exposure to TEE or having participated in a TEE rotation after the training course. An increase of 12.95% in post-test knowledge scores was observed. From the start to the end of the course, there was a significant reduction (p<0.001 for all) in the number of probe. During clinical performance evaluation, trainees were able to obtain all the required echocardiographic views unassisted but required a longer time and had more probe transitions when compared with an expert. A curriculum-based approach to TEE training for cardiology fellows can be complemented with kinematic analyses to objectify acquisition of manual skills during simulator-based training. Copyright © 2015 Elsevier Inc. All rights reserved.

Probing the magnetic field structure in Sgr A* on Black Hole Horizon Scales with Polarized Radiative Transfer Simulations

NASA Astrophysics Data System (ADS)

Gold, Roman; McKinney, Jonathan; Johnson, Michael; Doeleman, Sheperd; Event Horizon Telescope Collaboration

2016-03-01

Accreting black holes (BHs) are at the core of relativistic astrophysics as messengers of the strong-field regime of General Relativity and prime targets of several observational campaigns, including imaging the black hole shadow in SagA* and M87 with the Event Horizon Telescope. I will present results from general-relativistic, polarized radiatiative transfer models for the inner accretion flow in Sgr A*. The models use time dependent, global GRMHD simulations of hot accretion flows including standard-and-normal-evolution (SANE) and magnetically arrested disks (MAD). I present comparisons of these synthetic data sets to the most recent observations with the Event Horizon Telescope and show how the data distinguishes the models and probes the magnetic field structure.

SVD-aided pseudo principal-component analysis: A new method to speed up and improve determination of the optimum kinetic model from time-resolved data

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

Oang, Key Young; Yang, Cheolhee; Muniyappan, Srinivasan

Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model. In addition, the results of SAPPA for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of themore » same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy.« less

Selective and Sensitive Detection of Cyanide Based on the Displacement Strategy Using a Water-Soluble Fluorescent Probe.

PubMed

La, Ming; Hao, Yuanqiang; Wang, Zhaoyang; Han, Guo-Cheng; Qu, Lingbo

2016-01-01

A water-soluble fluorescent probe (C-GGH) was used for the highly sensitive and selective detection of cyanide (CN(-)) in aqueous media based on the displacement strategy. Due to the presence of the recognition unit GGH (Gly-Gly-His), the probe C-GGH can coordinate with Cu(2+) and consequently display ON-OFF type fluorescence response. Furthermore, the in situ formed nonfluorescent C-GGH-Cu(2+) complex can act as an effective OFF-ON type fluorescent probe for sensing CN(-) anion. Due to the strong binding affinity of CN(-) to Cu(2+), CN(-) can extract Cu(2+) from C-GGH-Cu(2+) complex, leading to the release of C-GGH and the recovery of fluorescent emission of the system. The probe C-GGH-Cu(2+) allowed detection of CN(-) in aqueous solution with a LOD (limit of detection) of 0.017 μmol/L which is much lower than the maximum contaminant level (1.9 μmol/L) for CN(-) in drinking water set by the WHO (World Health Organization). The probe also displayed excellent specificity for CN(-) towards other anions, including F(-), Cl(-), Br(-), I(-), SCN(-), PO4 (3-), N3 (-), NO3 (-), AcO(-), SO4 (2-), and CO3 (2-).

Selective and Sensitive Detection of Cyanide Based on the Displacement Strategy Using a Water-Soluble Fluorescent Probe

PubMed Central

La, Ming; Hao, Yuanqiang; Wang, Zhaoyang; Han, Guo-Cheng; Qu, Lingbo

2016-01-01

A water-soluble fluorescent probe (C-GGH) was used for the highly sensitive and selective detection of cyanide (CN−) in aqueous media based on the displacement strategy. Due to the presence of the recognition unit GGH (Gly-Gly-His), the probe C-GGH can coordinate with Cu2+ and consequently display ON-OFF type fluorescence response. Furthermore, the in situ formed nonfluorescent C-GGH-Cu2+ complex can act as an effective OFF-ON type fluorescent probe for sensing CN− anion. Due to the strong binding affinity of CN− to Cu2+, CN− can extract Cu2+ from C-GGH-Cu2+ complex, leading to the release of C-GGH and the recovery of fluorescent emission of the system. The probe C-GGH-Cu2+ allowed detection of CN− in aqueous solution with a LOD (limit of detection) of 0.017 μmol/L which is much lower than the maximum contaminant level (1.9 μmol/L) for CN− in drinking water set by the WHO (World Health Organization). The probe also displayed excellent specificity for CN− towards other anions, including F−, Cl−, Br−, I−, SCN−, PO4 3−, N3 −, NO3 −, AcO−, SO4 2−, and CO3 2−. PMID:26881185

Curriculum-Based Measurement of Oral Reading: Passage Equivalence and Probe-Set Development

ERIC Educational Resources Information Center

Christ, Theodore J.; Ardoin, Scott P.

2009-01-01

Curriculum-based measurement of reading (CBM-R) is used to estimate oral reading fluency. Unlike many traditional published tests, CBM-R materials are often comprised of 20 to 30 alternate forms/passages. Historically, CBM-R assessment materials were sampled from curricular materials. Recent research has documented the potentially deleterious…

Clinical tests of an ultrasonic periodontal probe

NASA Astrophysics Data System (ADS)

Hinders, Mark K.; Lynch, John E.; McCombs, Gayle B.

2002-05-01

A new ultrasonic periodontal probe has been developed that offers the potential for earlier detection of periodontal disease activity, non-invasive diagnosis, and greater reliability of measurement. A comparison study of the ultrasonic probe to both a manual probe, and a controlled-force probe was conducted to evaluate its clinical effectiveness. Twelve patients enrolled into this study. Two half-month examinations were conducted on each patient, scheduled one hour apart. A one-way analysis of variance was performed to compare the results for the three sets of probing depth measurements, followed by a repeated measures analysis to assess the reproducibility of the different probing techniques. These preliminary findings indicate that manual and ultrasonic probing measure different features of the pocket. Therefore, it is not obvious how the two depth measurements correspond to each other. However, both methods exhibited a similar tendency toward increasing pocket depths as Gingival Index scores increased. Based on the small sample size, further studies need to be conducted using a larger population of patients exhibiting a wider range of disease activity. In addition, studies that allow histological examination of the pocket after probing will help further evaluate the clinical effectiveness the ultrasonic probe. Future studies will also aid in the development of more effective automated feature recognition algorithms that convert the ultrasonic echoes into pocket depth readings.

Real-time data acquisition and telemetry based irrigation control system

DOEpatents

Slater, John M.; Svoboda, John M.

2005-12-13

A data acquisition and telemetry based control system for use in facilitating substantially real time management of an agricultural irrigation system. The soil moisture sensor includes a reader and a plurality of probes. The probes each include an electronic circuit having a moisture sensing capacitor in operative communication with the soil whose moisture is to be measured. Each probe also includes a receive/transmit antenna and the reader includes a transmit/receive antenna, so that as the reader passes near the probe, the reader transmits a digital excitation signal to the electronic circuit of the biodegradable probe via an inductive couple formed between the transmit/receive antenna of the reader and the receive/transmit coil of the probe. The electronic circuit uses an energy component of the excitation signal to generate a digital data signal which indicates the moisture content of the soil adjacent to the moisture sensing capacitor. The probe sends the data signal to the reader which then uses the data signal to develop a corresponding set of watering instructions which are then transmitted to a control module in communication with the irrigation system. The control module sends corresponding control signals to nozzles of the irrigation system causing the irrigation system to disperse water in a manner consistent with the moisture content data transmitted by the probes to the reader. Because the irrigation system moves continuously through the field to be irrigated, the moisture content data acquisition and resultant water dispersal by the irrigation system occur substantially in real time.

In vivo Raman measurement of levofloxacin lactate in blood using a nanoparticle-coated optical fiber probe

PubMed Central

Liu, Shupeng; Rong, Ming; Zhang, Heng; Chen, Na; Pang, Fufei; Chen, Zhenyi; Wang, Tingyun; Yan, Jianshe

2016-01-01

Monitoring drug concentrations in vivo is very useful for adjusting a drug dosage during treatment and for drug research. Specifically, cutting-edge “on-line” drug research relies on knowing how drugs are metabolized or how they interact with the blood in real-time. Thus, this study explored performing in vivo Raman measurements of the model drug levofloxacin lactate in the blood using a nanoparticle-coated optical fiber probe (optical fiber nano-probe). The results show that we were able to measure real-time changes in the blood concentration of levofloxacin lactate, suggesting that this technique could be helpful for performing drug analyses and drug monitoring in a clinical setting without repeatedly withdrawing blood from patients. PMID:27231590

Evolution of cooperative strategies from first principles.

PubMed

Burtsev, Mikhail; Turchin, Peter

2006-04-20

One of the greatest challenges in the modern biological and social sciences is to understand the evolution of cooperative behaviour. General outlines of the answer to this puzzle are currently emerging as a result of developments in the theories of kin selection, reciprocity, multilevel selection and cultural group selection. The main conceptual tool used in probing the logical coherence of proposed explanations has been game theory, including both analytical models and agent-based simulations. The game-theoretic approach yields clear-cut results but assumes, as a rule, a simple structure of payoffs and a small set of possible strategies. Here we propose a more stringent test of the theory by developing a computer model with a considerably extended spectrum of possible strategies. In our model, agents are endowed with a limited set of receptors, a set of elementary actions and a neural net in between. Behavioural strategies are not predetermined; instead, the process of evolution constructs and reconstructs them from elementary actions. Two new strategies of cooperative attack and defence emerge in simulations, as well as the well-known dove, hawk and bourgeois strategies. Our results indicate that cooperative strategies can evolve even under such minimalist assumptions, provided that agents are capable of perceiving heritable external markers of other agents.

Strong and Long Makes Short: Strong-Pump Strong-Probe Spectroscopy.

PubMed

Gelin, Maxim F; Egorova, Dassia; Domcke, Wolfgang

2011-01-20

We propose a new time-domain spectroscopic technique that is based on strong pump and probe pulses. The strong-pump strong-probe (SPSP) technique provides temporal resolution that is not limited by the durations of the pump and probe pulses. By numerically exact simulations of SPSP signals for a multilevel vibronic model, we show that the SPSP signals exhibit electronic and vibrational beatings on time scales which are significantly shorter than the pulse durations. This suggests the possible application of SPSP spectroscopy for the real-time investigation of molecular processes that cannot be temporally resolved by pump-probe spectroscopy with weak pump and probe pulses.

Selective recognition of DNA from olive leaves and olive oil by PNA and modified-PNA microarrays

PubMed Central

Rossi, Stefano; Calabretta, Alessandro; Tedeschi, Tullia; Sforza, Stefano; Arcioni, Sergio; Baldoni, Luciana; Corradini, Roberto; Marchelli, Rosangela

2012-01-01

PNA probes for the specific detection of DNA from olive oil samples by microarray technology were developed. The presence of as low as 5% refined hazelnut (Corylus avellana) oil in extra-virgin olive oil (Olea europaea L.) could be detected by using a PNA microarray. A set of two single nucleotide polymorphisms (SNPs) from the Actin gene of Olive was chosen as a model for evaluating the ability of PNA probes for discriminating olive cultivars. Both unmodified and C2-modified PNAs bearing an arginine side-chain were used, the latter showing higher sequence specificity. DNA extracted from leaves of three different cultivars (Ogliarola leccese, Canino and Frantoio) could be easily discriminated using a microarray with unmodified PNA probes, whereas discrimination of DNA from oil samples was more challenging, and could be obtained only by using chiral PNA probes. PMID:22772038

Effect of number of probes and their orientation on the calculation of several compressor face distortion descriptors

NASA Technical Reports Server (NTRS)

Stoll, F.; Tremback, J. W.; Arnaiz, H. H.

1979-01-01

A study was performed to determine the effects of the number and position of total pressure probes on the calculation of five compressor face distortion descriptors. This study used three sets of 320 steady state total pressure measurements that were obtained with a special rotating rake apparatus in wind tunnel tests of a mixed-compression inlet. The inlet was a one third scale model of the inlet on a YF-12 airplane, and it was tested in the wind tunnel at representative flight conditions at Mach numbers above 2.0. The study shows that large errors resulted in the calculation of the distortion descriptors even with a number of probes that were considered adequate in the past. There were errors as large as 30 and -50 percent in several distortion descriptors for a configuration consisting of eight rakes with five equal-area-weighted probes on each rake.

Cadaveric in-situ testing of optical coherence tomography system-based skull base surgery guidance

NASA Astrophysics Data System (ADS)

Sun, Cuiru; Khan, Osaama H.; Siegler, Peter; Jivraj, Jamil; Wong, Ronnie; Yang, Victor X. D.

2015-03-01

Optical Coherence Tomography (OCT) has extensive potential for producing clinical impact in the field of neurological diseases. A neurosurgical OCT hand-held forward viewing probe in Bayonet shape has been developed. In this study, we test the feasibility of integrating this imaging probe with modern navigation technology for guidance and monitoring of skull base surgery. Cadaver heads were used to simulate relevant surgical approaches for treatment of sellar, parasellar and skull base pathology. A high-resolution 3D CT scan was performed on the cadaver head to provide baseline data for navigation. The cadaver head was mounted on existing 3- or 4-point fixation systems. Tracking markers were attached to the OCT probe and the surgeon-probe-OCT interface was calibrated. 2D OCT images were shown in real time together with the optical tracking images to the surgeon during surgery. The intraoperative video and multimodality imaging data set, consisting of real time OCT images, OCT probe location registered to neurosurgical navigation were assessed. The integration of intraoperative OCT imaging with navigation technology provides the surgeon with updated image information, which is important to deal with tissue shifts and deformations during surgery. Preliminary results demonstrate that the clinical neurosurgical navigation system can provide the hand held OCT probe gross anatomical localization. The near-histological imaging resolution of intraoperative OCT can improve the identification of microstructural/morphology differences. The OCT imaging data, combined with the neurosurgical navigation tracking has the potential to improve image interpretation, precision and accuracy of the therapeutic procedure.

A new general model for predicting melting thermodynamics of complementary and mismatched B-form duplexes containing locked nucleic acids: application to probe design for digital PCR detection of somatic mutations.

PubMed

Hughesman, Curtis; Fakhfakh, Kareem; Bidshahri, Roza; Lund, H Louise; Haynes, Charles

2015-02-17

Advances in real-time polymerase chain reaction (PCR), as well as the emergence of digital PCR (dPCR) and useful modified nucleotide chemistries, including locked nucleic acids (LNAs), have created the potential to improve and expand clinical applications of PCR through their ability to better quantify and differentiate amplification products, but fully realizing this potential will require robust methods for designing dual-labeled hydrolysis probes and predicting their hybridization thermodynamics as a function of their sequence, chemistry, and template complementarity. We present here a nearest-neighbor thermodynamic model that accurately predicts the melting thermodynamics of a short oligonucleotide duplexed either to its perfect complement or to a template containing mismatched base pairs. The model may be applied to pure-DNA duplexes or to duplexes for which one strand contains any number and pattern of LNA substitutions. Perturbations to duplex stability arising from mismatched DNA:DNA or LNA:DNA base pairs are treated at the Gibbs energy level to maintain statistical significance in the regressed model parameters. This approach, when combined with the model's accounting of the temperature dependencies of the melting enthalpy and entropy, permits accurate prediction of T(m) values for pure-DNA homoduplexes or LNA-substituted heteroduplexes containing one or two independent mismatched base pairs. Terms accounting for changes in solution conditions and terminal addition of fluorescent dyes and quenchers are then introduced so that the model may be used to accurately predict and thereby tailor the T(m) of a pure-DNA or LNA-substituted hydrolysis probe when duplexed either to its perfect-match template or to a template harboring a noncomplementary base. The model, which builds on classic nearest-neighbor thermodynamics, should therefore be of use to clinicians and biologists who require probes that distinguish and quantify two closely related alleles in either a quantitative PCR or dPCR assay. This potential is demonstrated by using the model to design allele-specific probes that completely discriminate and quantify clinically relevant mutant alleles (BRAF V600E and KIT D816V) in a dPCR assay.

Characterizing the performance of an affordable, multichannel conductivity probe for density measurements in stratified flows

NASA Astrophysics Data System (ADS)

Subramanian, Balaji; Carminati, Marco; Luzzatto-Fegiz, Paolo

2017-11-01

In stratified flows, conductivity (combined with temperature) is often used to measure density. The conductivity probes typically used can resolve very fine spatial scales, but on the downside they are fragile, expensive, sensitive to environmental noise and have only single channel capability. Recently a low-cost, robust, arduino-based probe called Conduino was developed, which can be valuable in a wide range of applications where resolving extremely small spatial scales is not needed. This probe uses micro-USB connectors as actual conductivity sensors with a custom designed electronic board for simultaneous acquisition from multiple probes, with conductivity resolution comparable to commercially available PME conductivity probe. A detailed assessment of performance of this Conduino probe is described here. To establish time response and sensitivity as a function of electrode geometry, we build a variety of shapes for different kinds of applications, with tip spacing ranging from 0.5-2.5 mm, and with electrode length ranging from 2.3-6 mm. We set up a two-layer density profile and traverse it rapidly, yielding a time response comparable to PME. The Conduino's multi-channel capability is used to operate probe arrays, which helps to construct density fields in stratified flows.

Techniques for blade tip clearance measurements with capacitive probes

NASA Astrophysics Data System (ADS)

Steiner, Alexander

2000-07-01

This article presents a proven but advantageous concept for blade tip clearance evaluation in turbomachinery. The system is based on heavy duty probes and a high frequency (HF) and amplifying electronic unit followed by a signal processing unit. Measurements are taken under high temperature and other severe conditions such as ionization. Every single blade can be observed. The signals are digitally filtered and linearized in real time. The electronic set-up is highly integrated. Miniaturized versions of the electronic units exist. The small and robust units can be used in turbo engines in flight. With several probes at different angles in one radial plane further information is available. Shaft eccentricity or blade oscillations can be calculated.

Impact of Dynamic Specimen Shape Evolution on the Atom Probe Tomography Results of Doped Epitaxial Oxide Multilayers: Comparison of Experiment and Simulation

DOE PAGES

Madaan, Nitesh; Bao, Jie; Nandasiri, Manjula I.; ...

2015-08-31

The experimental atom probe tomography results from two different specimen orientations (top-down and side-ways) of a high oxygen ion conducting Samaria-doped-ceria/Scandia-stabilized-zirconia multilayer thin film solid oxide fuel cell electrolyte was correlated with level-set method based field evaporation simulations for the same specimen orientations. This experiment-theory correlation explains the dynamic specimen shape evolution and ion trajectory aberrations that can induce density artifacts in final reconstruction leading to inaccurate estimation of interfacial intermixing. This study highlights the need and importance of correlating experimental results with field evaporation simulations when using atom probe tomography for studying oxide heterostructure interfaces.

Simulating Energy Relaxation in Pump-Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids.

PubMed

Dettori, Riccardo; Ceriotti, Michele; Hunger, Johannes; Melis, Claudio; Colombo, Luciano; Donadio, Davide

2017-03-14

We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order.

PubMed

Aron, Miles; Browning, Richard; Carugo, Dario; Sezgin, Erdinc; Bernardino de la Serna, Jorge; Eggeling, Christian; Stride, Eleanor

2017-05-12

Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually characterized by the generalized polarization (GP) parameter. With the development of commercial microscopes equipped with spectral detectors, spectral imaging has become a convenient and powerful technique for measuring GP and other membrane properties. The existing tools for spectral image processing, however, are insufficient for processing the large data sets afforded by this technological advancement, and are unsuitable for processing images acquired with rapidly internalized fluorescent probes. Here we present a MATLAB spectral imaging toolbox with the aim of overcoming these limitations. In addition to common operations, such as the calculation of distributions of GP values, generation of pseudo-colored GP maps, and spectral analysis, a key highlight of this tool is reliable membrane segmentation for probes that are rapidly internalized. Furthermore, handling for hyperstacks, 3D reconstruction and batch processing facilitates analysis of data sets generated by time series, z-stack, and area scan microscope operations. Finally, the object size distribution is determined, which can provide insight into the mechanisms underlying changes in membrane properties and is desirable for e.g. studies involving model membranes and surfactant coated particles. Analysis is demonstrated for cell membranes, cell-derived vesicles, model membranes, and microbubbles with environmentally-sensitive probes Laurdan, carboxyl-modified Laurdan (C-Laurdan), Di-4-ANEPPDHQ, and Di-4-AN(F)EPPTEA (FE), for quantification of the local lateral density of lipids or lipid packing. The Spectral Imaging Toolbox is a powerful tool for the segmentation and processing of large spectral imaging datasets with a reliable method for membrane segmentation and no ability in programming required. The Spectral Imaging Toolbox can be downloaded from https://uk.mathworks.com/matlabcentral/fileexchange/62617-spectral-imaging-toolbox .

Determination of solute site occupancies within γ' precipitates in nickel-base superalloys via orientation-specific atom probe tomography

DOE PAGES

Meher, Subhashish; Rojhirunsakool, Tanaporn; Nandwana, Peeyush; ...

2015-04-28

In this study, the analytical limitations in atom probe tomography such as resolving a desired set of atomic planes, for solving complex materials science problems, have been overcome by employing a well-developed unique and reproducible crystallographic technique, involving synergetic coupling of orientation microscopy with atom probe tomography. The crystallographic information in atom probe reconstructions has been utilized to determine the solute site occupancies in Ni-Al-Cr based superalloys accurately. The structural information in atom probe reveals that both Al and Cr occupy the same sub-lattice within the L1 2-ordered g precipitates to form Ni 3(Al,Cr) precipitates in a Ni-14Al-7Cr(at.%) alloy. Interestingly,more » the addition of Co, which is a solid solution strengthener, to a Ni-14Al-7Cr alloy results in the partial reversal of Al site occupancy within g precipitates to form (Ni,Al) 3(Al,Cr,Co) precipitates. This unique evidence of reversal of Al site occupancy, resulting from the introduction of other solutes within the ordered structures, gives insights into the relative energetics of different sub-lattice sites when occupied by different solutes.« less

Directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S13 using tethered Fe(II).

PubMed Central

Heilek, G M; Noller, H F

1996-01-01

Directed hydroxyl radical probing was used to probe the rRNA neighborhood around protein S13 in the 30S ribosomal subunit. The unique cysteine at position 84 of S13 served as a tethering site for attachment of Fe(II)-1-(p-bromoacetamidobenzyl)-EDTA. Derivatized S13 (Fe-C84-S13) was then assembled into 30S ribosomal subunits by in vitro reconstitution with 16S rRNA and a mixture of the remaining 30S subunit proteins. Hydroxyl radicals generated from the tethered Fe(II) resulted in cleavage of the RNA backbone in two localized regions of the 3' major domain of 16S rRNA. One region spans nt 1308-1333 and is close to a site previously crosslinked to S13. A second set of cleavages is found in the 950/1230 helix. Both regions have been implicated in binding of S13 by previous chemical footprinting studies using base-specific chemical probes and solution-based hydroxyl radical probing. These results place both regions of 16S rRNA in proximity to position C84 of S13 in the three-dimensional structure of the 30S ribosomal subunit. PMID:8718688

Quantification of coronary microvascular resistance using angiographic images for volumetric blood flow measurement: in vivo validation

PubMed Central

Zhang, Zhang; Takarada, Shigeho

2011-01-01

Structural coronary microcirculation abnormalities are important prognostic determinants in clinical settings. However, an assessment of microvascular resistance (MR) requires a velocity wire. A first-pass distribution analysis technique to measure volumetric blood flow has been previously validated. The aim of this study was the in vivo validation of the MR measurement technique using first-pass distribution analysis. Twelve anesthetized swine were instrumented with a transit-time ultrasound flow probe on the proximal segment of the left anterior descending coronary artery (LAD). Microspheres were injected into the LAD to create a model of microvascular dysfunction. Adenosine (400 μg·kg−1·min−1) was used to produce maximum hyperemia. A region of interest in the LAD arterial bed was drawn to generate time-density curves using angiographic images. Volumetric blood flow measurements (Qa) were made using a time-density curve and the assumption that blood was momentarily replaced with contrast agent during the injection. Blood flow from the flow probe (Qp), coronary pressure (Pa), and right atrium pressure (Pv) were continuously recorded. Flow probe-based normalized MR (NMRp) and angiography-based normalized MR (NMRa) were calculated using Qp and Qa, respectively. In 258 measurements, Qa showed a strong correlation with the gold standard Qp (Qa = 0.90 Qp + 6.6 ml/min, r2 = 0.91, P < 0.0001). NMRa correlated linearly with NMRp (NMRa = 0.90 NMRp + 0.02 mmHg·ml−1·min−1, r2 = 0.91, P < 0.0001). Additionally, the Bland-Altman analysis showed a close agreement between NMRa and NMRp. In conclusion, a technique based on angiographic image data for quantifying NMR was validated using a swine model. This study provides a method to measure NMR without using a velocity wire, which can potentially be used to evaluate microvascular conditions during coronary arteriography. PMID:21398596

Current-Voltage and Floating-Potential characteristics of cylindrical emissive probes from a full-kinetic model based on the orbital motion theory

NASA Astrophysics Data System (ADS)

Chen, Xin; Sánchez-Arriaga, Gonzalo

2018-02-01

To model the sheath structure around an emissive probe with cylindrical geometry, the Orbital-Motion theory takes advantage of three conserved quantities (distribution function, transverse energy, and angular momentum) to transform the stationary Vlasov-Poisson system into a single integro-differential equation. For a stationary collisionless unmagnetized plasma, this equation describes self-consistently the probe characteristics. By solving such an equation numerically, parametric analyses for the current-voltage (IV) and floating-potential (FP) characteristics can be performed, which show that: (a) for strong emission, the space-charge effects increase with probe radius; (b) the probe can float at a positive potential relative to the plasma; (c) a smaller probe radius is preferred for the FP method to determine the plasma potential; (d) the work function of the emitting material and the plasma-ion properties do not influence the reliability of the floating-potential method. Analytical analysis demonstrates that the inflection point of an IV curve for non-emitting probes occurs at the plasma potential. The flat potential is not a self-consistent solution for emissive probes.

Rapid polymerase chain reaction-based screening assay for bacterial biothreat agents.

PubMed

Yang, Samuel; Rothman, Richard E; Hardick, Justin; Kuroki, Marcos; Hardick, Andrew; Doshi, Vishal; Ramachandran, Padmini; Gaydos, Charlotte A

2008-04-01

To design and evaluate a rapid polymerase chain reaction (PCR)-based assay for detecting Eubacteria and performing early screening for selected Class A biothreat bacterial pathogens. The authors designed a two-step PCR-based algorithm consisting of an initial broad-based universal detection step, followed by specific pathogen identification targeted for identification of the Class A bacterial biothreat agents. A region in the bacterial 16S rRNA gene containing a highly variable sequence flanked by clusters of conserved sequences was chosen as the target for the PCR assay design. A previously described highly conserved region located within the 16S rRNA amplicon was selected as the universal probe (UniProbe, Integrated DNA Technology, Coralville, IA). Pathogen-specific TaqMan probes were designed for Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Performance of the assay was assessed using genomic DNA extracted from the aforementioned biothreat-related organisms (inactivated or surrogate) and other common bacteria. The UniProbe detected the presence of all tested Eubacteria (31/31) with high analytical sensitivity. The biothreat-specific probes accurately identified organisms down to the closely related species and genus level, but were unable to discriminate between very close surrogates, such as Yersinia philomiragia and Bacillus cereus. A simple, two-step PCR-based assay proved capable of both universal bacterial detection and identification of select Class A bacterial biothreat and biothreat-related pathogens. Although this assay requires confirmatory testing for definitive species identification, the method has great potential for use in ED-based settings for rapid diagnosis in cases of suspected Category A bacterial biothreat agents.

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

PubMed Central

Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

2014-01-01

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism. PMID:25462574

Analysis of the HASI accelerometers data measured during the impact phase of the Huygens probe on the surface of Titan by means of a simulation with a finite-element model

NASA Astrophysics Data System (ADS)

Bettanini, C.; Zaccariotto, M.; Angrilli, F.

2008-04-01

The Huygens Atmospheric Structure Instrument (HASI) [Fulchignoni, M., Ferri, F., Angrilli, F., Bar-Nun, A., Barucci, M.A., Bianchini, G., Borucki, W., Coradini, M., Coustenis, A., Falkner, P., Flamini, E., Grard, R., Hamelin, M., Harri, A.M., Leppelmaier, G.W., Lopez-Moreno, J.J., McDonnell, J.A.M., McKay, C.P., Neubauer, F.M., Pedersen, A., Piacardi, G., Pirronello, V., Schwingenschuh, K., Seiff, A., Svedhem, H., Vanzani, V., Zarnecki, J.C., 2002. The characterisation of Titan atmosphere physical properties. Space Sci. Rev. 104, 395-431] was a very complete instrument suite installed on board the Huygens probe, the planetary lander of the Cassini Huygens Mission to Saturn system, which successfully completed its mission in January 2005. HASI comprised a set of accelerometers, temperature sensors, pressure transducers and permittivity analysers aimed at the investigation of Titan atmosphere, which were fully operative during a several hour-long parachuted descent from an altitude of 157 km to planetary surface. Accelerometers were the only instruments activated earlier, just after Cassini separation, and recorded data during all the mission phases from atmospheric entry to landing, providing essential information for elaborating probe trajectory as well as Titan atmospheric profiles [G. Colombatti, et al. Reconstruction of the trajectory of the Huygens probe using the Huygens Atmospheric Structure Instrument, this same PSS issue]. Although not specifically designed for monitoring very fast dynamic events, HASI accelerometers have also recorded the trace of probe impact with the planetary surface, building up along with the data from Huygens Surface Science Package (SSP) instrument [ Zarnecki, J.C., Leese, M.R., Garry, J.R.C., Ghafoor, N.A.L., Hathi, B., 2002. Huygens Surface Science Package. Space Sci. Rev. 104, 593-611] the only set of direct measurements of the mechanical properties of the Titan soil. Though not considered secondary with respect to SSP data, HASI data provide peculiar information related to the dynamic response of the whole Huygens probe when impacting the surface, whereas the SSP data were collected mainly by sensors located on a small penetrometer below the main probe dome. Therefore, although having a sensibly lower sampling frequency, HASI Accelerometer Subsystem (ACC) data complete the information of SSP data in the study of impact deceleration profiles, which can provide key information for the estimation of the mechanical parameters of the soil and get an insight of its consistency and composition. In the analysis of Huygens mission data some unexpected features were present in the ACC data sets, so a dedicated study was needed to investigate the presence of dynamic interferences during an acquisition and correct the impact signature. The developed method is based on dynamic analysis of the impact through a three-dimensional finite-element dynamic model of the Huygens probe and the results lead to a corrected interpretation of accelerometer readings and provided an improved description of key aspects of the planetary landing. Although some aspects of probe's state after impact need some further analysis, as for final resting attitude which is to date not completely agreed on, this study disclosed that the probe experienced a vertical decelerating action which is compatible with two possible scenarios: the first one implies the penetration in a soft substrate material followed by a lateral bounce out of the generated hole and the second one suggests the displacement of pebbles from the surface into the soil. Numerical elaboration of impact data calculated a 12 cm penetration into the surface, which may have been experienced either by the lower dome of the probe or from pebbles that were situated under the dome when contacting the planet. In either case after a few seconds of motion the Huygens probe finally rested above Titan's surface with a negligible penetration. Since HASI piezo-accelerometer design was driven by the need of high full-scale values to monitor critical events during entry and descent phase, it was not possible to reconstruct horizontal motion after main deceleration phase without consistent uncertainties due to the poor overall accuracy in a low-acceleration range.

Activation and binding in verbal working memory: a dual-process model for the recognition of nonwords.

PubMed

Oberauer, Klaus; Lange, Elke B

2009-02-01

The article presents a mathematical model of short-term recognition based on dual-process models and the three-component theory of working memory [Oberauer, K. (2002). Access to information in working memory: Exploring the focus of attention. Journal of Experimental Psychology: Learning, Memory, and Cognition, 28, 411-421]. Familiarity arises from activated representations in long-term memory, ignoring their relations; recollection retrieves bindings in the capacity-limited component of working memory. In three experiments participants encoded two short lists of nonwords for immediate recognition, one of which was then cued as irrelevant. Probes from the irrelevant list were rejected more slowly than new probes; this was also found with probes recombining letters of irrelevant nonwords, suggesting that familiarity arises from individual letters independent of their relations. When asked to accept probes whose letters were all in the relevant list, regardless of their conjunction, participants accepted probes preserving the original conjunctions faster than recombinations, showing that recollection accessed feature bindings automatically. The model fit the data best when familiarity depended only on matching letters, whereas recollection used binding information.

Intracellular probes for imaging oxygen concentration: how good are they?

NASA Astrophysics Data System (ADS)

Dmitriev, Ruslan I.; Papkovsky, Dmitri B.

2015-09-01

In the last decade a number of cell-permeable phosphorescence based probes for imaging of (intra)cellular oxygen (icO2) have been described. These small molecule, supramolecular and nanoparticle structures, although allowing analysis of hypoxia, local gradients and fluctuations in O2, responses to stimulation and drug treatment at sub-cellular level with high spatial and temporal resolution, differ significantly in their operational performance and applicability to different cell and tissue models. Here we discuss and compare these probes with respect to their staining efficiency, brightness, photostability, toxicity, cell specificity, compatibility with different cell and tissue models, and analytical performance. Merits and limitations of particular probes are highlighted and strategies for development of new high-performance O2 imaging probes defined. Key application areas in hypoxia research, stem cells, cancer biology and tissue physiology are also discussed.

Specific Detection of Clavibacter michiganensis subsp. sepedonicus by Amplification of Three Unique DNA Sequences Isolated by Subtraction Hybridization.

PubMed

Mills, D; Russell, B W; Hanus, J W

1997-08-01

ABSTRACT Three single-copy, unique DNA fragments, designated Cms50, Cms72, and Cms85, were isolated from strain CS3 of Clavibacter michiganensis subsp. sepedonicus by subtraction hybridization using driver DNA from C. michiganensis subsp. insidiosus, C. michiganensis subsp. michiganensis, and Rhodococcus facians. Radio-labeled probes made of these fragments and used in Southern blot analysis revealed each to be absolutely specific to all North American C. michiganensis subsp. sepedonicus strains tested, including plasmidless and nonmucoid strains. The probes have no homology with genomic DNA from related C. michiganensis subspecies insidiosus, michiganensis, and tessellarius, nor with DNA from 11 additional bacterial species and three unidentified strains, some of which have been previously reported to display cross-reactivity with C. michiganensis subsp. sepedonicus-specific antisera. The three fragments shared no homology, and they appeared to be separated from each other by at least 20 kbp in the CS3 genome. Internal primer sets permitted amplification of each fragment by the polymerase chain reaction (PCR) only from C. michiganensis subsp. sepedonicus DNA. In a PCR-based sensitivity assay using a primer set that amplifies Cms85, the lowest level of detection of C. michiganensis subsp. sepedonicus was 100 CFU per milliliter when cells were added to potato core fluid. Erroneous results that may arise from PCR artifacts and mutational events are, therefore, minimized by the redundancy of the primer sets, and the products should be verifiable with unique capture probes in sequence-based detection systems.

Dose verification of eye plaque brachytherapy using spectroscopic dosimetry.

PubMed

Jarema, T; Cutajar, D; Weaver, M; Petasecca, M; Lerch, M; Kejda, A; Rosenfeld, A

2016-09-01

Eye plaque brachytherapy has been developed and refined for the last 80 years, demonstrating effective results in the treatment of ocular malignancies. Current dosimetry techniques for eye plaque brachytherapy (such as TLD- and film-based techniques) are time consuming and cannot be used prior to treatment in a sterile environment. The measurement of the expected dose distribution within the eye, prior to insertion within the clinical setting, would be advantageous, as any errors in source loading will lead to an erroneous dose distribution and inferior treatment outcomes. This study investigated the use of spectroscopic dosimetry techniques for real-time quality assurance of I-125 based eye plaques, immediately prior to insertion. A silicon detector based probe, operating in spectroscopy mode was constructed, containing a small (1 mm(3)) silicon detector, mounted within a ceramic holder, all encapsulated within a rubber sheath to prevent water infiltration of the electronics. Preliminary tests of the prototype demonstrated that the depth dose distribution through the central axis of an I-125 based eye plaque may be determined from AAPM Task Group 43 recommendations to a deviation of 6 % at 3 mm depth, 7 % at 5 mm depth, 1 % at 10 mm depth and 13 % at 20 mm depth, with the deviations attributed to the construction of the probe. A new probe design aims to reduce these discrepancies, however the concept of spectroscopic dosimetry shows great promise for use in eye plaque quality assurance in the clinical setting.

Nonlinear Effects in Ultrasound Fields of Diagnostic-type Transducers Used for Kidney Stone Propulsion: Characterization in Water

PubMed Central

Karzova, M.; Cunitz, B.; Yuldashev, P.; Andriyakhina, Y.; Kreider, W.; Sapozhnikov, O.; Bailey, M.; Khokhlova, V.

2016-01-01

Newer imaging and therapeutic ultrasound technologies require higher in situ pressure levels compared to conventional diagnostic values. One example is the recently developed use of focused ultrasonic radiation force to move kidney stones and residual fragments out of the urinary collecting system. A commercial diagnostic 2.3 MHz C5-2 array probe is used to deliver the acoustic pushing pulses. The probe comprises 128 elements equally spaced at the 55 mm long convex cylindrical surface with 38 mm radius of curvature. The efficacy of the treatment can be increased by using higher transducer output to provide stronger pushing force; however, nonlinear acoustic saturation effect can be a limiting factor. In this work nonlinear propagation effects were analyzed for the C5-2 transducer using a combined measurement and modeling approach. Simulations were based on the 3D Westervelt equation; the boundary condition was set to match low power pressure beam scans. Focal waveforms simulated for increased output power levels were compared with the fiber-optic hydrophone measurements and were found in good agreement. It was shown that saturation effects do limit the acoustic pressure in the focal region of the transducer. This work has application to standard diagnostic probes and imaging. PMID:27087711

Nonlinear effects in ultrasound fields of diagnostic-type transducers used for kidney stone propulsion: Characterization in water

NASA Astrophysics Data System (ADS)

Karzova, M.; Cunitz, B.; Yuldashev, P.; Andriyakhina, Y.; Kreider, W.; Sapozhnikov, O.; Bailey, M.; Khokhlova, V.

2015-10-01

Newer imaging and therapeutic ultrasound technologies require higher in situ pressure levels compared to conventional diagnostic values. One example is the recently developed use of focused ultrasonic radiation force to move kidney stones and residual fragments out of the urinary collecting system. A commercial diagnostic 2.3 MHz C5-2 array probe is used to deliver the acoustic pushing pulses. The probe comprises 128 elements equally spaced at the 55 mm long convex cylindrical surface with 38 mm radius of curvature. The efficacy of the treatment can be increased by using higher intensity at the focus to provide stronger pushing force; however, nonlinear acoustic saturation can be a limiting factor. In this work nonlinear propagation effects were analyzed for the C5-2 transducer using a combined measurement and modeling approach. Simulations were based on the 3D Westervelt equation; the boundary condition was set to match the focal geometry of the beam as measured at a low power output. Focal waveforms simulated for increased output power levels were compared with the fiber-optic hydrophone measurements and were found in good agreement. It was shown that saturation effects do limit the acoustic pressure in the focal region of the transducer. This work has application to standard diagnostic probes and imaging.

Preparation of erosion and deposition investigations on plasma facing components in Wendelstein 7-X

NASA Astrophysics Data System (ADS)

Dhard, C. P.; Balden, M.; Braeuer, T.; Brezinsek, S.; Coenen, J. W.; Dudek, A.; Ehrke, G.; Hathiramani, D.; Klose, S.; König, R.; Laux, M.; Linsmeier, Ch; Manhard, A.; Masuzaki, S.; Mayer, M.; Motojima, G.; Naujoks, D.; Neu, R.; Neubauer, O.; Rack, M.; Ruset, C.; Schwarz-Selinger, T.; Pedersen, T. Sunn; Tokitani, M.; Unterberg, B.; Yajima, M.; W7-X Team1, The

2017-12-01

In the Wendelstein 7-X stellarator with its twisted magnetic geometry the investigation of plasma wall interaction processes in 3D plasma configurations is an important research subject. For the upcoming operation phase i.e. OP1.2, three different types of material probes have been installed within the plasma vessel for the erosion/deposition investigations in selected areas with largely different expected heat load levels, namely, ≤10 MW m-2 at the test divertor units (TDU), ≤500 kW m-2 at the baffles, heat shields and toroidal closures and ≤100 kW m-2 at the stainless steel wall panels. These include 18 exchangeable target elements at TDU, about 30 000 screw heads at graphite tiles and 44 wafer probes on wall panels, coated with marker layers. The layer thicknesses, surface morphologies and the impurity contents were pre-characterized by different techniques and subjected to various qualification tests. The positions of these probes were fixed based on the strike line locations on the divertor predicted by field line diffusion and EMC3/EIRENE modeling calculations for the OP1.2 plasma configurations and availability of locations on panels in direct view of the plasma. After the first half of the operation phase i.e. OP1.2a the probes will be removed to determine the erosion/deposition pattern by post-mortem analysis and replaced by a new set for the second half of the operation phase, OP1.2b.

Real-time prediction of queues at signalized intersections to support eco-driving applications.

DOT National Transportation Integrated Search

2014-10-01

The overall objective of this research is to develop models for predicting queue lengths at signalized intersections based on : the data from probe vehicles. The time and space coordinates of the probe vehicles going through signalized intersections ...

"Turn-off" fluorescent sensor for highly sensitive and specific simultaneous recognition of 29 famous green teas based on quantum dots combined with chemometrics.

PubMed

Liu, Li; Fan, Yao; Fu, Haiyan; Chen, Feng; Ni, Chuang; Wang, Jinxing; Yin, Qiaobo; Mu, Qingling; Yang, Tianming; She, Yuanbin

2017-04-22

Fluorescent "turn-off" sensors based on water-soluble quantum dots (QDs) have drawn increasing attention owing to their unique properties such as high fluorescence quantum yields, chemical stability and low toxicity. In this work, a novel method based on the fluorescence "turn-off" model with water-soluble CdTe QDs as the fluorescent probes for differentiation of 29 different famous green teas is established. The fluorescence of the QDs can be quenched in different degrees in light of positions and intensities of the fluorescent peaks for the green teas. Subsequently, with aid of classic partial least square discriminant analysis (PLSDA), all the green teas can be discriminated with high sensitivity, specificity and a satisfactory recognition rate of 100% for training set and 98.3% for prediction set, respectively. Especially, the "turn-off" fluorescence PLSDA model based on second-order derivatives (2nd der) with reduced least complexity (LVs = 3) was the most effective one for modeling. Most importantly, we further demonstrated the established "turn-off" fluorescent sensor mode has several significant advantages and appealing properties over the conventional fluorescent method for large-class-number classification (LCNC) of green teas. This work is, to the best of our knowledge, the first report on the rapid and effective identification of so many kinds of famous green teas based on the "turn-off" model of QDs combined with chemometrics, which also implies other potential applications on complex LCNC classification system with weak fluorescence or even without fluorescence to achieve higher detective response and specificity. Copyright © 2017 Elsevier B.V. All rights reserved.

Prediction model of potential hepatocarcinogenicity of rat hepatocarcinogens using a large-scale toxicogenomics database

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

Uehara, Takeki, E-mail: takeki.uehara@shionogi.co.jp; Toxicogenomics Informatics Project, National Institute of Biomedical Innovation, 7-6-8 Asagi, Ibaraki, Osaka 567-0085; Minowa, Yohsuke

2011-09-15

The present study was performed to develop a robust gene-based prediction model for early assessment of potential hepatocarcinogenicity of chemicals in rats by using our toxicogenomics database, TG-GATEs (Genomics-Assisted Toxicity Evaluation System developed by the Toxicogenomics Project in Japan). The positive training set consisted of high- or middle-dose groups that received 6 different non-genotoxic hepatocarcinogens during a 28-day period. The negative training set consisted of high- or middle-dose groups of 54 non-carcinogens. Support vector machine combined with wrapper-type gene selection algorithms was used for modeling. Consequently, our best classifier yielded prediction accuracies for hepatocarcinogenicity of 99% sensitivity and 97% specificitymore » in the training data set, and false positive prediction was almost completely eliminated. Pathway analysis of feature genes revealed that the mitogen-activated protein kinase p38- and phosphatidylinositol-3-kinase-centered interactome and the v-myc myelocytomatosis viral oncogene homolog-centered interactome were the 2 most significant networks. The usefulness and robustness of our predictor were further confirmed in an independent validation data set obtained from the public database. Interestingly, similar positive predictions were obtained in several genotoxic hepatocarcinogens as well as non-genotoxic hepatocarcinogens. These results indicate that the expression profiles of our newly selected candidate biomarker genes might be common characteristics in the early stage of carcinogenesis for both genotoxic and non-genotoxic carcinogens in the rat liver. Our toxicogenomic model might be useful for the prospective screening of hepatocarcinogenicity of compounds and prioritization of compounds for carcinogenicity testing. - Highlights: >We developed a toxicogenomic model to predict hepatocarcinogenicity of chemicals. >The optimized model consisting of 9 probes had 99% sensitivity and 97% specificity. >This model enables us to detect genotoxic as well as non-genotoxic hepatocarcinogens.« less

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe.

PubMed

Gertz, E Michael; Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees.

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

PubMed Central

Chowdhury, Salim Akhter; Lee, Woei-Jyh; Wangsa, Darawalee; Heselmeyer-Haddad, Kerstin; Ried, Thomas; Schwartz, Russell; Schäffer, Alejandro A.

2016-01-01

Advances in fluorescence in situ hybridization (FISH) make it feasible to detect multiple copy-number changes in hundreds of cells of solid tumors. Studies using FISH, sequencing, and other technologies have revealed substantial intra-tumor heterogeneity. The evolution of subclones in tumors may be modeled by phylogenies. Tumors often harbor aneuploid or polyploid cell populations. Using a FISH probe to estimate changes in ploidy can guide the creation of trees that model changes in ploidy and individual gene copy-number variations. We present FISHtrees 3.0, which implements a ploidy-based tree building method based on mixed integer linear programming (MILP). The ploidy-based modeling in FISHtrees includes a new formulation of the problem of merging trees for changes of a single gene into trees modeling changes in multiple genes and the ploidy. When multiple samples are collected from each patient, varying over time or tumor regions, it is useful to evaluate similarities in tumor progression among the samples. Therefore, we further implemented in FISHtrees 3.0 a new method to build consensus graphs for multiple samples. We validate FISHtrees 3.0 on a simulated data and on FISH data from paired cases of cervical primary and metastatic tumors and on paired breast ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). Tests on simulated data show improved accuracy of the ploidy-based approach relative to prior ploidyless methods. Tests on real data further demonstrate novel insights these methods offer into tumor progression processes. Trees for DCIS samples are significantly less complex than trees for paired IDC samples. Consensus graphs show substantial divergence among most paired samples from both sets. Low consensus between DCIS and IDC trees may help explain the difficulty in finding biomarkers that predict which DCIS cases are at most risk to progress to IDC. The FISHtrees software is available at ftp://ftp.ncbi.nih.gov/pub/FISHtrees. PMID:27362268

Teaching Functional Play Skills to a Young Child with Autism Spectrum Disorder through Video Self-Modeling

ERIC Educational Resources Information Center

Lee, Sharon Y.; Lo, Ya-yu; Lo, Yafen

2017-01-01

The researchers used a single-case, multiple probe design across three sets of toys (i.e., farm toy, doctor's clinic toy, and rescue toy) to examine the effects of video self-modeling (VSM) on the functional play skills of a 5-year-old child with autism spectrum disorder. The findings showed a functional relation between VSM and increased…

Design of a DNA chip for detection of unknown genetically modified organisms (GMOs).

PubMed

Nesvold, Håvard; Kristoffersen, Anja Bråthen; Holst-Jensen, Arne; Berdal, Knut G

2005-05-01

Unknown genetically modified organisms (GMOs) have not undergone a risk evaluation, and hence might pose a danger to health and environment. There are, today, no methods for detecting unknown GMOs. In this paper we propose a novel method intended as a first step in an approach for detecting unknown genetically modified (GM) material in a single plant. A model is designed where biological and combinatorial reduction rules are applied to a set of DNA chip probes containing all possible sequences of uniform length n, creating probes capable of detecting unknown GMOs. The model is theoretically tested for Arabidopsis thaliana Columbia, and the probabilities for detecting inserts and receiving false positives are assessed for various parameters for this organism. From a theoretical standpoint, the model looks very promising but should be tested further in the laboratory. The model and algorithms will be available upon request to the corresponding author.

Dual representation of item positions in verbal short-term memory: Evidence for two access modes.

PubMed

Lange, Elke B; Verhaeghen, Paul; Cerella, John

Memory sets of N = 1~5 digits were exposed sequentially from left-to-right across the screen, followed by N recognition probes. Probes had to be compared to memory list items on identity only (Sternberg task) or conditional on list position. Positions were probed randomly or in left-to-right order. Search functions related probe response times to set size. Random probing led to ramped, "Sternbergian" functions whose intercepts were elevated by the location requirement. Sequential probing led to flat search functions-fast responses unaffected by set size. These results suggested that items in STM could be accessed either by a slow search-on-identity followed by recovery of an associated location tag, or in a single step by following item-to-item links in study order. It is argued that this dual coding of location information occurs spontaneously at study, and that either code can be utilised at retrieval depending on test demands.

Model benchmarking and reference signals for angled-beam shear wave ultrasonic nondestructive evaluation (NDE) inspections

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Hopkins, Deborah; Datuin, Marvin; Warchol, Mark; Warchol, Lyudmila; Forsyth, David S.; Buynak, Charlie; Lindgren, Eric A.

2017-02-01

For model benchmark studies, the accuracy of the model is typically evaluated based on the change in response relative to a selected reference signal. The use of a side drilled hole (SDH) in a plate was investigated as a reference signal for angled beam shear wave inspection for aircraft structure inspections of fastener sites. Systematic studies were performed with varying SDH depth and size, and varying the ultrasonic probe frequency, focal depth, and probe height. Increased error was observed with the simulation of angled shear wave beams in the near-field. Even more significant, asymmetry in real probes and the inherent sensitivity of signals in the near-field to subtle test conditions were found to provide a greater challenge with achieving model agreement. To achieve quality model benchmark results for this problem, it is critical to carefully align the probe with the part geometry, to verify symmetry in probe response, and ideally avoid using reference signals from the near-field response. Suggested reference signals for angled beam shear wave inspections include using the `through hole' corner specular reflection signal and the full skip' signal off of the far wall from the side drilled hole.

Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database

PubMed Central

Butkiewicz, Mariusz; Lowe, Edward W.; Mueller, Ralf; Mendenhall, Jeffrey L.; Teixeira, Pedro L.; Weaver, C. David; Meiler, Jens

2013-01-01

With the rapidly increasing availability of High-Throughput Screening (HTS) data in the public domain, such as the PubChem database, methods for ligand-based computer-aided drug discovery (LB-CADD) have the potential to accelerate and reduce the cost of probe development and drug discovery efforts in academia. We assemble nine data sets from realistic HTS campaigns representing major families of drug target proteins for benchmarking LB-CADD methods. Each data set is public domain through PubChem and carefully collated through confirmation screens validating active compounds. These data sets provide the foundation for benchmarking a new cheminformatics framework BCL::ChemInfo, which is freely available for non-commercial use. Quantitative structure activity relationship (QSAR) models are built using Artificial Neural Networks (ANNs), Support Vector Machines (SVMs), Decision Trees (DTs), and Kohonen networks (KNs). Problem-specific descriptor optimization protocols are assessed including Sequential Feature Forward Selection (SFFS) and various information content measures. Measures of predictive power and confidence are evaluated through cross-validation, and a consensus prediction scheme is tested that combines orthogonal machine learning algorithms into a single predictor. Enrichments ranging from 15 to 101 for a TPR cutoff of 25% are observed. PMID:23299552

An Optimized Set of Fluorescence In Situ Hybridization Probes for Detection of Pancreatobiliary Tract Cancer in Cytology Brush Samples.

PubMed

Barr Fritcher, Emily G; Voss, Jesse S; Brankley, Shannon M; Campion, Michael B; Jenkins, Sarah M; Keeney, Matthew E; Henry, Michael R; Kerr, Sarah M; Chaiteerakij, Roongruedee; Pestova, Ekaterina V; Clayton, Amy C; Zhang, Jun; Roberts, Lewis R; Gores, Gregory J; Halling, Kevin C; Kipp, Benjamin R

2015-12-01

Pancreatobiliary cancer is detected by fluorescence in situ hybridization (FISH) of pancreatobiliary brush samples with UroVysion probes, originally designed to detect bladder cancer. We designed a set of new probes to detect pancreatobiliary cancer and compared its performance with that of UroVysion and routine cytology analysis. We tested a set of FISH probes on tumor tissues (cholangiocarcinoma or pancreatic carcinoma) and non-tumor tissues from 29 patients. We identified 4 probes that had high specificity for tumor vs non-tumor tissues; we called this set of probes pancreatobiliary FISH. We performed a retrospective analysis of brush samples from 272 patients who underwent endoscopic retrograde cholangiopancreatography for evaluation of malignancy at the Mayo Clinic; results were available from routine cytology and FISH with UroVysion probes. Archived residual specimens were retrieved and used to evaluate the pancreatobiliary FISH probes. Cutoff values for FISH with the pancreatobiliary probes were determined using 89 samples and validated in the remaining 183 samples. Clinical and pathologic evidence of malignancy in the pancreatobiliary tract within 2 years of brush sample collection was used as the standard; samples from patients without malignancies were used as negative controls. The validation cohort included 85 patients with malignancies (46.4%) and 114 patients with primary sclerosing cholangitis (62.3%). Samples containing cells above the cutoff for polysomy (copy number gain of ≥2 probes) were classified as positive in FISH with the UroVysion and pancreatobiliary probes. Multivariable logistic regression was used to estimate associations between clinical and pathology findings and results from FISH. The combination of FISH probes 1q21, 7p12, 8q24, and 9p21 identified cancer cells with 93% sensitivity and 100% specificity in pancreatobiliary tissue samples and were therefore included in the pancreatobiliary probe set. In the validation cohort of brush samples, pancreatobiliary FISH identified samples from patients with malignancy with a significantly higher level of sensitivity (64.7%) than the UroVysion probes (45.9%) (P < .001) or routine cytology analysis (18.8%) (P < .001), but similar specificity (92.9%, 90.8%, and 100.0% respectively). Factors significantly associated with detection of carcinoma, in adjusted analyses, included detection of polysomy by pancreatobiliary FISH (P < .001), a mass by cross-sectional imaging (P < .001), cancer cells by routine cytology (overall P = .003), as well as absence of primary sclerosing cholangitis (P = .011). We identified a set of FISH probes that detects cancer cells in pancreatobiliary brush samples from patients with and without primary sclerosing cholangitis with higher levels of sensitivity than UroVysion probes. Cytologic brushing test results and clinical features were independently associated with detection of cancer and might be used to identify patients with pancreatobiliary cancers. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.

PubMed

Gardiner, Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall, Anthony

2014-12-01

Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. © 2014 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

The Ising model coupled to 2d orders

NASA Astrophysics Data System (ADS)

Glaser, Lisa

2018-04-01

In this article we make first steps in coupling matter to causal set theory in the path integral. We explore the case of the Ising model coupled to the 2d discrete Einstein Hilbert action, restricted to the 2d orders. We probe the phase diagram in terms of the Wick rotation parameter β and the Ising coupling j and find that the matter and the causal sets together give rise to an interesting phase structure. The couplings give rise to five different phases. The causal sets take on random or crystalline characteristics as described in Surya (2012 Class. Quantum Grav. 29 132001) and the Ising model can be correlated or uncorrelated on the random orders and correlated, uncorrelated or anti-correlated on the crystalline orders. We find that at least one new phase transition arises, in which the Ising spins push the causal set into the crystalline phase.

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

Khachatryan, Vardan

A dedicated search is presented for new phenomena in inclusive 8- and 10-jet final states with low missing transverse momentum, with and without identification of jets originating from b quarks. The analysis is based on data from proton–proton collisions corresponding to an integrated luminosity of 19.7fb –1 collected with the CMS detector at the LHC at √s = 8TeV. The dominant multijet background expectations are obtained from low jet multiplicity control samples. Data agree well with the standard model background predictions, and limits are set in several benchmark models. Colorons (axigluons) with masses between 0.6 and 0.75 (up to 1.15)more » TeV are excluded at 95% confidence level. Similar exclusion limits for gluinos in R-parity violating supersymmetric scenarios are from 0.6 up to 1.1 TeV. Finally, these results comprise the first experimental probe of the coloron and axigluon models in multijet final states.« less

Introduction of argon beam coagulation functionality to robotic procedures using the ABC D-Flex probe: equivalency to an existing laparoscopic instrument

NASA Astrophysics Data System (ADS)

Merchel, Renée. A.; Barnes, Kelli S.; Taylor, Kenneth D.

2015-03-01

INTRODUCTION: The ABC® D-Flex Probe utilizes argon beam coagulation (ABC) technology to achieve hemostasis during minimally invasive surgery. A handle on the probe allows for integration with robotic surgical systems and introduces ABC to the robotic toolbox. To better understand the utility of D-Flex, this study compares the performance of the D-Flex probe to an existing ABC laparoscopic probe through ex vivo tissue analysis. METHODS: Comparisons were performed to determine the effect of four parameters: ABC device, tissue type, activation duration, and distance from tissue. Ten ABC D-Flex probes were used to create 30 burn samples for each comparison. Ex vivo bovine liver and porcine muscle were used as tissue models. The area and depth of each burn was measured using a light microscope. The resulting dimensional data was used to correlate tissue effect with each variable. RESULTS: D-Flex created burns which were smaller in surface area than the laparoscopic probe at all power levels. Additionally, D-Flex achieved thermal penetration levels equivalent to the laparoscopic probe. CONCLUSION: D-Flex implements a small 7F geometry which creates a more focused beam. When used with robotic precision, quick localized superficial hemostasis can be achieved with minimal collateral damage. Additionally, D-Flex achieved equivalent thermal penetration levels at lower power and argon flow-rate settings than the laparoscopic probe.

Multicolor fluorescent intravital live microscopy (FILM) for surgical tumor resection in a mouse xenograft model.

PubMed

Thurber, Greg M; Figueiredo, Jose L; Weissleder, Ralph

2009-11-30

Complete surgical resection of neoplasia remains one of the most efficient tumor therapies. However, malignant cell clusters are often left behind during surgery due to the inability to visualize and differentiate them against host tissue. Here we establish the feasibility of multicolor fluorescent intravital live microscopy (FILM) where multiple cellular and/or unique tissue compartments are stained simultaneously and imaged in real time. Theoretical simulations of imaging probe localization were carried out for three agents with specificity for cancer cells, stromal host response, or vascular perfusion. This transport analysis gave insight into the probe pharmacokinetics and tissue distribution, facilitating the experimental design and allowing predictions to be made about the localization of the probes in other animal models and in the clinic. The imaging probes were administered systemically at optimal time points based on the simulations, and the multicolor FILM images obtained in vivo were then compared to conventional pathological sections. Our data show the feasibility of real time in vivo pathology at cellular resolution and molecular specificity with excellent agreement between intravital and traditional in vitro immunohistochemistry. Multicolor FILM is an accurate method for identifying malignant tissue and cells in vivo. The imaging probes distributed in a manner similar to predictions based on transport principles, and these models can be used to design future probes and experiments. FILM can provide critical real time feedback and should be a useful tool for more effective and complete cancer resection.

On the improvement for charging large-scale flexible electrostatic actuators

NASA Astrophysics Data System (ADS)

Liao, Hsu-Ching; Chen, Han-Long; Su, Yu-Hao; Chen, Yu-Chi; Ko, Wen-Ching; Liou, Chang-Ho; Wu, Wen-Jong; Lee, Chih-Kung

2011-04-01

Recently, the development of flexible electret based electrostatic actuator has been widely discussed. The devices was shown to have high sound quality, energy saving, flexible structure and can be cut to any shape. However, achieving uniform charge on the electret diaphragm is one of the most critical processes needed to have the speaker ready for large-scale production. In this paper, corona discharge equipment contains multi-corona probes and grid bias was set up to inject spatial charges within the electret diaphragm. The optimal multi-corona probes system was adjusted to achieve uniform charge distribution of electret diaphragm. The processing conditions include the distance between the corona probes, the voltages of corona probe and grid bias, etc. We assembled the flexible electret loudspeakers first and then measured their sound pressure and beam pattern. The uniform charge distribution within the electret diaphragm based flexible electret loudspeaker provided us with the opportunity to shape the loudspeaker arbitrarily and to tailor the sound distribution per specifications request. Some of the potential futuristic applications for this device such as sound poster, smart clothes, and sound wallpaper, etc. were discussed as well.

A Versatile Technique for the In Vivo Imaging of Human Tumor Xenografts Using Near-Infrared Fluorochrome-Conjugated Macromolecule Probes

PubMed Central

Suemizu, Hiroshi; Kawai, Kenji; Higuchi, Yuichiro; Hashimoto, Haruo; Ogura, Tomoyuki; Itoh, Toshio; Sasaki, Erika; Nakamura, Masato

2013-01-01

Here, we present a versatile method for detecting human tumor xenografts in vivo, based on the enhanced permeability and retention (EPR) effect, using near-infrared (NIR) fluorochrome-conjugated macromolecule probes. Bovine serum albumin (BSA) and two immunoglobulins—an anti-human leukocyte antigen (HLA) monoclonal antibody and isotype control IgG2a—were labeled with XenoLight CF770 fluorochrome and used as NIR-conjugated macromolecule probes to study whole-body imaging in a variety of xenotransplantation mouse models. NIR fluorescent signals were observed in subcutaneously transplanted BxPC-3 (human pancreatic cancer) cells and HCT 116 (colorectal cancer) cells within 24 h of NIR-macromolecule probe injection, but the signal from the fluorochrome itself or from the NIR-conjugated small molecule (glycine) injection was not observed. The accuracy of tumor targeting was confirmed by the localization of the NIR-conjugated immunoglobulin within the T-HCT 116 xenograft (in which the orange-red fluorescent protein tdTomato was stably expressed by HCT 116 cells) in the subcutaneous transplantation model. However, there was no significant difference in the NIR signal intensity of the region of interest between the anti-HLA antibody group and the isotype control group in the subcutaneous transplantation model. Therefore, the antibody accumulation within the tumor in vivo is based on the EPR effect. The liver metastasis generated by an intrasplenic injection of T-HCT 116 cells was clearly visualized by the NIR-conjugated anti-HLA probe but not by the orange-red fluorescent signal derived from the tdTomato reporter. This result demonstrated the superiority of the NIR probes over the tdTomato reporter protein at enhancing tissue penetration. In another xenograft model, patient-derived xenografts (PDX) of LC11-JCK (human non-small cell lung cancer) were successfully visualized using the NIR-conjugated macromolecule probe without any genetic modification. These results suggested that NIR-conjugated macromolecule, preferably, anti-HLA antibody probe is a valuable tool for the detection of human tumors in experimental metastasis models using whole-body imaging. PMID:24358218

Boronate-Based Fluorescent Probes: Imaging Hydrogen Peroxide in Living Systems

PubMed Central

Lin, Vivian S.; Dickinson, Bryan C.; Chang, Christopher J.

2014-01-01

Hydrogen peroxide, a reactive oxygen species with unique chemical properties, is produced endogenously in living systems as a destructive oxidant to ward off pathogens or as a finely tuned second messenger in dynamic cellular signaling pathways. In order to understand the complex roles that hydrogen peroxide can play in biological systems, new tools to monitor hydrogen peroxide in its native settings, with high selectivity and sensitivity, are needed. Knowledge of organic synthetic reactivity provides the foundation for the molecular design of selective, functional hydrogen peroxide probes. A palette of fluorescent and luminescent probes that react chemoselectively with hydrogen peroxide has been developed, utilizing a boronate oxidation trigger. These indicators offer a variety of colors and in cellulo characteristics and have been used to examine hydrogen peroxide in a number of experimental setups, including in vitro fluorometry, confocal fluorescence microscopy, and flow cytometry. In this chapter, we provide an overview of the chemical features of these probes and information on their behavior to help researchers select the optimal probe and application. PMID:23791092

Intra-operative probe for brain cancer: feasibility study

NASA Astrophysics Data System (ADS)

Vu Thi, M. H.; Charon, Y.; Duval, M. A.; Lefebvre, F.; Menard, L.; Pitre, S.; Pinot, L.; Siebert, R.

2007-07-01

The present work aims a new medical probe for surgeons devoted to brain cancers, in particular glioblastoma multiforme. Within the last years, our group has started the development of a new intra-operative beta imaging probe. More recently, we took an alternative approach for the same application: a fluorescence probe. In both cases the purpose is to differentiate normal from tumor brain tissue. In a first step, we developed set-ups capable to measure autofluorescence. They are based on a dedicated epi-fluorescence design and on specific fiber optic probes. Relative signal amplitude, spectral shape and fluorescence lifetime measurements are foreseen to distinguish normal and cancer tissue by analyzing fluorophores like NADH, lipopigments and porphyrines. The autofluorescence spectra are recorded in the 460-640 nm range with a low resolution spectrometer. For lifetime measurements a fast detector (APD) is used together with a TCSPC-carte. Intrinsic wavelength- and time-resolutions are a few nm and 200 ps, respectively. Different samples have been analyzed to validate our new detection system and to allow a first configuration of our medical fluorescence probe. First results from the tissue measurements are shown.

Quantum algorithm for solving some discrete mathematical problems by probing their energy spectra

NASA Astrophysics Data System (ADS)

Wang, Hefeng; Fan, Heng; Li, Fuli

2014-01-01

When a probe qubit is coupled to a quantum register that represents a physical system, the probe qubit will exhibit a dynamical response only when it is resonant with a transition in the system. Using this principle, we propose a quantum algorithm for solving discrete mathematical problems based on the circuit model. Our algorithm has favorable scaling properties in solving some discrete mathematical problems.

Leaving out control groups: an internal contrast analysis of gene expression profiles in atrial fibrillation patients ‐ A systems biology approach to clinical categorization

PubMed Central

Vanhoutte, Kurt; de Asmundis, Carlo; Francesconi, Anna; Figys1, Jurgen; Steurs, Griet; Boussy, Tim; Roos, Markus; Mueller, Andreas; Massimo, Lucio; Paparella, Gaetano; Van Caelenberg, Kristien; Chierchia, Gian Battista; Sarkozy, Andrea; Y Terradellas, Pedro Brugada; Zizi, Martin

2009-01-01

Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical focus on potential entry pathways into the disease. We used a RMA (Robust Multichip Average) normalized Affymetrix micro-array data set from 10 AF patients (geo_accession #GSE2240). Four series of probes were selected based on physiopathogenic links with AF entryways: apoptosis (remodeling), MAP kinase (cell remodeling), OXPHOS (ability to sustain hemodynamic workload) and glycolysis (ischemia). Annotated probe lists were polled with Bioconductor packages in R (version 2.7.1). Genetic profile contrasts were analysed with hierarchical clustering and principal component analysis. The analysis revealed distinct patient groups for all probe sets. A substantial part (54% till 67%) of the variance is explained in the first 2 principal components. Genes in PC1/2 with high discriminatory value were selected and analyzed in detail. We aim for reliable molecular stratification of AF. We show that stratification is possible based on physiologically relevant gene sets. Genes with high contrast value are likely to give pathophysiological insight into permanent AF subtypes. PMID:19255648

Facile synthesis of a two-photon fluorescent probe based on pyrimidine 2-isothiocyanate and its application in bioimaging.

PubMed

Yang, Jie; Hu, Wei; Li, Huirong; Hou, Hanna; Tu, Yi; Liu, Bo

2018-04-18

Two-photon microscopy imaging has been widely applied in biological imaging, but the development of two-photon absorption probes is obviously lagging behind in the development of imaging technology. In this paper, a two-photon fluorescent probe (1) based on pyrimidine 2-isothiocyanate has been designed and synthesized through a simple method for two-photon biological imaging. Probe 1 was able to couple effectively with the amino groups on biomolecules. To verify the reactivity of the isothiocyanate group on probe 1 and the amine groups on the biomolecules, d-glucosamine was chosen as a model biomolecule to conjugate with probe 1. The result showed that probe 1 could effectively conjugate with d-glucosamine to synthesize probe 2, and the yield of probe 2 was 83%. After conjugating with d-glucosamine, linear absorption spectra, single-photon fluorescence spectra, and two-photon fluorescence spectra of probes 1 and 2 did not present significant changes. Probes 1 and 2 exhibited high fluorescence quantum yields (0.71-0.79) in toluene and chloroform. They also exhibited different photo-physical properties in solvents with different polarities. The two-photon absorption cross-section of probe 1 was 953 GM in toluene. In addition, probe 1 could be effectively conjugated with transferrin, and the conjugated probe (Tf-1) could be transported into Hep G2 cells through a receptor-mediated process for biological imaging. These results demonstrate that such probes are expected to have great potential applications in two-photon fluorescence bioimaging.

A Next-Generation Apparatus for Lithium Optical Lattice Experiments

NASA Astrophysics Data System (ADS)

Keshet, Aviv

Quantum simulation is emerging as an ambitious and active subfield of atomic physics. This thesis describes progress towards the goal of simulating condensed matter systems, in particular the physics of the Fermi-Hubbard model, using ultracold Lithium atoms in an optical lattice. A major goal of the quantum simulation program is to observe phase transitions of the Hubbard model, into Neal antiferromagnetic phases and d-wave superfluid phases. Phase transitions are generally accompanied by a change in an underlying correlation in a physical system. Such correlations may be most amenable to probing by looking at fluctuations in the system. Experimental techniques for probing density and magnetization fluctuations in a variety of atomic Fermi systems are developed. The suppression of density fluctuations (or atom "shot noise") in an ideal degenerate Fermi gas is observed by absorption imaging of time-of-flight expanded clouds. In-trap measurements of density and magnetization fluctuations are not easy to probe with absorption imaging, due to their extremely high attenuation. A method to probe these fluctuations based on speckle patterns, caused by fluctuations in the index of refraction for a detuned illumination beam, is developed and applied first to weakly interacting and then to strongly interacting in-trap gases. Fluctuation probes such as these will be a crucial tool in future quantum simulation of condensed matter systems. The quantum simulation experiments that we want to perform require a complex sequence of precisely timed computer controlled events. A distributed GUI-based control system designed with such experiments in mind, The Cicero Word Generator, is described. The system makes use of a client-server separation between a user interface for sequence design and a set of output hardware servers. Output hardware servers are designed to use standard National Instruments output cards, but the client-server nature allows this to be extended to other output hardware. Output sequences running on multiple servers and output cards can be synchronized using a shared clock. By using an FPGA-generated variable frequency clock, redundant buffers can be dramatically shortened, and a time resolution of 100ns achieved over effectively arbitrary sequence lengths. Experimental set-ups for producing, manipulating, and probing ultracold atomic gases can be quite complicated. To move forward with a quantum simulation program, it is necessary to have an apparatus that operates with a reliability that is not easily achieved in the face of this complexity. The design of a new apparatus is discussed. This Sodium-Lithium ultracold gas production machine has been engineered to incorporate as much experimental experience as possible to enhance its reliability. Particular attention has been paid to maximizing optical access and the utilization of this optical access, controlling the ambient temperature of the experiment, achieving a high vacuum, and simplifying subsystems where possible. The apparatus is now on the verge of producing degenerate gases, and should serve as a stable platform on which to perform future lattice quantum simulation experiments. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)

Electrical Resistance Based Damage Modeling of Multifunctional Carbon Fiber Reinforced Polymer Matrix Composites

NASA Astrophysics Data System (ADS)

Hart, Robert James

In the current thesis, the 4-probe electrical resistance of carbon fiber-reinforced polymer (CFRP) composites is utilized as a metric for sensing low-velocity impact damage. A robust method has been developed for recovering the directionally dependent electrical resistivities using an experimental line-type 4-probe resistance method. Next, the concept of effective conducting thickness was uniquely applied in the development of a brand new point-type 4-probe method for applications with electrically anisotropic materials. An extensive experimental study was completed to characterize the 4-probe electrical resistance of CFRP specimens using both the traditional line-type and new point-type methods. Leveraging the concept of effective conducting thickness, a novel method was developed for building 4-probe electrical finite element (FE) models in COMSOL. The electrical models were validated against experimental resistance measurements and the FE models demonstrated predictive capabilities when applied to CFRP specimens with varying thickness and layup. These new models demonstrated a significant improvement in accuracy compared to previous literature and could provide a framework for future advancements in FE modeling of electrically anisotropic materials. FE models were then developed in ABAQUS for evaluating the influence of prescribed localized damage on the 4-probe resistance. Experimental data was compiled on the impact response of various CFRP laminates, and was used in the development of quasi- static FE models for predicting presence of impact-induced delamination. The simulation-based delamination predictions were then integrated into the electrical FE models for the purpose of studying the influence of realistic damage patterns on electrical resistance. When the size of the delamination damage was moderate compared to the electrode spacing, the electrical resistance increased by less than 1% due to the delamination damage. However, for a specimen with large delamination extending beyond the electrode locations, the oblique resistance increased by 30%. This result suggests that for damage sensing applications, the spacing of electrodes relative to the size of the delamination is important. Finally CT image data was used to model 3-D void distributions and the electrical response of such specimens were compared to models with no voids. As the void content increased, the electrical resistance increased non-linearly. The relationship between void content and electrical resistance was attributed to a combination of three factors: (i) size and shape, (ii) orientation, and (iii) distribution of voids. As a whole, the current thesis provides a comprehensive framework for developing predictive, resistance-based damage sensing models for CFRP laminates of various layup and thickness.

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina.

PubMed

Bidard, Frédérique; Imbeaud, Sandrine; Reymond, Nancie; Lespinet, Olivier; Silar, Philippe; Clavé, Corinne; Delacroix, Hervé; Berteaux-Lecellier, Véronique; Debuchy, Robert

2010-06-18

The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.

Methods and compositions for efficient nucleic acid sequencing

DOEpatents

Drmanac, Radoje

2006-07-04

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Methods and compositions for efficient nucleic acid sequencing

DOEpatents

Drmanac, Radoje

2002-01-01

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Longitudinal measurement of extracellular matrix rigidity in 3D tumor models using particle-tracking microrheology.

PubMed

Jones, Dustin P; Hanna, William; El-Hamidi, Hamid; Celli, Jonathan P

2014-06-10

The mechanical microenvironment has been shown to act as a crucial regulator of tumor growth behavior and signaling, which is itself remodeled and modified as part of a set of complex, two-way mechanosensitive interactions. While the development of biologically-relevant 3D tumor models have facilitated mechanistic studies on the impact of matrix rheology on tumor growth, the inverse problem of mapping changes in the mechanical environment induced by tumors remains challenging. Here, we describe the implementation of particle-tracking microrheology (PTM) in conjunction with 3D models of pancreatic cancer as part of a robust and viable approach for longitudinally monitoring physical changes in the tumor microenvironment, in situ. The methodology described here integrates a system of preparing in vitro 3D models embedded in a model extracellular matrix (ECM) scaffold of Type I collagen with fluorescently labeled probes uniformly distributed for position- and time-dependent microrheology measurements throughout the specimen. In vitro tumors are plated and probed in parallel conditions using multiwell imaging plates. Drawing on established methods, videos of tracer probe movements are transformed via the Generalized Stokes Einstein Relation (GSER) to report the complex frequency-dependent viscoelastic shear modulus, G*(ω). Because this approach is imaging-based, mechanical characterization is also mapped onto large transmitted-light spatial fields to simultaneously report qualitative changes in 3D tumor size and phenotype. Representative results showing contrasting mechanical response in sub-regions associated with localized invasion-induced matrix degradation as well as system calibration, validation data are presented. Undesirable outcomes from common experimental errors and troubleshooting of these issues are also presented. The 96-well 3D culture plating format implemented in this protocol is conducive to correlation of microrheology measurements with therapeutic screening assays or molecular imaging to gain new insights into impact of treatments or biochemical stimuli on the mechanical microenvironment.

Computational Prediction and Validation of an Expert's Evaluation of Chemical Probes

PubMed Central

Litterman, Nadia K.; Lipinski, Christopher A.; Bunin, Barry A.; Ekins, Sean

2016-01-01

In a decade with over half a billion dollars of investment, more than 300 chemical probes have been identified to have biological activity through NIH funded screening efforts. We have collected the evaluations of an experienced medicinal chemist on the likely chemistry quality of these probes based on a number of criteria including literature related to the probe and potential chemical reactivity. Over 20% of these probes were found to be undesirable. Analysis of the molecular properties of these compounds scored as desirable suggested higher pKa, molecular weight, heavy atom count and rotatable bond number. We were particularly interested whether the human evaluation aspect of medicinal chemistry due diligence could be computationally predicted. We used a process of sequential Bayesian model building and iterative testing as we included additional probes. Following external validation of these methods and comparing different machine learning methods we identified Bayesian models with accuracy comparable to other measures of drug-likeness and filtering rules created to date. PMID:25244007

Ex vivo imaging of early dental caries within the interproximal space

NASA Astrophysics Data System (ADS)

Choo-Smith, Lin-P'ing; Hewko, Mark D.; Dufour, Marc L.; Fulton, Crystal; Qiu, Pingli; Gauthier, Bruno; Padioleau, Christian; Bisaillon, Charles-Etienne; Dong, Cecilia; Cleghorn, Blaine M.; Lamouche, Guy; Sowa, Michael G.

2009-02-01

Optical coherence tomography (OCT) is emerging as a technology that can potentially be used for the detection and monitoring of early dental enamel caries since it can provide high-resolution depth imaging of early lesions. To date, most caries detection optical technologies are well suited for examining caries at facial, lingual, incisal and occlusal surfaces. The approximal surfaces between adjacent teeth are difficult to examine due to lack of visual access and limited space for these new caries detection tools. Using a catheter-style probe developed at the NRC-Industrial Materials Institute, the probe was inserted into the interproximal space to examine the approximal surfaces with OCT imaging at 1310 nm. The probe was rotated continuously and translated axially to generate depth images in a spiral fashion. The probe was used in a mock tooth arch model consisting of extracted human teeth mounted with dental rope wax in their anatomically correct positions. With this ex vivo model, the probe provided images of the approximal surfaces revealing morphological structural details, regions of calculus, and especially regions of early dental caries (white spot lesions). Results were compared with those obtained from OCT imaging of individual samples where the approximal surfaces of extracted teeth are accessible on a lab-bench. Issues regarding access, regions of interest, and factors to be considered in an in vivo setting will be discussed. Future studies are aimed at using the probe in vivo with patient volunteers.

A multimodal spectroscopy system for real-time disease diagnosis

NASA Astrophysics Data System (ADS)

Šćepanović, Obrad R.; Volynskaya, Zoya; Kong, Chae-Ryon; Galindo, Luis H.; Dasari, Ramachandra R.; Feld, Michael S.

2009-04-01

The combination of reflectance, fluorescence, and Raman spectroscopy—termed multimodal spectroscopy (MMS)—provides complementary and depth-sensitive information about tissue composition. As such, MMS is a promising tool for disease diagnosis, particularly in atherosclerosis and breast cancer. We have developed an integrated MMS instrument and optical fiber spectral probe for simultaneous collection of all three modalities in a clinical setting. The MMS instrument multiplexes three excitation sources, a xenon flash lamp (370-740 nm), a nitrogen laser (337 nm), and a diode laser (830 nm), through the MMS probe to excite tissue and collect the spectra. The spectra are recorded on two spectrograph/charge-coupled device modules, one optimized for visible wavelengths (reflectance and fluorescence) and the other for the near-infrared (Raman), and processed to provide diagnostic parameters. We also describe the design and calibration of a unitary MMS optical fiber probe 2 mm in outer diameter, containing a single appropriately filtered excitation fiber and a ring of 15 collection fibers, with separate groups of appropriately filtered fibers for efficiently collecting reflectance, fluorescence, and Raman spectra from the same tissue location. A probe with this excitation/collection geometry has not been used previously to collect reflectance and fluorescence spectra, and thus physical tissue models ("phantoms") are used to characterize the probe's spectroscopic response. This calibration provides probe-specific modeling parameters that enable accurate extraction of spectral parameters. This clinical MMS system has been used recently to analyze artery and breast tissue in vivo and ex vivo.

The Measurement of Unsteady Surface Pressure Using a Remote Microphone Probe.

PubMed

Guan, Yaoyi; Berntsen, Carl R; Bilka, Michael J; Morris, Scott C

2016-12-03

Microphones are widely applied to measure pressure fluctuations at the walls of solid bodies immersed in turbulent flows. Turbulent motions with various characteristic length scales can result in pressure fluctuations over a wide frequency range. This property of turbulence requires sensing devices to have sufficient sensitivity over a wide range of frequencies. Furthermore, the small characteristic length scales of turbulent structures require small sensing areas and the ability to place the sensors in very close proximity to each other. The complex geometries of the solid bodies, often including large surface curvatures or discontinuities, require the probe to have the ability to be set up in very limited spaces. The development of a remote microphone probe, which is inexpensive, consistent, and repeatable, is described in the present communication. It allows for the measurement of pressure fluctuations with high spatial resolution and dynamic response over a wide range of frequencies. The probe is small enough to be placed within the interior of typical wind tunnel models. The remote microphone probe includes a small, rigid, and hollow tube that penetrates the model surface to form the sensing area. This tube is connected to a standard microphone, at some distance away from the surface, using a "T" junction. An experimental method is introduced to determine the dynamic response of the remote microphone probe. In addition, an analytical method for determining the dynamic response is described. The analytical method can be applied in the design stage to determine the dimensions and properties of the RMP components.

A transport model for non-local heating of electrons in ICP reactors

NASA Astrophysics Data System (ADS)

Chang, C. H.; Bose, Deepak

1998-10-01

A new model has been developed for non-local heating of electrons in ICP reactors, based on a hydrodynamic approach. The model has been derived using the electron momentum conservation in azimuthal direction with electromagnetic and frictional forces respectively as driving force and damper of harmonic oscillatory motion of electrons. The resulting transport equations include the convection of azimuthal electron momentum in radial and axial directions, thereby accounting for the non-local effects. The azimuthal velocity of electrons and the resulting electrical current are coupled to the Maxwell's relations, thus forming a self-consistent model for non-local heating. This model is being implemented along with a set of Navier-Stokes equations for plasma dynamics and gas flow to simulate low-pressure (few mTorr's) ICP discharges. Characteristics of nitrogen plasma in a TCP 300mm etch reactor is being studied. The results will be compared against the available Langmuir probe measurements [Collison et al. JVST-A 16(1),1998].

Control of the probe influence on the flow field in LP steam turbine

NASA Astrophysics Data System (ADS)

Kolovratník, Michal; Yun, Kukchol; Bartoš, Ondřej

For measuring the fine droplets properties in the wet steam expanding in the steam turbines the light extinction probes are usually used. The paper presents CFD modelling of the extinction probe influence on the wet steam flow field at the measurement position. The aim is to get a basic information about the influence of the flow field deviation on the measured data, in other words, of necessity to correct the measured data. The basic modelling procedure is described, as well as the supposed simplifications and the factor considering the change in the steam density in the measuring slot of the probe. The model is based on the experimental data that were achieved during the developmental measurements in the steam turbine 1090 MW in the power station Temelín. The experimental measurement was done in the cooperation with the Doosan Škoda Power s.r.o.

F-18 Labeled Diabody-Luciferase Fusion Proteins for Optical-ImmunoPET

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

Wu, Anna M.

2013-01-18

The goal of the proposed work is to develop novel dual-labeled molecular imaging probes for multimodality imaging. Based on small, engineered antibodies called diabodies, these probes will be radioactively tagged with Fluorine-18 for PET imaging, and fused to luciferases for optical (bioluminescence) detection. Performance will be evaluated and validated using a prototype integrated optical-PET imaging system, OPET. Multimodality probes for optical-PET imaging will be based on diabodies that are dually labeled with 18F for PET detection and fused to luciferases for optical imaging. 1) Two sets of fusion proteins will be built, targeting the cell surface markers CEA or HER2.more » Coelenterazine-based luciferases and variant forms will be evaluated in combination with native substrate and analogs, in order to obtain two distinct probes recognizing different targets with different spectral signatures. 2) Diabody-luciferase fusion proteins will be labeled with 18F using amine reactive [18F]-SFB produced using a novel microwave-assisted, one-pot method. 3) Sitespecific, chemoselective radiolabeling methods will be devised, to reduce the chance that radiolabeling will inactivate either the target-binding properties or the bioluminescence properties of the diabody-luciferase fusion proteins. 4) Combined optical and PET imaging of these dual modality probes will be evaluated and validated in vitro and in vivo using a prototype integrated optical-PET imaging system, OPET. Each imaging modality has its strengths and weaknesses. Development and use of dual modality probes allows optical imaging to benefit from the localization and quantitation offered by the PET mode, and enhances the PET imaging by enabling simultaneous detection of more than one probe.« less

SU-E-J-205: Monte Carlo Modeling of Ultrasound Probes for Real-Time Ultrasound Image-Guided Radiotherapy

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

Hristov, D; Schlosser, J; Bazalova, M

2014-06-01

Purpose: To quantify the effect of ultrasound (US) probe beam attenuation for radiation therapy delivered under real-time US image guidance by means of Monte Carlo (MC) simulations. Methods: MC models of two Philips US probes, an X6-1 matrix-array transducer and a C5-2 curved-array transducer, were built based on their CT images in the EGSnrc BEAMnrc and DOSXYZnrc codes. Due to the metal parts, the probes were scanned in a Tomotherapy machine with a 3.5 MV beam. Mass densities in the probes were assigned based on an electron density calibration phantom consisting of cylinders with mass densities between 0.2–8.0 g/cm{sup 3}.more » Beam attenuation due to the probes was measured in a solid water phantom for a 6 MV and 15 MV 15x15 cm{sup 2} beam delivered on a Varian Trilogy linear accelerator. The dose was measured with the PTW-729 ionization chamber array at two depths and compared to MC simulations. The extreme case beam attenuation expected in robotic US image guided radiotherapy for probes in upright position was quantified by means of MC simulations. Results: The 3.5 MV CT number to mass density calibration curve was found to be linear with R{sup 2} > 0.99. The maximum mass densities were 4.6 and 4.2 g/cm{sup 3} in the C5-2 and X6-1 probe, respectively. Gamma analysis of the simulated and measured doses revealed that over 98% of measurement points passed the 3%/3mm criteria for both probes and measurement depths. The extreme attenuation for probes in upright position was found to be 25% and 31% for the C5-2 and X6-1 probe, respectively, for both 6 and 15 MV beams at 10 cm depth. Conclusion: MC models of two US probes used for real-time image guidance during radiotherapy have been built. As a Result, radiotherapy treatment planning with the imaging probes in place can now be performed. J Schlosser is an employee of SoniTrack Systems, Inc. D Hristov has financial interest in SoniTrack Systems, Inc.« less

Imaging of oxygenation in 3D tissue models with multi-modal phosphorescent probes

NASA Astrophysics Data System (ADS)

Papkovsky, Dmitri B.; Dmitriev, Ruslan I.; Borisov, Sergei

2015-03-01

Cell-penetrating phosphorescence based probes allow real-time, high-resolution imaging of O2 concentration in respiring cells and 3D tissue models. We have developed a panel of such probes, small molecule and nanoparticle structures, which have different spectral characteristics, cell penetrating and tissue staining behavior. The probes are compatible with conventional live cell imaging platforms and can be used in different detection modalities, including ratiometric intensity and PLIM (Phosphorescence Lifetime IMaging) under one- or two-photon excitation. Analytical performance of these probes and utility of the O2 imaging method have been demonstrated with different types of samples: 2D cell cultures, multi-cellular spheroids from cancer cell lines and primary neurons, excised slices from mouse brain, colon and bladder tissue, and live animals. They are particularly useful for hypoxia research, ex-vivo studies of tissue physiology, cell metabolism, cancer, inflammation, and multiplexing with many conventional fluorophors and markers of cellular function.

Experimental and Computational Studies of the Flow Over a Sting Mounted Planetary Probe Configuration

NASA Technical Reports Server (NTRS)

Holden, Michael S.; Harvey, John K.; Boyd, Iain D.; George, Jyothish; Horvath, Thomas J.

1997-01-01

This paper summarizes the results of a series of experimental studies in the LENS shock tunnel and computations with DSMC and Navier Stokes codes which have been made to examine the aerothermal and flowfield characteristics of the flow over a sting-supported planetary probe configuration in hypervelocity air and nitrogen flows. The experimental program was conducted in the LENS hypervelocity shock tunnel at total enthalpies of 5and 10 MJkg for a range of reservoir pressure conditions from 70 to 500 bars. Heat transfer and pressure measurements were made on the front and rear face of the probe and along the supporting sting. High-speed and single shot schlieren photography were also employed to examine the flow over the model and the time to establish the flow in the base recirculation region. Predictions of the flowfield characteristics and the distributions of heat transfer and pressure were made with DSMC codes for rarefied flow conditions and with the Navier-Stokes solvers for the higher pressure conditions where the flows were assumed to be laminar. Analysis of the time history records from the heat transfer and pressure instrumentation on the face of the probe and in the base region indicated that the base flow was fully established in under 4 milliseconds from flow initiation or between 35 and 50 flow lengths based on base height. The measurements made in three different tunnel entries with two models of identical geometries but with different instrumentation packages, one prepared by NASA Langley and the second prepared by CUBRC, demonstrated good agreement between heat transfer measurements made with two different types of thin film and coaxial gage instrumentation. The measurements of heat transfer and pressure to the front face of the probe were in good agreement with theoretical predictions from both the DSMC and Navier Stokes codes. For the measurements made in low density flows, computations with the DSMC code were found to compare well with the pressure and heat transfer measurements on the sting, although the computed heat transfer rates in the recirculation region did not exhibit the same characteristics as the measurements. For the 10MJkg and 500 bar reservoir match point condition, the measurements and heat transfer along the sting from the first group of studies were in agreement with the Navier Stokes solutions for laminar conditions. A similar set of measurements made in later tests where the model was moved to a slightly different position in the test section indicated that the boundary layer in the reattachment compression region was close to transition or transitional where small changes in the test environment can result in larger than laminar heating rates. The maximum heating coefficients on the sting observed in the present studies was a small fraction of similar measurements obtained at nominally the same conditions in the HEG shock tunnel, where it is possible for transition to occur in the base flow, and in the low enthalpy studies conducted in the NASA Langley high Reynolds number Mach 10 tunnel where the base flow was shown to be turbulent. While the hybrid Navier- StokedDMSC calculations by Gochberg et al. (Reference 1) suggested that employing the Navier- Stokes calculations for the entire flowfield could be seriously in error in the base region for the 10 MJkg, 500 bar test case, similar calculations performed by Cornell, presented here, do not.

Neural Interfaces for Intracortical Recording: Requirements, Fabrication Methods, and Characteristics.

PubMed

Szostak, Katarzyna M; Grand, Laszlo; Constandinou, Timothy G

2017-01-01

Implantable neural interfaces for central nervous system research have been designed with wire, polymer, or micromachining technologies over the past 70 years. Research on biocompatible materials, ideal probe shapes, and insertion methods has resulted in building more and more capable neural interfaces. Although the trend is promising, the long-term reliability of such devices has not yet met the required criteria for chronic human application. The performance of neural interfaces in chronic settings often degrades due to foreign body response to the implant that is initiated by the surgical procedure, and related to the probe structure, and material properties used in fabricating the neural interface. In this review, we identify the key requirements for neural interfaces for intracortical recording, describe the three different types of probes-microwire, micromachined, and polymer-based probes; their materials, fabrication methods, and discuss their characteristics and related challenges.

An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats

PubMed Central

Valdés-Hernández, Pedro Antonio; Sumiyoshi, Akira; Nonaka, Hiroi; Haga, Risa; Aubert-Vásquez, Eduardo; Ogawa, Takeshi; Iturria-Medina, Yasser; Riera, Jorge J.; Kawashima, Ryuta

2011-01-01

Over the last decade, several papers have focused on the construction of highly detailed mouse high field magnetic resonance image (MRI) templates via non-linear registration to unbiased reference spaces, allowing for a variety of neuroimaging applications such as robust morphometric analyses. However, work in rats has only provided medium field MRI averages based on linear registration to biased spaces with the sole purpose of approximate functional MRI (fMRI) localization. This precludes any morphometric analysis in spite of the need of exploring in detail the neuroanatomical substrates of diseases in a recent advent of rat models. In this paper we present a new in vivo rat T2 MRI template set, comprising average images of both intensity and shape, obtained via non-linear registration. Also, unlike previous rat template sets, we include white and gray matter probabilistic segmentations, expanding its use to those applications demanding prior-based tissue segmentation, e.g., statistical parametric mapping (SPM) voxel-based morphometry. We also provide a preliminary digitalization of latest Paxinos and Watson atlas for anatomical and functional interpretations within the cerebral cortex. We confirmed that, like with previous templates, forepaw and hindpaw fMRI activations can be correctly localized in the expected atlas structure. To exemplify the use of our new MRI template set, were reported the volumes of brain tissues and cortical structures and probed their relationships with ontogenetic development. Other in vivo applications in the near future can be tensor-, deformation-, or voxel-based morphometry, morphological connectivity, and diffusion tensor-based anatomical connectivity. Our template set, freely available through the SPM extension website, could be an important tool for future longitudinal and/or functional extensive preclinical studies. PMID:22275894

Study of probe-sample distance for biomedical spectra measurement.

PubMed

Wang, Bowen; Fan, Shuzhen; Li, Lei; Wang, Cong

2011-11-02

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. 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. 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. 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.

Evaluation of a Wake Vortex Upset Model Based on Simultaneous Measurements of Wake Velocities and Probe-Aircraft Accelerations

NASA Technical Reports Server (NTRS)

Short, B. J.; Jacobsen, R. A.

1979-01-01

Simultaneous measurements were made of the upset responses experienced and the wake velocities encountered by an instrumented Learjet probe aircraft behind a Boeing 747 vortex-generating aircraft. The vortex-induced angular accelerations experienced could be predicted within 30% by a mathematical upset response model when the characteristics of the wake were well represented by the vortex model. The vortex model used in the present study adequately represented the wake flow field when the vortices dissipated symmetrically and only one vortex pair existed in the wake.

The von Neumann model of measurement in quantum mechanics

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

Mello, Pier A.

2014-01-08

We describe how to obtain information on a quantum-mechanical system by coupling it to a probe and detecting some property of the latter, using a model introduced by von Neumann, which describes the interaction of the system proper with the probe in a dynamical way. We first discuss single measurements, where the system proper is coupled to one probe with arbitrary coupling strength. The goal is to obtain information on the system detecting the probe position. We find the reduced density operator of the system, and show how Lüders rule emerges as the limiting case of strong coupling. The vonmore » Neumann model is then generalized to two probes that interact successively with the system proper. Now we find information on the system by detecting the position-position and momentum-position correlations of the two probes. The so-called 'Wigner's formula' emerges in the strong-coupling limit, while 'Kirkwood's quasi-probability distribution' is found as the weak-coupling limit of the above formalism. We show that successive measurements can be used to develop a state-reconstruction scheme. Finally, we find a generalized transform of the state and the observables based on the notion of successive measurements.« less

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

PubMed Central

González, Juan R; Carrasco, Josep L; Armengol, Lluís; Villatoro, Sergi; Jover, Lluís; Yasui, Yutaka; Estivill, Xavier

2008-01-01

Background MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample. Results Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace. Conclusion Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed. PMID:18522760

Physics-based analysis and control of human snoring

NASA Astrophysics Data System (ADS)

Sanchez, Yaselly; Wang, Junshi; Han, Pan; Xi, Jinxiang; Dong, Haibo

2017-11-01

In order to advance the understanding of biological fluid dynamics and its effects on the acoustics of human snoring, the study pursued a physics-based computational approach. From human magnetic resonance image (MRI) scans, the researchers were able to develop both anatomically and dynamically accurate airway-uvula models. With airways defined as rigid, and the uvula defined as flexible, computational models were created with various pharynx thickness and geometries. In order to determine vortex shedding with prescribed uvula movement, the uvula fluctuation was categorized by its specific parameters: magnitude, frequency, and phase lag. Uvula vibration modes were based on one oscillation, or one harmonic frequency, and pressure probes were located in seven different positions throughout the airway-uvula model. By taking fast Fourier transforms (FFT) from the pressure probe data, it was seen that four harmonics were created throughout the simulation within one oscillation of uvula movement. Of the four harmonics, there were two pressure probes which maintained high amplitudes and led the researcher to believe that different vortices formed with different snoring frequencies. This work is supported by the NSF Grant CBET-1605434.

Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site.

PubMed

Schneider, Samuel H; Boxer, Steven G

2016-09-15

IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.

Investigation of diocotron modes in toroidally trapped electron plasmas using non-destructive method

NASA Astrophysics Data System (ADS)

Lachhvani, Lavkesh; Pahari, Sambaran; Sengupta, Sudip; Yeole, Yogesh G.; Bajpai, Manu; Chattopadhyay, P. K.

2017-10-01

Experiments with trapped electron plasmas in a SMall Aspect Ratio Toroidal device (SMARTEX-C) have demonstrated a flute-like mode represented by oscillations on capacitive (wall) probes. Although analogous to diocotron mode observed in linear electron traps, the mode evolution in toroids can have interesting consequences due to the presence of in-homogeneous magnetic field. In SMARTEX-C, the probe signals are observed to undergo transition from small, near-sinusoidal oscillations to large amplitude, non-linear "double-peaked" oscillations. To interpret the wall probe signal and bring forth the dynamics, an expression for the induced current on the probe for an oscillating charge is derived, utilizing Green's Reciprocation Theorem. Equilibrium position, poloidal velocity of the charge cloud, and charge content of the cloud, required to compute the induced current, are estimated from the experiments. Signal through capacitive probes is thereby computed numerically for possible charge cloud trajectories. In order to correlate with experiments, starting with an intuitive guess of the trajectory, the model is evolved and tweaked to arrive at a signal consistent with experimentally observed probe signals. A possible vortex like dynamics is predicted, hitherto unexplored in toroidal geometries, for a limited set of experimental observations from SMARTEX-C. Though heuristic, a useful interpretation of capacitive probe data in terms of charge cloud dynamics is obtained.

Setting the magic angle for fast magic-angle spinning probes.

PubMed

Penzel, Susanne; Smith, Albert A; Ernst, Matthias; Meier, Beat H

2018-06-15

Fast magic-angle spinning, coupled with 1 H detection is a powerful method to improve spectral resolution and signal to noise in solid-state NMR spectra. Commercial probes now provide spinning frequencies in excess of 100 kHz. Then, one has sufficient resolution in the 1 H dimension to directly detect protons, which have a gyromagnetic ratio approximately four times larger than 13 C spins. However, the gains in sensitivity can quickly be lost if the rotation angle is not set precisely. The most common method of magic-angle calibration is to optimize the number of rotary echoes, or sideband intensity, observed on a sample of KBr. However, this typically uses relatively low spinning frequencies, where the spinning of fast-MAS probes is often unstable, and detection on the 13 C channel, for which fast-MAS probes are typically not optimized. Therefore, we compare the KBr-based optimization of the magic angle with two alternative approaches: optimization of the splitting observed in 13 C-labeled glycine-ethylester on the carbonyl due to the Cα-C' J-coupling, or optimization of the H-N J-coupling spin echo in the protein sample itself. The latter method has the particular advantage that no separate sample is necessary for the magic-angle optimization. Copyright © 2018. Published by Elsevier Inc.

Dissociable neural mechanisms underlying response-based and familiarity-based conflict in working memory.

PubMed

Nelson, James K; Reuter-Lorenz, Patricia A; Sylvester, Ching-Yune C; Jonides, John; Smith, Edward E

2003-09-16

Cognitive control requires the resolution of interference among competing and potentially conflicting representations. Such conflict can emerge at different points between stimulus input and response generation, with the net effect being that of compromising performance. The goal of this article was to dissociate the neural mechanisms underlying different sources of conflict to elucidate the architecture of the neural systems that implement cognitive control. By using functional magnetic resonance imaging and a verbal working memory task (item recognition), we examined brain activity related to two kinds of conflict with comparable behavioral consequences. In a trial of our item-recognition task, participants saw four letters, followed by a retention interval, and a probe letter that did or did not match one of the letters held in working memory (positive probe and negative probe, respectively). On some trials, conflict arose solely because of the current negative probe having a high familiarity, due to its membership in the immediately preceding trial's target set. On other trials, additional conflict arose because of the current negative probe having also been a positive probe on the immediately preceding trial, producing response-level conflict. Consistent with previous work, conflict due to high familiarity was associated with left prefrontal activation, but not with anterior cingulate activation. The response-conflict condition, when compared with high-familiarity conflict trials, was associated with anterior cingulate cortex activation, but with no additional left prefrontal activation. This double dissociation points to differing contributions of specific cortical areas to cognitive control, which are based on the source of conflict.

Comparing Cognitive Interviewing and Online Probing: Do They Find Similar Results?

ERIC Educational Resources Information Center

Meitinger, Katharina; Behr, Dorothée

2016-01-01

This study compares the application of probing techniques in cognitive interviewing (CI) and online probing (OP). Even though the probing is similar, the methods differ regarding typical mode setting, sample size, level of interactivity, and goals. We analyzed probing answers to the International Social Survey Programme item battery on specific…

sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters.

PubMed

Casel, Pierrot; Moreews, François; Lagarrigue, Sandrine; Klopp, Christophe

2009-07-16

Microarray is a powerful technology enabling to monitor tens of thousands of genes in a single experiment. Most microarrays are now using oligo-sets. The design of the oligo-nucleotides is time consuming and error prone. Genome wide microarray oligo-sets are designed using as large a set of transcripts as possible in order to monitor as many genes as possible. Depending on the genome sequencing state and on the assembly state the knowledge of the existing transcripts can be very different. This knowledge evolves with the different genome builds and gene builds. Once the design is done the microarrays are often used for several years. The biologists working in EADGENE expressed the need of up-to-dated annotation files for the oligo-sets they share including information about the orthologous genes of model species, the Gene Ontology, the corresponding pathways and the chromosomal location. The results of SigReannot on a chicken micro-array used in the EADGENE project compared to the initial annotations show that 23% of the oligo-nucleotide gene annotations were not confirmed, 2% were modified and 1% were added. The interest of this up-to-date annotation procedure is demonstrated through the analysis of real data previously published. SigReannot uses the oligo-nucleotide design procedure criteria to validate the probe-gene link and the Ensembl transcripts as reference for annotation. It therefore produces a high quality annotation based on reference gene sets.

Clinical utility of multiplex ligation-dependent probe amplification technique in identification of aetiology of unexplained mental retardation: a study in 203 Indian patients.

PubMed

Boggula, Vijay R; Shukla, Anju; Danda, Sumita; Hariharan, Sankar V; Nampoothiri, Sheela; Kumar, Rashmi; Phadke, Shubha R

2014-01-01

Developmental delay (DD)/mental retardation also described as intellectual disability (ID), is seen in 1-3 per cent of general population. Diagnosis continues to be a challenge at clinical level. With the advancement of new molecular cytogenetic techniques such as cytogenetic microarray (CMA), multiplex ligation-dependent probe amplification (MLPA) techniques, many microdeletion/microduplication syndromes with DD/ID are now delineated. MLPA technique can probe 40-50 genomic regions in a single reaction and is being used for evaluation of cases with DD/ID. In this study we evaluated the clinical utility of MLPA techniques with different probe sets to identify the aetiology of unexplained mental retardation in patients with ID/DD. A total of 203 randomly selected DD/ID cases with/without malformations were studied. MLPA probe sets for subtelomeric regions (P070/P036) and common microdeletions/microduplications (P245-A2) and X-chromosome (P106) were used. Positive cases with MLPA technique were confirmed using either fluorescence in situ hybridization (FISH) or follow up confirmatory MLPA probe sets. The overall detection rate was found to be 9.3 per cent (19 out of 203). The detection rates were 6.9 and 7.4 per cent for common microdeletion/microduplication and subtelomeric probe sets, respectively. No abnormality was detected with probe set for X-linked ID. The subtelomeric abnormalities detected included deletions of 1p36.33, 4p, 5p, 9p, 9q, 13q telomeric regions and duplication of 9pter. The deletions/duplications detected in non telomeric regions include regions for Prader Willi/Angelman regions, Williams syndrome, Smith Magenis syndrome and Velocardiofacial syndrome. Our results show that the use of P245-A2 and P070/P036-E1 probes gives good diagnostic yield. Though MLPA cannot probe the whole genome like cytogenetic microarray, due to its ease and relative low cost it is an important technique for evaluation of cases with DD/ID.

General equation for the differential pathlength factor of the frontal human head depending on wavelength and age.

PubMed

Scholkmann, Felix; Wolf, Martin

2013-10-01

Continuous-wave near-infrared spectroscopy and near-infrared imaging enable the measurement of relative concentration changes in oxy- and deoxyhemoglobin and thus hemodynamics and oxygenation. The accuracy of determined changes depends mainly on the modeling of the light transport through the probed tissue. Due to the highly scattering nature of tissue, the light path is longer than the source-detector separation (d). This is incorporated in modeling by multiplying d by a differential pathlength factor (DPF) which depends on several factors such as wavelength, age of the subject, and type of tissue. In the present work, we derive a general DPF equation for the frontal human head, incorporating dependency on wavelength and age, based on published data. We validated the equation using different data sets of experimentally determined DPFs from six independent studies.

Contact Versus Non-Contact Measurement of a Helicopter Main Rotor Composite Blade

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

Luczak, Marcin; Dziedziech, Kajetan; Peeters, Bart

2010-05-28

The dynamic characterization of lightweight structures is particularly complex as the impact of the weight of sensors and instrumentation (cables, mounting of exciters...) can distort the results. Varying mass loading or constraint effects between partial measurements may determine several errors on the final conclusions. Frequency shifts can lead to erroneous interpretations of the dynamics parameters. Typically these errors remain limited to a few percent. Inconsistent data sets however can result in major processing errors, with all related consequences towards applications based on the consistency assumption, such as global modal parameter identification, model-based damage detection and FRF-based matrix inversion in substructuring,more » load identification and transfer path analysis [1]. This paper addresses the subject of accuracy in the context of the measurement of the dynamic properties of a particular lightweight structure. It presents a comprehensive comparative study between the use of accelerometer, laser vibrometer (scanning LDV) and PU-probe (acoustic particle velocity and pressure) measurements to measure the structural responses, with as final aim the comparison of modal model quality assessment. The object of the investigation is a composite material blade from the main rotor of a helicopter. The presented results are part of an extensive test campaign performed with application of SIMO, MIMO, random and harmonic excitation, and the use of the mentioned contact and non-contact measurement techniques. The advantages and disadvantages of the applied instrumentation are discussed. Presented are real-life measurement problems related to the different set up conditions. Finally an analysis of estimated models is made in view of assessing the applicability of the various measurement approaches for successful fault detection based on modal parameters observation as well as in uncertain non-deterministic numerical model updating.« less

Contact Versus Non-Contact Measurement of a Helicopter Main Rotor Composite Blade

NASA Astrophysics Data System (ADS)

Luczak, Marcin; Dziedziech, Kajetan; Vivolo, Marianna; Desmet, Wim; Peeters, Bart; Van der Auweraer, Herman

2010-05-01

The dynamic characterization of lightweight structures is particularly complex as the impact of the weight of sensors and instrumentation (cables, mounting of exciters…) can distort the results. Varying mass loading or constraint effects between partial measurements may determine several errors on the final conclusions. Frequency shifts can lead to erroneous interpretations of the dynamics parameters. Typically these errors remain limited to a few percent. Inconsistent data sets however can result in major processing errors, with all related consequences towards applications based on the consistency assumption, such as global modal parameter identification, model-based damage detection and FRF-based matrix inversion in substructuring, load identification and transfer path analysis [1]. This paper addresses the subject of accuracy in the context of the measurement of the dynamic properties of a particular lightweight structure. It presents a comprehensive comparative study between the use of accelerometer, laser vibrometer (scanning LDV) and PU-probe (acoustic particle velocity and pressure) measurements to measure the structural responses, with as final aim the comparison of modal model quality assessment. The object of the investigation is a composite material blade from the main rotor of a helicopter. The presented results are part of an extensive test campaign performed with application of SIMO, MIMO, random and harmonic excitation, and the use of the mentioned contact and non-contact measurement techniques. The advantages and disadvantages of the applied instrumentation are discussed. Presented are real-life measurement problems related to the different set up conditions. Finally an analysis of estimated models is made in view of assessing the applicability of the various measurement approaches for successful fault detection based on modal parameters observation as well as in uncertain non-deterministic numerical model updating.

Computer- and Video-Based Instruction of Food-Preparation Skills: Acquisition, Generalization, and Maintenance

ERIC Educational Resources Information Center

Ayres, Kevin; Cihak, David

2010-01-01

The purpose of this study was to evaluate the effects of a computer-based video instruction (CBVI) program to teach life skills. Three middle school-aged students with intellectual disabilities were taught how to make a sandwich, use a microwave, and set the table with a CBVI software package. A multiple probe across behaviors design was used to…

Surface topography acquisition method for double-sided near-right-angle structured surfaces based on dual-probe wavelength scanning interferometry.

PubMed

Zhang, Tao; Gao, Feng; Jiang, Xiangqian

2017-10-02

This paper proposes an approach to measure double-sided near-right-angle structured surfaces based on dual-probe wavelength scanning interferometry (DPWSI). The principle and mathematical model is discussed and the measurement system is calibrated with a combination of standard step-height samples for both probes vertical calibrations and a specially designed calibration artefact for building up the space coordinate relationship of the dual-probe measurement system. The topography of the specially designed artefact is acquired by combining the measurement results with white light scanning interferometer (WLSI) and scanning electron microscope (SEM) for reference. The relative location of the two probes is then determined with 3D registration algorithm. Experimental validation of the approach is provided and the results show that the method is able to measure double-sided near-right-angle structured surfaces with nanometer vertical resolution and micrometer lateral resolution.

Probe and Sensors Development for Level Measurement of Fats, Oils and Grease in Grease Boxes

PubMed Central

Faria, José; Sousa, André; Reis, Arsénio; Filipe, Vitor; Barroso, João

2016-01-01

The wide spread of food outlets has become an environmental and sanitation infrastructure problem, due to Fats, Oils and Grease (FOG). A grease box is used at the industrials facilities to collect the FOG, in a specific time window, while its quality is good for recycling (e.g., biodiesel) and it is economically valuable. After this period, it will be disposed at a cost. For the proper management of the grease boxes, it is necessary to know the quantity of FOG inside the boxes, which is a major problem, as the boxes are sealed and permanently filled with water. The lack of homogeneity of the FOG renders it not detectable by current probes for level detection in liquids. In this article, the design, development and testing of a set of probes for FOG level measurement, based on the principles used in sensors for the detection of liquids inside containers, is described. The most suitable probe, based on the capacitance principle, together with the necessary hardware and software modules for data acquisition and transmission, was developed and tested. After the development phase, the probe was integrated on a metropolitan system for FOG collection and grease box management in partnership with a grease box management company. PMID:27649204

Unambiguous Identification of β-Tubulin as the Direct Cellular Target Responsible for the Cytotoxicity of Chalcone by Photoaffinity Labeling.

PubMed

Zhou, Bo; Yu, Xingxin; Zhuang, Chunlin; Villalta, Peter; Lin, Yong; Lu, Junxuan; Xing, Chengguo

2016-07-05

Chalcone is a simple and potentially privileged structure in medicinal chemistry with a diverse repertoire of biological activities, among which cytotoxicity is of particular interest. The sharp structure-activity relationship (SAR) for chalcone's cytotoxicity suggests structure-specific target interactions. Despite the numerous putative targets proposed, evidence for direct target interactions in cells is unavailable. In this study, guided by the sharp cytotoxic SAR, we developed a cytotoxic chalcone-based photoaffinity labeling (PAL) probe, (E)-3-(3-azidophenyl)-1-[3,5-dimethoxy-4-(prop-2-yn-1-yloxy)phenyl]-2-methylprop-2-en-1-one (C95; IC50 : 0.38±0.01 μm), along with two structurally similar non-cytotoxic probes. These probes were used to search for the direct cellular target responsible for chalcone's cytotoxicity through intact cell-based PAL experiments, in which β-tubulin was identified to specifically interact with the cytotoxic probe (i.e., C95) but not the non-cytotoxic probes. A set of phenotypical and biochemical assays further reinforced β-tubulin as the cytotoxic target of chalcones. Peptide mass quantitation by mass spectrometric analysis revealed one peptide potentially labeled by C95, providing information on chalcone's binding site on β-tubulin. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probe and Sensors Development for Level Measurement of Fats, Oils and Grease in Grease Boxes.

PubMed

Faria, José; Sousa, André; Reis, Arsénio; Filipe, Vitor; Barroso, João

2016-09-16

The wide spread of food outlets has become an environmental and sanitation infrastructure problem, due to Fats, Oils and Grease (FOG). A grease box is used at the industrials facilities to collect the FOG, in a specific time window, while its quality is good for recycling (e.g., biodiesel) and it is economically valuable. After this period, it will be disposed at a cost. For the proper management of the grease boxes, it is necessary to know the quantity of FOG inside the boxes, which is a major problem, as the boxes are sealed and permanently filled with water. The lack of homogeneity of the FOG renders it not detectable by current probes for level detection in liquids. In this article, the design, development and testing of a set of probes for FOG level measurement, based on the principles used in sensors for the detection of liquids inside containers, is described. The most suitable probe, based on the capacitance principle, together with the necessary hardware and software modules for data acquisition and transmission, was developed and tested. After the development phase, the probe was integrated on a metropolitan system for FOG collection and grease box management in partnership with a grease box management company.

Effect of structure variation of the aptamer-DNA duplex probe on the performance of displacement-based electrochemical aptamer sensors.

PubMed

Pang, Jie; Zhang, Ziping; Jin, Haizhu

2016-03-15

Electrochemical aptamer-based (E-AB) sensors employing electrode-immobilized, redox-tagged aptamer probes have emerged as a promising platform for the sensitive and quick detection of target analytes ranging from small molecules to proteins. Signal generation in this class of sensor is linked to change in electron transfer efficiency upon binding-induced change in flexibility/conformation of the aptamer probe. Because of this signaling mechanism, signal gains of these sensors can be improved by employing a displacement-based recognition system, which links target binding with a large-scale flexibility/conformation shift from the aptamer-DNA duplex to the single-stranded DNA or the native aptamer. Despite the relatively large number of displacement-based E-AB sensor samples, little attention has been paid to the structure variation of the aptamer-DNA duplex probe. Here we detail the effects of complementary length and position of the aptamer-DNA duplex probe on the performance of a model displacement-based E-AB sensor for ATP. We find that, greater background suppression and signal gain are observed with longer complementary length of the aptamer-DNA duplex probe. However, sensor equilibration time slows monotonically with increasing complementary length; and with too many target binding sites in aptamer sequence being occupied by the complementary DNA, the aptamer-target binding does not occur and no signal gain observed. We also demonstrate that signal gain of the displacement-based E-AB sensor is strongly dependent on the complementary position of the aptamer-DNA duplex probe, with complementary position located at the electrode-attached or redox-tagged end of the duplex probe, larger background suppression and signal increase than that of the middle position are observed. These results highlight the importance of rational structure design of the aptamer-DNA duplex probe and provide new insights into the optimization of displacement-based E-AB sensors. Copyright © 2015 Elsevier B.V. All rights reserved.

Learning through ferroelectric domain dynamics in solid-state synapses

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

Boyn, Soren; Grollier, Julie; Lecerf, Gwendal

In the brain, learning is achieved through the ability of synapses to reconfigure the strength by which they connect neurons (synaptic plasticity). In promising solid-state synapses called memristors, conductance can be finely tuned by voltage pulses and set to evolve according to a biological learning rule called spike-timing-dependent plasticity (STDP). Future neuromorphic architectures will comprise billions of such nanosynapses, which require a clear understanding of the physical mechanisms responsible for plasticity. Here we report on synapses based on ferroelectric tunnel junctions and show that STDP can be harnessed from inhomogeneous polarization switching. Through combined scanning probe imaging, electrical transport andmore » atomic-scale molecular dynamics, we demonstrate that conductance variations can be modelled by the nucleation-dominated reversal of domains. Finally, based on this physical model, our simulations show that arrays of ferroelectric nanosynapses can autonomously learn to recognize patterns in a predictable way, opening the path towards unsupervised learning in spiking neural networks.« less

Learning through ferroelectric domain dynamics in solid-state synapses

DOE PAGES

Boyn, Soren; Grollier, Julie; Lecerf, Gwendal; ...

2017-04-03

In the brain, learning is achieved through the ability of synapses to reconfigure the strength by which they connect neurons (synaptic plasticity). In promising solid-state synapses called memristors, conductance can be finely tuned by voltage pulses and set to evolve according to a biological learning rule called spike-timing-dependent plasticity (STDP). Future neuromorphic architectures will comprise billions of such nanosynapses, which require a clear understanding of the physical mechanisms responsible for plasticity. Here we report on synapses based on ferroelectric tunnel junctions and show that STDP can be harnessed from inhomogeneous polarization switching. Through combined scanning probe imaging, electrical transport andmore » atomic-scale molecular dynamics, we demonstrate that conductance variations can be modelled by the nucleation-dominated reversal of domains. Finally, based on this physical model, our simulations show that arrays of ferroelectric nanosynapses can autonomously learn to recognize patterns in a predictable way, opening the path towards unsupervised learning in spiking neural networks.« less

Design of 240,000 orthogonal 25mer DNA barcode probes.

PubMed

Xu, Qikai; Schlabach, Michael R; Hannon, Gregory J; Elledge, Stephen J

2009-02-17

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.

Design of 240,000 orthogonal 25mer DNA barcode probes

PubMed Central

Xu, Qikai; Schlabach, Michael R.; Hannon, Gregory J.; Elledge, Stephen J.

2009-01-01

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications. PMID:19171886

Development and construction of a comprehensive set of research diagnostics for the FLARE user facility

NASA Astrophysics Data System (ADS)

Yoo, Jongsoo; Jara-Almonte, J.; Majeski, S.; Frank, S.; Ji, H.; Yamada, M.

2016-10-01

FLARE (Facility for Laboratory Reconnection Experiments) will be operated as a flexible user facility, and so a complete set of research diagnostics is under development, including magnetic probe arrays, Langmuir probes, Mach probes, spectroscopic probes, and a laser interferometer. In order to accommodate the various requirements of users, large-scale (1 m), variable resolution (0.5-4 cm) magnetic probes have been designed, and are currently being prototyped. Moreover, a fully fiber-coupled laser interferometer has been designed to measure the line-integrated electron density. This fiber-coupled interferometer system will reduce the complexity of alignment processes and minimize maintenance of the system. Finally, improvements to the electrostatic probes and spectroscopic probes currently used in the Magnetic Reconnection Experiment (MRX) are discussed. The specifications of other subsystems, such as integrators and digitizers, are also presented. This work is supported by DoE Contract No. DE-AC0209CH11466.

Synthesis-identification integration: One-pot hydrothermal preparation of fluorescent nitrogen-doped carbon nanodots for differentiating nucleobases with the aid of multivariate chemometrics analysis.

PubMed

Zhuang, Qianfen; Cao, Wei; Ni, Yongnian; Wang, Yong

2018-08-01

Most of the conventional multidimensional differential sensors currently need at least two-step fabrication, namely synthesis of probe(s) and identification of multiple analytes by mixing of analytes with probe(s), and were conducted using multiple sensing elements or several devices. In the study, we chose five different nucleobases (adenine, cytosine, guanine, thymine, and uracil) as model analytes, and found that under hydrothermal conditions, sodium citrate could react directly with various nucleobases to yield different nitrogen-doped carbon nanodots (CDs). The CDs synthesized from different nucleobases exhibited different fluorescent properties, leading to their respective characteristic fluorescence spectra. Hence, we combined the fluorescence spectra of the CDs with advanced chemometrics like principle component analysis (PCA), hierarchical cluster analysis (HCA), K-nearest neighbor (KNN) and soft independent modeling of class analogy (SIMCA), to present a conceptually novel "synthesis-identification integration" strategy to construct a multidimensional differential sensor for nucleobase discrimination. Single-wavelength excitation fluorescence spectral data, single-wavelength emission fluorescence spectral data, and fluorescence Excitation-Emission Matrices (EEMs) of the CDs were respectively used as input data of the differential sensor. The results showed that the discrimination ability of the multidimensional differential sensor with EEM data set as input data was superior to those with single-wavelength excitation/emission fluorescence data set, suggesting that increasing the number of the data input could improve the discrimination power. Two supervised pattern recognition methods, namely KNN and SIMCA, correctly identified the five nucleobases with a classification accuracy of 100%. The proposed "synthesis-identification integration" strategy together with a multidimensional array of experimental data holds great promise in the construction of differential sensors. Copyright © 2018 Elsevier B.V. All rights reserved.

In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA.

PubMed

Hawkins, Melissa T R; Hofman, Courtney A; Callicrate, Taylor; McDonough, Molly M; Tsuchiya, Mirian T N; Gutiérrez, Eliécer E; Helgen, Kristofer M; Maldonado, Jesus E

2016-09-01

Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules. © 2015 John Wiley & Sons Ltd.

Identification of critical regulatory genes in cancer signaling network using controllability analysis

NASA Astrophysics Data System (ADS)

Ravindran, Vandana; Sunitha, V.; Bagler, Ganesh

2017-05-01

Cancer is characterized by a complex web of regulatory mechanisms which makes it difficult to identify features that are central to its control. Molecular integrative models of cancer, generated with the help of data from experimental assays, facilitate use of control theory to probe for ways of controlling the state of such a complex dynamic network. We modeled the human cancer signaling network as a directed graph and analyzed it for its controllability, identification of driver nodes and their characterization. We identified the driver nodes using the maximum matching algorithm and classified them as backbone, peripheral and ordinary based on their role in regulatory interactions and control of the network. We found that the backbone driver nodes were key to driving the regulatory network into cancer phenotype (via mutations) as well as for steering into healthy phenotype (as drug targets). This implies that while backbone genes could lead to cancer by virtue of mutations, they are also therapeutic targets of cancer. Further, based on their impact on the size of the set of driver nodes, genes were characterized as indispensable, dispensable and neutral. Indispensable nodes within backbone of the network emerged as central to regulatory mechanisms of control of cancer. In addition to probing the cancer signaling network from the perspective of control, our findings suggest that indispensable backbone driver nodes could be potentially leveraged as therapeutic targets. This study also illustrates the application of structural controllability for studying the mechanisms underlying the regulation of complex diseases.

Probing Protein Fold Space with a Simplified Model

PubMed Central

Minary, Peter; Levitt, Michael

2008-01-01

We probe the stability and near-native energy landscape of protein fold space using powerful conformational sampling methods together with simple reduced models and statistical potentials. Fold space is represented by a set of 280 protein domains spanning all topological classes and having a wide range of lengths (0-300 residues), amino acid composition, and number of secondary structural elements. The degrees of freedom are taken as the loop torsion angles. This choice preserves the native secondary structure but allows the tertiary structure to change. The proteins are represented by three-point per residue, three-dimensional models with statistical potentials derived from a knowledge-based study of known protein structures. When this space is sampled by a combination of Parallel Tempering and Equi-Energy Monte Carlo, we find that the three-point model captures the known stability of protein native structures with stable energy basins that are near-native (all-α: 4.77 Å, all-β: 2.93 Å, α/β: 3.09 Å, α+β: 4.89 Å on average and within 6 Å for 71.41 %, 92.85 %, 94.29 % and 64.28 % for all-α, all-β, α/β and α+β, classes respectively). Denatured structures also occur and these have interesting structural properties that shed light on the different landscape characteristics of α and β folds. We find that α/β proteins with alternating α and β segments (such as the beta-barrel) are more stable than proteins in other fold classes. PMID:18054792

Development of a high-speed VCSEL OCT system for real-time imaging of conscious patients larynx using a hand-held probe (Conference Presentation)

NASA Astrophysics Data System (ADS)

Rangarajan, Swathi; Chou, Li-Dek; Coughlan, Carolyn; Sharma, Giriraj; Wong, Brian J. F.; Ramalingam, Tirunelveli S.

2016-02-01

Fourier domain optical coherence tomography (FD-OCT) is a noninvasive imaging modality that has previously been used to image the human larynx. However, differences in anatomical geometry and short imaging range of conventional OCT limits its application in a clinical setting. In order to address this issue, we have developed a gradient-index (GRIN) lens rod-based hand-held probe in conjunction with a long imaging range 200 kHz Vertical-Cavity Surface Emitting Lasers (VCSEL) swept-source optical coherence tomography (SS-OCT) system for high speed real-time imaging of the human larynx in an office setting. This hand-held probe is designed to have a long and dynamically tunable working distance to accommodate the differences in anatomical geometry of human test subjects. A nominal working distance (~6 cm) of the probe is selected to have a lateral resolution <100 um within a depth of focus of 6.4 mm, which covers more than half of the 12 mm imaging range of the VCSEL laser. The maximum lateral scanning range of the probe at 6 cm working distance is approximately 8.4 mm, and imaging an area of 8.5 mm by 8.5 mm is accomplished within a second. Using the above system, we will demonstrate real-time cross-sectional OCT imaging of larynx during phonation in vivo in human and ex-vivo in pig vocal folds.

Set-relevance determines the impact of distractors on episodic memory retrieval.

PubMed

Kwok, Sze Chai; Shallice, Tim; Macaluso, Emiliano

2014-09-01

We investigated the interplay between stimulus-driven attention and memory retrieval with a novel interference paradigm that engaged both systems concurrently on each trial. Participants encoded a 45-min movie on Day 1 and, on Day 2, performed a temporal order judgment task during fMRI. Each retrieval trial comprised three images presented sequentially, and the task required participants to judge the temporal order of the first and the last images ("memory probes") while ignoring the second image, which was task irrelevant ("attention distractor"). We manipulated the content relatedness and the temporal proximity between the distractor and the memory probes, as well as the temporal distance between two probes. Behaviorally, short temporal distances between the probes led to reduced retrieval performance. Distractors that at encoding were temporally close to the first probe image reduced these costs, specifically when the distractor was content unrelated to the memory probes. The imaging results associated the distractor probe temporal proximity with activation of the right ventral attention network. By contrast, the precuneus was activated for high-content relatedness between distractors and probes and in trials including a short distance between the two memory probes. The engagement of the right ventral attention network by specific types of distractors suggests a link between stimulus-driven attention control and episodic memory retrieval, whereas the activation pattern of the precuneus implicates this region in memory search within knowledge/content-based hierarchies.

Cellular Oxygen and Nutrient Sensing in Microgravity Using Time-Resolved Fluorescence Microscopy

NASA Technical Reports Server (NTRS)

Szmacinski, Henryk

2003-01-01

Oxygen and nutrient sensing is fundamental to the understanding of cell growth and metabolism. This requires identification of optical probes and suitable detection technology without complex calibration procedures. Under this project Microcosm developed an experimental technique that allows for simultaneous imaging of intra- and inter-cellular events. The technique consists of frequency-domain Fluorescence Lifetime Imaging Microscopy (FLIM), a set of identified oxygen and pH probes, and methods for fabrication of microsensors. Specifications for electronic and optical components of FLIM instrumentation are provided. Hardware and software were developed for data acquisition and analysis. Principles, procedures, and representative images are demonstrated. Suitable lifetime sensitive oxygen, pH, and glucose probes for intra- and extra-cellular measurements of analyte concentrations have been identified and tested. Lifetime sensing and imaging have been performed using PBS buffer, culture media, and yeast cells as a model systems. Spectral specifications, calibration curves, and probes availability are also provided in the report.

Resolving Properties of Polymers and Nanoparticle Assembly through Coarse-Grained Computational Studies.

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

Grest, Gary S.

2017-09-01

Coupled length and time scales determine the dynamic behavior of polymers and polymer nanocomposites and underlie their unique properties. To resolve the properties over large time and length scales it is imperative to develop coarse grained models which retain the atomistic specificity. Here we probe the degree of coarse graining required to simultaneously retain significant atomistic details a nd access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using polyethylene as a model system, we probe how the coarse - graining scale affects themore » measured dynamics with different number methylene group s per coarse - grained beads. Using these models we simulate polyethylene melts for times over 500 ms to study the viscoelastic properties of well - entangled polymer melts and large nanoparticle assembly as the nanoparticles are driven close enough to form nanostructures.« less

When Interference Helps: Increasing Executive Load to Facilitate Deception Detection in the Concealed Information Test

PubMed Central

Visu-Petra, George; Varga, Mihai; Miclea, Mircea; Visu-Petra, Laura

2013-01-01

The possibility to enhance the detection efficiency of the Concealed Information Test (CIT) by increasing executive load was investigated, using an interference design. After learning and executing a mock crime scenario, subjects underwent three deception detection tests: an RT-based CIT, an RT-based CIT plus a concurrent memory task (CITMem), and an RT-based CIT plus a concurrent set-shifting task (CITShift). The concealed information effect, consisting in increased RT and lower response accuracy for probe items compared to irrelevant items, was evidenced across all three conditions. The group analyses indicated a larger difference between RTs to probe and irrelevant items in the dual-task conditions, but this difference was not translated in a significantly increased detection efficiency at an individual level. Signal detection parameters based on the comparison with a simulated innocent group showed accurate discrimination for all conditions. Overall response accuracy on the CITMem was highest and the difference between response accuracy to probes and irrelevants was smallest in this condition. Accuracy on the concurrent tasks (Mem and Shift) was high, and responses on these tasks were significantly influenced by CIT stimulus type (probes vs. irrelevants). The findings are interpreted in relation to the cognitive load/dual-task interference literature, generating important insights for research on the involvement of executive functions in deceptive behavior. PMID:23543918

Searches for pair production of third-generation squarks in √{s}=13 {TeV} pp collisions

NASA Astrophysics Data System (ADS)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; König, A.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rad, N.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Strauss, J.; Waltenberger, W.; Wulz, C.-E.; Chekhovsky, V.; Dvornikov, O.; Dydyshka, Y.; Emeliantchik, I.; Litomin, A.; Makarenko, V.; Mossolov, V.; Stefanovitch, R.; Suarez Gonzalez, J.; Zykunov, V.; Shumeiko, N.; Alderweireldt, S.; De Wolf, E. A.; Janssen, X.; Lauwers, J.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; Daci, N.; De Bruyn, I.; Deroover, K.; Lowette, S.; Moortgat, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Skovpen, K.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Brun, H.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Léonard, A.; Luetic, J.; Maerschalk, T.; Marinov, A.; Randle-conde, A.; Seva, T.; Vander Velde, C.; Vanlaer, P.; Vannerom, D.; Yonamine, R.; Zenoni, F.; Zhang, F.; Cimmino, A.; Cornelis, T.; Dobur, D.; Fagot, A.; Gul, M.; Khvastunov, I.; Poyraz, D.; Salva, S.; Schöfbeck, R.; Tytgat, M.; Van Driessche, W.; Yazgan, E.; Zaganidis, N.; Bakhshiansohi, H.; Beluffi, C.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; De Visscher, S.; Delaere, C.; Delcourt, M.; Francois, B.; Giammanco, A.; Jafari, A.; Komm, M.; Krintiras, G.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Piotrzkowski, K.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Wertz, S.; Beliy, N.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; De Oliveira Martins, C.; De Souza, S. Fonseca; Huertas Guativa, L. M.; Malbouisson, H.; Matos Figueiredo, D.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Pereira, A. Vilela; Ahuja, S.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Moon, C. S.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Fang, W.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Chen, Y.; Cheng, T.; Jiang, C. H.; Leggat, D.; Liu, Z.; Romeo, F.; Ruan, M.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Zhang, H.; Zhao, J.; Ban, Y.; Chen, G.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; González Hernández, C. F.; Ruiz Alvarez, J. D.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Sculac, T.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Ferencek, D.; Kadija, K.; Mesic, B.; Susa, T.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Tsiakkouri, D.; Finger, M.; Finger, M.; Carrera Jarrin, E.; El-khateeb, E.; Elgammal, S.; Mohamed, A.; Kadastik, M.; Perrini, L.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Ghosh, S.; Givernaud, A.; Gras, P.; de Monchenault, G. Hamel; Jarry, P.; Kucher, I.; Locci, E.; Machet, M.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Abdulsalam, A.; Antropov, I.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Chapon, E.; Charlot, C.; Davignon, O.; de Cassagnac, R. Granier; Jo, M.; Lisniak, S.; Miné, P.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Pigard, P.; Regnard, S.; Salerno, R.; Sirois, Y.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Zghiche, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Coubez, X.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Jansová, M.; Bihan, A.-C. Le; Van Hove, P.; Gadrat, S.; Beauceron, S.; Bernet, C.; Boudoul, G.; Carrillo Montoya, C. A.; Chierici, R.; Contardo, D.; Courbon, B.; Depasse, P.; El Mamouni, H.; Fan, J.; Fay, J.; Gascon, S.; Gouzevitch, M.; Grenier, G.; Ille, B.; Lagarde, F.; Laktineh, I. B.; Lethuillier, M.; Mirabito, L.; Pequegnot, A. L.; Perries, S.; Popov, A.; Sabes, D.; Sordini, V.; Vander Donckt, M.; Verdier, P.; Viret, S.; Toriashvili, T.; Tsamalaidze, Z.; Autermann, C.; Beranek, S.; Feld, L.; Kiesel, M. K.; Klein, K.; Lipinski, M.; Preuten, M.; Schomakers, C.; Schulz, J.; Verlage, T.; Zhukov, V.; Albert, A.; Brodski, M.; Dietz-Laursonn, E.; Duchardt, D.; Endres, M.; Erdmann, M.; Erdweg, S.; Esch, T.; Fischer, R.; Güth, A.; Hamer, M.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Knutzen, S.; Merschmeyer, M.; Meyer, A.; Millet, P.; Mukherjee, S.; Olschewski, M.; Padeken, K.; Pook, T.; Radziej, M.; Reithler, H.; Rieger, M.; Scheuch, F.; Sonnenschein, L.; Teyssier, D.; Thüer, S.; Cherepanov, V.; Flügge, G.; Kargoll, B.; Kress, T.; Künsken, A.; Lingemann, J.; Müller, T.; Nehrkorn, A.; Nowack, A.; Pistone, C.; Pooth, O.; Stahl, A.; Aldaya Martin, M.; Arndt, T.; Asawatangtrakuldee, C.; Beernaert, K.; Behnke, O.; Behrens, U.; Bin Anuar, A. A.; Borras, K.; Campbell, A.; Connor, P.; Contreras-Campana, C.; Costanza, F.; Pardos, C. Diez; Dolinska, G.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Eren, E.; Gallo, E.; Garay Garcia, J.; Geiser, A.; Gizhko, A.; Grados Luyando, J. M.; Grohsjean, A.; Gunnellini, P.; Harb, A.; Hauk, J.; Hempel, M.; Jung, H.; Kalogeropoulos, A.; Karacheban, O.; Kasemann, M.; Keaveney, J.; Kleinwort, C.; Korol, I.; Krücker, D.; Lange, W.; Lelek, A.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Mankel, R.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Ntomari, E.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Roland, B.; Sahin, M. Ö.; Saxena, P.; Schoerner-Sadenius, T.; Seitz, C.; Spannagel, S.; Stefaniuk, N.; Van Onsem, G. P.; Walsh, R.; Wissing, C.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Dreyer, T.; Garutti, E.; Gonzalez, D.; Haller, J.; Hoffmann, M.; Junkes, A.; Klanner, R.; Kogler, R.; Kovalchuk, N.; Lapsien, T.; Lenz, T.; Marchesini, I.; Marconi, D.; Meyer, M.; Niedziela, M.; Nowatschin, D.; Pantaleo, F.; Peiffer, T.; Perieanu, A.; Poehlsen, J.; Sander, C.; Scharf, C.; Schleper, P.; Schmidt, A.; Schumann, S.; Schwandt, J.; Stadie, H.; Steinbrück, G.; Stober, F. M.; Stöver, M.; Tholen, H.; Troendle, D.; Usai, E.; Vanelderen, L.; Vanhoefer, A.; Vormwald, B.; Akbiyik, M.; Barth, C.; Baur, S.; Baus, C.; Berger, J.; Butz, E.; Caspart, R.; Chwalek, T.; Colombo, F.; De Boer, W.; Dierlamm, A.; Fink, S.; Freund, B.; Friese, R.; Giffels, M.; Gilbert, A.; Goldenzweig, P.; Haitz, D.; Hartmann, F.; Heindl, S. M.; Husemann, U.; Katkov, I.; Kudella, S.; Mildner, H.; Mozer, M. U.; Müller, Th.; Plagge, M.; Quast, G.; Rabbertz, K.; Röcker, S.; Roscher, F.; Schröder, M.; Shvetsov, I.; Sieber, G.; Simonis, H. J.; Ulrich, R.; Wayand, S.; Weber, M.; Weiler, T.; Williamson, S.; Wöhrmann, C.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Giakoumopoulou, V. A.; Kyriakis, A.; Loukas, D.; Topsis-Giotis, I.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Tziaferi, E.; Evangelou, I.; Flouris, G.; Foudas, C.; Kokkas, P.; Loukas, N.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Filipovic, N.; Bencze, G.; Hajdu, C.; Horvath, D.; Sikler, F.; Veszpremi, V.; Vesztergombi, G.; Zsigmond, A. J.; Beni, N.; Czellar, S.; Karancsi, J.; Makovec, A.; Molnar, J.; Szillasi, Z.; Bartók, M.; Raics, P.; Trocsanyi, Z. L.; Ujvari, B.; Bahinipati, S.; Choudhury, S.; Mal, P.; Mandal, K.; Nayak, A.; Sahoo, D. K.; Sahoo, N.; Swain, S. K.; Bansal, S.; Beri, S. B.; Bhatnagar, V.; Chawla, R.; Bhawandeep, U.; Kalsi, A. K.; Kaur, A.; Kaur, M.; Kumar, R.; Kumari, P.; Mehta, A.; Mittal, M.; Singh, J. B.; Walia, G.; Kumar, Ashok; Bhardwaj, A.; Choudhary, B. C.; Garg, R. 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M.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Calabria, C.; Caputo, C.; Colaleo, A.; Creanza, D.; Cristella, L.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; Miniello, G.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Ranieri, A.; Selvaggi, G.; Sharma, A.; Silvestris, L.; Venditti, R.; Verwilligen, P.; Abbiendi, G.; Battilana, C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Chhibra, S. S.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Rossi, A. M.; Rovelli, T.; Siroli, G. 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M.; Lanza, G.; Lista, L.; Meola, S.; Paolucci, P.; Sciacca, C.; Thyssen, F.; Azzi, P.; Bacchetta, N.; Bellato, M.; Benato, L.; Biasotto, M.; Bisello, D.; Boletti, A.; Checchia, P.; Dall'Osso, M.; De Castro Manzano, P.; Dosselli, U.; Gasparini, F.; Gasparini, U.; Gozzelino, A.; Lacaprara, S.; Margoni, M.; Meneguzzo, A. T.; Pazzini, J.; Pozzobon, N.; Ronchese, P.; Simonetto, F.; Torassa, E.; Ventura, S.; Zanetti, M.; Zotto, P.; Zumerle, G.; Braghieri, A.; Fallavollita, F.; Magnani, A.; Montagna, P.; Ratti, S. P.; Re, V.; Riccardi, C.; Salvini, P.; Vai, I.; Vitulo, P.; Solestizi, L. Alunni; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Leonardi, R.; Mantovani, G.; Menichelli, M.; Saha, A.; Santocchia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fedi, G.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Spagnolo, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; Cipriani, M.; Del Re, D.; Diemoz, M.; Gelli, S.; Longo, E.; Margaroli, F.; Marzocchi, B.; Meridiani, P.; Organtini, G.; Paramatti, R.; Preiato, F.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bartosik, N.; Bellan, R.; Biino, C.; Cartiglia, N.; Cenna, F.; Costa, M.; Covarelli, R.; Degano, A.; Demaria, N.; Finco, L.; Kiani, B.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Monteil, E.; Monteno, M.; Obertino, M. M.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Ravera, F.; Romero, A.; Ruspa, M.; Sacchi, R.; Shchelina, K.; Sola, V.; Solano, A.; Staiano, A.; Traczyk, P.; Belforte, S.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Zanetti, A.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Lee, S.; Lee, S. W.; Oh, Y. D.; Sekmen, S.; Son, D. C.; Yang, Y. C.; Lee, A.; Kim, H.; Brochero Cifuentes, J. A.; Kim, T. J.; Cho, S.; Choi, S.; Go, Y.; Gyun, D.; Ha, S.; Hong, B.; Jo, Y.; Kim, Y.; Lee, K.; Lee, K. S.; Lee, S.; Lim, J.; Park, S. K.; Roh, Y.; Almond, J.; Kim, J.; Lee, H.; Oh, S. B.; Radburn-Smith, B. C.; Seo, S. h.; Yang, U. K.; Yoo, H. D.; Yu, G. B.; Choi, M.; Kim, H.; Kim, J. H.; Lee, J. S. H.; Park, I. C.; Ryu, G.; Ryu, M. S.; Choi, Y.; Goh, J.; Hwang, C.; Lee, J.; Yu, I.; Dudenas, V.; Juodagalvis, A.; Vaitkus, J.; Ahmed, I.; Ibrahim, Z. A.; Komaragiri, J. R.; Ali, M. A. B. Md; Mohamad Idris, F.; Abdullah, W. A. T. Wan; Yusli, M. N.; Zolkapli, Z.; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-De La Cruz, I.; Hernandez-Almada, A.; Lopez-Fernandez, R.; Magaña Villalba, R.; Mejia Guisao, J.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Oropeza Barrera, C.; Vazquez Valencia, F.; Carpinteyro, S.; Pedraza, I.; Salazar Ibarguen, H. A.; Uribe Estrada, C.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khan, W. A.; Saddique, A.; Shah, M. A.; Shoaib, M.; Waqas, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Bunkowski, K.; Byszuk, A.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Walczak, M.; Bargassa, P.; Da Cruz E. Silva, C. Beirão; Calpas, B.; Di Francesco, A.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Hollar, J.; Leonardo, N.; Lloret Iglesias, L.; Nemallapudi, M. V.; Rodrigues Antunes, J.; Seixas, J.; Toldaiev, O.; Vadruccio, D.; Varela, J.; Vischia, P.; Alexakhin, V.; Bunin, P.; Gavrilenko, M.; Golutvin, I.; Gorbunov, I.; Kamenev, A.; Karjavin, V.; Lanev, A.; Malakhov, A.; Matveev, V.; Palichik, V.; Perelygin, V.; Savina, M.; Shmatov, S.; Skatchkov, N.; Smirnov, V.; Voytishin, N.; Zarubin, A.; Chtchipounov, L.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Kuznetsova, E.; Murzin, V.; Oreshkin, V.; Sulimov, V.; Vorobyev, A.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Karneyeu, A.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Pozdnyakov, I.; Safronov, G.; Spiridonov, A.; Toms, M.; Vlasov, E.; Zhokin, A.; Bylinkin, A.; Markin, O.; Popova, E.; Zhemchugov, E.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Terkulov, A.; Baskakov, A.; Belyaev, A.; Boos, E.; Bunichev, V.; Dubinin, M.; Dudko, L.; Ershov, A.; Gribushin, A.; Klyukhin, V.; Kodolova, O.; Lokhtin, I.; Miagkov, I.; Obraztsov, S.; Petrushanko, S.; Savrin, V.; Blinov, V.; Skovpen, Y.; Shtol, D.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Elumakhov, D.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Cirkovic, P.; Devetak, D.; Dordevic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Barrio Luna, M.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Del Valle, A. Escalante; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Lopez, S. Goy; Hernandez, J. M.; Josa, M. I.; De Martino, E. Navarro; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; de Trocóniz, J. F.; Missiroli, M.; Moran, D.; Cuevas, J.; Fernandez Menendez, J.; Gonzalez Caballero, I.; González Fernández, J. R.; Palencia Cortezon, E.; Sanchez Cruz, S.; Suárez Andrés, I.; Vizan Garcia, J. M.; Cabrillo, I. J.; Calderon, A.; Curras, E.; Fernandez, M.; Garcia-Ferrero, J.; Gomez, G.; Lopez Virto, A.; Marco, J.; Martinez Rivero, C.; Matorras, F.; Piedra Gomez, J.; Rodrigo, T.; Ruiz-Jimeno, A.; Scodellaro, L.; Trevisani, N.; Vila, I.; Vilar Cortabitarte, R.; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Bloch, P.; Bocci, A.; Botta, C.; Camporesi, T.; Castello, R.; Cepeda, M.; Cerminara, G.; Chen, Y.; d'Enterria, D.; Dabrowski, A.; Daponte, V.; David, A.; De Gruttola, M.; De Roeck, A.; Di Marco, E.; Dobson, M.; Dorney, B.; du Pree, T.; Duggan, D.; Dünser, M.; Dupont, N.; Elliott-Peisert, A.; Everaerts, P.; Fartoukh, S.; Franzoni, G.; Fulcher, J.; Funk, W.; Gigi, D.; Gill, K.; Girone, M.; Glege, F.; Gulhan, D.; Gundacker, S.; Guthoff, M.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kieseler, J.; Kirschenmann, H.; Knünz, V.; Kornmayer, A.; Kortelainen, M. J.; Kousouris, K.; Krammer, M.; Lange, C.; Lecoq, P.; Lourenço, C.; Lucchini, M. T.; Malgeri, L.; Mannelli, M.; Martelli, A.; Meijers, F.; Merlin, J. A.; Mersi, S.; Meschi, E.; Milenovic, P.; Moortgat, F.; Morovic, S.; Mulders, M.; Neugebauer, H.; Orfanelli, S.; Orsini, L.; Pape, L.; Perez, E.; Peruzzi, M.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Racz, A.; Reis, T.; Rolandi, G.; Rovere, M.; Sakulin, H.; Sauvan, J. B.; Schäfer, C.; Schwick, C.; Seidel, M.; Sharma, A.; Silva, P.; Sphicas, P.; Steggemann, J.; Stoye, M.; Takahashi, Y.; Tosi, M.; Treille, D.; Triossi, A.; Tsirou, A.; Veckalns, V.; Veres, G. I.; Verweij, M.; Wardle, N.; Wöhri, H. K.; Zagozdzinska, A.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; Kotlinski, D.; Langenegger, U.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Casal, B.; Dissertori, G.; Dittmar, M.; Donegà, M.; Grab, C.; Heidegger, C.; Hits, D.; Hoss, J.; Kasieczka, G.; Lustermann, W.; Mangano, B.; Marionneau, M.; del Arbol, P. Martinez Ruiz; Masciovecchio, M.; Meinhard, M. T.; Meister, D.; Micheli, F.; Musella, P.; Nessi-Tedaldi, F.; Pandolfi, F.; Pata, J.; Pauss, F.; Perrin, G.; Perrozzi, L.; Quittnat, M.; Rossini, M.; Schönenberger, M.; Starodumov, A.; Tavolaro, V. R.; Theofilatos, K.; Wallny, R.; Aarrestad, T. K.; Amsler, C.; Caminada, L.; Canelli, M. F.; De Cosa, A.; Galloni, C.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Ngadiuba, J.; Pinna, D.; Rauco, G.; Robmann, P.; Salerno, D.; Yang, Y.; Zucchetta, A.; Candelise, V.; Doan, T. H.; Jain, Sh.; Khurana, R.; Konyushikhin, M.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Pozdnyakov, A.; Yu, S. S.; Kumar, Arun; Chang, P.; Chang, Y. H.; Chao, Y.; Chen, K. F.; Chen, P. H.; Fiori, F.; Hou, W.-S.; Hsiung, Y.; Liu, Y. F.; Lu, R.-S.; Miñano Moya, M.; Paganis, E.; Psallidas, A.; Tsai, J. f.; Asavapibhop, B.; Singh, G.; Srimanobhas, N.; Suwonjandee, N.; Adiguzel, A.; Bakirci, M. N.; Cerci, S.; Damarseckin, S.; Demiroglu, Z. S.; Dozen, C.; Dumanoglu, I.; Girgis, S.; Gokbulut, G.; Guler, Y.; Hos, I.; Kangal, E. E.; Kara, O.; Topaksu, A. Kayis; Kiminsu, U.; Oglakci, M.; Onengut, G.; Ozdemir, K.; Tali, B.; Turkcapar, S.; Zorbakir, I. S.; Zorbilmez, C.; Bilin, B.; Bilmis, S.; Isildak, B.; Karapinar, G.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Kaya, M.; Kaya, O.; Yetkin, E. A.; Yetkin, T.; Cakir, A.; Cankocak, K.; Sen, S.; Grynyov, B.; Levchuk, L.; Sorokin, P.; Aggleton, R.; Ball, F.; Beck, L.; Brooke, J. J.; Burns, D.; Clement, E.; Cussans, D.; Flacher, H.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Sakuma, T.; Seif El Nasr-storey, S.; Smith, D.; Smith, V. J.; Bell, K. W.; Belyaev, A.; Brew, C.; Brown, R. M.; Calligaris, L.; Cieri, D.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Williams, T.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Bundock, A.; Burton, D.; Casasso, S.; Citron, M.; Colling, D.; Corpe, L.; Dauncey, P.; Davies, G.; De Wit, A.; Della Negra, M.; Di Maria, R.; Dunne, P.; Elwood, A.; Futyan, D.; Haddad, Y.; Hall, G.; Iles, G.; James, T.; Lane, R.; Laner, C.; Lucas, R.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mastrolorenzo, L.; Nash, J.; Nikitenko, A.; Pela, J.; Penning, B.; Pesaresi, M.; Raymond, D. M.; Richards, A.; Rose, A.; Seez, C.; Summers, S.; Tapper, A.; Uchida, K.; Vazquez Acosta, M.; Virdee, T.; Wright, J.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Borzou, A.; Call, K.; Dittmann, J.; Hatakeyama, K.; Liu, H.; Pastika, N.; Bartek, R.; Dominguez, A.; Cooper, S. I.; Henderson, C.; Rumerio, P.; West, C.; Arcaro, D.; Avetisyan, A.; Bose, T.; Gastler, D.; Rankin, D.; Richardson, C.; Rohlf, J.; Sulak, L.; Zou, D.; Benelli, G.; Cutts, D.; Garabedian, A.; Hakala, J.; Heintz, U.; Hogan, J. M.; Jesus, O.; Kwok, K. H. M.; Laird, E.; Landsberg, G.; Mao, Z.; Narain, M.; Piperov, S.; Sagir, S.; Spencer, E.; Syarif, R.; Breedon, R.; Burns, D.; De La Barca Sanchez, M. Calderon; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Flores, C.; Funk, G.; Gardner, M.; Ko, W.; Lander, R.; Mclean, C.; Mulhearn, M.; Pellett, D.; Pilot, J.; Shalhout, S.; Shi, M.; Smith, J.; Squires, M.; Stolp, D.; Tos, K.; Tripathi, M.; Bravo, C.; Cousins, R.; Dasgupta, A.; Florent, A.; Hauser, J.; Ignatenko, M.; Mccoll, N.; Saltzberg, D.; Schnaible, C.; Valuev, V.; Weber, M.; Bouvier, E.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Ghiasi Shirazi, S. M. A.; Hanson, G.; Heilman, J.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Olmedo Negrete, M.; Paneva, M. I.; Shrinivas, A.; Si, W.; Wei, H.; Wimpenny, S.; Yates, B. R.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; Derdzinski, M.; Gerosa, R.; Holzner, A.; Klein, D.; Krutelyov, V.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Tadel, M.; Vartak, A.; Wasserbaech, S.; Welke, C.; Wood, J.; Würthwein, F.; Yagil, A.; Della Porta, G. Zevi; Amin, N.; Bhandari, R.; Bradmiller-Feld, J.; Campagnari, C.; Dishaw, A.; Dutta, V.; Franco Sevilla, M.; George, C.; Golf, F.; Gouskos, L.; Gran, J.; Heller, R.; Incandela, J.; Mullin, S. D.; Ovcharova, A.; Qu, H.; Richman, J.; Stuart, D.; Suarez, I.; Yoo, J.; Anderson, D.; Bendavid, J.; Bornheim, A.; Bunn, J.; Duarte, J.; Lawhorn, J. M.; Mott, A.; Newman, H. B.; Pena, C.; Spiropulu, M.; Vlimant, J. R.; Xie, S.; Zhu, R. Y.; Andrews, M. B.; Ferguson, T.; Paulini, M.; Russ, J.; Sun, M.; Vogel, H.; Vorobiev, I.; Weinberg, M.; Cumalat, J. P.; Ford, W. T.; Jensen, F.; Johnson, A.; Krohn, M.; Mulholland, T.; Stenson, K.; Wagner, S. R.; Alexander, J.; Chaves, J.; Chu, J.; Dittmer, S.; Mcdermott, K.; Mirman, N.; Kaufman, G. Nicolas; Patterson, J. R.; Rinkevicius, A.; Ryd, A.; Skinnari, L.; Soffi, L.; Tan, S. M.; Tao, Z.; Thom, J.; Tucker, J.; Wittich, P.; Zientek, M.; Winn, D.; Abdullin, S.; Albrow, M.; Apollinari, G.; Apresyan, A.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Cremonesi, M.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hare, D.; Harris, R. M.; Hasegawa, S.; Hirschauer, J.; Hu, Z.; Jayatilaka, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Klima, B.; Kreis, B.; Lammel, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, M.; Liu, T.; De Sá, R. Lopes; Lykken, J.; Maeshima, K.; Magini, N.; Marraffino, J. M.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mrenna, S.; Nahn, S.; O'Dell, V.; Pedro, K.; Prokofyev, O.; Rakness, G.; Ristori, L.; Sexton-Kennedy, E.; Soha, A.; Spalding, W. J.; Spiegel, L.; Stoynev, S.; Strait, J.; Strobbe, N.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vernieri, C.; Verzocchi, M.; Vidal, R.; Wang, M.; Weber, H. A.; Whitbeck, A.; Wu, Y.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Brinkerhoff, A.; Carnes, A.; Carver, M.; Curry, D.; Das, S.; Field, R. D.; Furic, I. K.; Konigsberg, J.; Korytov, A.; Low, J. F.; Ma, P.; Matchev, K.; Mei, H.; Mitselmakher, G.; Rank, D.; Shchutska, L.; Sperka, D.; Thomas, L.; Wang, J.; Wang, S.; Yelton, J.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Ackert, A.; Adams, T.; Askew, A.; Bein, S.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Prosper, H.; Santra, A.; Yohay, R.; Baarmand, M. M.; Bhopatkar, V.; Colafranceschi, S.; Hohlmann, M.; Noonan, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Jung, K.; Sandoval Gonzalez, I. D.; Varelas, N.; Wang, H.; Wu, Z.; Zakaria, M.; Zhang, J.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Snyder, C.; Tiras, E.; Wetzel, J.; Yi, K.; Anderson, I.; Blumenfeld, B.; Cocoros, A.; Eminizer, N.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Osherson, M.; Roskes, J.; Sarica, U.; Swartz, M.; Xiao, M.; Xin, Y.; You, C.; Al-bataineh, A.; Baringer, P.; Bean, A.; Boren, S.; Bowen, J.; Castle, J.; Forthomme, L.; Kenny, R. P.; Khalil, S.; Kropivnitskaya, A.; Majumder, D.; Mcbrayer, W.; Murray, M.; Sanders, S.; Stringer, R.; Tapia Takaki, J. D.; Wang, Q.; Ivanov, A.; Kaadze, K.; Maravin, Y.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Toda, S.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Calvert, B.; Eno, S. C.; Ferraioli, C.; Gomez, J. A.; Hadley, N. J.; Jabeen, S.; Kellogg, R. G.; Kolberg, T.; Kunkle, J.; Lu, Y.; Mignerey, A. C.; Ricci-Tam, F.; Shin, Y. H.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Abercrombie, D.; Allen, B.; Apyan, A.; Azzolini, V.; Barbieri, R.; Baty, A.; Bi, R.; Bierwagen, K.; Brandt, S.; Busza, W.; Cali, I. A.; D'Alfonso, M.; Demiragli, Z.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Hsu, D.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Krajczar, K.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Maier, B.; Marini, A. C.; Mcginn, C.; Mironov, C.; Narayanan, S.; Niu, X.; Paus, C.; Roland, C.; Roland, G.; Salfeld-Nebgen, J.; Stephans, G. S. F.; Tatar, K.; Varma, M.; Velicanu, D.; Veverka, J.; Wang, J.; Wang, T. W.; Wyslouch, B.; Yang, M.; Benvenuti, A. C.; Chatterjee, R. M.; Evans, A.; Hansen, P.; Kalafut, S.; Kao, S. C.; Kubota, Y.; Lesko, Z.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Claes, D. R.; Fangmeier, C.; Gonzalez Suarez, R.; Kamalieddin, R.; Kravchenko, I.; Malta Rodrigues, A.; Meier, F.; Monroy, J.; Siado, J. E.; Snow, G. R.; Stieger, B.; Alyari, M.; Dolen, J.; Godshalk, A.; Harrington, C.; Iashvili, I.; Kaisen, J.; Kharchilava, A.; Parker, A.; Rappoccio, S.; Roozbahani, B.; Alverson, G.; Barberis, E.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; De Lima, R. Teixeira; Trocino, D.; Wang, R.-J.; Wood, D.; Bhattacharya, S.; Charaf, O.; Hahn, K. A.; Kumar, A.; Mucia, N.; Odell, N.; Pollack, B.; Schmitt, M. H.; Sung, K.; Trovato, M.; Velasco, M.; Dev, N.; Hildreth, M.; Hurtado Anampa, K.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Planer, M.; Reinsvold, A.; Ruchti, R.; Smith, G.; Taroni, S.; Wayne, M.; Wolf, M.; Woodard, A.; Alimena, J.; Antonelli, L.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Francis, B.; Hart, A.; Hill, C.; Hughes, R.; Ji, W.; Liu, B.; Luo, W.; Puigh, D.; Winer, B. L.; Wulsin, H. W.; Cooperstein, S.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Lange, D.; Luo, J.; Marlow, D.; Medvedeva, T.; Mei, K.; Olsen, J.; Palmer, C.; Piroué, P.; Stickland, D.; Svyatkovskiy, A.; Tully, C.; Malik, S.; Barker, A.; Barnes, V. E.; Folgueras, S.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, A. W.; Khatiwada, A.; Miller, D. H.; Neumeister, N.; Schulte, J. F.; Shi, X.; Sun, J.; Wang, F.; Xie, W.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Chen, Z.; Ecklund, K. M.; Geurts, F. J. M.; Guilbaud, M.; Li, W.; Michlin, B.; Northup, M.; Padley, B. P.; Roberts, J.; Rorie, J.; Tu, Z.; Zabel, J.; Betchart, B.; Bodek, A.; de Barbaro, P.; Demina, R.; Duh, Y. t.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Hindrichs, O.; Khukhunaishvili, A.; Lo, K. H.; Tan, P.; Verzetti, M.; Agapitos, A.; Chou, J. P.; Gershtein, Y.; Gómez Espinosa, T. A.; Halkiadakis, E.; Heindl, M.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Kyriacou, S.; Lath, A.; Nash, K.; Saka, H.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Delannoy, A. G.; Foerster, M.; Heideman, J.; Riley, G.; Rose, K.; Spanier, S.; Thapa, K.; Bouhali, O.; Celik, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Huang, T.; Juska, E.; Kamon, T.; Mueller, R.; Pakhotin, Y.; Patel, R.; Perloff, A.; Perniè, L.; Rathjens, D.; Safonov, A.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Cowden, C.; Damgov, J.; De Guio, F.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Gurpinar, E.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Peltola, T.; Undleeb, S.; Volobouev, I.; Wang, Z.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Melo, A.; Ni, H.; Sheldon, P.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Barria, P.; Cox, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Neu, C.; Sinthuprasith, T.; Sun, X.; Wang, Y.; Wolfe, E.; Xia, F.; Clarke, C.; Harr, R.; Karchin, P. E.; Sturdy, J.; Belknap, D. A.; Buchanan, J.; Caillol, C.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ruggles, T.; Savin, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.

2017-05-01

Searches are presented for direct production of top or bottom squark pairs in proton-proton collisions at the CERN LHC. Two searches, based on complementary techniques, are performed in all-jet final states that are characterized by a significant imbalance in transverse momentum. An additional search requires the presence of a charged lepton isolated from other activity in the event. The data were collected in 2015 at a centre-of-mass energy of 13 {TeV} with the CMS detector and correspond to an integrated luminosity of 2.3 {fb}^{-1}. No statistically significant excess of events is found beyond the expected contribution from standard model processes. Exclusion limits are set in the context of simplified models of top or bottom squark pair production. Models with top and bottom squark masses up to 830 and 890 {GeV}, respectively, are probed for light neutralinos. For models with top squark masses of 675 {GeV}, neutralino masses up to 260 {GeV} are excluded at 95% confidence level.

The influence of crystal habit on the prediction of dry powder inhalation formulation performance using the cohesive-adhesive force balance approach.

PubMed

Hooton, Jennifer C; Jones, Matthew D; Harris, Haggis; Shur, Jagdeep; Price, Robert

2008-09-01

The aim of this investigation was to study the influence of crystalline habit of active pharmaceutical ingredients on the cohesive-adhesive force balance within model dry powder inhaler (DPI) formulations and the corresponding affect on DPI formulation performance. The cohesive-adhesive balance (CAB) approach to colloid probe atomic force microscopy (AFM) was employed to determine the cohesive and adhesive interactions of micronized budesonide particles against the {102} and {002} faces of budesonide single crystals and crystalline substrates of different sugars (cyclodextrin, lactose, trehalose, raffinose, and xylitol), respectively. These data were used to measure the relative level of cohesion and adhesion via CAB and the possible influence on in vitro performance of a carrier-based DPI formulation. Varying the crystal habit of the drug had a significant effect on the cohesive measurement of micronized budesonide probes, with the cohesive values on the {102} faces being approximately twice that on the {002} crystal faces. However, although different CAB values were measured with the sugars with respect to the crystal faces chosen for the cohesive-based measurement, the overall influence on the rank order of the CAB values was not directly influenced. For these data sets, the CAB gradient indicated that a decrease in the dominance of the adhesive forces led to a concomitant increase in fine particle delivery, reaching a plateau as the cohesive forces became dominant. The study suggested that crystal habit of the primary drug crystals influences the cohesive interactions and the resulting force balance measurements of colloid probe CAB analysis.

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

PubMed Central

2010-01-01

Background The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. Findings We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. Conclusions A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis. PMID:20565839

Fluorescent Probes for Single-Step Detection and Proteomic Profiling of Histone Deacetylases.

PubMed

Xie, Yusheng; Ge, Jingyan; Lei, Haipeng; Peng, Bo; Zhang, Huatang; Wang, Danyang; Pan, Sijun; Chen, Ganchao; Chen, Lanfang; Wang, Yi; Hao, Quan; Yao, Shao Q; Sun, Hongyan

2016-12-07

Histone deacetylases (HDACs) play important roles in regulating various physiological and pathological processes. Developing fluorescent probes capable of detecting HDAC activity can help further elucidate the roles of HDACs in biology. In this study, we first developed a set of activity-based fluorescent probes by incorporating the Kac residue and the O-NBD group. Upon enzymatic removal of the acetyl group in the Kac residue, the released free amine reacted intramolecularly with the O-NBD moiety, resulting in turn-on fluorescence. These designed probes are capable of detecting HDAC activity in a continuous fashion, thereby eliminating the extra step of fluorescence development. Remarkably, the amount of turn-on fluorescence can be as high as 50-fold, which is superior to the existing one-step HDAC fluorescent probes. Inhibition experiments further proved that the probes can serve as useful tools for screening HDAC inhibitors. Building on these results, we moved on and designed a dual-purpose fluorescent probe by introducing a diazirine photo-cross-linker into the probe. The resulting probe was not only capable of reporting enzymatic activity but also able to directly identify and capture the protein targets from the complex cellular environment. By combining a fluorometric method and in-gel fluorescence scanning technique, we found that epigenetic readers and erasers can be readily identified and differentiated using a single probe. This is not achievable with traditional photoaffinity probes. In light of the prominent properties and the diverse functions of this newly developed probe, we envision that it can provide a robust tool for functional analysis of HDACs and facilitate future drug discovery in epigenetics.

AKR1C1 as a Biomarker for Differentiating the Biological Effects of Combustible from Non-Combustible Tobacco Products.

PubMed

Woo, Sangsoon; Gao, Hong; Henderson, David; Zacharias, Wolfgang; Liu, Gang; Tran, Quynh T; Prasad, G L

2017-05-03

Smoking has been established as a major risk factor for developing oral squamous cell carcinoma (OSCC), but less attention has been paid to the effects of smokeless tobacco products. Our objective is to identify potential biomarkers to distinguish the biological effects of combustible tobacco products from those of non-combustible ones using oral cell lines. Normal human gingival epithelial cells (HGEC), non-metastatic (101A) and metastatic (101B) OSCC cell lines were exposed to different tobacco product preparations (TPPs) including cigarette smoke total particulate matter (TPM), whole-smoke conditioned media (WS-CM), smokeless tobacco extract in complete artificial saliva (STE), or nicotine (NIC) alone. We performed microarray-based gene expression profiling and found 3456 probe sets from 101A, 1432 probe sets from 101B, and 2717 probe sets from HGEC to be differentially expressed. Gene Set Enrichment Analysis (GSEA) revealed xenobiotic metabolism and steroid biosynthesis were the top two pathways that were upregulated by combustible but not by non-combustible TPPs. Notably, aldo-keto reductase genes, AKR1C1 and AKR1C2 , were the core genes in the top enriched pathways and were statistically upregulated more than eight-fold by combustible TPPs. Quantitative real time polymerase chain reaction (qRT-PCR) results statistically support AKR1C1 as a potential biomarker for differentiating the biological effects of combustible from non-combustible tobacco products.

AKR1C1 as a Biomarker for Differentiating the Biological Effects of Combustible from Non-Combustible Tobacco Products

PubMed Central

Woo, Sangsoon; Gao, Hong; Henderson, David; Zacharias, Wolfgang; Liu, Gang; Tran, Quynh T.; Prasad, G.L.

2017-01-01

Smoking has been established as a major risk factor for developing oral squamous cell carcinoma (OSCC), but less attention has been paid to the effects of smokeless tobacco products. Our objective is to identify potential biomarkers to distinguish the biological effects of combustible tobacco products from those of non-combustible ones using oral cell lines. Normal human gingival epithelial cells (HGEC), non-metastatic (101A) and metastatic (101B) OSCC cell lines were exposed to different tobacco product preparations (TPPs) including cigarette smoke total particulate matter (TPM), whole-smoke conditioned media (WS-CM), smokeless tobacco extract in complete artificial saliva (STE), or nicotine (NIC) alone. We performed microarray-based gene expression profiling and found 3456 probe sets from 101A, 1432 probe sets from 101B, and 2717 probe sets from HGEC to be differentially expressed. Gene Set Enrichment Analysis (GSEA) revealed xenobiotic metabolism and steroid biosynthesis were the top two pathways that were upregulated by combustible but not by non-combustible TPPs. Notably, aldo-keto reductase genes, AKR1C1 and AKR1C2, were the core genes in the top enriched pathways and were statistically upregulated more than eight-fold by combustible TPPs. Quantitative real time polymerase chain reaction (qRT-PCR) results statistically support AKR1C1 as a potential biomarker for differentiating the biological effects of combustible from non-combustible tobacco products. PMID:28467356

Input impedance of a probe-fed circular microstrip antenna with thick substrate

NASA Technical Reports Server (NTRS)

Davidovitz, M.; Lo, Y. T.

1986-01-01

A method of computing the input impedance for the probe fed circular microstrip antenna with thick dielectric substrate is presented. Utilizing the framework of the cavity model, the fields under the microstrip patch are expanded in a set of modes satisfying the boundary conditions on the eccentrically located probe, as well as on the cavity magnetic wall. A mode-matching technique is used to solve for the electric field at the junction between the cavity and the coaxial feed cable. The reflection coefficient of the transverse electromagnetic (TEM) mode incident in the coaxial cable is determined, from which the input impedance of the antenna is computed. Measured data are presented to verify the theoretical calculations. Results of the computation of various losses for the circular printed antenna as a function of substrate thickness are also included.

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

DOE PAGES

Cui, Yi; Hu, Dehong; Markillie, Lye Meng; ...

2017-10-04

Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes.more » This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2- 2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.« less

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

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

Cui, Yi; Hu, Dehong; Markillie, Lye Meng

Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes.more » This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2- 2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.« less

Aluminum nanostructures with strong visible-range SERS activity for versatile micropatterning of molecular security labels.

PubMed

Lay, Chee Leng; Koh, Charlynn Sher Lin; Wang, Jing; Lee, Yih Hong; Jiang, Ruibin; Yang, Yijie; Yang, Zhe; Phang, In Yee; Ling, Xing Yi

2018-01-03

The application of aluminum (Al)-based nanostructures for visible-range plasmonics, especially for surface-enhanced Raman scattering (SERS), currently suffers from inconsistent local electromagnetic field distributions and/or inhomogeneous distribution of probe molecules. Herein, we lithographically fabricate structurally uniform Al nanostructures which enable homogeneous adsorption of various probe molecules. Individual Al nanostructures exhibit strong local electromagnetic field enhancements, in turn leading to intense SERS activity. The average SERS enhancement factor (EF) for individual nanostructures exceeds 10 4 for non-resonant probe molecules in the visible spectrum. These Al nanostructures also retain more than 70% of their original SERS intensities after one-month storage, displaying superb stability under ambient conditions. We further achieve tunable polarization-dependent SERS responses using anisotropic Al nanostructures, facilitating the design of sophisticated SERS-based security labels. Our micron-sized security label comprises two-tier security features, including a machine-readable hybrid quick-response (QR) code overlaid with a set of ciphertexts. Our work demonstrates the versatility of Al-based structures in low-cost modern chemical nano-analytics and forgery protection.

Study of entry and landing probes for exploration of Titan

NASA Technical Reports Server (NTRS)

1979-01-01

Saturn's largest moon, Titan, is a totally unique planetary body which is certain to yield exciting new phenomena. Current information is lacking in detail to distinguish between a thin methane rich atmosphere and a thick nitrogen rich atmosphere. Therefore, both the thin and thick atmospheric models were used for the study of various Titan probe classes described in this report. The technical requirements, conceptual design, science return, schedule, cost and mission implications of three probe classes that could be used for exploration of Titan are defined. The three probe classes were based on a wide range of exploration mission possibilities.

Kinetic modeling of active plasma resonance spectroscopy

NASA Astrophysics Data System (ADS)

Oberrath, Jens

2016-09-01

The term ``active plasma resonance spectroscopy'' (APRS) refers to a plasma diagnostic method which employs the natural ability of plasmas to resonate close to the plasma frequency. Essential for this method is an appropriate model to determine the relation between the resonance parameters and demanded plasma parameters. Measurements with these probes in plasmas of a few Pa typically show a broadening of the spectrum that cannot be predicted by a fluid model. Thus, a kinetic model is necessary. A general kinetic model of APRS probes, which can be described in electorstatic approximation, valid for all pressures has been presented. This model is used to analyze the dynamic behavior of such probes by means of functional analytic methods. One of the main results is, that the system response function Y (ω) is given in terms of the matrix elements of the resolvent of the dynamic operator evaluated for values on the imaginary axis. The spectrum of this operator is continuous which implies a new phenomenon related to anomalous or non-collisional dissipation. Based on the scalar product, which is motivated by the kinetic free energy, the non-collisional damping can be interpreted: In a periodic state, the probe constantly emits plasma waves which propagate to ``infinity''. The free energy simply leaves the ``observation range'' of the probe which is recorded as damping. The kinetic damping, which depends on the mean kinetic energy of the electrons, is responsible for the broadening of a resonance peak in the measured spectrum of APRS probes. The ultimate goal is to determine explicit formulas for the relation between the broadening of the resonance peak and the ``equivalent electron temperature'', especially in the case of the spherical Impedance Probe and the Multipole Resonance Probe. Gratitude is expressed to the internal funding of Leuphana University, the BMBF via PluTO+, the DFG via Collaborative Research Center TR 87, and the Ruhr University Research School.

A novel suction/coagulation integrated probe for achieving better hemostasis: development and clinical use.

PubMed

Takahashi, Hidekazu; Haraguchi, Naotsugu; Nishimura, Junichi; Hata, Taishi; Matsuda, Chu; Yamamoto, Hirofumi; Mizushima, Tsunekazu; Mori, Masaki; Doki, Yuichiro; Nakajima, Kiyokazu

2018-06-01

Modern electrosurgical tools have a specific coagulation mode called "soft coagulation". However, soft coagulation has not been widely accepted for surgical operations. To optimize the soft coagulation environment, we developed a novel suction device integrated with an electrosurgical probe, called the "Suction ball coagulator" (SBC). In this study, we aimed to optimize the SBC design with a prototyping process involving a bench test and preclinical study; then, we aimed to demonstrate the feasibility, safety, and potential effectiveness of the SBC for laparoscopic surgery in clinical settings. SBC prototyping was performed with a bench test. Device optimization was performed in a preclinical study with a domestic swine bleeding model. Then, SBC was tested in a clinical setting during 17 clinical laparoscopic colorectal surgeries. In the bench tests, two tip hole sizes and patterns showed a good suction capacity. The preclinical study indicated the best tip shape for accuracy. In clinical use, no device-related adverse event was observed. Moreover, the SBC was feasible for prompt hemostasis and blunt dissections. In addition, SBC could evacuate vapors generated by tissue ablation using electroprobe during laparoscopic surgery. We successfully developed a novel, integrated suction/coagulation probe for hemostasis and commercialized it.

Gravity Probe B

NASA Image and Video Library

2003-07-11

Workers in the spacecraft processing facility on North Vandenberg Air Force Base get ready to begin processing the Gravity Probe B experiment, including setting up mechanical and electrical ground support equipment, making necessary connections and conditioning the spacecraft battery. The Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

Comparison of currents predicted by NASCAP/LEO model simulations with elementary Langmuir-type bare probe models for an insulated cable containing a single pinhole

NASA Technical Reports Server (NTRS)

Galofaro, Joel T.

1990-01-01

The behavior of a defect in the insulation of a short biased section of cable in a Low Earth Orbit (LEO) space environment was examined. Such studies are of the utmost importance for large space power systems where great quantities of cabling will be deployed. An insulated probe containing a pinhole was placed into a hypothetical high speed LEO plasma. The NASA Charging Analyzer Program (NASCAP/LEO) was used to explore sheath growth about the probe as a function of applied voltage and to predict I-V behavior. A set of independent current calculations using Langmuir's formulations for concentric spheres and coaxial cylinders were also performed. The case of concentric spheres was here extended to include the case of concentric hemispheres. Several simple Langmuir-type models were then constructed to bracket the current collected by the cable. The space-charge sheath radius and impact parameters were used to determine the proper current regime. I-V curves were plotted for the models and comparisons were made with NASCAP/LEO results. Finally, NASCAP/LEO potential contours and surface cell potential plots were examined to explain interesting features in the NASCAP/LEO I-V curve.

Shimming of a Magnet for Calibration of NMR Probes for the Muon g-2 Experiment

NASA Astrophysics Data System (ADS)

Bielajew, Rachel

2013-10-01

The Muon g-2 Experiment at Fermilab aims to measure the anomalous magnetic moment aμ ≡ (g-2)/2 of the muon to the precision of 0.14 parts per million. This experimental value of aμ can then be compared to the similarly precise theoretical predictions of the Standard Model in order to test the completeness of the model. The value of aμ is extracted from muons precessing in a magnetic field. The magnetic field will be measured with a set of 400 Nuclear Magnetic Resonance (NMR) probes, which have the ability to measure the field to a precision of tens of parts per billion. Before the Muon g-2 Experiment can take place, new NMR probes must be designed, built, and tested using a 1.45 Tesla test magnet at the University of Washington Center for Experimental Nuclear Physics and Astrophysics (CENPA). In order to achieve a significant signal from NMR probes, the magnetic field in which the probes are immersed must be extremely uniform. The existing magnet at CENPA has an approximately linear gradient in magnetic field of about 1 Gauss per centimeter in the smoothest direction. A pair of adjacent square Helmholtz coils was designed and built to create a linear gradient in order to cancel the existing gradient. The length of the NMR signals improved with the implementation of the coils. The results of the addition of the coils to the magnet on the signals from the NMR probes will be presented.

Optimum Design Rules for CMOS Hall Sensors

PubMed Central

Crescentini, Marco; Biondi, Michele; Romani, Aldo; Tartagni, Marco; Sangiorgi, Enrico

2017-01-01

This manuscript analyzes the effects of design parameters, such as aspect ratio, doping concentration and bias, on the performance of a general CMOS Hall sensor, with insight on current-related sensitivity, power consumption, and bandwidth. The article focuses on rectangular-shaped Hall probes since this is the most general geometry leading to shape-independent results. The devices are analyzed by means of 3D-TCAD simulations embedding galvanomagnetic transport model, which takes into account the Lorentz force acting on carriers due to a magnetic field. Simulation results define a set of trade-offs and design rules that can be used by electronic designers to conceive their own Hall probes. PMID:28375191

Optimum Design Rules for CMOS Hall Sensors.

PubMed

Crescentini, Marco; Biondi, Michele; Romani, Aldo; Tartagni, Marco; Sangiorgi, Enrico

2017-04-04

This manuscript analyzes the effects of design parameters, such as aspect ratio, doping concentration and bias, on the performance of a general CMOS Hall sensor, with insight on current-related sensitivity, power consumption, and bandwidth. The article focuses on rectangular-shaped Hall probes since this is the most general geometry leading to shape-independent results. The devices are analyzed by means of 3D-TCAD simulations embedding galvanomagnetic transport model, which takes into account the Lorentz force acting on carriers due to a magnetic field. Simulation results define a set of trade-offs and design rules that can be used by electronic designers to conceive their own Hall probes.

In vivo targeted peripheral nerve imaging with a nerve-specific nanoscale magnetic resonance probe.

PubMed

Zheng, Linfeng; Li, Kangan; Han, Yuedong; Wei, Wei; Zheng, Sujuan; Zhang, Guixiang

2014-11-01

Neuroimaging plays a pivotal role in clinical practice. Currently, computed tomography (CT), magnetic resonance imaging (MRI), ultrasonography, and positron emission tomography (PET) are applied in the clinical setting as neuroimaging modalities. There is no optimal imaging modality for clinical peripheral nerve imaging even though fluorescence/bioluminescence imaging has been used for preclinical studies on the nervous system. Some studies have shown that molecular and cellular MRI (MCMRI) can be used to visualize and image the cellular and molecular level of the nervous system. Other studies revealed that there are different pathological/molecular changes in the proximal and distal sites after peripheral nerve injury (PNI). Therefore, we hypothesized that in vivo peripheral nerve targets can be imaged using MCMRI with specific MRI probes. Specific probes should have higher penetrability for the blood-nerve barrier (BNB) in vivo. Here, a functional nanometre MRI probe that is based on nerve-specific proteins as targets, specifically, using a molecular antibody (mAb) fragment conjugated to iron nanoparticles as an MRI probe, was constructed for further study. The MRI probe allows for imaging the peripheral nerve targets in vivo. Copyright © 2014 Elsevier Ltd. All rights reserved.

Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting

PubMed Central

Ferguson-Smith, Malcolm A.

2018-01-01

In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus, which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds. PMID:29584697

Karyotype Evolution in Birds: From Conventional Staining to Chromosome Painting.

PubMed

Kretschmer, Rafael; Ferguson-Smith, Malcolm A; de Oliveira, Edivaldo Herculano Correa

2018-03-27

In the last few decades, there have been great efforts to reconstruct the phylogeny of Neoaves based mainly on DNA sequencing. Despite the importance of karyotype data in phylogenetic studies, especially with the advent of fluorescence in situ hybridization (FISH) techniques using different types of probes, the use of chromosomal data to clarify phylogenetic proposals is still minimal. Additionally, comparative chromosome painting in birds is restricted to a few orders, while in mammals, for example, virtually all orders have already been analyzed using this method. Most reports are based on comparisons using Gallus gallus probes, and only a small number of species have been analyzed with more informative sets of probes, such as those from Leucopternis albicollis and Gyps fulvus , which show ancestral macrochromosomes rearranged in alternative patterns. Despite this, it is appropriate to review the available cytogenetic information and possible phylogenetic conclusions. In this report, the authors gather both classical and molecular cytogenetic data and describe some interesting and unique characteristics of karyotype evolution in birds.

Public Data Set: Radially Scanning Magnetic Probes to Study Local Helicity Injection Dynamics

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

Richner, Nathan J; Bongard, Michael W; Fonck, Raymond J

This data set contains openly-documented, machine readable digital research data corresponding to figures published in N.J. Richner et al., 'Radially Scanning Magnetic Probes to Study Local Helicity Injection Dynamics,' accepted for publication in Rev. Sci. Instrum (2018).

Fluorescent diphenylphosphonate-based probes for detection of serine protease activity during inflammation.

PubMed

Edgington-Mitchell, Laura E; Barlow, Nicholas; Aurelio, Luigi; Samha, Aminath; Szabo, Monika; Graham, Bim; Bunnett, Nigel

2017-01-15

Activity-based probes are small molecules that covalently bind to the active site of a protease in an activity-dependent manner. We synthesized and characterized two fluorescent activity-based probes that target serine proteases with trypsin-like or elastase-like activity. We assessed the selectivity and potency of these probes against recombinant enzymes and demonstrated that while they are efficacious at labeling active proteases in complex protein mixtures in vitro, they are less valuable for in vivo studies. We used these probes to evaluate serine protease activity in two mouse models of acute inflammation, including pancreatitis and colitis. As anticipated, the activity of trypsin-like proteases was increased during pancreatitis. Levels of elastase-like proteases were low in pancreatic lysates and colonic luminal fluids, whether healthy or inflamed. Exogenously added recombinant neutrophil elastase was inhibited upon incubation with these samples, an effect that was augmented in inflamed samples compared to controls. These data suggest that endogenous inhibitors and elastase-degrading proteases are upregulated during inflammation. Copyright © 2016 Elsevier Ltd. All rights reserved.

A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse hybridization.

PubMed

Behr, T; Koob, C; Schedl, M; Mehlen, A; Meier, H; Knopp, D; Frahm, E; Obst, U; Schleifer, K; Niessner, R; Ludwig, W

2000-12-01

Complete 23S and almost complete 16S rRNA gene sequences were determined for the type strains of the validly described Enterococcus species, Melissococcus pluton and Tetragenococcus halophilus. A comprehensive set of rRNA targeted specific oligonucleotide hybridization probes was designed according to the multiple probe concept. In silico probe design and evaluation was performed using the respective tools of the ARB program package in combination with the ARB databases comprising the currently available 16S as well as 23S rRNA primary structures. The probes were optimized with respect to their application for reverse hybridization in microplate format. The target comprising 16S and 23S rDNA was amplified and labeled by PCR (polymerase chain reaction) using general primers targeting a wide spectrum of bacteria. Alternatively, amplification of two adjacent rDNA fragments of enterococci was performed by using specific primers. In vitro evaluation of the probe set was done including all Enterococcus type strains, and a selection of other representatives of the gram-positive bacteria with a low genomic DNA G+C content. The optimized probe set was used to analyze enriched drinking water samples as well as original samples from waste water treatment plants.

Nonlinear effects in ultrasound fields of diagnostic-type transducers used for kidney stone propulsion: Characterization in water

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

Karzova, M., E-mail: masha@acs366.phys.msu.ru; Physics Faculty, Moscow State University, Leninskie Gory, 119991 Moscow; Cunitz, B.

Newer imaging and therapeutic ultrasound technologies require higher in situ pressure levels compared to conventional diagnostic values. One example is the recently developed use of focused ultrasonic radiation force to move kidney stones and residual fragments out of the urinary collecting system. A commercial diagnostic 2.3 MHz C5-2 array probe is used to deliver the acoustic pushing pulses. The probe comprises 128 elements equally spaced at the 55 mm long convex cylindrical surface with 38 mm radius of curvature. The efficacy of the treatment can be increased by using higher intensity at the focus to provide stronger pushing force; however,more » nonlinear acoustic saturation can be a limiting factor. In this work nonlinear propagation effects were analyzed for the C5-2 transducer using a combined measurement and modeling approach. Simulations were based on the 3D Westervelt equation; the boundary condition was set to match the focal geometry of the beam as measured at a low power output. Focal waveforms simulated for increased output power levels were compared with the fiber-optic hydrophone measurements and were found in good agreement. It was shown that saturation effects do limit the acoustic pressure in the focal region of the transducer. This work has application to standard diagnostic probes and imaging.« less

Juno observes the dynamics of Jupiter's atmosphere

NASA Astrophysics Data System (ADS)

Ingersoll, Andrew P.; Juno Science Team

2017-10-01

Jupiter is a photogenic planet, but our knowledge of the deep atmosphere is limited. Remote sensing observations have traditionally probed within and above the cloud tops, which are in the 0.5-1.0 bar pressure range. Dynamical models have focused on explaining this data set. Microwave observations from Earth probe down to the 5-10 bar range, which overlaps with the predicted base of the water cloud. The Galileo probe yielded data on winds, composition, temperature gradients, clouds, radiant flux, and lightning down to 22 bars, but only at one place on the planet. Further, the traditional observations are constrained to cover low and middle latitudes. In contrast, Juno's camera and infrared radiometer, JunoCam and JIRAM, have yielded images of the poles that show cyclonic vortices in polygonal arrangements. Juno's microwave radiometer yields latitude-altitude cross sections that show dynamical features of the ammonia distribution down to 50-100 bars. And Jupiter's gravity field yields information about the winds at thousands of km depth, where the pressures are tens of kbars. In this talk I will summarize the Juno observations that pertain to the dynamics of Jupiter's atmosphere and I will offer some of my own interpretations. The new data raise as many questions as answers, but that is as it should be. As Ed Stone said during a Voyager encounter, "If we knew all the answers before we got there, we wouldn't be learning anything."

The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization

PubMed Central

2013-01-01

Background Hybridization based assays and capture systems depend on the specificity of hybridization between a probe and its intended target. A common guideline in the construction of DNA microarrays, for instance, is that avoiding complementary stretches of more than 15 nucleic acids in a 50 or 60-mer probe will eliminate sequence specific cross-hybridization reactions. Here we present a study of the behavior of partially matched oligonucleotide pairs with complementary stretches starting well below this threshold complementarity length – in silico, in solution, and at the microarray surface. The modeled behavior of pairs of oligonucleotide probes and their targets suggests that even a complementary stretch of sequence 12 nt in length would give rise to specific cross-hybridization. We designed a set of binding partners to a 50-mer oligonucleotide containing complementary stretches from 6 nt to 21 nt in length. Results Solution melting experiments demonstrate that stable partial duplexes can form when only 12 bp of complementary sequence are present; surface hybridization experiments confirm that a signal close in magnitude to full-strength signal can be obtained from hybridization of a 12 bp duplex within a 50mer oligonucleotide. Conclusions Microarray and other molecular capture strategies that rely on a 15 nt lower complementarity bound for eliminating specific cross-hybridization may not be sufficiently conservative. PMID:23445545

Peptide nucleic acid probe-based fluorescence melting curve analysis for rapid screening of common JAK2, MPL, and CALR mutations.

PubMed

Park, Joonhong; Song, Minsik; Jang, Woori; Chae, Hyojin; Lee, Gun Dong; Kim, KyungTak; Park, Heekyung; Kim, Myungshin; Kim, Yonggoo

2017-02-01

We developed and evaluated the feasibility of peptide nucleic acid (PNA)-based fluorescence melting curve analysis (FMCA) to detect common mutations in myeloproliferative neoplasms (MPNs). We have set up two separate reactions of PNA-based FMCA: JAK2 V617F &CALR p.Leu367fs*46 (set A) and MPL W515L/K &CALR p.Lys385fs*47 (set B). Clinical usefulness was validated with allele-specific real-time PCR, fragment analysis, Sanger sequencing in 57 BCR-ABL1-negative MPNs. The limit of detection (LOD) of PNA-based FMCA was approximately 10% for each mutation and interference reactions using mixtures of different mutations were not observed. Non-specific amplification was not observed in normal control. PNA-based FMCA was able to detect all JAK2 V617F (n=20), CALR p.Leu367fs*46 (n=10) and p.Lys385fs*47 (n=8). Three of six MPL mutations were detected except three samples with low mutant concentration in out of LOD. JAK2 exon 12 mutations (n=7) were negative without influencing V617F results. Among six variant CALR exon 9 mutations, two were detected by this method owing to invading of probe binding site. PNA-based FMCA for detecting common JAK2, MPL, and CALR mutations is a rapid, simple, and sensitive technique in BCR-ABL1-negative MPNs with >10% mutant allele at the time of initial diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Development of practical red fluorescent probe for cytoplasmic calcium ions with greatly improved cell-membrane permeability.

PubMed

Hirabayashi, Kazuhisa; Hanaoka, Kenjiro; Egawa, Takahiro; Kobayashi, Chiaki; Takahashi, Shodai; Komatsu, Toru; Ueno, Tasuku; Terai, Takuya; Ikegaya, Yuji; Nagano, Tetsuo; Urano, Yasuteru

2016-10-01

Fluorescence imaging of calcium ions (Ca(2+)) has become an essential technique for investigation of signaling pathways involving Ca(2+) as a second messenger. But, Ca(2+) signaling is involved in many biological phenomena, and therefore simultaneous visualization of Ca(2+) and other biomolecules (multicolor imaging) would be particularly informative. For this purpose, we set out to develop a fluorescent probe for Ca(2+) that would operate in a different color region (red) from that of probes for other molecules, many of which show green fluorescence, as exemplified by green fluorescent protein (GFP). We previously developed a red fluorescent probe for monitoring cytoplasmic Ca(2+) concentration, based on our established red fluorophore, TokyoMagenta (TM), but there remained room for improvement, especially as regards efficiency of introduction into cells. We considered that this issue was probably mainly due to limited water solubility of the probe. So, we designed and synthesized a red-fluorescent probe with improved water solubility. We confirmed that this Ca(2+) red-fluorescent probe showed high cell-membrane permeability with bright fluorescence. It was successfully applied to fluorescence imaging of not only live cells, but also brain slices, and should be practically useful for multicolor imaging studies of biological mechanisms. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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.

Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour

PubMed Central

Wynn, Michelle L.; Kulesa, Paul M.; Schnell, Santiago

2012-01-01

Follow-the-leader chain migration is a striking cell migratory behaviour observed during vertebrate development, adult neurogenesis and cancer metastasis. Although cell–cell contact and extracellular matrix (ECM) cues have been proposed to promote this phenomenon, mechanisms that underlie chain migration persistence remain unclear. Here, we developed a quantitative agent-based modelling framework to test mechanistic hypotheses of chain migration persistence. We defined chain migration and its persistence based on evidence from the highly migratory neural crest model system, where cells within a chain extend and retract filopodia in short-lived cell contacts and move together as a collective. In our agent-based simulations, we began with a set of agents arranged as a chain and systematically probed the influence of model parameters to identify factors critical to the maintenance of the chain migration pattern. We discovered that chain migration persistence requires a high degree of directional bias in both lead and follower cells towards the target. Chain migration persistence was also promoted when lead cells maintained cell contact with followers, but not vice-versa. Finally, providing a path of least resistance in the ECM was not sufficient alone to drive chain persistence. Our results indicate that chain migration persistence depends on the interplay of directional cell movement and biased cell–cell contact. PMID:22219399

Wireless network of stand-alone end effect probes for soil in situ permittivity measurements over the 100MHZ-6GHz frequency range

NASA Astrophysics Data System (ADS)

Demontoux, François; Bircher, Simone; Ruffié, Gilles; Bonnaudiin, Fabrice; Wigneron, Jean-Pierre; Kerr, Yann

2017-04-01

Microwave remote sensing and non-destructive analysis are a powerful way to provide properties estimation of materials. Numerous applications using microwave frequency behavior of materials (remote sensing above land surfaces, non-destructive analysis…) are strongly dependent on the material's permittivity (i.e. dielectric properties). This permittivity depends on numerous parameters such as moisture, texture, temperature, frequency or bulk density. Permittivity measurements are generally carried out in the laboratory. Additionally, dielectric mixing models allow, over a restricted range of conditions, the assessment of a material's permittivity. in-situ measurements are more difficult to obtain. Some in situ measurement probes based on permittivity properties of soil exist (e.g. Time Domain Reflectometers and Transmissometers, capacitance and impedance sensors). They are dedicated to the acquisition of soil moisture data based on permittivity (mainly the real part) estimations over a range of frequencies from around 50 MHz to 1 or 2 GHz. Other Dielectric Assessment Kits exist but they are expensive and they are rather dedicated to laboratory measurements. Furthermore, the user can't address specific issues related to particular materials (e.g. organic soils) or specific measurement conditions (in situ long time records). At the IMS Laboratory we develop probes for in situ soil permittivity measurements (real and imaginary parts) in the 0.5 - 6 GHz frequency range. They are based on the end effect phenomenon of a coaxial waveguide and so are called end effect probes in this paper. The probes can be connected to a portable Vector Network Analyzer (VNA, ANRITSU MS2026A) for the S11 coefficient measurements needed to compute permittivity. It is connected to a PC to record data using an USB connection. This measurement set-up is already used for in situ measurement of soil properties in the framework of the European Space Agency's (ESA) SMOS space mission. However, it should be useful to install many probes on the same site to obtain permittivity measurements over a large area. To reach this goal, the probes should communicate with each other to send data to a record device. Furthermore, it is needed to record measurements over a long time period (many months) to study the in-situ dielectric soil property variations according to changing weather conditions and seasonal trends. The goal of the research work presented is to develop a dielectric sensor system based on end effect probes able to communicate the data using wireless technology. It must be stand-alone from an electric and data recording point of view so it must integrate a VNA circuit instead of the ANRITSU VNA used for the moment. The LoRa wireless technology has been selected because of its low electric consumption and the large distance between equipment available. LoRaWAN™ is a Low Power Wide Area Network specification intended for wireless battery operated devices. The LoRaWAN data rates range from 0.3 kbps to 50 kbps which is sufficient for our probes' data exchanges. We will present the work done to perform the VNA and the LoRa communication board as well as the work done to improve the probes and the permittivity computation algorithm.

Diffraction modeling of finite subband EFC probing on dark hole contrast with WFIRST-CGI shaped pupil coronagraph

NASA Astrophysics Data System (ADS)

Zhou, Hanying; Krist, John; Nemati, Bijan

2016-08-01

Current coronagraph instrument design (CGI), as a part of a proposed NASA WFIRST (Wide-Field InfraRed Survey Telescope) mission, allocates two subband filters per full science band in order to contain system complexity and cost. We present our detailed investigation results on the adequacy of such limited number of finite subband filters in achieving full band dark hole contrast with shaped pupil coronagraph. The study is based on diffraction propagation modeling with realistic WFIRST optics, where each subband's complex field estimation is obtained, using Electric Field Conjugation (EFC) wavefront sensing / control algorithm, from pairwise pupil plane deformable mirror (DM) probing and image plane intensity averaging of the resulting fields of multiple (subband) wavelengths. Multiple subband choices and probing and control strategies are explored, including standard subband probing; mixed wavelength and/or weighted Jacobian matrix; subband probing with intensity subtraction; and extended subband probing with intensity subtraction. Overall, the investigation shows that the achievable contrast with limited number of finite subband EFC probing is about 2 2.5x worse than the designed post-EFC contrast for current SPC design. The result suggests that for future shaped pupil design, slightly larger over intended full bandwidth should be considered if it will be used with limited subbands for probing.

Validation of Afterbody Aeroheating Predictions for Planetary Probes: Status and Future Work

NASA Technical Reports Server (NTRS)

Wright, Michael J.; Brown, James L.; Sinha, Krishnendu; Candler, Graham V.; Milos, Frank S.; Prabhu, DInesh K.

2005-01-01

A review of the relevant flight conditions and physical models for planetary probe afterbody aeroheating calculations is given. Readily available sources of afterbody flight data and published attempts to computationally simulate those flights are summarized. A current status of the application of turbulence models to afterbody flows is presented. Finally, recommendations for additional analysis and testing that would reduce our uncertainties in our ability to accurately predict base heating levels are given.

Experimental validation of a theoretical model of dual wavelength photoacoustic (PA) excitation in fluorophores

NASA Astrophysics Data System (ADS)

Märk, Julia; Theiss, Christoph; Schmitt, Franz-Josef; Laufer, Jan

2015-03-01

Fluorophores, such as exogenous dyes and genetically expressed proteins, exhibit radiative relaxation with long excited state lifetimes. This can be exploited for PA detection based on dual wavelength excitation using pump and probe wavelengths that coincide with the absorption and emission spectra, respectively. While the pump pulse raises the fluorophore to a long-lived excited state, simultaneous illumination with the probe pulse reduces the excited state lifetime due to stimulated emission (SE).This leads to a change in thermalized energy, and hence PA signal amplitude, compared to single wavelength illumination. By introducing a time delay between pump and probe pulses, the change in PA amplitude can be modulated. Since the effect is not observed in endogenous chromophores, it provides a contrast mechanism for the detection of fluorophores via PA difference imaging. In this study, a theoretical model of the PA signal generation in fluorophores was developed and experimentally validated. The model is based on a system of coupled rate equations, which describe the spatial and temporal changes in the population of the molecular energy levels of a fluorophore as a function of pump-probe energy and concentration. This allows the prediction of the thermalized energy distribution, and hence the time-resolved PA signal amplitude. The model was validated by comparing its predictions to PA signals measured in solutions of rhodamine 6G, a well-known laser dye, and Atto680, a NIR fluorophore.

Attentional bias to threat in the general population is contingent on target competition, not on attentional control settings.

PubMed

Wirth, Benedikt Emanuel; Wentura, Dirk

2018-04-01

Dot-probe studies usually find an attentional bias towards threatening stimuli only in anxious participants. Here, we investigated under what conditions such a bias occurs in unselected samples. According to contingent-capture theory, an irrelevant cue only captures attention if it matches an attentional control setting. Therefore, we first tested the hypothesis that an attentional control setting tuned to threat must be activated in (non-anxious) individuals. In Experiment 1, we used a dot-probe task with a manipulation of attentional control settings ('threat' - set vs. control set). Surprisingly, we found an (anxiety-independent) attentional bias to angry faces that was not moderated by attentional control settings. Since we presented two stimuli (i.e., a target and a distractor) on the target screen in Experiment 1 (a necessity to realise the test of contingent capture), but most dot-probe studies only employ a single target, we conducted Experiment 2 to test the hypothesis that attentional bias in the general population is contingent on target competition. Participants performed a dot-probe task, involving presentation of a stand-alone target or a target competing with a distractor. We found an (anxiety-independent) attentional bias towards angry faces in the latter but not the former condition. This suggests that attentional bias towards angry faces in unselected samples is not contingent on attentional control settings but on target competition.

Analysis of non-contact and contact probe-to-sample thermal exchange for quantitative measurements of thin film and nanostructure thermal conductivity by the scanning hot probe method

NASA Astrophysics Data System (ADS)

Wilson, Adam A.

The ability to measure thermal properties of thin films and nanostructured materials is an important aspect of many fields of academic study. A strategy especially well-suited for nanoscale investigations of these properties is the scanning hot probe technique, which is unique in its ability to non-destructively interrogate the thermal properties with high resolution, both laterally as well as through the thickness of the material. Strategies to quantitatively determine sample thermal conductivity depend on probe calibration. State of the art calibration strategies assume that the area of thermal exchange between probe and sample does not vary with sample thermal conductivity. However, little investigation has gone into determining whether or not that assumption is valid. This dissertation provides a rigorous study into the probe-to-sample heat transfer through the air gap at diffusive distances for a variety of values of sample thermal conductivity. It is demonstrated that the thermal exchange radius and gap/contact thermal resistance varies with sample thermal conductivity as well as tip-to-sample clearance in non-contact mode. In contact mode, it is demonstrated that higher thermal conductivity samples lead to a reduction in thermal exchange radius for Wollaston probe tips. Conversely, in non-contact mode and in contact mode for sharper probe tips where air contributes the most to probe-to-sample heat transfer, the opposite trend occurs. This may be attributed to the relatively strong solid-to-solid conduction occurring between probe and sample for the Wollaston probes. A three-dimensional finite element (3DFE) model was developed to investigate how the calibrated thermal exchange parameters vary with sample thermal conductivity when calibrating the probe via the intersection method in non-contact mode at diffusive distances. The 3DFE model was then used to explore the limits of sensitivity of the experiment for a range of simulated experimental conditions. It is determined that, when operating the scanning hot probe technique in air at standard temperature and pressure using Wollaston probes, the technique is capable of measuring, within 20% uncertainty, samples with values of thermal conductivity up to 10 Wm-1K-1 in contact mode and up to 2 Wm-1K-1 in non-contact mode. By increasing the thermal conductivity of the probe's surroundings (i.e. changing air to a more conductive gas), sensitivity in non-contact mode to sample thermal conductivity is improved, which suggests potential for future investigations using non-contact scanning hot probe to measure thermal conductivity of higher thermal conductivity samples. The ability of the technique to differentiate thin films from the substrate is investigated, and the sensitivity of the technique to thin films and samples with anisotropic properties is explored. The models (both analytical and finite element) developed and reported in this dissertation lead to the ability to measure samples which, by the standard procedure before this work, were unable to be accurately measured. While other techniques failed to be able to successfully interrogate the film thermal conductivity of a full set of double-wall carbon nanotubes infused into polymers, the methods developed in this work allowed non-contact scanning hot probe measurements to be successfully performed to obtain the film thermal conductivity for each sample. Finite element simulations accounting for the anisotropy of these thin film on sample materials show similar trends with independently measured in-plane thermal conductivity for the only two (of five) samples in the set which were successfully able to be measured by the independent technique. Investigations in contact mode with high resolution Pd probes, whose probe-to-sample clearance is difficult to control in a repeatable fashion, show that surface roughness affects the thermal contact resistance. This can lead to values of reported sample thermal conductivity which are misleading, when using the standard calibrated thermal exchange parameters on samples with significantly different surface roughness than the calibration samples. This affect was taken into account to report sample thermal conductivity of Bi2Te3 nanoflakes.

Modeling flow for modified concentric cylinder rheometer geometry

NASA Astrophysics Data System (ADS)

Ekeruche, Karen; Connelly, Kelly; Kavehpour, H. Pirouz

2016-11-01

Rheology experiments on biological fluids can be difficult when samples are limited in volume, sensitive to degradation, and delicate to extract from tissues. A probe-like geometry has been developed to perform shear creep experiments on biological fluids and to use the creep response to characterize fluid material properties. This probe geometry is a modified concentric cylinder setup, where the gap is large and we assume the inner cylinder rotates in an infinite fluid. To validate this assumption we perform shear creep tests with the designed probe on Newtonian and non-Newtonian fluids and vary the outer cylinder container diameter. We have also created a numerical model based on the probe geometry setup to compare with experimental results at different outer cylinder diameters. A creep test is modeled by applying rotation to the inner cylinder and solving for the deformation of the fluid throughout the gap. Steady state viscosity values are calculated from creep compliance curves and compared between experimental and numerical results.

Multispectral Photoacoustic Imaging of Tumor Protease Activity with a Gold Nanocage-Based Activatable Probe.

PubMed

Liu, Cheng; Li, Shiying; Gu, Yanjuan; Xiong, Huahua; Wong, Wing-Tak; Sun, Lei

2018-05-07

Tumor proteases have been recognized as significant regulators in the tumor microenvironment, but the current strategies for in vivo protease imaging have tended to focus on the development of a probe design rather than the investigation of a novel imaging strategy by leveraging the imaging technique and probe. Herein, it is the first report to investigate the ability of multispectral photoacoustic imaging (PAI) to estimate the distribution of protease cleavage sites inside living tumor tissue by using an activatable photoacoustic (PA) probe. The protease MMP-2 is selected as the target. In this probe, gold nanocages (GNCs) with an absorption peak at ~ 800 nm and fluorescent dye molecules with an absorption peak at ~ 680 nm are conjugated via a specific enzymatic peptide substrate. Upon enzymatic activation by MMP-2, the peptide substrate is cleaved and the chromophores are released. Due to the different retention speeds of large GNCs and small dye molecules, the probe alters its intrinsic absorption profile and produces a distinct change in the PA signal. A multispectral PAI technique that can distinguish different chromophores based on intrinsic PA spectral signatures is applied to estimate the signal composition changes and indicate the cleavage interaction sites. Finally, the multispectral PAI technique with the activatable probe is tested in solution, cultured cells, and a subcutaneous tumor model in vivo. Our experiment in solution with enzyme ± inhibitor, cell culture ± inhibitor, and in vivo tumor model with administration of the developed probe ± inhibitor demonstrated the probe was cleaved by the targeted enzyme. Particularly, the in vivo estimation of the cleavage site distribution was validated with the result of ex vivo immunohistochemistry analysis. This novel synergy of the multispectral PAI technique and the activatable probe is a potential strategy for the distribution estimation of tumor protease activity in vivo.

Tides and tidal stress: Applications to Europa

NASA Astrophysics Data System (ADS)

Hurford, Terry Anthony, Jr.

A review of analytical techniques and documentation of previously inaccessible mathematical formulations is applied to study of Jupiter's satellite Europa. Compared with numerical codes that are commonly used to model global tidal effects, analytical models of tidal deformation give deeper insight into the mechanics of tides, and can better reveal the nature of the dependence of observable effects on key parameters. I develop analytical models for tidal deformation of multi-layered bodies. Previous studies of Europa, based on numerical computation, only to show isolated examples from parameter space. My results show a systematic dependence of tidal response on the thicknesses and material parameters of Europa's core, rocky mantle, liquid water ocean, and outer layer of ice. As in the earlier work, I restrict these studies to incompressible materials. Any set of Love numbers h 2 and k 2 which describe a planet's tidal deformation, could be fit by a range of ice thickness values, by adjusting other parameters such as mantle rigidity or core size, an important result for mission planning. Inclusion of compression into multilayer models has been addressed analytically, uncovering several issues that are not explicit in the literature. Full evaluation with compression is here restricted to a uniform sphere. A set of singularities in the classical solution, which correspond to instabilities due to self-gravity has been identified and mapped in parameter space. The analytical models of tidal response yield the stresses anywhere within the body, including on its surface. Crack patterns (such as cycloids) on Europa are probably controlled by these stresses. However, in contrast to previous studies which used a thin shell approximation of the tidal stress, I consider how other tidal models compare with the observed tectonic features. In this way the relationship between Europa's surface tectonics and the global tidal distortion can be constrained. While large-scale tidal deformations probe internal structure deep within a body, small-scale deformations can probe internal structure at shallower depths. I have used photoclinometry to obtain topographic profiles across terrain adjacent to Europan ridges to detect the effects of loading on the lithosphere. Lithospheric thicknesses have been determined and correlated with types and ages of terrain.

Shock probes in a one-dimensional Katz-Lebowitz-Spohn model

NASA Astrophysics Data System (ADS)

Chatterjee, Sakuntala; Barma, Mustansir

2008-06-01

We consider shock probes in a one-dimensional driven diffusive medium with nearest-neighbor Ising interaction (KLS model). Earlier studies based on an approximate mapping of the present system to an effective zero-range process concluded that the exponents characterizing the decays of several static and dynamical correlation functions of the probes depend continuously on the strength of the Ising interaction. On the contrary, our numerical simulations indicate that over a substantial range of the interaction strength, these exponents remain constant and their values are the same as in the case of no interaction (when the medium executes an ASEP). We demonstrate this by numerical studies of several dynamical correlation functions for two probes and also for a macroscopic number of probes. Our results are consistent with the expectation that the short-ranged correlations induced by the Ising interaction should not affect the large time and large distance properties of the system, implying that scaling forms remain the same as in the medium with no interactions present.

Probing eukaryotic cell mechanics via mesoscopic simulations

NASA Astrophysics Data System (ADS)

Pivkin, Igor V.; Lykov, Kirill; Nematbakhsh, Yasaman; Shang, Menglin; Lim, Chwee Teck

2017-11-01

We developed a new mesoscopic particle based eukaryotic cell model which takes into account cell membrane, cytoskeleton and nucleus. The breast epithelial cells were used in our studies. To estimate the viscoelastic properties of cells and to calibrate the computational model, we performed micropipette aspiration experiments. The model was then validated using data from microfluidic experiments. Using the validated model, we probed contributions of sub-cellular components to whole cell mechanics in micropipette aspiration and microfluidics experiments. We believe that the new model will allow to study in silico numerous problems in the context of cell biomechanics in flows in complex domains, such as capillary networks and microfluidic devices.

Density Waves in Saturn's Rings from Cassini Radio Occultations

NASA Astrophysics Data System (ADS)

French, R. G.; Rappaport, N. J.; Marouf, E. A.; McGhee, C. A.

2005-12-01

The Cassini Radio Science Team conducted a set of optimized diametric occultations by Saturn and its rings from May to September 2005, providing 11 separate probes of Saturn's ionosphere and atmosphere, and 12 optical depth profiles of the complete ring system. Each event was observed by the stations of the Deep Space Net (DSN) at three radio frequencies (S, X, Ka bands, with corresponding wavelengths of ? = 13, 3.6, and 0.9 cm). Very accurate pointing by the spacecraft and ground antennas resulted in stable baseline signal levels, and the relatively large ring opening angle (B=19-25°) permitted us to probe even quite dense ring regions with excellent SNR. The RSS occultation technique enables us to recover very fine detailed radial structure by correcting for diffraction effects. Multiple occultation chords, covering a variety of ring longitudes and ring opening angles, reveal the structure of the rings in remarkable detail, including density and bending waves, satellite wakes, and subtle variations at the 100-m radius scale. Janus and Epimetheus are responsible for a particularly rich set of density waves, and their coorbital interactions result in a complex interplay of time-variable ring structure over the 8-year libration period of the two satellites. We compare the first-order 2:1, 4:3, 5:4, and 6:5 coorbital density waves from multiple occultation chords to linear density wave models based on a dynamical model of the orbital exchange between the moons. From the observed dispersion relation of the wave crests, we infer the surface mass density and eccentricity gradient of particle streamlines, and match the detailed shapes of the wave crests using a non-linear analysis. Second-order coorbital features are also evident, and there are even hints of third-order density waves in the high SNR radio occultation data.

Investigating the neural bases for intra-subject cognitive efficiency changes using functional magnetic resonance imaging

PubMed Central

Rao, Neena K.; Motes, Michael A.; Rypma, Bart

2014-01-01

Several fMRI studies have examined brain regions mediating inter-subject variability in cognitive efficiency, but none have examined regions mediating intra-subject variability in efficiency. Thus, the present study was designed to identify brain regions involved in intra-subject variability in cognitive efficiency via participant-level correlations between trial-level reaction time (RT) and trial-level fMRI BOLD percent signal change on a processing speed task. On each trial, participants indicated whether a digit-symbol probe-pair was present or absent in an array of nine digit-symbol probe-pairs while fMRI data were collected. Deconvolution analyses, using RT time-series models (derived from the proportional scaling of an event-related hemodynamic response function model by trial-level RT), were used to evaluate relationships between trial-level RTs and BOLD percent signal change. Although task-related patterns of activation and deactivation were observed in regions including bilateral occipital, bilateral parietal, portions of the medial wall such as the precuneus, default mode network regions including anterior cingulate, posterior cingulate, bilateral temporal, right cerebellum, and right cuneus, RT-BOLD correlations were observed in a more circumscribed set of regions. Positive RT-BOLD correlations, where fast RTs were associated with lower BOLD percent signal change, were observed in regions including bilateral occipital, bilateral parietal, and the precuneus. RT-BOLD correlations were not observed in the default mode network indicating a smaller set of regions associated with intra-subject variability in cognitive efficiency. The results are discussed in terms of a distributed area of regions that mediate variability in the cognitive efficiency that might underlie processing speed differences between individuals. PMID:25374527

Investigating the neural bases for intra-subject cognitive efficiency changes using functional magnetic resonance imaging.

PubMed

Rao, Neena K; Motes, Michael A; Rypma, Bart

2014-01-01

Several fMRI studies have examined brain regions mediating inter-subject variability in cognitive efficiency, but none have examined regions mediating intra-subject variability in efficiency. Thus, the present study was designed to identify brain regions involved in intra-subject variability in cognitive efficiency via participant-level correlations between trial-level reaction time (RT) and trial-level fMRI BOLD percent signal change on a processing speed task. On each trial, participants indicated whether a digit-symbol probe-pair was present or absent in an array of nine digit-symbol probe-pairs while fMRI data were collected. Deconvolution analyses, using RT time-series models (derived from the proportional scaling of an event-related hemodynamic response function model by trial-level RT), were used to evaluate relationships between trial-level RTs and BOLD percent signal change. Although task-related patterns of activation and deactivation were observed in regions including bilateral occipital, bilateral parietal, portions of the medial wall such as the precuneus, default mode network regions including anterior cingulate, posterior cingulate, bilateral temporal, right cerebellum, and right cuneus, RT-BOLD correlations were observed in a more circumscribed set of regions. Positive RT-BOLD correlations, where fast RTs were associated with lower BOLD percent signal change, were observed in regions including bilateral occipital, bilateral parietal, and the precuneus. RT-BOLD correlations were not observed in the default mode network indicating a smaller set of regions associated with intra-subject variability in cognitive efficiency. The results are discussed in terms of a distributed area of regions that mediate variability in the cognitive efficiency that might underlie processing speed differences between individuals.

Speeded Probed Recall Is Affected by Grouping.

PubMed

Morra, Sergio; Epidendio, Valentina

2015-01-01

Most of the evidence from previous studies on speeded probed recall supported primacy-gradient models of serial order representation. Two experiments investigated the effect of grouping on speeded probed recall. Six-word lists, followed by a number between 1 and 6, were presented for speeded recall of the word in the position indicated by the number. Grouping was manipulated through interstimulus intervals. In both experiments, a significant Position × Grouping interaction was found in RT. It is concluded that the results are not consistent with models of order representation only based on a primacy gradient. Possible alternative representations of serial order are also discussed; a case is made for a holistic order representation.

Electron temperature and heat load measurements in the COMPASS divertor using the new system of probes

NASA Astrophysics Data System (ADS)

Adamek, J.; Seidl, J.; Horacek, J.; Komm, M.; Eich, T.; Panek, R.; Cavalier, J.; Devitre, A.; Peterka, M.; Vondracek, P.; Stöckel, J.; Sestak, D.; Grover, O.; Bilkova, P.; Böhm, P.; Varju, J.; Havranek, A.; Weinzettl, V.; Lovell, J.; Dimitrova, M.; Mitosinkova, K.; Dejarnac, R.; Hron, M.; The COMPASS Team; The EUROfusion MST1 Team

2017-11-01

A new system of probes was recently installed in the divertor of tokamak COMPASS in order to investigate the ELM energy density with high spatial and temporal resolution. The new system consists of two arrays of rooftop-shaped Langmuir probes (LPs) used to measure the floating potential or the ion saturation current density and one array of Ball-pen probes (BPPs) used to measure the plasma potential with a spatial resolution of ~3.5 mm. The combination of floating BPPs and LPs yields the electron temperature with microsecond temporal resolution. We report on the design of the new divertor probe arrays and first results of electron temperature profile measurements in ELMy H-mode and L-mode. We also present comparative measurements of the parallel heat flux using the new probe arrays and fast infrared termography (IR) data during L-mode with excellent agreement between both techniques using a heat power transmission coefficient γ  =  7. The ELM energy density {{\\varepsilon }\\parallel } was measured during a set of NBI assisted ELMy H-mode discharges. The peak values of {{\\varepsilon }\\parallel } were compared with those predicted by model and with experimental data from JET, AUG and MAST with a good agreement.

Universal Oligonucleotide Microarray for Sub-Typing of Influenza A Virus

PubMed Central

Ryabinin, Vladimir A.; Kostina, Elena V.; Maksakova, Galiya A.; Neverov, Alexander A.; Chumakov, Konstantin M.; Sinyakov, Alexander N.

2011-01-01

A universal microchip was developed for genotyping Influenza A viruses. It contains two sets of oligonucleotide probes allowing viruses to be classified by the subtypes of hemagglutinin (H1–H13, H15, H16) and neuraminidase (N1–N9). Additional sets of probes are used to detect H1N1 swine influenza viruses. Selection of probes was done in two steps. Initially, amino acid sequences specific to each subtype were identified, and then the most specific and representative oligonucleotide probes were selected. Overall, between 19 and 24 probes were used to identify each subtype of hemagglutinin (HA) and neuraminidase (NA). Genotyping included preparation of fluorescently labeled PCR amplicons of influenza virus cDNA and their hybridization to microarrays of specific oligonucleotide probes. Out of 40 samples tested, 36 unambiguously identified HA and NA subtypes of Influenza A virus. PMID:21559081

ISS Plasma Interaction: Measurements and Modeling

NASA Technical Reports Server (NTRS)

Barsamian, H.; Mikatarian, R.; Alred, J.; Minow, J.; Koontz, S.

2004-01-01

Ionospheric plasma interaction effects on the International Space Station are discussed in the following paper. The large structure and high voltage arrays of the ISS represent a complex system interacting with LEO plasma. Discharge current measurements made by the Plasma Contactor Units and potential measurements made by the Floating Potential Probe delineate charging and magnetic induction effects on the ISS. Based on theoretical and physical understanding of the interaction phenomena, a model of ISS plasma interaction has been developed. The model includes magnetic induction effects, interaction of the high voltage solar arrays with ionospheric plasma, and accounts for other conductive areas on the ISS. Based on these phenomena, the Plasma Interaction Model has been developed. Limited verification of the model has been performed by comparison of Floating Potential Probe measurement data to simulations. The ISS plasma interaction model will be further tested and verified as measurements from the Floating Potential Measurement Unit become available, and construction of the ISS continues.

Magnetic monopole search with the MoEDAL test trapping detector

NASA Astrophysics Data System (ADS)

Katre, Akshay

2016-11-01

IMoEDAL is designed to search for monopoles produced in high-energy Large Hadron Collider (LHC) collisions, based on two complementary techniques: nucleartrack detectors for high-ionisation signatures and other highly ionising avatars of new physics, and trapping volumes for direct magnetic charge measurements with a superconducting magnetometer. The MoEDAL test trapping detector array deployed in 2012, consisting of over 600 aluminium samples, was analysed and found to be consistent with zero trapped magnetic charge. Stopping acceptances are obtained from a simulation of monopole propagation in matter for a range of charges and masses, allowing to set modelindependent and model-dependent limits on monopole production cross sections. Multiples of the fundamental Dirac magnetic charge are probed for the first time at the LHC.

Evaluation of a CdTe semiconductor based compact γ camera for sentinel lymph node imaging.

PubMed

Russo, Paolo; Curion, Assunta S; Mettivier, Giovanni; Esposito, Michela; Aurilio, Michela; Caracò, Corradina; Aloj, Luigi; Lastoria, Secondo

2011-03-01

The authors assembled a prototype compact gamma-ray imaging probe (MediPROBE) for sentinel lymph node (SLN) localization. This probe is based on a semiconductor pixel detector. Its basic performance was assessed in the laboratory and clinically in comparison with a conventional gamma camera. The room-temperature CdTe pixel detector (1 mm thick) has 256 x 256 square pixels arranged with a 55 microm pitch (sensitive area 14.08 x 14.08 mm2), coupled pixel-by-pixel via bump-bonding to the Medipix2 photon-counting readout CMOS integrated circuit. The imaging probe is equipped with a set of three interchangeable knife-edge pinhole collimators (0.94, 1.2, or 2.1 mm effective diameter at 140 keV) and its focal distance can be regulated in order to set a given field of view (FOV). A typical FOV of 70 mm at 50 mm skin-to-collimator distance corresponds to a minification factor 1:5. The detector is operated at a single low-energy threshold of about 20 keV. For 99 mTc, at 50 mm distance, a background-subtracted sensitivity of 6.5 x 10(-3) cps/kBq and a system spatial resolution of 5.5 mm FWHM were obtained for the 0.94 mm pinhole; corresponding values for the 2.1 mm pinhole were 3.3 x 10(-2) cps/kBq and 12.6 mm. The dark count rate was 0.71 cps. Clinical images in three patients with melanoma indicate detection of the SLNs with acquisition times between 60 and 410 s with an injected activity of 26 MBq 99 mTc and prior localization with standard gamma camera lymphoscintigraphy. The laboratory performance of this imaging probe is limited by the pinhole collimator performance and the necessity of working in minification due to the limited detector size. However, in clinical operative conditions, the CdTe imaging probe was effective in detecting SLNs with adequate resolution and an acceptable sensitivity. Sensitivity is expected to improve with the future availability of a larger CdTe detector permitting operation at shorter distances from the patient skin.

On the Tuning of High-Resolution NMR Probes

PubMed Central

Pöschko, Maria Theresia; Schlagnitweit, Judith; Huber, Gaspard; Nausner, Martin; Horničáková, Michaela; Desvaux, Hervé; Müller, Norbert

2014-01-01

Three optimum conditions for the tuning of NMR probes are compared: the conventional tuning optimum, which is based on radio-frequency pulse efficiency, the spin noise tuning optimum based on the line shape of the spin noise signal, and the newly introduced frequency shift tuning optimum, which minimizes the frequency pushing effect on strong signals. The latter results if the radiation damping feedback field is not in perfect quadrature to the precessing magnetization. According to the conventional RLC (resistor–inductor–capacitor) resonant circuit model, the optima should be identical, but significant deviations are found experimentally at low temperatures, in particular on cryogenically cooled probes. The existence of different optima with respect to frequency pushing and spin noise line shape has important consequences on the nonlinearity of spin dynamics at high polarization levels and the implementation of experiments on cold probes. PMID:25210000

Portable LED-induced autofluorescence imager with a probe of L shape for oral cancer diagnosis

NASA Astrophysics Data System (ADS)

Huang, Ting-Wei; Lee, Yu-Cheng; Cheng, Nai-Lun; Yan, Yung-Jhe; Chiang, Hou-Chi; Chiou, Jin-Chern; Mang, Ou-Yang

2015-08-01

The difference of spectral distribution between lesions of epithelial cells and normal cells after excited fluorescence is one of methods for the cancer diagnosis. In our previous work, we developed a portable LED Induced autofluorescence (LIAF) imager contained the multiple wavelength of LED excitation light and multiple filters to capture ex-vivo oral tissue autofluorescence images. Our portable system for detection of oral cancer has a probe in front of the lens for fixing the object distance. The shape of the probe is cone, and it is not convenient for doctor to capture the oral image under an appropriate view angle in front of the probe. Therefore, a probe of L shape containing a mirror is proposed for doctors to capture the images with the right angles, and the subjects do not need to open their mouse constrainedly. Besides, a glass plate is placed in probe to prevent the liquid entering in the body, but the light reflected from the glass plate directly causes the light spots inside the images. We set the glass plate in front of LED to avoiding the light spots. When the distance between the glasses plate and the LED model plane is less than the critical value, then we can prevent the light spots caused from the glasses plate. The experiments show that the image captured with the new probe that the glasses plate placed in the back-end of the probe has no light spots inside the image.

Molecular Inversion Probe Analysis of Gene Copy Alterations Reveals Distinct Categories of Colorectal Carcinoma

PubMed Central

Ji, Hanlee; Kumm, Jochen; Zhang, Michael; Farnam, Kyle; Salari, Keyan; Faham, Malek; Ford, James M.; Davis, Ronald W.

2006-01-01

Genomic instability is a major feature of neoplastic development in colorectal carcinoma and other cancers. Specific genomic instability events, such as deletions in chromosomes and other alterations in gene copy number, have potential utility as biologically relevant prognostic biomarkers. For example, genomic deletions on chromosome arm 18q are an indicator of colorectal carcinoma behavior and potentially useful as a prognostic indicator. Adapting a novel genomic technology called molecular inversion probes which can determine gene copy alterations, such as genomic deletions, we designed a set of probes to interrogate several hundred individual exons of >200 cancer genes with an overall distribution covering all chromosome arms. In addition, >100 probes were designed in close proximity of microsatellite markers on chromosome arm 18q. We analyzed a set of colorectal carcinoma cell lines and primary colorectal tumor samples for gene copy alterations and deletion mutations in exons. Based on clustering analysis, we distinguished the different categories of genomic instability among the colorectal cancer cell lines. Our analysis of primary tumors uncovered several distinct categories of colorectal carcinoma, each with specific patterns of 18q deletions and deletion mutations in specific genes. This finding has potential clinical ramifications given the application of 18q loss of heterozygosity events as a potential indicator for adjuvant treatment in stage II colorectal carcinoma. PMID:16912164

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

Shi, Zhemin; Department of Physical Electronics, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552; Taguchi, Dai

The details of turnover process of spontaneous polarization and associated carrier motions in indium-tin oxide/poly-(vinylidene-trifluoroethylene)/pentacene/Au capacitor were analyzed by coupling displacement current measurement (DCM) and electric-field-induced optical second-harmonic generation (EFISHG) measurement. A model was set up from DCM results to depict the relationship between electric field in semiconductor layer and applied external voltage, proving that photo illumination effect on the spontaneous polarization process lied in variation of semiconductor conductivity. The EFISHG measurement directly and selectively probed the electric field distribution in semiconductor layer, modifying the model and revealing detailed carrier behaviors involving photo illumination effect, dipole reversal, and interfacial chargingmore » in the device. A further decrease of DCM current in the low voltage region under illumination was found as the result of illumination effect, and the result was argued based on the changing of the total capacitance of the double-layer capacitors.« less

Estimating Genomic Distance from DNA Sequence Location in Cell Nuclei by a Random Walk Model

NASA Astrophysics Data System (ADS)

van den Engh, Ger; Sachs, Rainer; Trask, Barbara J.

1992-09-01

The folding of chromatin in interphase cell nuclei was studied by fluorescent in situ hybridization with pairs of unique DNA sequence probes. The sites of DNA sequences separated by 100 to 2000 kilobase pairs (kbp) are distributed in interphase chromatin according to a random walk model. This model provides the basis for calculating the spacing of sequences along the linear DNA molecule from interphase distance measurements. An interphase mapping strategy based on this model was tested with 13 probes from a 4-megabase pair (Mbp) region of chromosome 4 containing the Huntington disease locus. The results confirmed the locations of the probes and showed that the remaining gap in the published maps of this region is negligible in size. Interphase distance measurements should facilitate construction of chromosome maps with an average marker density of one per 100 kbp, approximately ten times greater than that achieved by hybridization to metaphase chromosomes.

Quantitative validation of an air-coupled ultrasonic probe model by Interferometric laser tomography

NASA Astrophysics Data System (ADS)

Revel, G. M.; Pandarese, G.; Cavuto, A.

2012-06-01

The present paper describes the quantitative validation of a finite element (FE) model of the ultrasound beam generated by an air coupled non-contact ultrasound transducer. The model boundary conditions are given by vibration velocities measured by laser vibrometry on the probe membrane. The proposed validation method is based on the comparison between the simulated 3D pressure field and the pressure data measured with interferometric laser tomography technique. The model details and the experimental techniques are described in paper. The analysis of results shows the effectiveness of the proposed approach and the possibility to quantitatively assess and predict the generated acoustic pressure field, with maximum discrepancies in the order of 20% due to uncertainty effects. This step is important for determining in complex problems the real applicability of air-coupled probes and for the simulation of the whole inspection procedure, also when the component is designed, so as to virtually verify its inspectability.

Difference in thermodynamics between two types of esophageal temperature probes: Insights from an experimental study.

PubMed

Gianni, Carola; Atoui, Moustapha; Mohanty, Sanghamitra; Trivedi, Chintan; Bai, Rong; Al-Ahmad, Amin; Burkhardt, J David; Gallinghouse, G Joseph; Hranitzky, Patrick M; Horton, Rodney P; Sanchez, Javier E; Di Biase, Luigi; Lakkireddy, Dhanunjaya R; Natale, Andrea

2016-11-01

Luminal esophageal temperature monitoring is performed with a variety of temperature probes, but little is known about the relationship between the structure of a given probe and its thermodynamic characteristics. The purpose of this study was to evaluate the difference in thermodynamics between a 9Fr standard esophageal probe and an 18Fr esophageal stethoscope. In the experimental setting, each probe was submerged in a constant temperature water bath maintained at 42°C; in the patient setting, we monitored the temperature with both probes at the same time. The time constant of the stethoscope was higher than that of the probe (33.5 vs 8.3 s). Compared to the probe, the mean temperature measured by the stethoscope at 10 seconds was significantly lower (22.5°C ± 0.4°C vs 33.5°C ± 0.3°C, P<.0001), whereas the time to reach the peak temperature was significantly longer (132.6 ± 5.9 s vs 38.8 ± 1.0 s, P<.0001). Even in the ablation cases we observed that when the esophageal probe reached a peak temperature of 39.6°C ± 0.3°C, the esophageal stethoscope still displayed a temperature of 37.3°C ± 0.2°C (a mean of 2.39°C ± 0.3°C lower, P<.0001), showing a <0.5°C increase in temperature half of the times. The 18Fr esophageal stethoscope has a significantly slower time response compared to the 9Fr esophageal probe. In the clinical setting, this might result in a considerable underestimation of the luminal esophageal temperature with potentially fatal consequences. Copyright © 2016 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Patterns of Limnohabitans Microdiversity across a Large Set of Freshwater Habitats as Revealed by Reverse Line Blot Hybridization

PubMed Central

Jezbera, Jan; Jezberová, Jitka; Kasalický, Vojtěch; Šimek, Karel; Hahn, Martin W.

2013-01-01

Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization) probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S–23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus) patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of these bacteria. Instead, our observations suggest that the genus Limnohabitans, as well as its R-BT subgroup, represent ecologically heterogeneous taxa, which underwent pronounced ecological diversification. PMID:23554898

A magnetic nanobead-based bioassay provides sensitive detection of single- and biplex bacterial DNA using a portable AC susceptometer

PubMed Central

Strömberg, Mattias; Zardán Gómez de la Torre, Teresa; Nilsson, Mats; Svedlindh, Peter; Strømme, Maria

2014-01-01

Bioassays relying on magnetic read-out using probe-tagged magnetic nanobeads are potential platforms for low-cost biodiagnostic devices for pathogen detection. For optimal assay performance it is crucial to apply an easy, efficient and robust bead-probe conjugation protocol. In this paper, sensitive (1.5 pM) singleplex detection of bacterial DNA sequences is demonstrated in a portable AC susceptometer by a magnetic nanobead-based bioassay principle; the volume-amplified magnetic nanobead detection assay (VAM-NDA). Two bead sizes, 100 and 250 nm, are investigated along with a highly efficient, rapid, robust, and stable conjugation chemistry relying on the avidin–biotin interaction for bead-probe attachment. Avidin-biotin conjugation gives easy control of the number of detection probes per bead; thus allowing for systematic investigation of the impact of varying the detection probe surface coverage upon bead immobilization in rolling circle amplified DNA-coils. The existence of an optimal surface coverage is discussed. Biplex VAM-NDA detection is for the first time demonstrated in the susceptometer: Semi-quantitative results are obtained and it is concluded that the concentration of DNA-coils in the incubation volume is of crucial importance for target quantification. The present findings bring the development of commercial biodiagnostic devices relying on the VAM–NDA further towards implementation in point-of-care and outpatient settings. PMID:24174315

Group normalization for genomic data.

PubMed

Ghandi, Mahmoud; Beer, Michael A

2012-01-01

Data normalization is a crucial preliminary step in analyzing genomic datasets. The goal of normalization is to remove global variation to make readings across different experiments comparable. In addition, most genomic loci have non-uniform sensitivity to any given assay because of variation in local sequence properties. In microarray experiments, this non-uniform sensitivity is due to different DNA hybridization and cross-hybridization efficiencies, known as the probe effect. In this paper we introduce a new scheme, called Group Normalization (GN), to remove both global and local biases in one integrated step, whereby we determine the normalized probe signal by finding a set of reference probes with similar responses. Compared to conventional normalization methods such as Quantile normalization and physically motivated probe effect models, our proposed method is general in the sense that it does not require the assumption that the underlying signal distribution be identical for the treatment and control, and is flexible enough to correct for nonlinear and higher order probe effects. The Group Normalization algorithm is computationally efficient and easy to implement. We also describe a variant of the Group Normalization algorithm, called Cross Normalization, which efficiently amplifies biologically relevant differences between any two genomic datasets.

Group Normalization for Genomic Data

PubMed Central

Ghandi, Mahmoud; Beer, Michael A.

2012-01-01

Data normalization is a crucial preliminary step in analyzing genomic datasets. The goal of normalization is to remove global variation to make readings across different experiments comparable. In addition, most genomic loci have non-uniform sensitivity to any given assay because of variation in local sequence properties. In microarray experiments, this non-uniform sensitivity is due to different DNA hybridization and cross-hybridization efficiencies, known as the probe effect. In this paper we introduce a new scheme, called Group Normalization (GN), to remove both global and local biases in one integrated step, whereby we determine the normalized probe signal by finding a set of reference probes with similar responses. Compared to conventional normalization methods such as Quantile normalization and physically motivated probe effect models, our proposed method is general in the sense that it does not require the assumption that the underlying signal distribution be identical for the treatment and control, and is flexible enough to correct for nonlinear and higher order probe effects. The Group Normalization algorithm is computationally efficient and easy to implement. We also describe a variant of the Group Normalization algorithm, called Cross Normalization, which efficiently amplifies biologically relevant differences between any two genomic datasets. PMID:22912661

Huygens Titan Probe Trajectory Reconstruction Using Traditional Methods and the Program to Optimize Simulated Trajectories II

NASA Technical Reports Server (NTRS)

Striepe, Scott A.; Blanchard, Robert C.; Kirsch, Michael F.; Fowler, Wallace T.

2007-01-01

On January 14, 2005, ESA's Huygens probe separated from NASA's Cassini spacecraft, entered the Titan atmosphere and landed on its surface. As part of NASA Engineering Safety Center Independent Technical Assessment of the Huygens entry, descent, and landing, and an agreement with ESA, NASA provided results of all EDL analyses and associated findings to the Huygens project team prior to probe entry. In return, NASA was provided the flight data from the probe so that trajectory reconstruction could be done and simulation models assessed. Trajectory reconstruction of the Huygens entry probe at Titan was accomplished using two independent approaches: a traditional method and a POST2-based method. Results from both approaches are discussed in this paper.

Final Report fir DE-SC0005507 (A1618): The Development of an Improved Cloud Microphysical Product for Model and Remote Sensing Evaluation using RACORO Observations

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

McFarquhar, Greg M.

2012-09-21

We proposed to analyze data collected during the Routine Aerial Facilities (AAF) Clouds with Low Optical Water Depths (CLOWD) Optical Radiative Observations (RACORO) in order to develop an integrated product of cloud microphysical properties (number concentration of drops in different size bins, total liquid drop concentration integrated over all bin sizes, liquid water content LWC, extinction of liquid clouds, effective radius of water drops, and radar reflectivity factor) that could be used to evaluate large-eddy simulations (LES), general circulation models (GCMs) and ground-based remote sensing retrievals, and to develop cloud parameterizations with the end goal of improving the modeling ofmore » cloud processes and properties and their impact on atmospheric radiation. We have completed the development of this microphysical database. We investigated the differences in the size distributions measured by the Cloud and Aerosol Spectrometer (CAS) and the Forward Scattering Probe (FSSP), between the one dimensional cloud imaging probe (1DC) and the two-dimensional cloud imaging probe (2DC), and between the bulk LWCs measured by the Gerber probe against those derived from the size resolved probes.« less

Persistence of Microbial Contamination on Transvaginal Ultrasound Probes despite Low-Level Disinfection Procedure

PubMed Central

M'Zali, Fatima; Bounizra, Carole; Leroy, Sandrine; Mekki, Yahia; Quentin-Noury, Claudine; Kann, Michael

2014-01-01

Aim of the Study In many countries, Low Level Disinfection (LLD) of covered transvaginal ultrasound probes is recommended between patients' examinations. The aim of this study was to evaluate the antimicrobial efficacy of LLD under routine conditions on a range of microorganisms. Materials and Methods Samples were taken over a six month period in a private French Radiology Center. 300 specimens derived from endovaginal ultrasound probes were analyzed after disinfection of the probe with wipes impregnated with a quaternary ammonium compound and chlorhexidine. Human papillomavirus (HPV) was sought in the first set of s100 samples, Chlamydia trachomatis and mycoplasmas were searched in the second set of 100 samples, bacteria and fungi in the third 100 set samples. HPV, C. trachomatis and mycoplasmas were detected by PCR amplification. PCR positive samples were subjected to a nuclease treatment before an additional PCR assay to assess the likely viable microorganisms. Bacteria and fungi were investigated by conventional methods. Results A substantial persistence of microorganisms was observed on the disinfected probes: HPV DNA was found on 13% of the samples and 7% in nuclease-resistant form. C. trachomatis DNA was detected on 20% of the probes by primary PCR but only 2% after nuclease treatment, while mycoplasma DNA was amplified in 8% and 4%, respectively. Commensal and/or environmental bacterial flora was present on 86% of the probes, occasionally in mixed culture, and at various levels (10->3000 CFU/probe); Staphylococcus aureus was cultured from 4% of the probes (10-560 CFU/probe). No fungi were isolated. Conclusion Our findings raise concerns about the efficacy of impregnated towels as a sole mean for disinfection of ultrasound probes. Although the ultrasound probes are used with disposable covers, our results highlight the potential risk of cross contamination between patients during ultrasound examination and emphasize the need for reviewing the disinfection procedure. PMID:24695371

Development of the STPX Spheromak System

NASA Astrophysics Data System (ADS)

Williams, R. L.; Clark, J.; Weatherford, C. A.

2015-11-01

The progress made in starting up the STPX Spheromak system, which is now installed at the Florida A&M University, is reviewed. Experimental, computational and theoretical activities are underway. The control system for firing the magnetized coaxial plasma gun and for collecting data from the diagnostic probes, based on LabView, is being tested and adapted. Preliminary results of testing the installed magnetic field probes, Langmuir triple probes, cylindrical ion probes, and optical diagnostics will be discussed. Progress in modeling this spheromak using simulation codes, such as NIMROD, will be discussed. Progress in investigating the use of algebraic topology to describe this spheromak will be reported.

ALEX neutral beam probe

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

Pourrezaei, K.

1982-01-01

A neutral beam probe capable of measuring plasma space potential in a fully 3-dimensional magnetic field geometry has been developed. This neutral beam was successfully used to measure an arc target plasma contained within the ALEX baseball magnetic coil. A computer simulation of the experiment was performed to refine the experimental design and to develop a numerical model for scaling the ALEX neutral beam probe to other cases of fully 3-dimensional magnetic field. Based on this scaling a 30 to 50 keV neutral cesium beam probe capable of measuring space potential in the thermal barrier region of TMX Upgrade wasmore » designed.« less

Scanning laser vibrometry and luminol photomicrography to map cavitational activity around ultrasonic scalers

NASA Astrophysics Data System (ADS)

Felver, Bernhard; King, David C.; Lea, Simon C.; Price, Gareth J.; Walmsley, A. Damien

2008-06-01

Ultrasonic dental scalers are clinically used to remove deposits from tooth surfaces. A metal probe, oscillating at ultrasonic frequencies, is used to chip away deposits from the teeth. To reduce frictional heating, water flows over the operated probe in which a bi-product, cavitation, may be generated. The aim of this study is characterise probe oscillations using scanning laser vibrometry and to relate the recorded data to the occurrence of cavitation that is mapped in the course of this research. Scanning laser vibrometry (Polytec models 300-F/S and 400-3D) was used to measure the movement of various designs of operating probes and to locate vibration nodes / anti-nodes at different generator power settings and contact loads (100g and 200g). Cavitation mapping was performed by photographing the emission from a luminol solution with a digital camera (Artemis ICX285). The scaler design influences the number and location of vibration node / anti-node points. For all ultrasonic probes, the highest displacement amplitude values were recorded at the tip. The highest amounts of cavitation around the probes were recorded at the second anti-node measured from the tip. Broad, beaver-tale shaped probes produced more cavitation than slim shaped ones. The design also influences the amount of inertial cavitation around the operated instrument. The clinical relevance is that broad, beaver-tale shaped probes are unlikely to reach subgingival areas of the tooth. Further research is required to design probes that will be clinically superior to cleaning this area of the tooth.

Determination of matrix composition based on solute-solute nearest-neighbor distances in atom probe tomography.

PubMed

De Geuser, F; Lefebvre, W

2011-03-01

In this study, we propose a fast automatic method providing the matrix concentration in an atom probe tomography (APT) data set containing two phases or more. The principle of this method relies on the calculation of the relative amount of isolated solute atoms (i.e., not surrounded by a similar solute atom) as a function of a distance d in the APT reconstruction. Simulated data sets have been generated to test the robustness of this new tool and demonstrate that rapid and reproducible results can be obtained without the need of any user input parameter. The method has then been successfully applied to a ternary Al-Zn-Mg alloy containing a fine dispersion of hardening precipitates. The relevance of this method for direct estimation of matrix concentration is discussed and compared with the existing methodologies. Copyright © 2010 Wiley-Liss, Inc.

A Plasma Diagnostic Set for the Study of a Variable Specific Impulse Magnetoplasma Rocket

NASA Astrophysics Data System (ADS)

Squire, J. P.; Chang-Diaz, F. R.; Bengtson Bussell, R., Jr.; Jacobson, V. T.; Wootton, A. J.; Bering, E. A.; Jack, T.; Rabeau, A.

1997-11-01

The Advanced Space Propulsion Laboratory (ASPL) is developing a Variable Specific Impulse Magnetoplasma Rocket (VASIMR) using an RF heated magnetic mirror operated asymmetrically. We will describe the initial set of plasma diagnostics and data acquisition system being developed and installed on the VASIMR experiment. A U.T. Austin team is installing two fast reciprocating probes: a quadruple Langmuir and a Mach probe. These measure electron density and temperature profiles, electrostatic plasma fluctuations, and plasma flow profiles. The University of Houston is developing an array of 20 highly directional Retarding Potential Analyzers (RPA) for measuring ion energy distribution function profiles in the rocket plume, giving a measurement of total thrust. We have also developed a CAMAC based data acquisition system using LabView running on a Power Macintosh communicating through a 2 MB/s serial highway. We will present data from initial plasma operations and discuss future diagnostic development.

Teaching Meal Planning to Youth with Mental Retardation in Natural Settings.

ERIC Educational Resources Information Center

Arnold-Reid, Gae S.; And Others

1997-01-01

Three adolescent roommates with mild mental retardation were provided training in planning nutritious meals based on the food groups. A multiple probe design across individuals was used to evaluate training efficacy. Results indicated that the training procedures were effective in increasing healthy food choices. All participants maintained 100%…

Evidence-Based Practice: A Matrix for Predicting Phonological Generalization

ERIC Educational Resources Information Center

Gierut, Judith A.; Hulse, Lauren E.

2010-01-01

This paper describes a matrix for clinical use in the selection of phonological treatment targets to induce generalization, and in the identification of probe sounds to monitor during the course of intervention. The matrix appeals to a set of factors that have been shown to promote phonological generalization in the research literature, including…

Identification of squid species by melting temperature shifts on fluorescence melting curve analysis (FMCA) using single dual-labeled probe

NASA Astrophysics Data System (ADS)

Koh, Eunjung; Song, Ha Jeong; Kwon, Na Young; Kim, Gi Won; Lee, Kwang Ho; Jo, Soyeon; Park, Sujin; Park, Jihyun; Park, Eun Kyeong; Hwang, Seung Yong

2017-06-01

Real time PCR is a standard method for identification of species. One of limitations of the qPCR is that there would be false-positive result due to mismatched hybridization between target sequence and probe depending on the annealing temperature in the PCR condition. As an alternative, fluorescence melting curve analysis (FMCA) could be applied for species identification. FMCA is based on a dual-labeled probe. Even with subtle difference of target sequence, there are visible melting temperature (Tm) shift. One of FMCA applications is distinguishing organisms distributed and consumed globally as popular food ingredients. Their prices are set by species or country of origin. However, counterfeiting or distributing them without any verification procedure are becoming social problems and threatening food safety. Besides distinguishing them in naked eye is very difficult and almost impossible in any processed form. Therefore, it is necessary to identify species in molecular level. In this research three species of squids which have 1-2 base pair differences each are selected as samples since they have the same issue. We designed a probe which perfectly matches with one species and the others mismatches 2 and 1 base pair respectively and labeled with fluorophore and quencher. In an experiment with a single probe, we successfully distinguished them by Tm shift depending on the difference of base pair. By combining FMCA and qPCR chip, smaller-scale assay with higher sensitivity and resolution could be possible, andc furthermore, enabling results analysis with smart phone would realize point-of-care testing (POCT).

Design Optimization for Interferometric Space-Based 21-cm Power Spectrum Measurements

NASA Astrophysics Data System (ADS)

Pober, Jonathan

2018-06-01

Observations of the highly-redshifted 21 cm hyperfine line of neutral hydrogen (HI) are one of the most promising probes for the future of cosmology. At redshifts z > 30, the HI signal is likely the only measurable emission, as luminous objects have yet to form. At these very low radio frequencies, however, the earth’s ionosphere becomes opaque — necessitating observations from space. The major challenge to neutral hydrogen cosmology (at all redshifts) lies in the presence of bright foreground emission, which can dominate the HI signal by as much as eight orders of magnitude at the highest redshifts. The only method for extracting the cosmological signal relies on the spectral smoothness of the foregrounds; since each frequency of the HI signal probes a different redshift, the cosmological emission is essentially uncorrelated from frequency to frequency. The key challenge for designing an experiment lies in maintaining the spectral smoothness of the foregrounds. If the frequency response of the instrument introduces spectral structure (or at least, a residual that cannot be calibrated out at the necessary precision), it quickly becomes impossible to distinguish the cosmological signal from the foregrounds. This principle has guided the design of ground-based experiments like the Precision Array for Probing the Epoch of Reionization (PAPER) and the Hydrogen Epoch of Reionization Array (HERA). However, there still exists no unifying framework for turning this design "philosophy" into a robust, quantitative set of performance metrics and specifications. In this talk, I will present updates on the efforts of my research group to translate lessons learned from ground-based experiments into a fully traceable set of mission requirements for Cosmic Dawn Mapper or other space-based 21 cm interferometer.

Diode-laser-based therapy device

NASA Astrophysics Data System (ADS)

Udrea, Mircea V.; Nica, Adriana S.; Florian, Mariana; Poenaru, Daniela; Udrea, Gabriela; Lungeanu, Mihaela; Sporea, Dan G.; Vasiliu, Virgil V.; Vieru, Roxana

2004-10-01

A new therapy laser device is presented. The device consists of a central unit and different types of laser probes. The laser probe model SL7-650 delivers seven red (650 nm), 5 mW diode lasers convergent beams. The beams converge at about 30 cm in front of the laser probe and the irradiated area might be varied by simple displacement of the laser probe with respect to the target. The laser probe SL1-808 emits single infrared laser beam up to 500 mW. The efficiency of the use of this device in physiotherapy, and rheumatology, has been put into evidence after years of testing. Dermatology and microsurgery are users of infrared powerful laser probes. The device has successfully passed technical and clinical tests in order to be certified. The laser device design and some medical results are given.

An ALuc-Based Molecular Tension Probe for Sensing Intramolecular Protein-Protein Interactions.

PubMed

Kim, Sung-Bae; Nishihara, Ryo; Suzuki, Koji

2016-01-01

Optical imaging of protein-protein interactions (PPIs) facilitates comprehensive elucidation of intracellular molecular events. The present protocol demonstrates an optical measure for visualizing molecular tension triggered by any PPI in mammalian cells. A unique design of single-chain probes was fabricated, in which a full-length artificial luciferase (ALuc(®)) was sandwiched between two model proteins of interest, e.g., FKBP and FRB. A molecular tension probe comprising ALuc23 greatly enhances the bioluminescence in response to varying concentrations of rapamycin, and named "tension probe (TP)." The basic probe design can be further modified towards eliminating the C-terminal end of ALuc and was found to improve signal-to-background ratios, named "combinational probe." TPs may become an important addition to the tool box of bioassays in the determination of protein dynamics of interest in mammalian cells.

SU-F-J-182: Investigation of Systems for Improved Accuracy in Clinical Y-90 Percent Delivered Calculations

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

McBeth, R; Elder, D; Kesner, A

2016-06-15

Purpose: Y-90 Selective Internal Radiation Therapy (SIRT) is used to treat liver tumors, and by nature has variability in the percent of the intended dose that is actually delivered. To determine the quality of the administration, pre and post activity measurements are taken, and used to infer percent delivered. Vendor specifications indicate the use of an ion chamber to take these measurements. In our work, we investigated the accuracy of ion chambers, and compared them to other detector systems. Methods: We have built phantoms, phantom holders, and protocols, which allow us to measure our Y90 doses with varying apparatuses: amore » dose calibrator, a Geiger-counter, an ion chamber, a crystal based thyroid probe, and a gamma camera. We have set up a system that has enabled us to gather data by measuring clinical Y90 doses as they are used in the clinic using all of the instrumental methods. Five initial doses (25 measurements/acquisitions) have been taken at the time of this abstract submission. Results: Our initial results show that measurements acquired using scintillation based detectors (thyroid probe and gamma camera) correlate better with the gold standard (i.e. the dose calibrator). Pearson correlations between the dose calibrator measurements and the GM counter, Ion chamber, thyroid probe, and gamma camera were found to be 0.88, 0.83, 0.98, 0.99, respectively. More acquisitions and analysis are planned to determine the precision of the systems, as well as optimal energy window settings. Conclusion: It is likely that current standard practice can be improved using scintillation crystal based detectors. Such systems are more sensitive, can integrate signal, and can use energy discrimination. Furthermore, phantoms can be built to integrate with probe and gamma camera systems that are robust and provide reproducibility. Future work will include expanded acquisition and analysis.« less

Partition-based acquisition model for speed up navigated beta-probe surface imaging

NASA Astrophysics Data System (ADS)

Monge, Frédéric; Shakir, Dzhoshkun I.; Navab, Nassir; Jannin, Pierre

2016-03-01

Although gross total resection in low-grade glioma surgery leads to a better patient outcome, the in-vivo control of resection borders remains challenging. For this purpose, navigated beta-probe systems combined with 18F-based radiotracer, relying on activity distribution surface estimation, have been proposed to generate reconstructed images. The clinical relevancy has been outlined by early studies where intraoperative functional information is leveraged although inducing low spatial resolution in reconstruction. To improve reconstruction quality, multiple acquisition models have been proposed. They involve the definition of attenuation matrix for designing radiation detection physics. Yet, they require high computational power for efficient intraoperative use. To address the problem, we propose a new acquisition model called Partition Model (PM) considering an existing model where coefficients of the matrix are taken from a look-up table (LUT). Our model is based upon the division of the LUT into averaged homogeneous values for assigning attenuation coefficients. We validated our model using in vitro datasets, where tumors and peri-tumoral tissues have been simulated. We compared our acquisition model with the o_-the-shelf LUT and the raw method. Acquisition models outperformed the raw method in term of tumor contrast (7.97:1 mean T:B) but with a difficulty of real-time use. Both acquisition models reached the same detection performance with references (0.8 mean AUC and 0.77 mean NCC), where PM slightly improves the mean tumor contrast up to 10.1:1 vs 9.9:1 with the LUT model and more importantly, it reduces the mean computation time by 7.5%. Our model gives a faster solution for an intraoperative use of navigated beta-probe surface imaging system, with improved image quality.

Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions

PubMed Central

Sükösd, Zsuzsanna; Swenson, M. Shel; Kjems, Jørgen; Heitsch, Christine E.

2013-01-01

Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always improves over the original minimum free energy (MFE) structure. However, the amount of improvement varies with the sequence, exhibiting a correlation with MFE accuracy. Further analysis of this correlation shows that accurate MFE base pairs are typically preserved in a data-directed prediction, whereas inaccurate ones are not. Thus, the positive predictive value of common base pairs is consistently higher than the directed prediction accuracy. Finally, we confirm sequence dependencies in the directability of thermodynamic predictions and investigate the potential for greater accuracy improvements in the worst performing test sequence. PMID:23325843

Critical capacity, travel time delays and travel time distribution of rapid mass transit systems

NASA Astrophysics Data System (ADS)

Legara, Erika Fille; Monterola, Christopher; Lee, Kee Khoon; Hung, Gih Guang

2014-07-01

We set up a mechanistic agent-based model of a rapid mass transit system. Using empirical data from Singapore's unidentifiable smart fare card, we validate our model by reconstructing actual travel demand and duration of travel statistics. We subsequently use this model to investigate two phenomena that are known to significantly affect the dynamics within the RTS: (1) overloading in trains and (2) overcrowding in the RTS platform. We demonstrate that by varying the loading capacity of trains, a tipping point emerges at which an exponential increase in the duration of travel time delays is observed. We also probe the impact on the rail system dynamics of three types of passenger growth distribution across stations: (i) Dirac delta, (ii) uniform and (iii) geometric, which is reminiscent of the effect of land use on transport. Under the assumption of a fixed loading capacity, we demonstrate the dependence of a given origin-destination (OD) pair on the flow volume of commuters in station platforms.

Search for a low-mass pseudoscalar Higgs boson produced in association with a $$b\\bar{b}$$ pair in pp collisions at √s = 8 TeV

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

Khachatryan, Vardan

A search is reported for a light pseudoscalar Higgs boson decaying to a pair of τ leptons, produced in association with amore » $$b\\bar{b}$$ pair, in the context of two-Higgs-doublet models. The results are based on pp collision data at a centre-of-mass energy of 8 TeV collected by the CMS experiment at the LHC and corresponding to an integrated luminosity of 19.7 fb -1. Pseudoscalar boson masses between 25 and 80 GeV are probed. There was no evidence for a pseudoscalar boson found and upper limits were set on the production cross section times branching fraction to t pairs between 7 and 39 pb at the 95% confidence level. This search excludes a pseudoscalar Higgs boson with mass below 80 GeV, in Type II two-Higgs-doublet models with a negative coupling of standard model-like Higgs boson to down-type fermions.« less

Search for a low-mass pseudoscalar Higgs boson produced in association with a $$b\\bar{b}$$ pair in pp collisions at √s = 8 TeV

DOE PAGES

Khachatryan, Vardan

2016-05-06

A search is reported for a light pseudoscalar Higgs boson decaying to a pair of τ leptons, produced in association with amore » $$b\\bar{b}$$ pair, in the context of two-Higgs-doublet models. The results are based on pp collision data at a centre-of-mass energy of 8 TeV collected by the CMS experiment at the LHC and corresponding to an integrated luminosity of 19.7 fb -1. Pseudoscalar boson masses between 25 and 80 GeV are probed. There was no evidence for a pseudoscalar boson found and upper limits were set on the production cross section times branching fraction to t pairs between 7 and 39 pb at the 95% confidence level. This search excludes a pseudoscalar Higgs boson with mass below 80 GeV, in Type II two-Higgs-doublet models with a negative coupling of standard model-like Higgs boson to down-type fermions.« less

Search for light bosons in decays of the 125 GeV Higgs boson in proton-proton collisions at √{s}=8 TeV

NASA Astrophysics Data System (ADS)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; König, A.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rad, N.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Strauss, J.; Waltenberger, W.; Wulz, C.-E.; Dvornikov, O.; Makarenko, V.; Zykunov, V.; Mossolov, V.; Shumeiko, N.; Gonzalez, J. Suarez; Alderweireldt, S.; De Wolf, E. A.; Janssen, X.; Lauwers, J.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Zeid, S. Abu; Blekman, F.; D'Hondt, J.; Daci, N.; De Bruyn, I.; Deroover, K.; Lowette, S.; Moortgat, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Brun, H.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Léonard, A.; Luetic, J.; Maerschalk, T.; Marinov, A.; Randle-conde, A.; Seva, T.; Velde, C. Vander; Vanlaer, P.; Vannerom, D.; Yonamine, R.; Zenoni, F.; Zhang, F.; Cimmino, A.; Cornelis, T.; Dobur, D.; Fagot, A.; Garcia, G.; Gul, M.; Khvastunov, I.; Poyraz, D.; Salva, S.; Schöfbeck, R.; Sharma, A.; Tytgat, M.; Van Driessche, W.; Yazgan, E.; Zaganidis, N.; Bakhshiansohi, H.; Beluffi, C.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; De Visscher, S.; Delaere, C.; Delcourt, M.; Francois, B.; Giammanco, A.; Jafari, A.; Jez, P.; Komm, M.; Krintiras, G.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Nuttens, C.; Piotrzkowski, K.; Quertenmont, L.; Selvaggi, M.; Marono, M. Vidal; Wertz, S.; Beliy, N.; Júnior, W. L. Aldá; Alves, F. L.; Alves, G. A.; Brito, L.; Hensel, C.; Moraes, A.; Pol, M. E.; Teles, P. Rebello; Chagas, E. Belchior Batista Das; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; De Oliveira Martins, C.; De Souza, S. Fonseca; Guativa, L. M. Huertas; Malbouisson, H.; Figueiredo, D. Matos; Herrera, C. 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Vilar; Abbaneo, D.; Auffray, E.; Auzinger, G.; Bachtis, M.; Baillon, P.; Ball, A. H.; Barney, D.; Bloch, P.; Bocci, A.; Bonato, A.; Botta, C.; Camporesi, T.; Castello, R.; Cepeda, M.; Cerminara, G.; D'Alfonso, M.; d'Enterria, D.; Dabrowski, A.; Daponte, V.; David, A.; De Gruttola, M.; De Roeck, A.; Di Marco, E.; Dobson, M.; Dorney, B.; du Pree, T.; Duggan, D.; Dünser, M.; Dupont, N.; Elliott-Peisert, A.; Fartoukh, S.; Franzoni, G.; Fulcher, J.; Funk, W.; Gigi, D.; Gill, K.; Girone, M.; Glege, F.; Gulhan, D.; Gundacker, S.; Guthoff, M.; Hammer, J.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kieseler, J.; Kirschenmann, H.; Knünz, V.; Kornmayer, A.; Kortelainen, M. J.; Kousouris, K.; Krammer, M.; Lange, C.; Lecoq, P.; Lourenço, C.; Lucchini, M. T.; Malgeri, L.; Mannelli, M.; Martelli, A.; Meijers, F.; Merlin, J. A.; Mersi, S.; Meschi, E.; Milenovic, P.; Moortgat, F.; Morovic, S.; Mulders, M.; Neugebauer, H.; Orfanelli, S.; Orsini, L.; Pape, L.; Perez, E.; Peruzzi, M.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Racz, A.; Reis, T.; Rolandi, G.; Rovere, M.; Ruan, M.; Sakulin, H.; Sauvan, J. B.; Schäfer, C.; Schwick, C.; Seidel, M.; Sharma, A.; Silva, P.; Sphicas, P.; Steggemann, J.; Stoye, M.; Takahashi, Y.; Tosi, M.; Treille, D.; Triossi, A.; Tsirou, A.; Veckalns, V.; Veres, G. I.; Verweij, M.; Wardle, N.; Zagozdzinska, A.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; Kotlinski, D.; Langenegger, U.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Casal, B.; Dissertori, G.; Dittmar, M.; Donegà, M.; Grab, C.; Heidegger, C.; Hits, D.; Hoss, J.; Kasieczka, G.; Lecomte, P.; Lustermann, W.; Mangano, B.; Marionneau, M.; del Arbol, P. Martinez Ruiz; Masciovecchio, M.; Meinhard, M. T.; Meister, D.; Micheli, F.; Musella, P.; Nessi-Tedaldi, F.; Pandolfi, F.; Pata, J.; Pauss, F.; Perrin, G.; Perrozzi, L.; Quittnat, M.; Rossini, M.; Schönenberger, M.; Starodumov, A.; Tavolaro, V. R.; Theofilatos, K.; Wallny, R.; Aarrestad, T. K.; Amsler, C.; Caminada, L.; Canelli, M. F.; De Cosa, A.; Galloni, C.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Ngadiuba, J.; Pinna, D.; Rauco, G.; Robmann, P.; Salerno, D.; Yang, Y.; Zucchetta, A.; Candelise, V.; Doan, T. H.; Jain, Sh.; Khurana, R.; Konyushikhin, M.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Pozdnyakov, A.; Yu, S. S.; Kumar, Arun; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Chen, P. H.; Dietz, C.; Fiori, F.; Hou, W.-S.; Hsiung, Y.; Liu, Y. F.; Lu, R.-S.; Moya, M. Miñano; Paganis, E.; Psallidas, A.; Tsai, J. f.; Tzeng, Y. M.; Asavapibhop, B.; Singh, G.; Srimanobhas, N.; Suwonjandee, N.; Adiguzel, A.; Cerci, S.; Damarseckin, S.; Demiroglu, Z. S.; Dozen, C.; Dumanoglu, I.; Girgis, S.; Gokbulut, G.; Guler, Y.; Hos, I.; Kangal, E. E.; Kara, O.; Topaksu, A. Kayis; Kiminsu, U.; Oglakci, M.; Onengut, G.; Ozdemir, K.; Cerci, D. Sunar; Topakli, H.; Turkcapar, S.; Zorbakir, I. S.; Zorbilmez, C.; Bilin, B.; Bilmis, S.; Isildak, B.; Karapinar, G.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Kaya, M.; Kaya, O.; Yetkin, E. A.; Yetkin, T.; Cakir, A.; Cankocak, K.; Sen, S.; Grynyov, B.; Levchuk, L.; Sorokin, P.; Aggleton, R.; Ball, F.; Beck, L.; Brooke, J. J.; Burns, D.; Clement, E.; Cussans, D.; Flacher, H.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Sakuma, T.; El Nasr-storey, S. Seif; Smith, D.; Smith, V. J.; Bell, K. W.; Belyaev, A.; Brew, C.; Brown, R. M.; Calligaris, L.; Cieri, D.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Williams, T.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Bundock, A.; Burton, D.; Casasso, S.; Citron, M.; Colling, D.; Corpe, L.; Dauncey, P.; Davies, G.; De Wit, A.; Negra, M. Della; Di Maria, R.; Dunne, P.; Elwood, A.; Futyan, D.; Haddad, Y.; Hall, G.; Iles, G.; James, T.; Lane, R.; Laner, C.; Lucas, R.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mastrolorenzo, L.; Nash, J.; Nikitenko, A.; Pela, J.; Penning, B.; Pesaresi, M.; Raymond, D. M.; Richards, A.; Rose, A.; Seez, C.; Summers, S.; Tapper, A.; Uchida, K.; Acosta, M. Vazquez; Virdee, T.; Wright, J.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leslie, D.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Borzou, A.; Call, K.; Dittmann, J.; Hatakeyama, K.; Liu, H.; Pastika, N.; Cooper, S. I.; Henderson, C.; Rumerio, P.; West, C.; Arcaro, D.; Avetisyan, A.; Bose, T.; Gastler, D.; Rankin, D.; Richardson, C.; Rohlf, J.; Sulak, L.; Zou, D.; Benelli, G.; Berry, E.; Cutts, D.; Garabedian, A.; Hakala, J.; Heintz, U.; Hogan, J. M.; Jesus, O.; Kwok, K. H. M.; Laird, E.; Landsberg, G.; Mao, Z.; Narain, M.; Piperov, S.; Sagir, S.; Spencer, E.; Syarif, R.; Breedon, R.; Breto, G.; Burns, D.; De La Barca Sanchez, M. Calderon; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Flores, C.; Funk, G.; Gardner, M.; Gunion, J.; Ko, W.; Lander, R.; Mclean, C.; Mulhearn, M.; Pellett, D.; Pilot, J.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Bravo, C.; Cousins, R.; Dasgupta, A.; Everaerts, P.; Florent, A.; Hauser, J.; Ignatenko, M.; Mccoll, N.; Saltzberg, D.; Schnaible, C.; Takasugi, E.; Valuev, V.; Weber, M.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Shirazi, S. M. A. Ghiasi; Hanson, G.; Heilman, J.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Negrete, M. Olmedo; Paneva, M. I.; Shrinivas, A.; Si, W.; Wei, H.; Wimpenny, S.; Yates, B. R.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; Derdzinski, M.; Gerosa, R.; Holzner, A.; Klein, D.; Krutelyov, V.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Tadel, M.; Vartak, A.; Wasserbaech, S.; Welke, C.; Wood, J.; Würthwein, F.; Yagil, A.; Porta, G. Zevi Della; Amin, N.; Bhandari, R.; Bradmiller-Feld, J.; Campagnari, C.; Dishaw, A.; Dutta, V.; Sevilla, M. Franco; George, C.; Golf, F.; Gouskos, L.; Gran, J.; Heller, R.; Incandela, J.; Mullin, S. D.; Ovcharova, A.; Qu, H.; Richman, J.; Stuart, D.; Suarez, I.; Yoo, J.; Anderson, D.; Apresyan, A.; Bendavid, J.; Bornheim, A.; Bunn, J.; Chen, Y.; Duarte, J.; Lawhorn, J. M.; Mott, A.; Newman, H. B.; Pena, C.; Spiropulu, M.; Vlimant, J. R.; Xie, S.; Zhu, R. Y.; Andrews, M. B.; Azzolini, V.; Ferguson, T.; Paulini, M.; Russ, J.; Sun, M.; Vogel, H.; Vorobiev, I.; Weinberg, M.; Cumalat, J. P.; Ford, W. T.; Jensen, F.; Johnson, A.; Krohn, M.; Mulholland, T.; Stenson, K.; Wagner, S. R.; Alexander, J.; Chaves, J.; Chu, J.; Dittmer, S.; Mcdermott, K.; Mirman, N.; Kaufman, G. Nicolas; Patterson, J. R.; Rinkevicius, A.; Ryd, A.; Skinnari, L.; Soffi, L.; Tan, S. M.; Tao, Z.; Thom, J.; Tucker, J.; Wittich, P.; Zientek, M.; Winn, D.; Abdullin, S.; Albrow, M.; Apollinari, G.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Cremonesi, M.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hare, D.; Harris, R. M.; Hasegawa, S.; Hirschauer, J.; Hu, Z.; Jayatilaka, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Klima, B.; Kreis, B.; Lammel, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; De Sá, R. Lopes; Lykken, J.; Maeshima, K.; Magini, N.; Marraffino, J. M.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mrenna, S.; Nahn, S.; O'Dell, V.; Pedro, K.; Prokofyev, O.; Rakness, G.; Ristori, L.; Sexton-Kennedy, E.; Soha, A.; Spalding, W. J.; Spiegel, L.; Stoynev, S.; Strobbe, N.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vernieri, C.; Verzocchi, M.; Vidal, R.; Wang, M.; Weber, H. A.; Whitbeck, A.; Wu, Y.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Brinkerhoff, A.; Carnes, A.; Carver, M.; Curry, D.; Das, S.; Field, R. D.; Furic, I. K.; Konigsberg, J.; Korytov, A.; Low, J. F.; Ma, P.; Matchev, K.; Mei, H.; Mitselmakher, G.; Rank, D.; Shchutska, L.; Sperka, D.; Thomas, L.; Wang, J.; Wang, S.; Yelton, J.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Ackert, A.; Adams, J. R.; Adams, T.; Askew, A.; Bein, S.; Diamond, B.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Prosper, H.; Santra, A.; Yohay, R.; Baarmand, M. M.; Bhopatkar, V.; Colafranceschi, S.; Hohlmann, M.; Noonan, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Jung, K.; Kurt, P.; O'Brien, C.; Gonzalez, I. D. Sandoval; Turner, P.; Varelas, N.; Wang, H.; Wu, Z.; Zakaria, M.; Zhang, J.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Snyder, C.; Tiras, E.; Wetzel, J.; Yi, K.; Anderson, I.; Blumenfeld, B.; Cocoros, A.; Eminizer, N.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Osherson, M.; Roskes, J.; Sarica, U.; Swartz, M.; Xiao, M.; Xin, Y.; You, C.; Al-bataineh, A.; Baringer, P.; Bean, A.; Boren, S.; Bowen, J.; Bruner, C.; Castle, J.; Forthomme, L.; Kenny, R. P.; Khalil, S.; Kropivnitskaya, A.; Majumder, D.; Mcbrayer, W.; Murray, M.; Sanders, S.; Stringer, R.; Takaki, J. D. Tapia; Wang, Q.; Ivanov, A.; Kaadze, K.; Maravin, Y.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Toda, S.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Calvert, B.; Eno, S. C.; Ferraioli, C.; Gomez, J. A.; Hadley, N. J.; Jabeen, S.; Kellogg, R. G.; Kolberg, T.; Kunkle, J.; Lu, Y.; Mignerey, A. C.; Ricci-Tam, F.; Shin, Y. H.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Abercrombie, D.; Allen, B.; Apyan, A.; Barbieri, R.; Baty, A.; Bi, R.; Bierwagen, K.; Brandt, S.; Busza, W.; Cali, I. A.; Demiragli, Z.; Di Matteo, L.; Ceballos, G. Gomez; Goncharov, M.; Hsu, D.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Krajczar, K.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Maier, B.; Marini, A. C.; Mcginn, C.; Mironov, C.; Narayanan, S.; Niu, X.; Paus, C.; Roland, C.; Roland, G.; Salfeld-Nebgen, J.; Stephans, G. S. F.; Sumorok, K.; Tatar, K.; Varma, M.; Velicanu, D.; Veverka, J.; Wang, J.; Wang, T. W.; Wyslouch, B.; Yang, M.; Zhukova, V.; Benvenuti, A. C.; Chatterjee, R. M.; Evans, A.; Finkel, A.; Gude, A.; Hansen, P.; Kalafut, S.; Kao, S. C.; Kubota, Y.; Lesko, Z.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bartek, R.; Bloom, K.; Claes, D. R.; Dominguez, A.; Fangmeier, C.; Suarez, R. Gonzalez; Kamalieddin, R.; Kravchenko, I.; Rodrigues, A. Malta; Meier, F.; Monroy, J.; Siado, J. E.; Snow, G. R.; Stieger, B.; Alyari, M.; Dolen, J.; George, J.; Godshalk, A.; Harrington, C.; Iashvili, I.; Kaisen, J.; Kharchilava, A.; Kumar, A.; Parker, A.; Rappoccio, S.; Roozbahani, B.; Alverson, G.; Barberis, E.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; De Lima, R. Teixeira; Trocino, D.; Wang, R.-J.; Wood, D.; Bhattacharya, S.; Charaf, O.; Hahn, K. A.; Kubik, A.; Kumar, A.; Mucia, N.; Odell, N.; Pollack, B.; Schmitt, M. H.; Sung, K.; Trovato, M.; Velasco, M.; Dev, N.; Hildreth, M.; Anampa, K. Hurtado; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Planer, M.; Reinsvold, A.; Ruchti, R.; Smith, G.; Taroni, S.; Wayne, M.; Wolf, M.; Woodard, A.; Alimena, J.; Antonelli, L.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Francis, B.; Hart, A.; Hill, C.; Hughes, R.; Ji, W.; Liu, B.; Luo, W.; Puigh, D.; Winer, B. L.; Wulsin, H. W.; Cooperstein, S.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Lange, D.; Luo, J.; Marlow, D.; Donald, J. Mc; Medvedeva, T.; Mei, K.; Mooney, M.; Olsen, J.; Palmer, C.; Piroué, P.; Stickland, D.; Svyatkovskiy, A.; Tully, C.; Zuranski, A.; Malik, S.; Barker, A.; Barnes, V. E.; Folgueras, S.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, A. W.; Khatiwada, A.; Miller, D. H.; Neumeister, N.; Schulte, J. F.; Shi, X.; Sun, J.; Wang, F.; Xie, W.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Chen, Z.; Ecklund, K. M.; Geurts, F. J. M.; Guilbaud, M.; Li, W.; Michlin, B.; Northup, M.; Padley, B. P.; Redjimi, R.; Roberts, J.; Rorie, J.; Tu, Z.; Zabel, J.; Betchart, B.; Bodek, A.; de Barbaro, P.; Demina, R.; Duh, Y. t.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Hindrichs, O.; Khukhunaishvili, A.; Lo, K. H.; Tan, P.; Verzetti, M.; Agapitos, A.; Chou, J. P.; Contreras-Campana, E.; Gershtein, Y.; Espinosa, T. A. Gómez; Halkiadakis, E.; Heindl, M.; Hidas, D.; Hughes, E.; Kaplan, S.; Elayavalli, R. Kunnawalkam; Kyriacou, S.; Lath, A.; Nash, K.; Saka, H.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Delannoy, A. G.; Foerster, M.; Heideman, J.; Riley, G.; Rose, K.; Spanier, S.; Thapa, K.; Bouhali, O.; Celik, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Huang, T.; Juska, E.; Kamon, T.; Mueller, R.; Pakhotin, Y.; Patel, R.; Perloff, A.; Perniè, L.; Rathjens, D.; Rose, A.; Safonov, A.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Cowden, C.; Damgov, J.; De Guio, F.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Gurpinar, E.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Peltola, T.; Undleeb, S.; Volobouev, I.; Wang, Z.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Melo, A.; Ni, H.; Sheldon, P.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Barria, P.; Cox, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Neu, C.; Sinthuprasith, T.; Sun, X.; Wang, Y.; Wolfe, E.; Xia, F.; Clarke, C.; Harr, R.; Karchin, P. E.; Sturdy, J.; Belknap, D. A.; Buchanan, J.; Caillol, C.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ruggles, T.; Savin, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.

2017-10-01

A search is presented for decays beyond the standard model of the 125 GeV Higgs bosons to a pair of light bosons, based on models with extended scalar sectors. Light boson masses between 5 and 62.5 GeV are probed in final states containing four τ leptons, two muons and two b quarks, or two muons and two τ leptons. The results are from data in proton-proton collisions corresponding to an integrated luminosity of 19.7 fb-1, accumulated by the CMS experiment at the LHC at a center-of-mass energy of 8 TeV. No evidence for such exotic decays is found in the data. Upper limits are set on the product of the cross section and branching fraction for several signal processes. The results are also compared to predictions of two-Higgs-doublet models, including those with an additional scalar singlet. [Figure not available: see fulltext.

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

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

Cui, Yi; Hu, Dehong; Markillie, Lye Meng

Quantitative gene expression analysis in intact single cells can be achieved using single molecule- based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple FISH sub-probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific binding of sub-probes and tissue autofluorescence, limiting its accuracy. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on blinking frequencies of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses blinking frequency patterns, emitted frommore » a transcript bound to multiple sub-probes, which are distinct from blinking patterns emitted from partial or nonspecifically bound sub-probes and autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2, and their ratio (Nkx2-2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct blinking frequency patterns, laying the foundation for reliable single-cell transcriptomics.« less

Gravity Probe B

NASA Image and Video Library

2003-07-13

In the spacecraft processing facility on North Vandenberg Air Force Base, workers prepare to remove the soft shipping cover from the Gravity Probe B experiment. Immediate processing includes setting up mechanical and electrical ground support equipment, making necessary connections and conditioning the spacecraft battery. The Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

Gravity Probe B

NASA Image and Video Library

2003-07-11

Workers in the spacecraft processing facility on North Vandenberg Air Force Base get ready to begin processing the Gravity Probe B experiment. Mechanical and electrical ground support equipment will be set up and necessary connections made with the spacecraft. Spacecraft battery conditioning will also begin. The Gravity Probe B will launch a payload of four gyroscopes into low-Earth polar orbit to test two extraordinary predictions of Albert Einstein’s general theory of relativity: the geodetic effect (how space and time are warped by the presence of the Earth) and frame dragging (how Earth’s rotation drags space and time around with it). Once in orbit, for 18 months each gyroscope’s spin axis will be monitored as it travels through local spacetime, observing and measuring these effects. The experiment was developed by Stanford University, Lockheed Martin and NASA’s Marshall Space Flight Center.

Imaging on a Shoestring: Cost-Effective Technologies for Probing Vadose Zone Transport Processes

NASA Astrophysics Data System (ADS)

Corkhill, C.; Bridge, J. W.; Barns, G.; Fraser, R.; Romero-Gonzalez, M.; Wilson, R.; Banwart, S.

2010-12-01

Key barriers to the widespread uptake of imaging technology for high spatial resolution monitoring of porous media systems are cost and accessibility. X-ray tomography, magnetic resonance imaging (MRI), gamma and neutron radiography require highly specialised equipment, controlled laboratory environments and/or access to large synchrotron facilities. Here we present results from visible light, fluorescence and autoradiographic imaging techniques developed at low cost and applied in standard analytical laboratories, adapted where necessary at minimal capital expense. UV-visible time lapse fluorescence imaging (UV-vis TLFI) in a transparent thin bed chamber enabled microspheres labelled with fluorescent dye and a conservative fluorophore solute (disodium fluorescein) to be measured simultaneously in saturated, partially-saturated and actively draining quartz sand to elucidate empirical values for colloid transport and deposition parameters distributed throughout the flow field, independently of theoretical approximations. Key results include the first experimental quantification of the effects of ionic strength and air-water interfacial area on colloid deposition above a capillary fringe, and the first direct observations of particle mobilisation and redeposition by moving saturation gradients during drainage. UV-vis imaging was also used to study biodegradation and reactive transport in a variety of saturated conditions, applying fluorescence as a probe for oxygen and nitrate concentration gradients, pH, solute transport parameters, reduction of uranium, and mapping of two-dimensional flow fields around a model dipole flow borehole system to validate numerical models. Costs are low: LED excitation sources (< US 50), flow chambers (US 200) and detectors (although a complete scientific-grade CCD set-up costs around US$ 8000, robust datasets can be obtained using a commercial digital SLR camera) mean that set-ups can be flexible to meet changing experimental requirements. The critical limitations of UV-vis fluorescence imaging are the need for reliable fluorescent probes suited to the experimental objective, and the reliance on thin-bed (2D) transparent porous media. Autoradiographic techniques address some of these limitations permit imaging of key biogeochemical processes in opaque media using radioactive probes, without the need for specialised radiation sources. We present initial calibration data for the use of autoradiography to monitor transport parameters for radionuclides (99-technetium), and a novel application of a radioactive salt tracer as a probe for pore water content, in model porous media systems.

Towards the integration, annotation and association of historical microarray experiments with RNA-seq.

PubMed

Chavan, Shweta S; Bauer, Michael A; Peterson, Erich A; Heuck, Christoph J; Johann, Donald J

2013-01-01

Transcriptome analysis by microarrays has produced important advances in biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the development of an effective disease subtyping via cluster assignment, and a 70 gene risk score. Both enabled an improved molecular understanding of MM, and have provided prognostic information for the purposes of clinical management. Many researchers are now transitioning to Next Generation Sequencing (NGS) approaches and RNA-seq in particular, due to its discovery-based nature, improved sensitivity, and dynamic range. Additionally, RNA-seq allows for the analysis of gene isoforms, splice variants, and novel gene fusions. Given the voluminous amounts of historical microarray data, there is now a need to associate and integrate microarray and RNA-seq data via advanced bioinformatic approaches. Custom software was developed following a model-view-controller (MVC) approach to integrate Affymetrix probe set-IDs, and gene annotation information from a variety of sources. The tool/approach employs an assortment of strategies to integrate, cross reference, and associate microarray and RNA-seq datasets. Output from a variety of transcriptome reconstruction and quantitation tools (e.g., Cufflinks) can be directly integrated, and/or associated with Affymetrix probe set data, as well as necessary gene identifiers and/or symbols from a diversity of sources. Strategies are employed to maximize the annotation and cross referencing process. Custom gene sets (e.g., MM 70 risk score (GEP-70)) can be specified, and the tool can be directly assimilated into an RNA-seq pipeline. A novel bioinformatic approach to aid in the facilitation of both annotation and association of historic microarray data, in conjunction with richer RNA-seq data, is now assisting with the study of MM cancer biology.

Neurocircuitry models of posttraumatic stress disorder and extinction: human neuroimaging research--past, present, and future.

PubMed

Rauch, Scott L; Shin, Lisa M; Phelps, Elizabeth A

2006-08-15

The prevailing neurocircuitry models of anxiety disorders have been amygdalocentric in form. The bases for such models have progressed from theoretical considerations, extrapolated from research in animals, to in vivo human imaging data. For example, one current model of posttraumatic stress disorder (PTSD) has been highly influenced by knowledge from rodent fear conditioning research. Given the phenomenological parallels between fear conditioning and the pathogenesis of PTSD, we have proposed that PTSD is characterized by exaggerated amygdala responses (subserving exaggerated acquisition of fear associations and expression of fear responses) and deficient frontal cortical function (mediating deficits in extinction and the capacity to suppress attention/response to trauma-related stimuli), as well as deficient hippocampal function (mediating deficits in appreciation of safe contexts and explicit learning/memory). Neuroimaging studies have yielded convergent findings in support of this model. However, to date, neuroimaging investigations of PTSD have not principally employed conditioning and extinction paradigms per se. The recent development of such imaging probes now sets the stage for directly testing hypotheses regarding the neural substrates of fear conditioning and extinction abnormalities in PTSD.

"Gap hunting" to characterize clustered probe signals in Illumina methylation array data.

PubMed

Andrews, Shan V; Ladd-Acosta, Christine; Feinberg, Andrew P; Hansen, Kasper D; Fallin, M Daniele

2016-01-01

The Illumina 450k array has been widely used in epigenetic association studies. Current quality-control (QC) pipelines typically remove certain sets of probes, such as those containing a SNP or with multiple mapping locations. An additional set of potentially problematic probes are those with DNA methylation distributions characterized by two or more distinct clusters separated by gaps. Data-driven identification of such probes may offer additional insights for downstream analyses. We developed a procedure, termed "gap hunting," to identify probes showing clustered distributions. Among 590 peripheral blood samples from the Study to Explore Early Development, we identified 11,007 "gap probes." The vast majority (9199) are likely attributed to an underlying SNP(s) or other variant in the probe, although SNP-affected probes exist that do not produce a gap signals. Specific factors predict which SNPs lead to gap signals, including type of nucleotide change, probe type, DNA strand, and overall methylation state. These expected effects are demonstrated in paired genotype and 450k data on the same samples. Gap probes can also serve as a surrogate for the local genetic sequence on a haplotype scale and can be used to adjust for population stratification. The characteristics of gap probes reflect potentially informative biology. QC pipelines may benefit from an efficient data-driven approach that "flags" gap probes, rather than filtering such probes, followed by careful interpretation of downstream association analyses. Our results should translate directly to the recently released Illumina EPIC array given the similar chemistry and content design.

Analysis of the Negative-SET Behaviors in Cu/ZrO2/Pt Devices

NASA Astrophysics Data System (ADS)

Liu, Sen; Zhao, Xiaolong; Li, Qingjiang; Li, Nan; Wang, Wei; Liu, Qi; Xu, Hui

2016-12-01

Metal oxide-based electrochemical metallization memory (ECM) shows promising performance for next generation non-volatile memory. The negative-SET behavior has been observed in various oxide-based ECM devices. But the underlying mechanism of this behavior remains unaddressed and the role of the metal cation and oxygen vacancy in this behavior is unclear. In this work, we have observed two kinds of negative-SET (labeled as N-SET1 and N-SET2) behaviors in our Cu/ZrO2/Pt devices. Both the two behaviors can result in hard breakdown due to the high compliance current in reset process. The I-V characteristic shows that the two negative-SET behaviors have an obvious difference in operation voltage. Using four-probe resistance measurement method, the resistance-temperature characteristics of the ON-state after various negative-SET behaviors have been studied. The temperature dependence results demonstrate that the N-SET1 behavior is dominated by Cu conductive filament (CF) reformation caused by the Cu CF overgrowth phenomenon while the N-SET2 is related to the formation of oxygen vacancy CF. This work may provide a comprehensive understanding of the switching mechanism in oxide-based ECM devices.

Integrating prior knowledge in multiple testing under dependence with applications to detecting differential DNA methylation.

PubMed

Kuan, Pei Fen; Chiang, Derek Y

2012-09-01

DNA methylation has emerged as an important hallmark of epigenetics. Numerous platforms including tiling arrays and next generation sequencing, and experimental protocols are available for profiling DNA methylation. Similar to other tiling array data, DNA methylation data shares the characteristics of inherent correlation structure among nearby probes. However, unlike gene expression or protein DNA binding data, the varying CpG density which gives rise to CpG island, shore and shelf definition provides exogenous information in detecting differential methylation. This article aims to introduce a robust testing and probe ranking procedure based on a nonhomogeneous hidden Markov model that incorporates the above-mentioned features for detecting differential methylation. We revisit the seminal work of Sun and Cai (2009, Journal of the Royal Statistical Society: Series B (Statistical Methodology)71, 393-424) and propose modeling the nonnull using a nonparametric symmetric distribution in two-sided hypothesis testing. We show that this model improves probe ranking and is robust to model misspecification based on extensive simulation studies. We further illustrate that our proposed framework achieves good operating characteristics as compared to commonly used methods in real DNA methylation data that aims to detect differential methylation sites. © 2012, The International Biometric Society.

Sequential Multiplex Analyte Capturing for Phosphoprotein Profiling*

PubMed Central

Poetz, Oliver; Henzler, Tanja; Hartmann, Michael; Kazmaier, Cornelia; Templin, Markus F.; Herget, Thomas; Joos, Thomas O.

2010-01-01

Microarray-based sandwich immunoassays can simultaneously detect dozens of proteins. However, their use in quantifying large numbers of proteins is hampered by cross-reactivity and incompatibilities caused by the immunoassays themselves. Sequential multiplex analyte capturing addresses these problems by repeatedly probing the same sample with different sets of antibody-coated, magnetic suspension bead arrays. As a miniaturized immunoassay format, suspension bead array-based assays fulfill the criteria of the ambient analyte theory, and our experiments reveal that the analyte concentrations are not significantly changed. The value of sequential multiplex analyte capturing was demonstrated by probing tumor cell line lysates for the abundance of seven different receptor tyrosine kinases and their degree of phosphorylation and by measuring the complex phosphorylation pattern of the epidermal growth factor receptor in the same sample from the same cavity. PMID:20682761

Multiplex real-time PCR assays for the identification of the potato cyst and tobacco cyst nematodes

USDA-ARS?s Scientific Manuscript database

TaqMan primer-probe sets were developed for the detection and identification of potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis using two-tube, multiplex real-time PCR. One tube contained a primer-probe set specific for G. pallida (pale cyst nematode) multiplexed with another prim...

Distributed force probe bending model of critical dimension atomic force microscopy bias

NASA Astrophysics Data System (ADS)

Ukraintsev, Vladimir A.; Orji, Ndubuisi G.; Vorburger, Theodore V.; Dixson, Ronald G.; Fu, Joseph; Silver, Rick M.

2013-04-01

Critical dimension atomic force microscopy (CD-AFM) is a widely used reference metrology technique. To characterize modern semiconductor devices, small and flexible probes, often 15 to 20 nm in diameter, are used. Recent studies have reported uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements. To understand the source of these variations, tip-sample interactions between high aspect ratio features and small flexible probes, and their influence on measurement bias, should be carefully studied. Using theoretical and experimental procedures, one-dimensional (1-D) and two-dimensional (2-D) models of cylindrical probe bending relevant to carbon nanotube (CNT) AFM probes were developed and tested. An earlier 1-D bending model was refined, and a new 2-D distributed force (DF) model was developed. Contributions from several factors were considered, including: probe misalignment, CNT tip apex diameter variation, probe bending before snapping, and distributed van der Waals-London force. A method for extracting Hamaker probe-surface interaction energy from experimental probe-bending data was developed. Comparison of the new 2-D model with 1-D single point force (SPF) model revealed a difference of about 28% in probe bending. A simple linear relation between biases predicted by the 1-D SPF and 2-D DF models was found. The results suggest that probe bending can be on the order of several nanometers and can partially explain the observed CD-AFM probe-to-probe variation. New 2-D and three-dimensional CD-AFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

Dual-wavelength pump-probe microscopy analysis of melanin composition

NASA Astrophysics Data System (ADS)

Thompson, Andrew; Robles, Francisco E.; Wilson, Jesse W.; Deb, Sanghamitra; Calderbank, Robert; Warren, Warren S.

2016-11-01

Pump-probe microscopy is an emerging technique that provides detailed chemical information of absorbers with sub-micrometer spatial resolution. Recent work has shown that the pump-probe signals from melanin in human skin cancers correlate well with clinical concern, but it has been difficult to infer the molecular origins of these differences. Here we develop a mathematical framework to describe the pump-probe dynamics of melanin in human pigmented tissue samples, which treats the ensemble of individual chromophores that make up melanin as Gaussian absorbers with bandwidth related via Frenkel excitons. Thus, observed signals result from an interplay between the spectral bandwidths of the individual underlying chromophores and spectral proximity of the pump and probe wavelengths. The model is tested using a dual-wavelength pump-probe approach and a novel signal processing method based on gnomonic projections. Results show signals can be described by a single linear transition path with different rates of progress for different individual pump-probe wavelength pairs. Moreover, the combined dual-wavelength data shows a nonlinear transition that supports our mathematical framework and the excitonic model to describe the optical properties of melanin. The novel gnomonic projection analysis can also be an attractive generic tool for analyzing mixing paths in biomolecular and analytical chemistry.

Dual-wavelength pump-probe microscopy analysis of melanin composition

PubMed Central

Thompson, Andrew; Robles, Francisco E.; Wilson, Jesse W.; Deb, Sanghamitra; Calderbank, Robert; Warren, Warren S.

2016-01-01

Pump-probe microscopy is an emerging technique that provides detailed chemical information of absorbers with sub-micrometer spatial resolution. Recent work has shown that the pump-probe signals from melanin in human skin cancers correlate well with clinical concern, but it has been difficult to infer the molecular origins of these differences. Here we develop a mathematical framework to describe the pump-probe dynamics of melanin in human pigmented tissue samples, which treats the ensemble of individual chromophores that make up melanin as Gaussian absorbers with bandwidth related via Frenkel excitons. Thus, observed signals result from an interplay between the spectral bandwidths of the individual underlying chromophores and spectral proximity of the pump and probe wavelengths. The model is tested using a dual-wavelength pump-probe approach and a novel signal processing method based on gnomonic projections. Results show signals can be described by a single linear transition path with different rates of progress for different individual pump-probe wavelength pairs. Moreover, the combined dual-wavelength data shows a nonlinear transition that supports our mathematical framework and the excitonic model to describe the optical properties of melanin. The novel gnomonic projection analysis can also be an attractive generic tool for analyzing mixing paths in biomolecular and analytical chemistry. PMID:27833147

Flow Characterization Studies of the 10-MW TP3 Arc-Jet Facility: Probe Sweeps

NASA Technical Reports Server (NTRS)

Goekcen, Tahir; Alunni, Antonella I.

2016-01-01

This paper reports computational simulations and analysis in support of calibration and flow characterization tests in a high enthalpy arc-jet facility at NASA Ames Research Center. These tests were conducted in the NASA Ames 10-MW TP3 facility using flat-faced stagnation calorimeters at six conditions corresponding to the steps of a simulated flight heating profile. Data were obtained using a conical nozzle test configuration in which the models were placed in a free jet downstream of the nozzle. Experimental surveys of arc-jet test flow with pitot pressure and heat flux probes were also performed at these arc-heater conditions, providing assessment of the flow uniformity and valuable data for the flow characterization. Two different sets of pitot pressure and heat probes were used: 9.1-mm sphere-cone probes (nose radius of 4.57 mm or 0.18 in) with null-point heat flux gages, and 15.9-mm (0.625 in) diameter hemisphere probes with Gardon gages. The probe survey data clearly show that the test flow in the TP3 facility is not uniform at most conditions (not even axisymmetric at some conditions), and the extent of non-uniformity is highly dependent on various arc-jet parameters such as arc current, mass flow rate, and the amount of cold-gas injection at the arc-heater plenum. The present analysis comprises computational fluid dynamics simulations of the nonequilibrium flowfield in the facility nozzle and test box, including the models tested. Comparisons of computations with the experimental measurements show reasonably good agreement except at the extreme low pressure conditions of the facility envelope.

The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: towards a computationally efficient analysis without informative priors

NASA Astrophysics Data System (ADS)

Pellejero-Ibanez, Marcos; Chuang, Chia-Hsun; Rubiño-Martín, J. A.; Cuesta, Antonio J.; Wang, Yuting; Zhao, Gongbo; Ross, Ashley J.; Rodríguez-Torres, Sergio; Prada, Francisco; Slosar, Anže; Vazquez, Jose A.; Alam, Shadab; Beutler, Florian; Eisenstein, Daniel J.; Gil-Marín, Héctor; Grieb, Jan Niklas; Ho, Shirley; Kitaura, Francisco-Shu; Percival, Will J.; Rossi, Graziano; Salazar-Albornoz, Salvador; Samushia, Lado; Sánchez, Ariel G.; Satpathy, Siddharth; Seo, Hee-Jong; Tinker, Jeremy L.; Tojeiro, Rita; Vargas-Magaña, Mariana; Brownstein, Joel R.; Nichol, Robert C.; Olmstead, Matthew D.

2017-07-01

We develop a new computationally efficient methodology called double-probe analysis with the aim of minimizing informative priors (those coming from extra probes) in the estimation of cosmological parameters. Using our new methodology, we extract the dark energy model-independent cosmological constraints from the joint data sets of the Baryon Oscillation Spectroscopic Survey (BOSS) galaxy sample and Planck cosmic microwave background (CMB) measurements. We measure the mean values and covariance matrix of {R, la, Ωbh2, ns, log(As), Ωk, H(z), DA(z), f(z)σ8(z)}, which give an efficient summary of the Planck data and two-point statistics from the BOSS galaxy sample. The CMB shift parameters are R=√{Ω _m H_0^2} r(z_*) and la = πr(z*)/rs(z*), where z* is the redshift at the last scattering surface, and r(z*) and rs(z*) denote our comoving distance to the z* and sound horizon at z*, respectively; Ωb is the baryon fraction at z = 0. This approximate methodology guarantees that we will not need to put informative priors on the cosmological parameters that galaxy clustering is unable to constrain, I.e. Ωbh2 and ns. The main advantage is that the computational time required for extracting these parameters is decreased by a factor of 60 with respect to exact full-likelihood analyses. The results obtained show no tension with the flat Λ cold dark matter (ΛCDM) cosmological paradigm. By comparing with the full-likelihood exact analysis with fixed dark energy models, on one hand we demonstrate that the double-probe method provides robust cosmological parameter constraints that can be conveniently used to study dark energy models, and on the other hand we provide a reliable set of measurements assuming dark energy models to be used, for example, in distance estimations. We extend our study to measure the sum of the neutrino mass using different methodologies, including double-probe analysis (introduced in this study), full-likelihood analysis and single-probe analysis. From full-likelihood analysis, we obtain Σmν < 0.12 (68 per cent), assuming ΛCDM and Σmν < 0.20 (68 per cent) assuming owCDM. We also find that there is degeneracy between observational systematics and neutrino masses, which suggests that one should take great care when estimating these parameters in the case of not having control over the systematics of a given sample.

Polyketide intermediate mimics as probes for revealing cryptic stereochemistry of ketoreductase domains.

PubMed

Li, Yang; Fiers, William D; Bernard, Steffen M; Smith, Janet L; Aldrich, Courtney C; Fecik, Robert A

2014-12-19

Among natural product families, polyketides have shown the most promise for combinatorial biosynthesis of natural product-like libraries. Though recent research in the area has provided many mechanistic revelations, a basic-level understanding of kinetic and substrate tolerability is still needed before the full potential of combinatorial biosynthesis can be realized. We have developed a novel set of chemical probes for the study of ketoreductase domains of polyketide synthases. This chemical tool-based approach was validated using the ketoreductase of pikromycin module 2 (PikKR2) as a model system. Triketide substrate mimics 12 and 13 were designed to increase stability (incorporating a nonhydrolyzable thioether linkage) and minimize nonessential functionality (truncating the phosphopantetheinyl arm). PikKR2 reduction product identities as well as steady-state kinetic parameters were determined by a combination of LC-MS/MS analysis of synthetic standards and a NADPH consumption assay. The d-hydroxyl product is consistent with bioinformatic analysis and results from a complementary biochemical and molecular biological approach. When compared to widely employed substrates in previous studies, diketide 63 and trans-decalone 64, substrates 12 and 13 showed 2-10 fold lower K(M) values (2.4 ± 0.8 and 7.8 ± 2.7 mM, respectively), indicating molecular recognition of intermediate-like substrates. Due to an abundance of the nonreducable enol-tautomer, the k(cat) values were attenuated by as much as 15-336 fold relative to known substrates. This study reveals the high stereoselectivity of PikKR2 in the face of gross substrate permutation, highlighting the utility of a chemical probe-based approach in the study of polyketide ketoreductases.

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

NASA Technical Reports Server (NTRS)

Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

2001-01-01

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

PROBES FOR THE SPECIFIC DETECTION OF CRYPTOSPORIDIUM PARVUM

EPA Science Inventory

A probe set, consisting of two synthetic oligonucleotides each tagged with a fluorescent reporter molecule, has been developed for specific detection of Cryptosporidium parvum.Each probe strand detects ribosomal RNA from a range of isolates of this species, and the combination is...

THz pulses from 4th generation X-ray light sources: Perspectives for fully synchronized THz pump X-ray probe experiments

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

Gensch, M.

2010-02-03

In this paper the prospects of terahertz (THz) pulses generated at 4th generation X-ray light sources are presented on the example of recent results from a prototype set-up at the soft X-ray FEL FLASH. It is shown, that the THz pulses from the relativistic ultra short electron bunches have unique properties, that at FLASH are utilized for novel THz pump X-ray probe experiments with a robust few fs resolution. Based on these experiences it is discussed, how future facilities can benefit from implementation of similar or further improved instrumentation.

Integrated cosmological probes: Extended analysis

NASA Astrophysics Data System (ADS)

Nicola, Andrina; Refregier, Alexandre; Amara, Adam

2017-04-01

Recent progress in cosmology has relied on combining different cosmological probes. In an earlier work, we implemented an integrated approach to cosmology where the probes are combined into a common framework at the map level. This has the advantage of taking full account of the correlations between the different probes, to provide a stringent test of systematics and of the validity of the cosmological model. We extend this analysis to include not only cosmic microwave background (CMB) temperature, galaxy clustering, and weak lensing from the Sloan Digital Sky Survey (SDSS) but also CMB lensing, weak lensing from Dark Energy Survey Science Verification (DES SV) data, type Ia supernova, and H0 measurements. This yields 12 auto- and cross-power spectra which include the CMB temperature power spectrum, cosmic shear, galaxy clustering, galaxy-galaxy lensing, CMB lensing cross-correlation along with other cross-correlations, as well as background probes. Furthermore, we extend the treatment of systematic uncertainties by studying the impact of intrinsic alignments, baryonic corrections, residual foregrounds in the CMB temperature, and calibration factors for the different power spectra. For Λ CDM , we find results that are consistent with our earlier work. Given our enlarged data set and systematics treatment, this confirms the robustness of our analysis and results. Furthermore, we find that our best-fit cosmological model gives a good fit to all the data we consider with no signs of tensions within our analysis. We also find our constraints to be consistent with those found by the joint analysis of the WMAP9, SPT, and ACT CMB experiments and the KiDS weak lensing survey. Comparing with the Planck Collaboration results, we see a broad agreement, but there are indications of a tension from the marginalized constraints in most pairs of cosmological parameters. Since our analysis includes CMB temperature Planck data at 10 <ℓ<610 , the tension appears to arise between the Planck high-ℓ modes and the other measurements. Furthermore, we find the constraints on the probe calibration parameters to be in agreement with expectations, showing that the data sets are mutually consistent. In particular, this yields a confirmation of the amplitude calibration of the weak lensing measurements from the SDSS, DES SV, and Planck CMB lensing from our integrated analysis.

Einstein Inflationary Probe (EIP)

NASA Technical Reports Server (NTRS)

Hinshaw, Gary

2004-01-01

I will discuss plans to develop a concept for the Einstein Inflation Probe: a mission to detect gravity waves from inflation via the unique signature they impart to the cosmic microwave background (CMB) polarization. A sensitive CMB polarization satellite may be the only way to probe physics at the grand-unified theory (GUT) scale, exceeding by 12 orders of magnitude the energies studied at the Large Hadron Collider. A detection of gravity waves would represent a remarkable confirmation of the inflationary paradigm and set the energy scale at which inflation occurred when the universe was a fraction of a second old. Even a strong upper limit to the gravity wave amplitude would be significant, ruling out many common models of inflation, and pointing to inflation occurring at much lower energy, if at all. Measuring gravity waves via the CMB polarization will be challenging. We will undertake a comprehensive study to identify the critical scientific requirements for the mission and their derived instrumental performance requirements. At the core of the study will be an assessment of what is scientifically and experimentally optimal within the scope and purpose of the Einstein Inflation Probe.

Docosahexaenoic acid conjugated near infrared flourescence probe for in vivo early tumor diagnosis

NASA Astrophysics Data System (ADS)

Li, Siwen; Cao, Jie; Qin, Jingyi; Zhang, Xin; Achilefu, Samuel; Qian, Zhiyu; Gu, Yueqing

2013-02-01

Docosahexaenoic acid(DHA) is an omega-3 C22 natural fatty acid with six cis double bonds and as a constituent of membranes used as a precursor for metabolic and biochemical path ways. In this manuscript,we describe the synthesis of near-infrared(NIR) flourescence ICG-Der-01 labeled DHA for in vitro and vivo tumor targeting.The structure of the probe was intensively characterized by UV and MS. The in vitro and vivo tumor targeting abilities of the DHA-based NIR probes were investigeted in MCF-7 cells and MCF-7 xenograft mice model differently by confocal microscopy and CCD camera. The cell cytotoxicity were tested in tumor cells MCF-7 .The results shows that the DHA-based NIR probes have high affinity with the tumor both in vitro and vivo.In addition ,we also found that the DHA-based NIR probes have the apparent cytotoxicity on MCF-7 cells .which demonstrated that DHA was conjugated with other antitumor drug could increase the abilities of antirumor efficacy .So DHA-ICG-Der-01 is a promising optical agent for diagnosis of tumors especially in their early stage.

A support vector machine designed to identify breasts at high risk using multi-probe generated REIS signals: a preliminary assessment

NASA Astrophysics Data System (ADS)

Gur, David; Zheng, Bin; Lederman, Dror; Dhurjaty, Sreeram; Sumkin, Jules; Zuley, Margarita

2010-02-01

A new resonance-frequency based electronic impedance spectroscopy (REIS) system with multi-probes, including one central probe and six external probes that are designed to contact the breast skin in a circular form with a radius of 60 millimeters to the central ("nipple") probe, has been assembled and installed in our breast imaging facility. We are conducting a prospective clinical study to test the performance of this REIS system in identifying younger women (< 50 years old) at higher risk for having or developing breast cancer. In this preliminary analysis, we selected a subset of 100 examinations. Among these, 50 examinations were recommended for a biopsy due to detection of a highly suspicious breast lesion and 50 were determined negative during mammography screening. REIS output signal sweeps that we used to compute an initial feature included both amplitude and phase information representing differences between corresponding (matched) EIS signal values acquired from the left and right breasts. A genetic algorithm was applied to reduce the feature set and optimize a support vector machine (SVM) to classify the REIS examinations into "biopsy recommended" and "non-biopsy" recommended groups. Using the leave-one-case-out testing method, the classification performance as measured by the area under the receiver operating characteristic (ROC) curve was 0.816 +/- 0.042. This pilot analysis suggests that the new multi-probe-based REIS system could potentially be used as a risk stratification tool to identify pre-screened young women who are at higher risk of having or developing breast cancer.

Extracting Primordial Non-Gaussianity from Large Scale Structure in the Post-Planck Era

NASA Astrophysics Data System (ADS)

Dore, Olivier

Astronomical observations have become a unique tool to probe fundamental physics. Cosmology, in particular, emerged as a data-driven science whose phenomenological modeling has achieved great success: in the post-Planck era, key cosmological parameters are measured to percent precision. A single model reproduces a wealth of astronomical observations involving very distinct physical processes at different times. This success leads to fundamental physical questions. One of the most salient is the origin of the primordial perturbations that grew to form the large-scale structures we now observe. More and more cosmological observables point to inflationary physics as the origin of the structure observed in the universe. Inflationary physics predict the statistical properties of the primordial perturbations and it is thought to be slightly non-Gaussian. The detection of this small deviation from Gaussianity represents the next frontier in early Universe physics. To measure it would provide direct, unique and quantitative insights about the physics at play when the Universe was only a fraction of a second old, thus probing energies untouchable otherwise. En par with the well-known relic gravitational wave radiation -- the famous ``B-modes'' -- it is one the few probes of inflation. This departure from Gaussianity leads to very specific signature in the large scale clustering of galaxies. Observing large-scale structure, we can thus establish a direct connection with fundamental theories of the early universe. In the post-Planck era, large-scale structures are our most promising pathway to measuring this primordial signal. Current estimates suggests that the next generation of space or ground based large scale structure surveys (e.g. the ESA EUCLID or NASA WFIRST missions) might enable a detection of this signal. This potential huge payoff requires us to solidify the theoretical predictions supporting these measurements. Even if the exact signal we are looking for is of unknown amplitude, it is obvious that we must measure it as well as these ground breaking data set will permit. We propose to develop the supporting theoretical work to the point where the complete non-gaussianian signature can be extracted from these data sets. We will do so by developing three complementary directions: - We will develop the appropriate formalism to measure and model galaxy clustering on the largest scales. - We will study the impact of non-Gaussianity on higher-order statistics, the most promising statistics for our purpose.. - We will explicit the connection between these observables and the microphysics of a large class of inflation models, but also identify fundamental limitations to this interpretation.

Hints on the nature of dark matter from the properties of Milky Way satellites

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

Anderhalden, Donnino; Diemand, Juerg; Schneider, Aurel

2013-03-01

The nature of dark matter is still unknown and one of the most fundamental scientific mysteries. Although successfully describing large scales, the standard cold dark matter model (CDM) exhibits possible shortcomings on galactic and sub-galactic scales. It is exactly at these highly non-linear scales where strong astrophysical constraints can be set on the nature of the dark matter particle. While observations of the Lyman-α forest probe the matter power spectrum in the mildly non-linear regime, satellite galaxies of the Milky Way provide an excellent laboratory as a test of the underlying cosmology on much smaller scales. Here we present resultsmore » from a set of high resolution simulations of a Milky Way sized dark matter halo in eight distinct cosmologies: CDM, warm dark matter (WDM) with a particle mass of 2 keV and six different cold plus warm dark matter (C+WDM) models, varying the fraction, f{sub wdm}, and the mass, m{sub wdm}, of the warm component. We used three different observational tests based on Milky Way satellite observations: the total satellite abundance, their radial distribution and their mass profile. We show that the requirement of simultaneously satisfying all three constraints sets very strong limits on the nature of dark matter. This shows the power of a multi-dimensional small scale approach in ruling out models which would be still allowed by large scale observations.« less

Spin and chirality effects in antler-topology processes at high energy $${e^+e^-}$$ colliders

DOE PAGES

Choi, S. Y.; Christensen, N. D.; Salmon, D.; ...

2015-10-01

We perform a model-independent investigation of spin and chirality correlation effects in the antler-topology processes e +e -→P +P -→(ℓ+D0)(ℓ-D¯0) at high-energy e +e - colliders with polarized beams. Generally the production process e +e -→P +P - can occur not only through the s-channel exchange of vector bosons, V0 , including the neutral Standard Model (SM) gauge bosons, γ and Z, but also through the s- and t-channel exchanges of new neutral states, S0 and T0 , and the u-channel exchange of new doubly charged states, U-- . The general set of (non-chiral) three-point couplings of the new particlesmore » and leptons allowed in a renormalizable quantum field theory is considered. The general spin and chirality analysis is based on the threshold behavior of the excitation curves for P +P - pair production in e +e - collisions with longitudinal- and transverse-polarized beams, the angular distributions in the production process and also the production-decay angular correlations. In the first step, we present the observables in the helicity formalism. Subsequently, we show how a set of observables can be designed for determining the spins and chiral structures of the new particles without any model assumptions. Finally, taking into account a typical set of approximately chiral invariant scenarios, we demonstrate how the spin and chirality effects can be probed experimentally at a high-energy e +e - collider.« less

Spin and chirality effects in antler-topology processes at high energy $$\\varvec{e^+e^-}$$ e + e - colliders

DOE PAGES

Choi, S. Y.; Christensen, N. D.; Salmon, D.; ...

2015-10-01

We perform a model-independent investigation of spin and chirality correlation effects in the antler-topology processes e+e−→P+P−→(ℓ+D0)(ℓ−D¯0) at high-energy e+e− colliders with polarized beams. Generally the production process e+e−→P+P− can occur not only through the s-channel exchange of vector bosons, V0 , including the neutral Standard Model (SM) gauge bosons, γ and Z, but also through the s- and t-channel exchanges of new neutral states, S0 and T0 , and the u-channel exchange of new doubly charged states, U−− . The general set of (non-chiral) three-point couplings of the new particles and leptons allowed in a renormalizable quantum field theory ismore » considered. The general spin and chirality analysis is based on the threshold behavior of the excitation curves for P+P− pair production in e+e− collisions with longitudinal- and transverse-polarized beams, the angular distributions in the production process and also the production-decay angular correlations. In the first step, we present the observables in the helicity formalism. Subsequently, we show how a set of observables can be designed for determining the spins and chiral structures of the new particles without any model assumptions. Finally, taking into account a typical set of approximately chiral invariant scenarios, we demonstrate how the spin and chirality effects can be probed experimentally at a high-energy e+e− collider.« less

Spin and chirality effects in antler-topology processes at high energy $${e^+e^-}$$ colliders

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

Choi, S. Y.; Christensen, N. D.; Salmon, D.

We perform a model-independent investigation of spin and chirality correlation effects in the antler-topology processes e +e -→P +P -→(ℓ+D0)(ℓ-D¯0) at high-energy e +e - colliders with polarized beams. Generally the production process e +e -→P +P - can occur not only through the s-channel exchange of vector bosons, V0 , including the neutral Standard Model (SM) gauge bosons, γ and Z, but also through the s- and t-channel exchanges of new neutral states, S0 and T0 , and the u-channel exchange of new doubly charged states, U-- . The general set of (non-chiral) three-point couplings of the new particlesmore » and leptons allowed in a renormalizable quantum field theory is considered. The general spin and chirality analysis is based on the threshold behavior of the excitation curves for P +P - pair production in e +e - collisions with longitudinal- and transverse-polarized beams, the angular distributions in the production process and also the production-decay angular correlations. In the first step, we present the observables in the helicity formalism. Subsequently, we show how a set of observables can be designed for determining the spins and chiral structures of the new particles without any model assumptions. Finally, taking into account a typical set of approximately chiral invariant scenarios, we demonstrate how the spin and chirality effects can be probed experimentally at a high-energy e +e - collider.« less

Effective Radius of Ice Cloud Particle Populations Derived from Aircraft Probes

NASA Technical Reports Server (NTRS)

Heymsfield, Andrew J.; Schmitt, Carl; Bansemer, Aaron; vanZadelhoff, Gerd-Jan; McGill, Matthew J.; Twohy, Cynthia

2005-01-01

The effective radius(r(sub e)) is a crucial variable in representing the radiative properties of cloud layers in general circulation models. This parameter is proportional to the condensed water content (CWC) divided by the extinction (sigma). For ice cloud layers, parameterizations for r(sub e), have been developed from aircraft in-situ measurements 1) indirectly, using data obtained from particle spectrometer probes and assumptions or observations about particle shape and mass to get the ice water content (IWC) and area to get sigma, and recently 2) from probes that measure IWC and sigma directly. This study compares [IWC/sigma] derived from the two methods using data sets acquired from comparable instruments on two aircraft, one sampling clouds at mid-levels and the other at upper-levels during the CRYSTAL-FACE field program in Florida in 2002. The sigma and IWC derived by each method are compared and evaluated in different ways for each aircraft data set. Direct measurements of sigma exceed those derived indirectly by a factor of two to two and a half. The IWC probes, relying on ice sublimation, appear to measure accurately except when the IWC is high or the particles too large to sublimate completely during the short transit time through the probe. The IWC estimated from the particle probes are accurate when direct measurements are available to provide constraints and useful information in high IWC/large particle situations. Because of the discrepancy in sigma estimates between the direct and indirect approaches, there is a factor of 2 to 3 difference in [IWC/sigma] between them. Although there are significant uncertainties involved in its use, comparisons with several independent data sources suggest that the indirect method is the more accurate of the two approaches. However, experiments are needed to resolve the source of the discrepancy in sigma.

Spectroscopic and Statistical Techniques for Information Recovery in Metabonomics and Metabolomics

NASA Astrophysics Data System (ADS)

Lindon, John C.; Nicholson, Jeremy K.

2008-07-01

Methods for generating and interpreting metabolic profiles based on nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and chemometric analysis methods are summarized and the relative strengths and weaknesses of NMR and chromatography-coupled MS approaches are discussed. Given that all data sets measured to date only probe subsets of complex metabolic profiles, we describe recent developments for enhanced information recovery from the resulting complex data sets, including integration of NMR- and MS-based metabonomic results and combination of metabonomic data with data from proteomics, transcriptomics, and genomics. We summarize the breadth of applications, highlight some current activities, discuss the issues relating to metabonomics, and identify future trends.

Spectroscopic and statistical techniques for information recovery in metabonomics and metabolomics.

PubMed

Lindon, John C; Nicholson, Jeremy K

2008-01-01

Methods for generating and interpreting metabolic profiles based on nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and chemometric analysis methods are summarized and the relative strengths and weaknesses of NMR and chromatography-coupled MS approaches are discussed. Given that all data sets measured to date only probe subsets of complex metabolic profiles, we describe recent developments for enhanced information recovery from the resulting complex data sets, including integration of NMR- and MS-based metabonomic results and combination of metabonomic data with data from proteomics, transcriptomics, and genomics. We summarize the breadth of applications, highlight some current activities, discuss the issues relating to metabonomics, and identify future trends.

Random walks of colloidal probes in viscoelastic materials

NASA Astrophysics Data System (ADS)

Khan, Manas; Mason, Thomas G.

2014-04-01

To overcome limitations of using a single fixed time step in random walk simulations, such as those that rely on the classic Wiener approach, we have developed an algorithm for exploring random walks based on random temporal steps that are uniformly distributed in logarithmic time. This improvement enables us to generate random-walk trajectories of probe particles that span a highly extended dynamic range in time, thereby facilitating the exploration of probe motion in soft viscoelastic materials. By combining this faster approach with a Maxwell-Voigt model (MVM) of linear viscoelasticity, based on a slowly diffusing harmonically bound Brownian particle, we rapidly create trajectories of spherical probes in soft viscoelastic materials over more than 12 orders of magnitude in time. Appropriate windowing of these trajectories over different time intervals demonstrates that random walk for the MVM is neither self-similar nor self-affine, even if the viscoelastic material is isotropic. We extend this approach to spatially anisotropic viscoelastic materials, using binning to calculate the anisotropic mean square displacements and creep compliances along different orthogonal directions. The elimination of a fixed time step in simulations of random processes, including random walks, opens up interesting possibilities for modeling dynamics and response over a highly extended temporal dynamic range.

Identification of neonatal hearing impairment: ear-canal measurements of acoustic admittance and reflectance in neonates.

PubMed

Keefe, D H; Folsom, R C; Gorga, M P; Vohr, B R; Bulen, J C; Norton, S J

2000-10-01

1) To describe broad bandwidth measurements of acoustic admittance (Y) and energy reflectance (R) in the ear canals of neonates. 2) To describe a means for evaluating when a YR response is valid. 3) To describe the relations between these YR measurements and age, gender, left/right ear, and selected risk factors. YR responses were obtained at four test sites in well babies without risk indicators, well babies with at least one risk indicator, and graduates of neonatal intensive care units. YR responses were measured using a chirp stimulus at moderate levels over a frequency range from 250 to 8000 Hz. The system was calibrated based on measurements in a set of cylindrical tubes. The probe assembly was inserted in the ear canal of the neonate, and customized software was used for data acquisition. YR responses were measured in over 4000 ears, and half of the responses were used in exploratory data analyses. The particular YR variables chosen for analysis were energy reflectance, equivalent volume and acoustic conductance. Based on the view that unduly large negative equivalent volumes at low frequencies were physically impossible, it was concluded that approximately 13% of the YR responses showed evidence of improper probe seal in the ear canal. To test how these outliers influenced the overall pattern of YR responses, analyses were conducted both on the full data set (N = 2081) and the data set excluding outliers (N = 1825). The YR responses averaged over frequency varied with conceptional age (conception to date of test), gender, left/right ear, and selected risk factors; in all cases, significant effects were observed more frequently in the data set excluding outliers. After excluding outliers and controlling for conceptional age effects, the dichotomous risk factors accounting for the greatest variance in the YR responses were, in rank order, cleft lip and palate, aminoglycoside therapy, low birth weight, history of ventilation, and low APGAR scores. In separate analyses, YR responses varied in the first few days after birth. An analysis showed that the use of a YR test criterion to assess the quality of probe seal may help control the false-positive rate in evoked otoacoustic emission testing. This is the first report of wideband YR responses in neonates. Data were acquired in a few seconds, but the responses are highly sensitive to whether the probe is fully sealed in the ear canal. A real-time acoustic test of probe fit is proposed to better address the probe seal problem. The YR responses provide information on middle-ear status that varies over the neonatal age range and that is sensitive to the presence or absence of risk factors, ear, and gender differences. Thus, a YR test may have potential for use in neonatal screening tests for hearing loss.

Noise of a model counterrotation propeller with reduced aft rotor diameter at simulated takeoff/approach conditions (F7/A3)

NASA Technical Reports Server (NTRS)

Woodward, Richard P.; Gordon, Eliott B.

1988-01-01

A model high-speed advanced counterrotation propeller, F7/A3, was tested in the NASA Lewis Research Center 9 by 15 foot Anechoic Wind Tunnel at simulated takeoff/approach conditions of 0.2 Mach number. Acoustic measurements were taken with an axially translating microphone probe, and with a polar microphone probe which was fixed to the propeller nacelle and could take both sideline and circumferential acoustic surveys. Aerodynamic measurements were also made to establish propeller operating conditions. The propeller was run at two setting angles (front angle/rear angle) of 36.4/43.5 and 41.1/46.4 degrees, forward rotor tip speeds from 165 to 259 m/sec, rotor spacings from 8.48 to 14.99 cm based on pitch change axis separation, and angles of attack to 16 degrees. The aft rotor diameter was 85 percent of the forward rotor diameter to reduce tip vortex-aft rotor interaction as a major interaction noise source. Results are compared with equal diameter F7/A7 data which was previously obtained under similar operating conditions. The aft rotor-alone tone was 7 dB lower for the reduced diameter aft rotor, due to reduced tip speed at constant rpm. Interaction tone levels for the F7/A3 propeller were higher at minimum row spacing and lower at maximum spacing.

Review on Dark Photon

NASA Astrophysics Data System (ADS)

Curciarello, Francesca

2016-04-01

e+e- collider experiments at the intensity frontier are naturally suited to probe the existence of a force beyond the Standard Model between WIMPs, the most viable dark matter candidates. The mediator of this new force, known as dark photon, should be a new vector gauge boson very weakly coupled to the Standard Model photon. No significant signal has been observed so far. I will report on current limits set on the coupling factor ɛ2 between the photon and the dark photon by e+e- collider experiments.

Science with the space-based interferometer LISA. IV: probing inflation with gravitational waves

NASA Astrophysics Data System (ADS)

Bartolo, Nicola; Caprini, Chiara; Domcke, Valerie; Figueroa, Daniel G.; Garcia-Bellido, Juan; Chiara Guzzetti, Maria; Liguori, Michele; Matarrese, Sabino; Peloso, Marco; Petiteau, Antoine; Ricciardone, Angelo; Sakellariadou, Mairi; Sorbo, Lorenzo; Tasinato, Gianmassimo

2016-12-01

We investigate the potential for the LISA space-based interferometer to detect the stochastic gravitational wave background produced from different mechanisms during inflation. Focusing on well-motivated scenarios, we study the resulting contributions from particle production during inflation, inflationary spectator fields with varying speed of sound, effective field theories of inflation with specific patterns of symmetry breaking and models leading to the formation of primordial black holes. The projected sensitivities of LISA are used in a model-independent way for various detector designs and configurations. We demonstrate that LISA is able to probe these well-motivated inflationary scenarios beyond the irreducible vacuum tensor modes expected from any inflationary background.

Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification.

PubMed

Oberthuer, André; Berthold, Frank; Warnat, Patrick; Hero, Barbara; Kahlert, Yvonne; Spitz, Rüdiger; Ernestus, Karen; König, Rainer; Haas, Stefan; Eils, Roland; Schwab, Manfred; Brors, Benedikt; Westermann, Frank; Fischer, Matthias

2006-11-01

To develop a gene expression-based classifier for neuroblastoma patients that reliably predicts courses of the disease. Two hundred fifty-one neuroblastoma specimens were analyzed using a customized oligonucleotide microarray comprising 10,163 probes for transcripts with differential expression in clinical subgroups of the disease. Subsequently, the prediction analysis for microarrays (PAM) was applied to a first set of patients with maximally divergent clinical courses (n = 77). The classification accuracy was estimated by a complete 10-times-repeated 10-fold cross validation, and a 144-gene predictor was constructed from this set. This classifier's predictive power was evaluated in an independent second set (n = 174) by comparing results of the gene expression-based classification with those of risk stratification systems of current trials from Germany, Japan, and the United States. The first set of patients was accurately predicted by PAM (cross-validated accuracy, 99%). Within the second set, the PAM classifier significantly separated cohorts with distinct courses (3-year event-free survival [EFS] 0.86 +/- 0.03 [favorable; n = 115] v 0.52 +/- 0.07 [unfavorable; n = 59] and 3-year overall survival 0.99 +/- 0.01 v 0.84 +/- 0.05; both P < .0001) and separated risk groups of current neuroblastoma trials into subgroups with divergent outcome (NB2004: low-risk 3-year EFS 0.86 +/- 0.04 v 0.25 +/- 0.15, P < .0001; intermediate-risk 1.00 v 0.57 +/- 0.19, P = .018; high-risk 0.81 +/- 0.10 v 0.56 +/- 0.08, P = .06). In a multivariate Cox regression model, the PAM predictor classified patients of the second set more accurately than risk stratification of current trials from Germany, Japan, and the United States (P < .001; hazard ratio, 4.756 [95% CI, 2.544 to 8.893]). Integration of gene expression-based class prediction of neuroblastoma patients may improve risk estimation of current neuroblastoma trials.

Pharmacophore modeling using Site-Identification by Ligand Competitive Saturation (SILCS) with multiple probe molecules

PubMed Central

Yu, Wenbo; Lakkaraju, Sirish Kaushik; Raman, E. Prabhu; Fang, Lei; MacKerell, Alexander D.

2015-01-01

Receptor-based pharmacophore modeling is an efficient computer-aided drug design technique that uses the structure of the target protein to identify novel leads. However, most methods consider protein flexibility and desolvation effects in a very approximate way, which may limit their use in practice. The Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling protocol (SILCS-Pharm) was introduced recently to address these issues as SILCS naturally takes both protein flexibility and desolvation effects into account by using full MD simulations to determine 3D maps of the functional group-affinity patterns on a target receptor. In the present work, the SILCS-Pharm protocol is extended to use a wider range of probe molecules including benzene, propane, methanol, formamide, acetaldehyde, methylammonium, acetate and water. This approach removes the previous ambiguity brought by using water as both the hydrogen-bond donor and acceptor probe molecule. The new SILCS-Pharm protocol is shown to yield improved screening results as compared to the previous approach based on three target proteins. Further validation of the new protocol using five additional protein targets showed improved screening compared to those using common docking methods, further indicating improvements brought by the explicit inclusion of additional feature types associated with the wider collection of probe molecules in the SILCS simulations. The advantage of using complementary features and volume constraints, based on exclusion maps of the protein defined from the SILCS simulations, is presented. In addition, re-ranking using SILCS-based ligand grid free energies is shown to enhance the diversity of identified ligands for the majority of targets. These results suggest that the SILCS-Pharm protocol will be of utility in rational drug design. PMID:25622696

Nonlinear information fusion algorithms for data-efficient multi-fidelity modelling.

PubMed

Perdikaris, P; Raissi, M; Damianou, A; Lawrence, N D; Karniadakis, G E

2017-02-01

Multi-fidelity modelling enables accurate inference of quantities of interest by synergistically combining realizations of low-cost/low-fidelity models with a small set of high-fidelity observations. This is particularly effective when the low- and high-fidelity models exhibit strong correlations, and can lead to significant computational gains over approaches that solely rely on high-fidelity models. However, in many cases of practical interest, low-fidelity models can only be well correlated to their high-fidelity counterparts for a specific range of input parameters, and potentially return wrong trends and erroneous predictions if probed outside of their validity regime. Here we put forth a probabilistic framework based on Gaussian process regression and nonlinear autoregressive schemes that is capable of learning complex nonlinear and space-dependent cross-correlations between models of variable fidelity, and can effectively safeguard against low-fidelity models that provide wrong trends. This introduces a new class of multi-fidelity information fusion algorithms that provide a fundamental extension to the existing linear autoregressive methodologies, while still maintaining the same algorithmic complexity and overall computational cost. The performance of the proposed methods is tested in several benchmark problems involving both synthetic and real multi-fidelity datasets from computational fluid dynamics simulations.

Monitoring the injured brain: registered, patient specific atlas models to improve accuracy of recovered brain saturation values

NASA Astrophysics Data System (ADS)

Clancy, Michael; Belli, Antonio; Davies, David; Lucas, Samuel J. E.; Su, Zhangjie; Dehghani, Hamid

2015-07-01

The subject of superficial contamination and signal origins remains a widely debated topic in the field of Near Infrared Spectroscopy (NIRS), yet the concept of using the technology to monitor an injured brain, in a clinical setting, poses additional challenges concerning the quantitative accuracy of recovered parameters. Using high density diffuse optical tomography probes, quantitatively accurate parameters from different layers (skin, bone and brain) can be recovered from subject specific reconstruction models. This study assesses the use of registered atlas models for situations where subject specific models are not available. Data simulated from subject specific models were reconstructed using the 8 registered atlas models implementing a regional (layered) parameter recovery in NIRFAST. A 3-region recovery based on the atlas model yielded recovered brain saturation values which were accurate to within 4.6% (percentage error) of the simulated values, validating the technique. The recovered saturations in the superficial regions were not quantitatively accurate. These findings highlight differences in superficial (skin and bone) layer thickness between the subject and atlas models. This layer thickness mismatch was propagated through the reconstruction process decreasing the parameter accuracy.

Experimental Investigation of Subsonic Turbulent Boundary Layer Flow Over a Wall-Mounted Axisymmetric Hill

NASA Technical Reports Server (NTRS)

Bell, James H.; Heineck, James T.; Zilliac, Gregory; Mehta, Rabindra D.; Long, Kurtis R.

2016-01-01

An important goal for modern fluid mechanics experiments is to provide datasets which present a challenge for Computational Fluid Dynamics simulations to reproduce. Such "CFD validation experiments" should be well-characterized and well-documented, and should investigate flows which are difficult for CFD to calculate. It is also often convenient for the experiment to be challenging for CFD in some aspects while simple in others. This report is part of the continuing documentation of a series of experiments conducted to characterize the flow around an axisymmetric, modified-cosine-shaped, wall-mounted hill named "FAITH" (Fundamental Aero Investigates The Hill). Computation of this flow is easy in some ways - subsonic flow over a simple shape - while being complex in others - separated flow and boundary layer interactions. The primary set of experiments were performed on a 15.2 cm high, 45.7 cm base diameter machined aluminum model that was tested at mean speeds of 50 m/s (Reynolds Number based on height = 500,000). The ratio of model height to boundary later height was approximately 3. The flow was characterized using surface oil flow visualization, Cobra probe to determine point-wise steady and unsteady 3D velocities, Particle Image Velocimetry (PIV) to determine 3D velocities and turbulence statistics along specified planes, Pressure Sensitive Paint (PSP) to determine mean surface pressures, and Fringe Imaging Skin Friction (FISF) to determine surface skin friction magnitude and direction. A set of pathfinder experiments were also performed in a water channel on a smaller scale (5.1 cm high, 15.2 cm base diameter) sintered nylon model. The water channel test was conducted at a mean test section speed of 3 cm/s (Reynolds Number of 1500), but at the same ratio of model height to boundary layer thickness. Dye injection from both the model and an upstream rake was used to visualize the flow. This report summarizes the experimental set-up, techniques used, and data acquired. It also describes some details of the dataset that is being constructed for use by other researchers, especially the CFD community.

Determining confounding sensitivities in eddy current thin film measurements

NASA Astrophysics Data System (ADS)

Gros, Ethan; Udpa, Lalita; Smith, James A.; Wachs, Katelyn

2017-02-01

Eddy current (EC) techniques are widely used in industry to measure the thickness of non-conductive films on a metal substrate. This is done by using a system whereby a coil carrying a high-frequency alternating current is used to create an alternating magnetic field at the surface of the instrument's probe. When the probe is brought near a conductive surface, the alternating magnetic field will induce ECs in the conductor. The substrate characteristics and the distance of the probe from the substrate (the coating thickness) affect the magnitude of the ECs. The induced currents load the probe coil affecting the terminal impedance of the coil. The measured probe impedance is related to the lift off between coil and conductor as well as conductivity of the test sample. For a known conductivity sample, the probe impedance can be converted into an equivalent film thickness value. The EC measurement can be confounded by a number of measurement parameters. It was the goal of this research to determine which physical properties of the measurement set-up and sample can adversely affect the thickness measurement. The eddy-current testing was performed using a commercially available, hand-held eddy-current probe (ETA3.3H spring-loaded eddy probe running at 8 MHz) that comes with a stand to hold the probe. The stand holds the probe and adjusts the probe on the z-axis to help position the probe in the correct area as well as make precise measurements. The signal from the probe was sent to a hand-held readout, where the results are recorded directly in terms of liftoff or film thickness. Understanding the effect of certain factors on the measurements of film thickness, will help to evaluate how accurate the ETA3.3H spring-loaded eddy probe was at measuring film thickness under varying experimental conditions. This research studied the effects of a number of factors such as i) conductivity, ii) edge effect, iii) surface finish of base material and iv) cable condition.

On CD-AFM bias related to probe bending

NASA Astrophysics Data System (ADS)

Ukraintsev, V. A.; Orji, N. G.; Vorburger, T. V.; Dixson, R. G.; Fu, J.; Silver, R. M.

2012-03-01

Critical Dimension AFM (CD-AFM) is a widely used reference metrology. To characterize modern semiconductor devices, very small and flexible probes, often 15 nm to 20 nm in diameter, are now frequently used. Several recent publications have reported on uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements [1,2]. Results obtained in this work suggest that probe bending can be on the order of several nanometers and thus potentially can explain much of the observed CD-AFM probe-to-probe bias variation. We have developed and experimentally tested one-dimensional (1D) and two-dimensional (2D) models to describe the bending of cylindrical probes. An earlier 1D bending model reported by Watanabe et al. [3] was refined. Contributions from several new phenomena were considered, including: probe misalignment, diameter variation near the carbon nanotube tip (CNT) apex, probe bending before snapping, distributed van der Waals-London force, etc. The methodology for extraction of the Hamaker probe-surface interaction energy from experimental probe bending data was developed. To overcome limitations of the 1D model, a new 2D distributed force (DF) model was developed. Comparison of the new model with the 1D single point force (SPF) model revealed about 27 % difference in probe bending bias between the two. A simple linear relation between biases predicted by the 1D SPF and 2D DF models was found. This finding simplifies use of the advanced 2D DF model of probe bending in various CD-AFM applications. New 2D and three-dimensional (3D) CDAFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

The special role of item-context associations in the direct-access region of working memory.

PubMed

Campoy, Guillermo

2017-09-01

The three-embedded-component model of working memory (WM) distinguishes three representational states corresponding to three WM regions: activated long-term memory, direct-access region (DAR), and focus of attention. Recent neuroimaging research has revealed that access to the DAR is associated with enhanced hippocampal activity. Because the hippocampus mediates the encoding and retrieval of item-context associations, it has been suggested that this hippocampal activation is a consequence of the fact that item-context associations are particularly strong and accessible in the DAR. This study provides behavioral evidence for this view using an item-recognition task to assess the effect of non-intentional encoding and maintenance of item-location associations across WM regions. Five pictures of human faces were sequentially presented in different screen locations followed by a recognition probe. Visual cues immediately preceding the probe indicated the location thereof. When probe stimuli appeared in the same location that they had been presented within the memory set, the presentation of the cue was expected to elicit the activation of the corresponding WM representation through the just-established item-location association, resulting in faster recognition. Results showed this same-location effect, but only for items that, according to their serial position within the memory set, were held in the DAR.

Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays

PubMed Central

Binder, Hans; Fasold, Mario; Glomb, Torsten

2009-01-01

Background Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates. Methodology/Principal Findings The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G) and the particular type of mismatched pairings formed in cross-allelic probe/target duplexes constitute sources of systematic biases of the probe signals with consequences for genotyping and copy number estimates. The poly-G effect seems to be related to the crowded arrangement of probes which facilitates complex formation of neighboring probes with at minimum three adjacent G's in their sequence. Conclusions The applied method of “triple-averaging” represents a model-free approach to estimate the mean intensity contributions of different sequence motifs which can be applied in calibration algorithms to correct signal values for sequence effects. Rules for appropriate sequence corrections are suggested. PMID:19924253

Novel Handheld Magnetometer Probe Based on Magnetic Tunnelling Junction Sensors for Intraoperative Sentinel Lymph Node Identification

PubMed Central

Cousins, A.; Balalis, G. L.; Thompson, S. K.; Forero Morales, D.; Mohtar, A.; Wedding, A. B.; Thierry, B.

2015-01-01

Using magnetic tunnelling junction sensors, a novel magnetometer probe for the identification of the sentinel lymph node using magnetic tracers was developed. Probe performance was characterised in vitro and validated in a preclinical swine model. Compared to conventional gamma probes, the magnetometer probe showed excellent spatial resolution of 4.0 mm, and the potential to detect as few as 5 μg of magnetic tracer. Due to the high sensitivity of the magnetometer, all first-tier nodes were identified in the preclinical experiments, and there were no instances of false positive or false negative detection. Furthermore, these preliminary data encourage the application of the magnetometer probe for use in more complex lymphatic environments, such as in gastrointestinal cancers, where the sentinel node is often in close proximity to other non-sentinel nodes, and high spatial resolution detection is required. PMID:26038833

Development and Application of Wide Bandwidth Magneto-Resistive Sensor Based Eddy Current Probe

NASA Technical Reports Server (NTRS)

Wincheski, Russell A.; Simpson, John

2010-01-01

The integration of magneto-resistive sensors into eddy current probes can significantly expand the capabilities of conventional eddy current nondestructive evaluation techniques. The room temperature solid-state sensors have typical bandwidths in the megahertz range and resolutions of tens of microgauss. The low frequency sensitivity of magneto-resistive sensors has been capitalized upon in previous research to fabricate very low frequency eddy current sensors for deep flaw detection in multilayer conductors. In this work a modified probe design is presented to expand the capabilities of the device. The new probe design incorporates a dual induction source enabling operation from low frequency deep flaw detection to high frequency high resolution near surface material characterization. Applications of the probe for the detection of localized near surface conductivity anomalies are presented. Finite element modeling of the probe is shown to be in good agreement with experimental measurements.

Modelling studies in aqueous solution of lanthanide (III) chelates designed for nuclear magnetic resonance biomedical applications

NASA Astrophysics Data System (ADS)

Henriques, E. S.; Geraldes, C. F. G. C.; Ramos, M. J.

Molecular dynamics simulations and complementary modelling studies have been carried out for the [Gd(DOTA)·(H2O)]- and [Tm(DOTP)]5- chelates in aqueous media, to provide a better understanding of several structural and dynamical properties of these versatile nuclear magnetic resonance (NMR) probes, including coordination shells and corresponding water exchange mechanisms, and interactions of these complexes with alkali metal ions. This knowledge is of key importance in the areas of 1H relaxation and shift reagents for NMR applications in medical diagnosis. A new refinement of our own previously developed set of parameters for these Ln(III) chelates has been used, and is reported here. Calculations of water mean residence times suggest a reassessment of the characterization of the chelates' second coordination shell, one where the simple spherical distribution model is discarded in favour of a more detailed approach. Na+ probe interaction maps are in good agreement with the available site location predictions derived from 23Na NMR shifts.

Correlated adiabatic and isocurvature cosmic microwave background fluctuations in the wake of the results from the wilkinson microwave anisotropy probe.

PubMed

Väliviita, Jussi; Muhonen, Vesa

2003-09-26

In general correlated models, in addition to the usual adiabatic component with a spectral index n(ad1) there is another adiabatic component with a spectral index n(ad2) generated by entropy perturbation during inflation. We extend the analysis of a correlated mixture of adiabatic and isocurvature cosmic microwave background fluctuations of the Wilkinson Microwave Anisotropy Probe (WMAP) group, who set the two adiabatic spectral indices equal. Allowing n(ad1) and n(ad2) to vary independently we find that the WMAP data favor models where the two adiabatic components have opposite spectral tilts. Using the WMAP data only, the 2sigma upper bound for the isocurvature fraction f(iso) of the initial power spectrum at k(0)=0.05 Mpc(-1) increases somewhat, e.g., from 0.76 of n(ad2)=n(ad1) models to 0.84 with a prior n(iso)<1.84 for the isocurvature spectral index.

Resolving Dynamic Properties of Polymers through Coarse-Grained Computational Studies

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

Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora

2016-02-05

Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly modeled. In this paper, we probe the degree of coarse graining required to simultaneously retain significant atomistic details and access large length and time scales. The degree of coarse graining in turn sets the minimum length scale instrumental in defining polymer properties and dynamics. Using linear polyethylene as a model system, we probe how the coarse-graining scale affects the measured dynamics. Iterative Boltzmann inversion ismore » used to derive coarse-grained potentials with 2–6 methylene groups per coarse-grained bead from a fully atomistic melt simulation. We show that atomistic detail is critical to capturing large-scale dynamics. Finally, using these models we simulate polyethylene melts for times over 500 μs to study the viscoelastic properties of well-entangled polymer melts.« less

A resource for benchmarking the usefulness of protein structure models.

PubMed

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

In Vivo Imaging of Immuno-Spin Trapped Radicals With Molecular Magnetic Resonance Imaging in a Diabetic Mouse Model

PubMed Central

Towner, Rheal A.; Smith, Nataliya; Saunders, Debra; Henderson, Michael; Downum, Kristen; Lupu, Florea; Silasi-Mansat, Robert; Ramirez, Dario C.; Gomez-Mejiba, Sandra E.; Bonini, Marcelo G.; Ehrenshaft, Marilyn; Mason, Ronald P.

2012-01-01

Oxidative stress plays a major role in diabetes. In vivo levels of membrane-bound radicals (MBRs) in a streptozotocin-induced diabetic mouse model were uniquely detected by combining molecular magnetic resonance imaging (mMRI) and immunotrapping techniques. An anti-DMPO (5,5-dimethyl-1-pyrroline N-oxide) antibody (Ab) covalently bound to an albumin (BSA)-Gd (gadolinium)-DTPA (diethylene triamine penta acetic acid)-biotin MRI contrast agent (anti-DMPO probe), and mMRI, were used to detect in vivo levels of DMPO-MBR adducts in kidneys, livers, and lungs of diabetic mice, after DMPO administration. Magnetic resonance signal intensities, which increase in the presence of a Gd-based molecular probe, were significantly higher within the livers, kidneys, and lungs of diabetic animals administered the anti-DMPO probe compared with controls. Fluorescence images validated the location of the anti-DMPO probe in excised tissues via conjugation of streptavidin-Cy3, which targeted the probe biotin moiety, and immunohistochemistry was used to validate the presence of DMPO adducts in diabetic mouse livers. This is the first report of noninvasively imaging in vivo levels of MBRs within any disease model. This method can be specifically applied toward diabetes models for in vivo assessment of free radical levels, providing an avenue to more fully understand the role of free radicals in diabetes. PMID:22698922

Portable oral cancer detection using a miniature confocal imaging probe with a large field of view

NASA Astrophysics Data System (ADS)

Wang, Youmin; Raj, Milan; McGuff, H. Stan; Bhave, Gauri; Yang, Bin; Shen, Ting; Zhang, Xiaojing

2012-06-01

We demonstrate a MEMS micromirror enabled handheld confocal imaging probe for portable oral cancer detection, where a comparatively large field of view (FOV) was generated through the programmable Lissajous scanning pattern of the MEMS micromirror. Miniaturized handheld MEMS confocal imaging probe was developed, and further compared with the desktop confocal prototype under clinical setting. For the handheld confocal imaging system, optical design simulations using CODE VR® shows the lateral and axial resolution to be 0.98 µm and 4.2 µm, where experimental values were determined to be 3 µm and 5.8 µm, respectively, with a FOV of 280 µm×300 µm. Fast Lissajous imaging speed up to 2 fps was realized with improved Labview and Java based real-time imaging software. Properties such as 3D imaging through autofocusing and mosaic imaging for extended lateral view (6 mm × 8 mm) were examined for carcinoma real-time pathology. Neoplastic lesion tissues of giant cell fibroma and peripheral ossifying fibroma, the fibroma inside the paraffin box and ex vivo gross tissues were imaged by the bench-top and handheld imaging modalities, and further compared with commercial microscope imaging results. The MEMS scanner-based handheld confocal imaging probe shows great promise as a potential clinical tool for oral cancer diagnosis and treatment.

A faculty development workshop in narrative-based reflective writing.

PubMed

Boudreau, J Donald; Liben, Stephen; Fuks, Abraham

2012-08-01

Narrative approaches are used increasingly in the health professions with a range of objectives. We must acquaint educators with this burgeoning field and prepare them for the incorporation of story-telling in their pedagogical practices. The authors describe a template for a faculty development workshop designed to foster self-reflection through the use of narrative techniques and prepare clinical teachers to deploy such approaches. The design is based on a six-year experience in delivering introductory workshops in narrative approaches to medical teachers. The workshops, which served as a model for the template, have been offered to a total of 92 clinicians being trained to mentor medical students. A generic template is described. It includes a table of core concepts from narrative theory, a set of probing questions useful in a basic technical analysis of texts and a list of initiating prompts for exercises in reflective writing. A workshop organized and deployed using this template is deliverable over a half-day. The model has proven to be feasible and highly valued by participants. It can be adapted for other contexts by educators across the continuum of health professional education.

Multiplexed fibre optic sensing in the distal lung (Conference Presentation)

NASA Astrophysics Data System (ADS)

Choudhary, Tushar R.; Tanner, Michael G.; Megia-Fernandez, Alicia; Harrington, Kerrianne; Wood, Harry A.; Chankeshwara, Sunay; Zhu, Patricia; Choudhury, Debaditya; Yu, Fei; Thomson, Robert R.; Duncan, Rory R.; Dhaliwal, Kevin; Bradley, Mark

2017-02-01

We present a toolkit for a multiplexed pH and oxygen sensing probe in the distal lung using multicore fibres. Measuring physiological relevant parameters like pH and oxygen is of significant importance in understanding changes associated with disease pathology. We present here, a single multicore fibre based pH and oxygen sensing probe which can be used with a standard bronchoscope to perform in vivo measurements in the distal lung. The multiplexed probe consists of fluorescent pH sensors (fluorescein based) and oxygen sensors (Palladium porphyrin complex based) covalently bonded to silica microspheres (10 µm) loaded on the distal facet of a 19 core (10 µm core diameter) multicore fibre (total diameter of 150 µm excluding coating). Pits are formed by selectively etching the cores using hydrofluoric acid, multiplexing is achieved through the self-location of individual probes on differing cores. This architecture can be expanded to include probes for further parameters. Robust measurements are demonstrated of self-referencing fluorophores, not limited by photobleaching, with short (100ms) measurement times at low ( 10µW) illumination powers. We have performed on bench calibration and tests of in vitro tissue models and in an ovine whole lung model to validate our sensors. The pH sensor is demonstrated in the physiologically relevant range of pH 5 to pH 8.5 and with an accuracy of ± 0.05 pH units. The oxygen sensor is demonstrated in gas mixtures downwards from 20% oxygen and in liquid saturated with 20% oxygen mixtures ( 8mg/L) down to full depletion (0mg/L) with 0.5mg/L accuracy.

Determination of propranolol hydrochloride in pharmaceutical preparations using near infrared spectrometry with fiber optic probe and multivariate calibration methods.

PubMed

Marques Junior, Jucelino Medeiros; Muller, Aline Lima Hermes; Foletto, Edson Luiz; da Costa, Adilson Ben; Bizzi, Cezar Augusto; Irineu Muller, Edson

2015-01-01

A method for determination of propranolol hydrochloride in pharmaceutical preparation using near infrared spectrometry with fiber optic probe (FTNIR/PROBE) and combined with chemometric methods was developed. Calibration models were developed using two variable selection models: interval partial least squares (iPLS) and synergy interval partial least squares (siPLS). The treatments based on the mean centered data and multiplicative scatter correction (MSC) were selected for models construction. A root mean square error of prediction (RMSEP) of 8.2 mg g(-1) was achieved using siPLS (s2i20PLS) algorithm with spectra divided into 20 intervals and combination of 2 intervals (8501 to 8801 and 5201 to 5501 cm(-1)). Results obtained by the proposed method were compared with those using the pharmacopoeia reference method and significant difference was not observed. Therefore, proposed method allowed a fast, precise, and accurate determination of propranolol hydrochloride in pharmaceutical preparations. Furthermore, it is possible to carry out on-line analysis of this active principle in pharmaceutical formulations with use of fiber optic probe.

Low energy probes of PeV scale sfermions

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

Altmannshofer, Wolfgang; Harnik, Roni; Zupan, Jure

2013-11-27

We derive bounds on squark and slepton masses in mini-split supersymmetry scenario using low energy experiments. In this setup gauginos are at the TeV scale, while sfermions are heavier by a loop factor. We cover the most sensitive low energy probes including electric dipole moments (EDMs), meson oscillations and charged lepton flavor violation (LFV) transitions. A leading log resummation of the large logs of gluino to sfermion mass ratio is performed. A sensitivity to PeV squark masses is obtained at present from kaon mixing measurements. A number of observables, including neutron EDMs, mu->e transitions and charmed meson mixing, will startmore » probing sfermion masses in the 100 TeV-1000 TeV range with the projected improvements in the experimental sensitivities. We also discuss the implications of our results for a variety of models that address the flavor hierarchy of quarks and leptons. We find that EDM searches will be a robust probe of models in which fermion masses are generated radiatively, while LFV searches remain sensitive to simple-texture based flavor models.« less

A Real-Time Method for Estimating Viscous Forebody Drag Coefficients

NASA Technical Reports Server (NTRS)

Whitmore, Stephen A.; Hurtado, Marco; Rivera, Jose; Naughton, Jonathan W.

2000-01-01

This paper develops a real-time method based on the law of the wake for estimating forebody skin-friction coefficients. The incompressible law-of-the-wake equations are numerically integrated across the boundary layer depth to develop an engineering model that relates longitudinally averaged skin-friction coefficients to local boundary layer thickness. Solutions applicable to smooth surfaces with pressure gradients and rough surfaces with negligible pressure gradients are presented. Model accuracy is evaluated by comparing model predictions with previously measured flight data. This integral law procedure is beneficial in that skin-friction coefficients can be indirectly evaluated in real-time using a single boundary layer height measurement. In this concept a reference pitot probe is inserted into the flow, well above the anticipated maximum thickness of the local boundary layer. Another probe is servomechanism-driven and floats within the boundary layer. A controller regulates the position of the floating probe. The measured servomechanism position of this second probe provides an indirect measurement of both local and longitudinally averaged skin friction. Simulation results showing the performance of the control law for a noisy boundary layer are then presented.

Development and utilization of new diagnostics for dense-phase pneumatic transport. Quarterly technical progress report, October 1-December 31, 1989

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

Louge, M. Y.; Jenkins, J. T.

The main objective of this work is to develop probes for local measurements of solid velocity and holdup in dense gas-solid flows. In particular, capacitance probes are designed to measure local, time-dependent particle concentrations. In addition, a new optical fiber probe based on laser-induced-phosphorescence is developed to measure particle velocities. The principles for the capacitance and optical diagnostics were given in our first and second quarterly reports. In this reporting period, we have demonstrated with success the feasibility of the optical fiber probe. Another objective of this work is to develop a model of dense-phase conveying and to test thismore » model in a setup that incorporates our diagnostics. In this period, as a prelude to these modeling efforts scheduled for the third year of the contract, we have carried out additional computer simulations of rapid granular flows to verify the theories of Jenkins and Richman (1988) on the anisotropy of the second moment in simple shear. 2 refs., 5 figs.« less

Single top quark production as a probe of anomalous tqγ and tqZ couplings at the FCC-ee

NASA Astrophysics Data System (ADS)

Khanpour, Hamzeh; Khatibi, Sara; Yanehsari, Morteza Khatiri; Najafabadi, Mojtaba Mohammadi

2017-12-01

In this paper, a detailed study to probe the top quark Flavour-Changing Neutral Currents (FCNC) tqγ and tqZ at the future e-e+ collider FCC-ee in two different center-of-mass energies of 240 and 350 GeV is presented. A set of useful variables are proposed and used in a multivariate technique to separate signal e-e+ → Z / γ → t q bar (t bar q) from Standard Model background processes. The study includes a fast detector simulation based on the DELPHES package to consider the detector effects. The upper limits on the FCNC branching ratios at 95% confidence level (CL) in terms of the integrated luminosity are presented. It is shown that with 300 fb-1 of integrated luminosity of data, FCC-ee would be able to exclude the effective coupling strengths above O (10-4 -10-5) which is corresponding to branching fraction of O (0.01 - 0.001)%. We show that moving to a high-luminosity regime leads to a significant improvement on the upper bounds on the top quark FCNC couplings to a photon or a Z boson.

Noise of a model high speed counterrotation propeller at simulated takeoff/approach conditions (F7/A7)

NASA Technical Reports Server (NTRS)

Woodward, Richard P.

1987-01-01

A high speed advanced counterrotation propeller, was tested in the NASA-Lewis 9 x 15 foot Anechoic Wind Tunnel at simulated takeoff/approach conditions of 0.2 Mach number. Acoustic measurements were taken with fixed floor microphones, an axially translating microphone probe, and with a polar microphone probe which was fixed to the propeller nacelle and could take both sideline and circumferential acoustic surveys. Aerodynamic measurements were also made to establish the propeller operating conditions. The propeller was run over a range of blade setting angles from 36.4/36.5 to 41.1/39.4 deg, tip speeds from 165 to 259 m/sec, rotor spacings from 1.56 to 3.63 based on forward rotor tip chord to aerodynamic separation, and angles of attack to + or - 16 deg. First order rotor alone tones showed highest directivity levels near the propeller plane, while interaction tone showed high levels throughout sideline directivity, especially toward the propeller rotation axis. Interaction tone levels were sensitive to propeller row spacing while rotor alone tones showed little spacing effect. There is a decreased noise level associated with higher propeller blade numbers for the same overall propeller thrust.

An individually tailored treatment programme for improved oral hygiene: introduction of a new course of action in health education for patients with periodontitis.

PubMed

Jönsson, B; Ohrn, K; Oscarson, N; Lindberg, P

2009-08-01

To describe and evaluate an individually tailored treatment programme based on a behavioural medicine approach to oral hygiene self-care for patients with chronic periodontitis. Two experimental single-case studies with multiple-baseline design across different self-administered oral hygiene behaviours were conducted. Cognitive Behavioural techniques were used to organize the strategies for the intervention and the approach to counselling was inspired by and structured in accordance with Motivational Interviewing. The central features in the programme were the individual analysis of knowledge and oral hygiene habits, individually set goals for oral hygiene behaviour, practice of manual dexterity for oral hygiene aids, continuous self-monitoring of the behaviour and prevention of relapse. Both participants reached the predecided criteria for clinical significance in reducing plaque and bleeding on probing. Reductions of periodontal probing depth were achieved as well. The positive results remained stable throughout the 2-year study period. The successful application of this educational model suggests that it could be used as a method for tailoring interventions targeted to oral hygiene for patients with periodontal conditions. The programme will now be tested in a larger randomized controlled trial.

Colposcopic imaging using visible-light optical coherence tomography.

PubMed

Duan, Lian; McRaven, Michael D; Liu, Wenzhong; Shu, Xiao; Hu, Jianmin; Sun, Cheng; Veazey, Ronald S; Hope, Thomas J; Zhang, Hao F

2017-05-01

High-resolution colposcopic optical coherence tomography (OCT) provides key anatomical measures, such as thickness and minor traumatic injury of vaginal epithelium, of the female reproductive tract noninvasively. This information can be helpful in both fundamental investigations in animal models and disease screenings in humans. We present a fiber-based visible-light OCT and two probe designs for colposcopic application. One probe conducts circular scanning using a DC motor, and the other probe is capable of three-dimensional imaging over a 4.6 × 4.6 - mm 2 area using a pair of galvo scanners. Using this colposcopic vis-OCT with both probes, we acquired high-resolution images from whole isolated macaque vaginal samples and identified biopsy lesions.

Colposcopic imaging using visible-light optical coherence tomography

NASA Astrophysics Data System (ADS)

Duan, Lian; McRaven, Michael D.; Liu, Wenzhong; Shu, Xiao; Hu, Jianmin; Sun, Cheng; Veazey, Ronald S.; Hope, Thomas J.; Zhang, Hao F.

2017-05-01

High-resolution colposcopic optical coherence tomography (OCT) provides key anatomical measures, such as thickness and minor traumatic injury of vaginal epithelium, of the female reproductive tract noninvasively. This information can be helpful in both fundamental investigations in animal models and disease screenings in humans. We present a fiber-based visible-light OCT and two probe designs for colposcopic application. One probe conducts circular scanning using a DC motor, and the other probe is capable of three-dimensional imaging over a 4.6×4.6-mm2 area using a pair of galvo scanners. Using this colposcopic vis-OCT with both probes, we acquired high-resolution images from whole isolated macaque vaginal samples and identified biopsy lesions.

Validation of single-fluid and two-fluid magnetohydrodynamic models of the helicity injected torus spheromak experiment with the NIMROD code

NASA Astrophysics Data System (ADS)

Akcay, Cihan; Kim, Charlson C.; Victor, Brian S.; Jarboe, Thomas R.

2013-08-01

We present a comparison study of 3-D pressureless resistive MHD (rMHD) and 3-D presureless two-fluid MHD models of the Helicity Injected Torus with Steady Inductive helicity injection (HIT-SI). HIT-SI is a current drive experiment that uses two geometrically asymmetric helicity injectors to generate and sustain toroidal plasmas. The comparable size of the collisionless ion skin depth di to the resistive skin depth predicates the importance of the Hall term for HIT-SI. The simulations are run with NIMROD, an initial-value, 3-D extended MHD code. The modeled plasma density and temperature are assumed uniform and constant. The helicity injectors are modeled as oscillating normal magnetic and parallel electric field boundary conditions. The simulations use parameters that closely match those of the experiment. The simulation output is compared to the formation time, plasma current, and internal and surface magnetic fields. Results of the study indicate 2fl-MHD shows quantitative agreement with the experiment while rMHD only captures the qualitative features. The validity of each model is assessed based on how accurately it reproduces the global quantities as well as the temporal and spatial dependence of the measured magnetic fields. 2fl-MHD produces the current amplification Itor/Iinj and formation time τf demonstrated by HIT-SI with similar internal magnetic fields. rMHD underestimates Itor/Iinj and exhibits much a longer τf. Biorthogonal decomposition (BD), a powerful mathematical tool for reducing large data sets, is employed to quantify how well the simulations reproduce the measured surface magnetic fields without resorting to a probe-by-probe comparison. BD shows that 2fl-MHD captures the dominant surface magnetic structures and the temporal behavior of these features better than rMHD.

Investigating High-School Students' Reasoning Strategies when They Solve Linear Equations

ERIC Educational Resources Information Center

Huntley, Mary Ann; Marcus, Robin; Kahan, Jeremy; Miller, Jane Lincoln

2007-01-01

A cross-curricular structured-probe task-based clinical interview study with 44 pairs of third-year high-school mathematics students, most of whom were high achieving, was conducted to investigate their approaches to a variety of algebra problems. This paper presents results from one problem that involved solving a set of three linear equations of…

A new diagnostic real-time PCR method for huanglongbing detection in citrus root tissue

USDA-ARS?s Scientific Manuscript database

Citrus fibrous root tissue was evaluated as an alternative source material for Huanglongbing (HLB) diagnosis by real-time PCR using primer-probe set TXCChlb, developed in the present study based on 16S rDNA of “Candidatus Liberibacter asiaticus” (CLas). Real-time PCR data obtained with DNA samples p...

Development of a Microarray-Based Tool To Characterize Vaginal Bacterial Fluctuations and Application to a Novel Antibiotic Treatment for Bacterial Vaginosis

PubMed Central

Cruciani, Federica; Biagi, Elena; Severgnini, Marco; Consolandi, Clarissa; Calanni, Fiorella; Donders, Gilbert; Brigidi, Patrizia

2015-01-01

The healthy vaginal microbiota is generally dominated by lactobacilli that confer antimicrobial protection and play a crucial role in health. Bacterial vaginosis (BV) is the most prevalent lower genital tract infection in women in reproductive age and is characterized by a shift in the relative abundances of Lactobacillus spp. to a greater abundance of strictly anaerobic bacteria. In this study, we designed a new phylogenetic microarray-based tool (VaginArray) that includes 17 probe sets specific for the most representative bacterial groups of the human vaginal ecosystem. This tool was implemented using the ligase detection reaction-universal array (LDR-UA) approach. The entire probe set properly recognized the specific targets and showed an overall sensitivity of 6 to 12 ng per probe. The VaginArray was applied to assess the efficacy of rifaximin vaginal tablets for the treatment of BV, analyzing the vaginal bacterial communities of 22 BV-affected women treated with rifaximin vaginal tablets at a dosage of 25 mg/day for 5 days. Our results showed the ability of rifaximin to reduce the growth of various BV-related bacteria (Atopobium vaginae, Prevotella, Megasphaera, Mobiluncus, and Sneathia spp.), with the highest antibiotic susceptibility for A. vaginae and Sneathia spp. Moreover, we observed an increase of Lactobacillus crispatus levels in the subset of women who maintained remission after 1 month of therapy, opening new perspectives for the treatment of BV. PMID:25733514

An Approximation to the Adaptive Exponential Integrate-and-Fire Neuron Model Allows Fast and Predictive Fitting to Physiological Data.

PubMed

Hertäg, Loreen; Hass, Joachim; Golovko, Tatiana; Durstewitz, Daniel

2012-01-01

For large-scale network simulations, it is often desirable to have computationally tractable, yet in a defined sense still physiologically valid neuron models. In particular, these models should be able to reproduce physiological measurements, ideally in a predictive sense, and under different input regimes in which neurons may operate in vivo. Here we present an approach to parameter estimation for a simple spiking neuron model mainly based on standard f-I curves obtained from in vitro recordings. Such recordings are routinely obtained in standard protocols and assess a neuron's response under a wide range of mean-input currents. Our fitting procedure makes use of closed-form expressions for the firing rate derived from an approximation to the adaptive exponential integrate-and-fire (AdEx) model. The resulting fitting process is simple and about two orders of magnitude faster compared to methods based on numerical integration of the differential equations. We probe this method on different cell types recorded from rodent prefrontal cortex. After fitting to the f-I current-clamp data, the model cells are tested on completely different sets of recordings obtained by fluctuating ("in vivo-like") input currents. For a wide range of different input regimes, cell types, and cortical layers, the model could predict spike times on these test traces quite accurately within the bounds of physiological reliability, although no information from these distinct test sets was used for model fitting. Further analyses delineated some of the empirical factors constraining model fitting and the model's generalization performance. An even simpler adaptive LIF neuron was also examined in this context. Hence, we have developed a "high-throughput" model fitting procedure which is simple and fast, with good prediction performance, and which relies only on firing rate information and standard physiological data widely and easily available.

Predicting the partitioning of biological compounds between room-temperature ionic liquids and water by means of the solvation-parameter model.

PubMed

Padró, Juan M; Ponzinibbio, Agustín; Mesa, Leidy B Agudelo; Reta, Mario

2011-03-01

The partition coefficients, P(IL/w), for different probe molecules as well as for compounds of biological interest between the room-temperature ionic liquids (RTILs) 1-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF(6)], 1-hexyl-3-methylimidazolium hexafluorophosphate, [HMIM][PF(6)], 1-octyl-3-methylimidazolium tetrafluoroborate, [OMIM][BF(4)] and water were accurately measured. [BMIM][PF(6)] and [OMIM][BF(4)] were synthesized by adapting a procedure from the literature to a simpler, single-vessel and faster methodology, with a much lesser consumption of organic solvent. We employed the solvation-parameter model to elucidate the general chemical interactions involved in RTIL/water partitioning. With this purpose, we have selected different solute descriptor parameters that measure polarity, polarizability, hydrogen-bond-donor and hydrogen-bond-acceptor interactions, and cavity formation for a set of specifically selected probe molecules (the training set). The obtained multiparametric equations were used to predict the partition coefficients for compounds not present in the training set (the test set), most being of biological interest. Partial solubility of the ionic liquid in water (and water into the ionic liquid) was taken into account to explain the obtained results. This fact has not been deeply considered up to date. Solute descriptors were obtained from the literature, when available, or else calculated through commercial software. An excellent agreement between calculated and experimental log P(IL/w) values was obtained, which demonstrated that the resulting multiparametric equations are robust and allow predicting partitioning for any organic molecule in the biphasic systems studied.

Energetic ion loss detector on the Alcator C-Mod tokamak.

PubMed

Pace, D C; Granetz, R S; Vieira, R; Bader, A; Bosco, J; Darrow, D S; Fiore, C; Irby, J; Parker, R R; Parkin, W; Reinke, M L; Terry, J L; Wolfe, S M; Wukitch, S J; Zweben, S J

2012-07-01

A scintillator-based energetic ion loss detector has been successfully commissioned on the Alcator C-Mod tokamak. This probe is located just below the outer midplane, where it captures ions of energies up to 2 MeV resulting from ion cyclotron resonance heating. After passing through a collimating aperture, ions impact different regions of the scintillator according to their gyroradius (energy) and pitch angle. The probe geometry and installation location are determined based on modeling of expected lost ions. The resulting probe is compact and resembles a standard plasma facing tile. Four separate fiber optic cables view different regions of the scintillator to provide phase space resolution. Evolving loss levels are measured during ion cyclotron resonance heating, including variation dependent upon individual antennae.

MPAI (mass probes aided ionization) method for total analysis of biomolecules by mass spectrometry.

PubMed

Honda, Aki; Hayashi, Shinichiro; Hifumi, Hiroki; Honma, Yuya; Tanji, Noriyuki; Iwasawa, Naoko; Suzuki, Yoshio; Suzuki, Koji

2007-01-01

We have designed and synthesized various mass probes, which enable us to effectively ionize various molecules to be detected with mass spectrometry. We call the ionization method using mass probes the "MPAI (mass probes aided ionization)" method. We aim at the sensitive detection of various biological molecules, and also the detection of bio-molecules by a single mass spectrometry serially without changing the mechanical settings. Here, we review mass probes for small molecules with various functional groups and mass probes for proteins. Further, we introduce newly developed mass probes for proteins for highly sensitive detection.

The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: Double-probe measurements from BOSS galaxy clustering and Planck data – towards an analysis without informative priors

DOE PAGES

Pellejero-Ibanez, Marco; Chuang, Chia -Hsun; Rubino-Martin, J. A.; ...

2016-03-28

Here, we develop a new methodology called double-probe analysis with the aim of minimizing informative priors in the estimation of cosmological parameters. We extract the dark-energy-model-independent cosmological constraints from the joint data sets of Baryon Oscillation Spectroscopic Survey (BOSS) galaxy sample and Planck cosmic microwave background (CMB) measurement. We measure the mean values and covariance matrix of {R, l a, Ω bh 2, n s, log(A s), Ω k, H(z), D A(z), f(z)σ 8(z)}, which give an efficient summary of Planck data and 2-point statistics from BOSS galaxy sample, where R = √Ω mH 2 0, and l a =more » πr(z *)/r s(z *), z * is the redshift at the last scattering surface, and r(z *) and r s(z *) denote our comoving distance to z * and sound horizon at z * respectively. The advantage of this method is that we do not need to put informative priors on the cosmological parameters that galaxy clustering is not able to constrain well, i.e. Ω bh 2 and n s. Using our double-probe results, we obtain Ω m = 0.304 ± 0.009, H 0 = 68.2 ± 0.7, and σ 8 = 0.806 ± 0.014 assuming ΛCDM; and Ω k = 0.002 ± 0.003 and w = –1.00 ± 0.07 assuming owCDM. The results show no tension with the flat ΛCDM cosmological paradigm. By comparing with the full-likelihood analyses with fixed dark energy models, we demonstrate that the double-probe method provides robust cosmological parameter constraints which can be conveniently used to study dark energy models. We extend our study to measure the sum of neutrino mass and obtain Σm ν < 0.10/0.22 (68%/95%) assuming ΛCDM and Σm ν < 0.26/0.52 (68%/95%) assuming wCDM. This paper is part of a set that analyses the final galaxy clustering dataset from BOSS.« less

The unsuitability of implantable Doppler probes for the early detection of renal vascular complications – a porcine model for prevention of renal transplant loss

PubMed Central

Jespersen, Bente; Møldrup, Ulla; Keller, Anna K.

2017-01-01

Background Vascular occlusion is a rare, but serious complication after kidney transplantation often resulting in graft loss. We therefore aimed to develop an experimental porcine model for stepwise reduction of the renal venous blood flow and to compare an implantable Doppler probe and microdialysis for fast detection of vascular occlusion. Methods In 20 pigs, implantable Doppler probes were placed on the renal artery and vein and a microdialysis catheter was placed in the renal cortex. An arterial flowprobe served as gold standard. Following two-hour baseline measurements, the pigs were randomised to stepwise venous occlusion, complete venous occlusion, complete arterial occlusion or controls. Results All parameters were stable through baseline measurements. Glutamate and lactate measured by microdialysis increased significantly (p = 0.02 and p = 0.03 respectively) 30 minutes after a 2/3 (66%) reduction in renal blood flow. The implantable Doppler probe was not able to detect flow changes until there was total venous occlusion. Microdialysis detected changes in local metabolism after both arterial and venous occlusion; the implantable Doppler probe could only detect vascular occlusions on the vessel it was placed. Conclusions We developed a new model for stepwise renal venous blood flow occlusion. Furthermore, the first comparison of the implantable Doppler probe and microdialysis for detection of renal vascular occlusions was made. The implantable Doppler probe could only detect flow changes after a complete occlusion, whereas microdialysis detected changes earlier, and could detect both arterial and venous occlusion. Based on these results, the implantable Doppler probe for early detection of vascular occlusions cannot be recommended. PMID:28542429

Paramagnetic 19F NMR and Electrospray Ionization Mass Spectrometric Studies of Substituted Pyridine Complexes of Chromium(III): Models for Potential Use of 19F NMR to Probe Cr(III)-Nucleotide Interaction1

PubMed Central

Rhodes, Nicholas R.; Belmore, Ken; Cassady, Carolyn J.; Vincent, John B.

2013-01-01

The synthesis and characterization of chromium basic carboxylate complexes, [Cr3(O2CR)6L3]+, containing trifluoroacetate, 3-fluoropyridine, 3-trifluoromethylpyridine, and 4-trifluoromethylpyridine are described. The substituted pyridine ligands are used as models of DNA bases to determine whether 19F NMR would be a potentially useful probe of the binding of Cr3+ to DNA. The 19F NMR resonances of the coordinated ligands, while broadened by delocalization of unpaired electron density from the S=3/2 chromic centers, are readily discernable, and the contact shifts are of sufficient magnitude that the signals from coordinated and free ligands can easily be differentiated. Thus, 19F NMR appears to be a potentially useful probe of the binding of Cr3+ to DNA containing F-labeled bases. Additionally, electrospray MS is shown to be a convenient method to establish the identity of chromium basic carboxylate assemblies. PMID:24222929

Measurement of electron density using reactance cutoff probe

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

You, K. H.; Seo, B. H.; Kim, J. H.

2016-05-15

This paper proposes a new measurement method of electron density using the reactance spectrum of the plasma in the cutoff probe system instead of the transmission spectrum. The highly accurate reactance spectrum of the plasma-cutoff probe system, as expected from previous circuit simulations [Kim et al., Appl. Phys. Lett. 99, 131502 (2011)], was measured using the full two-port error correction and automatic port extension methods of the network analyzer. The electron density can be obtained from the analysis of the measured reactance spectrum, based on circuit modeling. According to the circuit simulation results, the reactance cutoff probe can measure themore » electron density more precisely than the previous cutoff probe at low densities or at higher pressure. The obtained results for the electron density are presented and discussed for a wide range of experimental conditions, and this method is compared with previous methods (a cutoff probe using the transmission spectrum and a single Langmuir probe).« less

Cutoff Probe for Tokamak SOL Measurement

NASA Astrophysics Data System (ADS)

Na, Byung-Keun; You, Kwang-Ho; Kim, Dae-Woong; You, Shin-Jae; Kim, Jung-Hyung; Chang, Hong-Young

2013-09-01

Since a cutoff probe was developed, there have been a lot of improvements in methodology and analysis for low temperature plasmas. However, in order to apply the cutoff probe to the Tokamak scrape-off layer (SOL), three important issues should be solved - speed, thermal protection, and short-distance (a few mm) wave propagation in magnetized plasmas. In this presentation, the improvement of cutoff probe for Tokamak is shown. The above problems can be solved using the following methods: (a) the cutoff probe can be used with short impulse of a few nano-seconds for speed improvement. (b) Ceramic covers were used for thermal protection. (c) In magnetized plasmas, the cutoff peak can be analyzed using circuit modeling and CST Microwave studio. To verify the proposed methods, the cutoff probe was applied to a Helicon plasma, and the results were compared to laser Thomson scattering results. Based on the result in the Helicon plasma, the cutoff probe will be applied to far-SOL region at the KSTAR 2013 campaign, and SOL region at the later campaign.

Targeting of deep-brain structures in nonhuman primates using MR and CT Images

NASA Astrophysics Data System (ADS)

Chen, Antong; Hines, Catherine; Dogdas, Belma; Bone, Ashleigh; Lodge, Kenneth; O'Malley, Stacey; Connolly, Brett; Winkelmann, Christopher T.; Bagchi, Ansuman; Lubbers, Laura S.; Uslaner, Jason M.; Johnson, Colena; Renger, John; Zariwala, Hatim A.

2015-03-01

In vivo gene delivery in central nervous systems of nonhuman primates (NHP) is an important approach for gene therapy and animal model development of human disease. To achieve a more accurate delivery of genetic probes, precise stereotactic targeting of brain structures is required. However, even with assistance from multi-modality 3D imaging techniques (e.g. MR and CT), the precision of targeting is often challenging due to difficulties in identification of deep brain structures, e.g. the striatum which consists of multiple substructures, and the nucleus basalis of meynert (NBM), which often lack clear boundaries to supporting anatomical landmarks. Here we demonstrate a 3D-image-based intracranial stereotactic approach applied toward reproducible intracranial targeting of bilateral NBM and striatum of rhesus. For the targeting we discuss the feasibility of an atlas-based automatic approach. Delineated originally on a high resolution 3D histology-MR atlas set, the NBM and the striatum could be located on the MR image of a rhesus subject through affine and nonrigid registrations. The atlas-based targeting of NBM was compared with the targeting conducted manually by an experienced neuroscientist. Based on the targeting, the trajectories and entry points for delivering the genetic probes to the targets could be established on the CT images of the subject after rigid registration. The accuracy of the targeting was assessed quantitatively by comparison between NBM locations obtained automatically and manually, and finally demonstrated qualitatively via post mortem analysis of slices that had been labelled via Evan Blue infusion and immunohistochemistry.

Assimilation of Biophysical Neuronal Dynamics in Neuromorphic VLSI.

PubMed

Wang, Jun; Breen, Daniel; Akinin, Abraham; Broccard, Frederic; Abarbanel, Henry D I; Cauwenberghs, Gert

2017-12-01

Representing the biophysics of neuronal dynamics and behavior offers a principled analysis-by-synthesis approach toward understanding mechanisms of nervous system functions. We report on a set of procedures assimilating and emulating neurobiological data on a neuromorphic very large scale integrated (VLSI) circuit. The analog VLSI chip, NeuroDyn, features 384 digitally programmable parameters specifying for 4 generalized Hodgkin-Huxley neurons coupled through 12 conductance-based chemical synapses. The parameters also describe reversal potentials, maximal conductances, and spline regressed kinetic functions for ion channel gating variables. In one set of experiments, we assimilated membrane potential recorded from one of the neurons on the chip to the model structure upon which NeuroDyn was designed using the known current input sequence. We arrived at the programmed parameters except for model errors due to analog imperfections in the chip fabrication. In a related set of experiments, we replicated songbird individual neuron dynamics on NeuroDyn by estimating and configuring parameters extracted using data assimilation from intracellular neural recordings. Faithful emulation of detailed biophysical neural dynamics will enable the use of NeuroDyn as a tool to probe electrical and molecular properties of functional neural circuits. Neuroscience applications include studying the relationship between molecular properties of neurons and the emergence of different spike patterns or different brain behaviors. Clinical applications include studying and predicting effects of neuromodulators or neurodegenerative diseases on ion channel kinetics.

Ensemble stump classifiers and gene expression signatures in lung cancer.

PubMed

Frey, Lewis; Edgerton, Mary; Fisher, Douglas; Levy, Shawn

2007-01-01

Microarray data sets for cancer tumor tissue generally have very few samples, each sample having thousands of probes (i.e., continuous variables). The sparsity of samples makes it difficult for machine learning techniques to discover probes relevant to the classification of tumor tissue. By combining data from different platforms (i.e., data sources), data sparsity is reduced, but this typically requires normalizing data from the different platforms, which can be non-trivial. This paper proposes a variant on the idea of ensemble learners to circumvent the need for normalization. To facilitate comprehension we build ensembles of very simple classifiers known as decision stumps--decision trees of one test each. The Ensemble Stump Classifier (ESC) identifies an mRNA signature having three probes and high accuracy for distinguishing between adenocarcinoma and squamous cell carcinoma of the lung across four data sets. In terms of accuracy, ESC outperforms a decision tree classifier on all four data sets, outperforms ensemble decision trees on three data sets, and simple stump classifiers on two data sets.

Chemical Probes for Molecular Imaging and Detection of Hydrogen Sulfide and Reactive Sulfur Species in Biological Systems

PubMed Central

2014-01-01

Hydrogen sulfide (H2S), a gaseous species produced by both bacteria and higher eukaryotic organisms, including mammalian vertebrates, has attracted attention in recent years for its contributions to human health and disease. H2S has been proposed as a cytoprotectant and gasotransmitter in many tissue types, including mediating vascular tone in blood vessels as well as neuromodulation in the brain. The molecular mechanisms dictating how H2S affects cellular signaling and other physiological events remain insufficiently understood. Furthermore, the involvement of H2S in metal-binding interactions and formation of related RSS such as sulfane sulfur may contribute to other distinct signaling pathways. Owing to its widespread biological roles and unique chemical properties, H2S is an appealing target for chemical biology approaches to elucidate its production, trafficking, and downstream function. In this context, reaction-based fluorescent probes offer a versatile set of screening tools to visualize H2S pools in living systems. Three main strategies used in molecular probe development for H2S detection include azide and nitro group reduction, nucleophilic attack, and CuS precipitation. Each of these approaches exploit the strong nucleophilicity and reducing potency of H2S to achieve selectivity over other biothiols. In addition, a variety of methods have been developed for the detection of other reactive sulfur species (RSS), including sulfite and bisulfite, as well as sulfane sulfur species and related modifications such as S-nitrosothiols. Access to this growing chemical toolbox of new molecular probes for H2S and related RSS sets the stage for applying these developing technologies to probe reactive sulfur biology in living systems. PMID:25474627

A novel pooled-sample multiplex luminex assay for high-throughput measurement of relative telomere length.

PubMed

Jasmine, Farzana; Shinkle, Justin; Sabarinathan, Mekala; Ahsan, Habibul; Pierce, Brandon L; Kibriya, Muhammad G

2018-03-12

Relative telomere length (RTL) is a potential biomarker of aging and risk for chronic disease. Previously, we developed a probe-based RTL assay on Luminex platform, where probes for Telomere (T) and reference gene (R) for a given DNA sample were tested in a single well. Here, we describe a method of pooling multiple samples in one well to increase the throughput and cost-effectiveness. We used four different microbeads for the same T-probe and four different microbeads for the same R-probe. Each pair of probe sets were hybridized to DNA in separate plates and then pooled in a single plate for all the subsequent steps. We used DNA samples from 60 independent individuals and repeated in multiple batches to test the precision. The precision was good to excellent with Intraclass correlation coefficient (ICC) of 0.908 (95% CI 0.856-0.942). More than 67% of the variation in the RTL could be explained by sample-to-sample variation; less than 0.1% variation was due to batch-to-batch variation and 0.3% variation was explained by bead-to-bead variation. We increased the throughput of RTL Luminex assay from 60 to 240 samples per run. The new assay was validated against the original Luminex assay without pooling (r = 0.79, P = 1.44 × 10 -15 ). In an independent set of samples (n = 550), the new assay showed a negative correlation of RTL with age (r = -0.41), a result providing external validation for the method. We describe a novel high throughput pooled-sample multiplex Luminex assay for RTL with good to excellent precision suitable for large-scale studies. © 2018 Wiley Periodicals, Inc.

Simplified Real-Time Multiplex Detection of Loop-Mediated Isothermal Amplification Using Novel Mediator Displacement Probes with Universal Reporters.

PubMed

Becherer, Lisa; Bakheit, Mohammed; Frischmann, Sieghard; Stinco, Silvina; Borst, Nadine; Zengerle, Roland; von Stetten, Felix

2018-04-03

A variety of real-time detection techniques for loop-mediated isothermal amplification (LAMP) based on the change in fluorescence intensity during DNA amplification enable simultaneous detection of multiple targets. However, these techniques depend on fluorogenic probes containing target-specific sequences. That complicates the adaption to different targets leading to time-consuming assay optimization. Here, we present the first universal real-time detection technique for multiplex LAMP. The novel approach allows simple assay design and is easy to implement for various targets. The innovation features a mediator displacement probe and a universal reporter. During amplification of target DNA the mediator is displaced from the mediator displacement probe. Then it hybridizes to the reporter generating a fluorescence signal. The novel mediator displacement (MD) detection was validated against state-of-the-art molecular beacon (MB) detection by means of a HIV-1 RT-LAMP: MD surpassed MB detection by accelerated probe design (MD: 10 min, MB: 3-4 h), shorter times to positive (MD 4.1 ± 0.1 min shorter than MB, n = 36), improved signal-to-noise fluorescence ratio (MD: 5.9 ± 0.4, MB: 2.7 ± 0.4; n = 15), and showed equally good or better analytical performance parameters. The usability of one universal mediator-reporter set in different multiplex assays was successfully demonstrated for a biplex RT-LAMP of HIV-1 and HTLV-1 and a biplex LAMP of Haemophilus ducreyi and Treponema pallidum, both showing good correlation between target concentration and time to positive. Due to its simple implementation it is suggested to extend the use of the universal mediator-reporter sets to the detection of various other diagnostic panels.

Integrated sensor biopsy device for real time tissue metabolism analysis

NASA Astrophysics Data System (ADS)

Delgado Alonso, Jesus; Lieberman, Robert A.; DiCarmine, Paul M.; Berry, David; Guzman, Narciso; Marpu, Sreekar B.

2018-02-01

Current methods for guiding cancer biopsies rely almost exclusively on images derived from X-ray, ultrasound, or magnetic resonance, which essentially characterize suspected lesions based only on tissue density. This paper presents a sensor integrated biopsy device for in situ tissue analysis that will enable biopsy teams to measure local tissue chemistry in real time during biopsy procedures, adding a valuable new set of parameters to augment and extend conventional image guidance. A first demonstrator integrating three chemical and biochemical sensors was tested in a mice strain that is a spontaneous breast cancer model. In all cases, the multisensory probe was able to discriminate between healthy tissue, the edge of the tumor, and total insertion inside the cancer tissue, recording real-time information about tissue metabolism.