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.

Quantitative Real-Time PCR using the Thermo Scientific Solaris qPCR Assay

PubMed Central

Ogrean, Christy; Jackson, Ben; Covino, James

2010-01-01

The Solaris qPCR Gene Expression Assay is a novel type of primer/probe set, designed to simplify the qPCR process while maintaining the sensitivity and accuracy of the assay. These primer/probe sets are pre-designed to >98% of the human and mouse genomes and feature significant improvements from previously available technologies. These improvements were made possible by virtue of a novel design algorithm, developed by Thermo Scientific bioinformatics experts. Several convenient features have been incorporated into the Solaris qPCR Assay to streamline the process of performing quantitative real-time PCR. First, the protocol is similar to commonly employed alternatives, so the methods used during qPCR are likely to be familiar. Second, the master mix is blue, which makes setting the qPCR reactions easier to track. Third, the thermal cycling conditions are the same for all assays (genes), making it possible to run many samples at a time and reducing the potential for error. Finally, the probe and primer sequence information are provided, simplifying the publication process. Here, we demonstrate how to obtain the appropriate Solaris reagents using the GENEius product search feature found on the ordering web site (www.thermo.com/solaris) and how to use the Solaris reagents for performing qPCR using the standard curve method. PMID:20567213

Developing the Alphabetic Principle to Aid Text-Based Augmentative and Alternative Communication Use by Adults With Low Speech Intelligibility and Intellectual Disabilities.

PubMed

Schmidt-Naylor, Anna C; Saunders, Kathryn J; Brady, Nancy C

2017-05-17

We explored alphabet supplementation as an augmentative and alternative communication strategy for adults with minimal literacy. Study 1's goal was to teach onset-letter selection with spoken words and assess generalization to untaught words, demonstrating the alphabetic principle. Study 2 incorporated alphabet supplementation within a naming task and then assessed effects on speech intelligibility. Three men with intellectual disabilities (ID) and low speech intelligibility participated. Study 1 used a multiple-probe design, across three 20-word sets, to show that our computer-based training improved onset-letter selection. We also probed generalization to untrained words. Study 2 taught onset-letter selection for 30 new words chosen for functionality. Five listeners transcribed speech samples of the 30 words in 2 conditions: speech only and speech with alphabet supplementation. Across studies 1 and 2, participants demonstrated onset-letter selection for at least 90 words. Study 1 showed evidence of the alphabetic principle for some but not all word sets. In study 2, participants readily used alphabet supplementation, enabling listeners to understand twice as many words. This is the first demonstration of alphabet supplementation in individuals with ID and minimal literacy. The large number of words learned holds promise both for improving communication and providing a foundation for improved literacy.

Immunohistochemistry and alternative FISH testing in breast cancer with HER2 equivocal amplification.

PubMed

Agersborg, Sally; Mixon, Christopher; Nguyen, Thanh; Aithal, Sramila; Sudarsanam, Sucha; Blocker, Forrest; Weiss, Lawrence; Gasparini, Robert; Jiang, Shiping; Chen, Wayne; Hess, Gregory; Albitar, Maher

2018-03-22

While HER2 testing is well established in directing appropriate treatment for breast cancer, a small percentage of cases show equivocal results by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Alternative probes may be used in equivocal cases. We present a single community-based institution's experience in further evaluating these cases. Between 2014 and 2016, 4255 samples were submitted for HER2 amplification testing by alternative probes, TP53, RAI1, and RARA. Of the patients tested by FISH, 505/3908 (12.9%) also had IHC data. Most (73.9%) FISH equivocal cases remained equivocal after IHC testing. However, 50.5% of equivocal cases were classified as HER2 amplified by alternative probes. Most cases were positive by more than one probe: 78% of positive cases by RAI1 and 73.9% by TP53. There was a significant difference between IHC and FISH alternative testing (p < 0.0001) among the equivocal cases by conventional FISH testing, 44% of IHC negative cases became positive while 36% of the positive IHC cases became negative by alternative FISH testing. Available data showed that 41% of patients were treated with palbociclib and were positive by alternative FISH. The prevalence of double HER2 equivocal cases and the discrepancy between IHC and alternative FISH testing suggest that FISH alternative testing using both RAI1 and TP53 probes is necessary for conclusive classification. Because almost half of FISH equivocal cases converted to HER2 amplified upon alternative testing, clinical studies to determine the benefit of anti-HER2 therapy in these patients are urgently needed.

Feature singletons attract spatial attention independently of feature priming

PubMed Central

Yashar, Amit; White, Alex L.; Fang, Wanghaoming; Carrasco, Marisa

2017-01-01

People perform better in visual search when the target feature repeats across trials (intertrial feature priming [IFP]). Here, we investigated whether repetition of a feature singleton's color modulates stimulus-driven shifts of spatial attention by presenting a probe stimulus immediately after each singleton display. The task alternated every two trials between a probe discrimination task and a singleton search task. We measured both stimulus-driven spatial attention (via the distance between the probe and singleton) and IFP (via repetition of the singleton's color). Color repetition facilitated search performance (IFP effect) when the set size was small. When the probe appeared at the singleton's location, performance was better than at the opposite location (stimulus-driven attention effect). The magnitude of this attention effect increased with the singleton's set size (which increases its saliency) but did not depend on whether the singleton's color repeated across trials, even when the previous singleton had been attended as a search target. Thus, our findings show that repetition of a salient singleton's color affects performance when the singleton is task relevant and voluntarily attended (as in search trials). However, color repetition does not affect performance when the singleton becomes irrelevant to the current task, even though the singleton does capture attention (as in probe trials). Therefore, color repetition per se does not make a singleton more salient for stimulus-driven attention. Rather, we suggest that IFP requires voluntary selection of color singletons in each consecutive trial. PMID:28800369

Feature singletons attract spatial attention independently of feature priming.

PubMed

Yashar, Amit; White, Alex L; Fang, Wanghaoming; Carrasco, Marisa

2017-08-01

People perform better in visual search when the target feature repeats across trials (intertrial feature priming [IFP]). Here, we investigated whether repetition of a feature singleton's color modulates stimulus-driven shifts of spatial attention by presenting a probe stimulus immediately after each singleton display. The task alternated every two trials between a probe discrimination task and a singleton search task. We measured both stimulus-driven spatial attention (via the distance between the probe and singleton) and IFP (via repetition of the singleton's color). Color repetition facilitated search performance (IFP effect) when the set size was small. When the probe appeared at the singleton's location, performance was better than at the opposite location (stimulus-driven attention effect). The magnitude of this attention effect increased with the singleton's set size (which increases its saliency) but did not depend on whether the singleton's color repeated across trials, even when the previous singleton had been attended as a search target. Thus, our findings show that repetition of a salient singleton's color affects performance when the singleton is task relevant and voluntarily attended (as in search trials). However, color repetition does not affect performance when the singleton becomes irrelevant to the current task, even though the singleton does capture attention (as in probe trials). Therefore, color repetition per se does not make a singleton more salient for stimulus-driven attention. Rather, we suggest that IFP requires voluntary selection of color singletons in each consecutive trial.

A novel HRM assay for differentiating classical strains and highly pathogenic strains of type 2 porcine reproductive and respiratory syndrome virus.

PubMed

Sun, Junying; Bingga, Gali; Liu, Zhicheng; Zhang, Chunhong; Shen, Haiyan; Guo, Pengju; Zhang, Jianfeng

2018-06-01

Differentiation of classical strains and highly pathogenic strains of porcine reproductive and respiratory syndrome virus is crucial for effective vaccination programs and epidemiological studies. We used nested PCR and high resolution melting curve analysis with unlabeled probe to distinguish between the classical and the highly pathogenic strains of this virus. Two sets of primers and a 20 bp unlabeled probe were designed from the NSP3 gene. The unlabeled probe included two mutations specific for the classical and highly pathogenic strains of the virus. An additional primer set from the NSP2 gene of the highly pathogenic vaccine strain JXA1-R was used to detect its exclusive single nucleotide polymorphism. We tested 107 clinical samples, 21 clinical samples were positive for PRRSV (consistent with conventional PCR assay), among them four were positive for the classical strain with the remainder 17 for the highly pathogenic strain. Around 10 °C difference between probe melting temperatures showed the high discriminatory power of this method. Among highly pathogenic positive samples, three samples were determined as positive for JXA1-R vaccine-related strain with a 95% genotype confidence percentage. All these genotyping results using the high resolution melting curve assay were confirmed with DNA sequencing. This unlabeled probe method provides an alternative means to differentiate the classical strains from the highly pathogenic porcine reproductive and respiratory syndrome virus strains rapidly and accurately. Copyright © 2018. Published by Elsevier Ltd.

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.

Pioneer Jupiter orbiter probe mission 1980, probe description

NASA Technical Reports Server (NTRS)

Defrees, R. E.

1974-01-01

The adaptation of the Saturn-Uranus Atmospheric Entry Probe (SUAEP) to a Jupiter entry probe is summarized. This report is extracted from a comprehensive study of Jovian missions, atmospheric model definitions and probe subsystem alternatives.

Utility of Alternate, Noncentromeric Chromosome 17 Reference Probe for Human Epidermal Growth Factor Receptor Fluorescence In Situ Hybridization Testing in Breast Cancer Cases.

PubMed

Pai, Trupti; Shet, Tanuja; Patil, Asawari; Shetty, Omshree; Singh, Angad; Desai, Sangeeta B

2018-05-01

Context PathVysion-a US Food and Drug Administration-approved dual-probe human epidermal growth factor receptor ( HER2) fluorescence in situ hybridization (FISH) assay-provides the HER2: CEP17 ratio, a centromeric enumeration probe ratio for determining HER2 status in breast cancers. However, pericentromeric amplifications might then skew the HER2: CEP17 ratio, underestimating the HER2 status, which calls into question the use of CEP17 as the reference probe. Objective To analyze the utility of a noncentromeric chromosome 17 reference locus ( D17S122) to assess HER2 gene status in cases showing "nonclassical" FISH patterns with the CEP17 probe. Design The HER2 status of breast cancers accessioned in the years 2015-2017, displaying "nonclassical" or "equivocal" results by the PathVysion (Abbott Molecular Inc, Des Plaines, Illinois) HER2 DNA Probe Kit were reflex tested using an alternate FISH probe (ZytoLight SPEC/D17S122, ZytoVision, Bremerhaven, Germany) and interpreted with American Society of Clinical Oncology/College of American Pathologists 2013 guidelines. Results Of 37 cases, 17 were FISH equivocal. With the alternate D17S122 probe, 13 (76.4%) were reclassified as amplified, 3 (17.6%) as nonamplified, and a single case retained an equivocal result. Of the 17 cases with a chromosome 17 polysomy pattern, disomy, polysomy, and monosomy patterns were seen with 14 cases, 2 cases, and 1 case, respectively. Within the 17 cases with polysomy pattern, 3 (17.6%) demonstrated an unusual colocalization pattern of HER2 and CEP17, which was not observed with the alternate probe. Conclusions The denominator-stable alternate probe is a useful adjunct in the diagnostic armamentarium to analyze HER2 status in cases with FISH equivocal and complex patterns.

Infrared laser sealing of porcine vascular tissues using a 1,470 nm diode laser: Preliminary in vivo studies.

PubMed

Cilip, Christopher M; Kerr, Duane; Latimer, Cassandra A; Rosenbury, Sarah B; Giglio, Nicholas C; Hutchens, Thomas C; Nau, William H; Fried, Nathaniel M

2017-04-01

Infrared (IR) lasers are being explored as an alternative to radiofrequency (RF) and ultrasonic (US) devices for rapid hemostasis with minimal collateral zones of thermal damage and tissue necrosis. Previously, a 1,470 nm IR laser sealed and cut ex vivo porcine renal arteries of 1-8 mm diameter in 2 seconds, yielding burst pressures greater than 1,200 mmHg and thermal coagulation zones less than 3 mm. This preliminary study describes in vivo testing of a handheld laser probe in a porcine model. A handheld prototype with vessel/tissue clasping mechanism was tested on 73 blood vessels less than 6 mm diameter using 1,470 nm laser power of 35 W for 1-5 seconds. Device power settings, irradiation time, tissue type, vessel diameter, and histology sample number were recorded for each procedure. The probe was evaluated for hemostasis after sealing isolated and bundled arteriole/venous (A/V) vasculature of porcine abdomen and hind leg. Sealed vessel samples were collected for histological analysis of lateral thermal damage. Hemostasis was achieved in 57 of 73 seals (78%). The probe consistently sealed vasculature in small bowel mesentery, mesometrium, and gastrosplenic and epiploic regions. Seal performance was less consistent on hind leg vasculature including saphenous arteries/bundles and femoral and iliac arteries. Collagen denaturation averaged 1.6 ± 0.9 mm in eight samples excised for histologic examination. A handheld laser probe sealed porcine vessels, in vivo. Further probe development and laser parameter optimization is necessary before infrared lasers may be evaluated as an alternative to RF and US vessel sealing devices. Lasers Surg. Med. 49:366-371, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.

PubMed

Chitturi, Neelima; Balagannavar, Govindkumar; Chandrashekar, Darshan S; Abinaya, Sadashivam; Srini, Vasan S; Acharya, Kshitish K

2013-12-27

Standard 3' Affymetrix gene expression arrays have contributed a significantly higher volume of existing gene expression data than other microarray platforms. These arrays were designed to identify differentially expressed genes, but not their alternatively spliced transcript forms. No resource can currently identify expression pattern of specific mRNA forms using these microarray data, even though it is possible to do this. We report a web server for expression profiling of alternatively spliced transcripts using microarray data sets from 31 standard 3' Affymetrix arrays for human, mouse and rat species. The tool has been experimentally validated for mRNAs transcribed or not-detected in a human disease condition (non-obstructive azoospermia, a male infertility condition). About 4000 gene expression datasets were downloaded from a public repository. 'Good probes' with complete coverage and identity to latest reference transcript sequences were first identified. Using them, 'Transcript specific probe-clusters' were derived for each platform and used to identify expression status of possible transcripts. The web server can lead the user to datasets corresponding to specific tissues, conditions via identifiers of the microarray studies or hybridizations, keywords, official gene symbols or reference transcript identifiers. It can identify, in the tissues and conditions of interest, about 40% of known transcripts as 'transcribed', 'not-detected' or 'differentially regulated'. Corresponding additional information for probes, genes, transcripts and proteins can be viewed too. We identified the expression of transcripts in a specific clinical condition and validated a few of these transcripts by experiments (using reverse transcription followed by polymerase chain reaction). The experimental observations indicated higher agreements with the web server results, than contradictions. The tool is accessible at http://resource.ibab.ac.in/TIPMaP. The newly developed online tool forms a reliable means for identification of alternatively spliced transcript-isoforms that may be differentially expressed in various tissues, cell types or physiological conditions. Thus, by making better use of existing data, TIPMaP avoids the dependence on precious tissue-samples, in experiments with a goal to establish expression profiles of alternative splice forms--at least in some cases.

A novel universal real-time PCR system using the attached universal duplex probes for quantitative analysis of nucleic acids.

PubMed

Yang, Litao; Liang, Wanqi; Jiang, Lingxi; Li, Wenquan; Cao, Wei; Wilson, Zoe A; Zhang, Dabing

2008-06-04

Real-time PCR techniques are being widely used for nucleic acids analysis, but one limitation of current frequently employed real-time PCR is the high cost of the labeled probe for each target molecule. We describe a real-time PCR technique employing attached universal duplex probes (AUDP), which has the advantage of generating fluorescence by probe hydrolysis and strand displacement over current real-time PCR methods. AUDP involves one set of universal duplex probes in which the 5' end of the fluorescent probe (FP) and a complementary quenching probe (QP) lie in close proximity so that fluorescence can be quenched. The PCR primer pair with attached universal template (UT) and the FP are identical to the UT sequence. We have shown that the AUDP technique can be used for detecting multiple target DNA sequences in both simplex and duplex real-time PCR assays for gene expression analysis, genotype identification, and genetically modified organism (GMO) quantification with comparable sensitivity, reproducibility, and repeatability with other real-time PCR methods. The results from GMO quantification, gene expression analysis, genotype identification, and GMO quantification using AUDP real-time PCR assays indicate that the AUDP real-time PCR technique has been successfully applied in nucleic acids analysis, and the developed AUDP real-time PCR technique will offer an alternative way for nucleic acid analysis with high efficiency, reliability, and flexibility at low cost.

Developing the Alphabetic Principle to Aid Text-Based Augmentative and Alternative Communication Use by Adults With Low Speech Intelligibility and Intellectual Disabilities

PubMed Central

Schmidt-Naylor, Anna C.; Brady, Nancy C.

2017-01-01

Purpose We explored alphabet supplementation as an augmentative and alternative communication strategy for adults with minimal literacy. Study 1's goal was to teach onset-letter selection with spoken words and assess generalization to untaught words, demonstrating the alphabetic principle. Study 2 incorporated alphabet supplementation within a naming task and then assessed effects on speech intelligibility. Method Three men with intellectual disabilities (ID) and low speech intelligibility participated. Study 1 used a multiple-probe design, across three 20-word sets, to show that our computer-based training improved onset-letter selection. We also probed generalization to untrained words. Study 2 taught onset-letter selection for 30 new words chosen for functionality. Five listeners transcribed speech samples of the 30 words in 2 conditions: speech only and speech with alphabet supplementation. Results Across studies 1 and 2, participants demonstrated onset-letter selection for at least 90 words. Study 1 showed evidence of the alphabetic principle for some but not all word sets. In study 2, participants readily used alphabet supplementation, enabling listeners to understand twice as many words. Conclusions This is the first demonstration of alphabet supplementation in individuals with ID and minimal literacy. The large number of words learned holds promise both for improving communication and providing a foundation for improved literacy. PMID:28474087

RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing1[C][W][OA

PubMed Central

Loraine, Ann E.; McCormick, Sheila; Estrada, April; Patel, Ketan; Qin, Peng

2013-01-01

Pollen grains of Arabidopsis (Arabidopsis thaliana) contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing patterns of pollen transcripts will improve our understanding of pollen and allow investigation of tissue-specific splicing in plants. Most Arabidopsis pollen transcriptome studies have used the ATH1 microarray, which does not assay splice variants and lacks specific probe sets for many genes. To investigate the pollen transcriptome, we performed high-throughput sequencing (RNA-Seq) of Arabidopsis pollen and seedlings for comparison. Gene expression was more diverse in seedling, and genes involved in cell wall biogenesis were highly expressed in pollen. RNA-Seq detected at least 4,172 protein-coding genes expressed in pollen, including 289 assayed only by nonspecific probe sets. Additional exons and previously unannotated 5′ and 3′ untranslated regions for pollen-expressed genes were revealed. We detected regions in the genome not previously annotated as expressed; 14 were tested and 12 were confirmed by polymerase chain reaction. Gapped read alignments revealed 1,908 high-confidence new splicing events supported by 10 or more spliced read alignments. Alternative splicing patterns in pollen and seedling were highly correlated. For most alternatively spliced genes, the ratio of variants in pollen and seedling was similar, except for some encoding proteins involved in RNA splicing. This study highlights the robustness of splicing patterns in plants and the importance of ongoing annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser. PMID:23590974

Design and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp.

PubMed

Hug, Laura A; Salehi, Maryam; Nuin, Paulo; Tillier, Elisabeth R; Edwards, Elizabeth A

2011-08-01

Dehalococcoides spp. are an industrially relevant group of Chloroflexi bacteria capable of reductively dechlorinating contaminants in groundwater environments. Existing Dehalococcoides genomes revealed a high level of sequence identity within this group, including 98 to 100% 16S rRNA sequence identity between strains with diverse substrate specificities. Common molecular techniques for identification of microbial populations are often not applicable for distinguishing Dehalococcoides strains. Here we describe an oligonucleotide microarray probe set designed based on clustered Dehalococcoides genes from five different sources (strain DET195, CBDB1, BAV1, and VS genomes and the KB-1 metagenome). This "pangenome" probe set provides coverage of core Dehalococcoides genes as well as strain-specific genes while optimizing the potential for hybridization to closely related, previously unknown Dehalococcoides strains. The pangenome probe set was compared to probe sets designed independently for each of the five Dehalococcoides strains. The pangenome probe set demonstrated better predictability and higher detection of Dehalococcoides genes than strain-specific probe sets on nontarget strains with <99% average nucleotide identity. An in silico analysis of the expected probe hybridization against the recently released Dehalococcoides strain GT genome and additional KB-1 metagenome sequence data indicated that the pangenome probe set performs more robustly than the combined strain-specific probe sets in the detection of genes not included in the original design. The pangenome probe set represents a highly specific, universal tool for the detection and characterization of Dehalococcoides from contaminated sites. It has the potential to become a common platform for Dehalococcoides-focused research, allowing meaningful comparisons between microarray experiments regardless of the strain examined.

Blade tip timing (BTT) uncertainties

NASA Astrophysics Data System (ADS)

Russhard, Pete

2016-06-01

Blade Tip Timing (BTT) is an alternative technique for characterising blade vibration in which non-contact timing probes (e.g. capacitance or optical probes), typically mounted on the engine casing (figure 1), and are used to measure the time at which a blade passes each probe. This time is compared with the time at which the blade would have passed the probe if it had been undergoing no vibration. For a number of years the aerospace industry has been sponsoring research into Blade Tip Timing technologies that have been developed as tools to obtain rotor blade tip deflections. These have been successful in demonstrating the potential of the technology, but rarely produced quantitative data, along with a demonstration of a traceable value for measurement uncertainty. BTT technologies have been developed under a cloak of secrecy by the gas turbine OEM's due to the competitive advantages it offered if it could be shown to work. BTT measurements are sensitive to many variables and there is a need to quantify the measurement uncertainty of the complete technology and to define a set of guidelines as to how BTT should be applied to different vehicles. The data shown in figure 2 was developed from US government sponsored program that bought together four different tip timing system and a gas turbine engine test. Comparisons showed that they were just capable of obtaining measurement within a +/-25% uncertainty band when compared to strain gauges even when using the same input data sets.

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.

A novel universal real-time PCR system using the attached universal duplex probes for quantitative analysis of nucleic acids

PubMed Central

Yang, Litao; Liang, Wanqi; Jiang, Lingxi; Li, Wenquan; Cao, Wei; Wilson, Zoe A; Zhang, Dabing

2008-01-01

Background Real-time PCR techniques are being widely used for nucleic acids analysis, but one limitation of current frequently employed real-time PCR is the high cost of the labeled probe for each target molecule. Results We describe a real-time PCR technique employing attached universal duplex probes (AUDP), which has the advantage of generating fluorescence by probe hydrolysis and strand displacement over current real-time PCR methods. AUDP involves one set of universal duplex probes in which the 5' end of the fluorescent probe (FP) and a complementary quenching probe (QP) lie in close proximity so that fluorescence can be quenched. The PCR primer pair with attached universal template (UT) and the FP are identical to the UT sequence. We have shown that the AUDP technique can be used for detecting multiple target DNA sequences in both simplex and duplex real-time PCR assays for gene expression analysis, genotype identification, and genetically modified organism (GMO) quantification with comparable sensitivity, reproducibility, and repeatability with other real-time PCR methods. Conclusion The results from GMO quantification, gene expression analysis, genotype identification, and GMO quantification using AUDP real-time PCR assays indicate that the AUDP real-time PCR technique has been successfully applied in nucleic acids analysis, and the developed AUDP real-time PCR technique will offer an alternative way for nucleic acid analysis with high efficiency, reliability, and flexibility at low cost. PMID:18522756

Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids: a comparative study in hexaploid chrysanthemum.

PubMed

Grandke, Fabian; Singh, Priyanka; Heuven, Henri C M; de Haan, Jorn R; Metzler, Dirk

2016-08-24

Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing technologies. While genotype classification is an established noise reduction step in diploids, it gains complexity with increasing ploidy levels. Eventually, the errors produced by misclassifications exceed the benefits of genotype classes. Alternatively, continuous genotype values can be used for association analysis in higher polyploids. We associated continuous genotypes to three different traits and compared the results to the output of the genotype caller SuperMASSA. Linear, Bayesian and partial least squares regression were applied, to determine if the use of continuous genotypes is limited to a specific method. A disease, a flowering and a growth trait with h (2) of 0.51, 0.78 and 0.91 were associated with a hexaploid chrysanthemum genotypes. The data set consisted of 55,825 probes and 228 samples. We were able to detect associating probes using continuous genotypes for multiple traits, using different regression methods. The identified probe sets were overlapping, but not identical between the methods. Baysian regression was the most restrictive method, resulting in ten probes for one trait and none for the others. Linear and partial least squares regression led to numerous associating probes. Association based on genotype classes resulted in similar values, but missed several significant probes. A simulation study was used to successfully validate the number of associating markers. Association of various phenotypic traits with continuous genotypes is successful with both uni- and multivariate regression methods. Genotype calling does not improve the association and shows no advantages in this study. Instead, use of continuous genotypes simplifies the analysis, saves computational time and results more potential markers.

Clinical Potential of Quantum Dots

PubMed Central

Iga, Arthur M.; Robertson, John H. P.; Winslet, Marc C.; Seifalian, Alexander M.

2007-01-01

Advances in nanotechnology have led to the development of novel fluorescent probes called quantum dots. Quantum dots have revolutionalized the processes of tagging molecules within research settings and are improving sentinel lymph node mapping and identification in vivo studies. As the unique physical and chemical properties of these fluorescent probes are being unraveled, new potential methods of early cancer detection, rapid spread and therapeutic management, that is, photodynamic therapy are being explored. Encouraging results of optical and real time identification of sentinel lymph nodes and lymph flow using quantum dots in vivo models are emerging. Quantum dots have also superseded many of the limitations of organic fluorophores and are a promising alternative as a research tool. In this review, we examine the promising clinical potential of quantum dots, their hindrances for clinical use and the current progress in abrogating their inherent toxicity. PMID:18317518

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

Comparison of Two Methods for Detecting Alternative Splice Variants Using GeneChip® Exon Arrays

PubMed Central

Fan, Wenhong; Stirewalt, Derek L.; Radich, Jerald P.; Zhao, Lueping

2011-01-01

The Affymetrix GeneChip Exon Array can be used to detect alternative splice variants. Microarray Detection of Alternative Splicing (MIDAS) and Partek® Genomics Suite (Partek® GS) are among the most popular analytical methods used to analyze exon array data. While both methods utilize statistical significance for testing, MIDAS and Partek® GS could produce somewhat different results due to different underlying assumptions. Comparing MIDAS and Partek® GS is quite difficult due to their substantially different mathematical formulations and assumptions regarding alternative splice variants. For meaningful comparison, we have used the previously published generalized probe model (GPM) which encompasses both MIDAS and Partek® GS under different assumptions. We analyzed a colon cancer exon array data set using MIDAS, Partek® GS and GPM. MIDAS and Partek® GS produced quite different sets of genes that are considered to have alternative splice variants. Further, we found that GPM produced results similar to MIDAS as well as to Partek® GS under their respective assumptions. Within the GPM, we show how discoveries relating to alternative variants can be quite different due to different assumptions. MIDAS focuses on relative changes in expression values across different exons within genes and tends to be robust but less efficient. Partek® GS, however, uses absolute expression values of individual exons within genes and tends to be more efficient but more sensitive to the presence of outliers. From our observations, we conclude that MIDAS and Partek® GS produce complementary results, and discoveries from both analyses should be considered. PMID:23675234

Thermodynamically optimal whole-genome tiling microarray design and validation.

PubMed

Cho, Hyejin; Chou, Hui-Hsien

2016-06-13

Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations. Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome. This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design.

Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations.

PubMed

Chen, Xiangnan; Li, Huanzheng; Mao, Yijian; Xu, Xueqin; Lv, Jiaojiao; Zhou, Lili; Lin, Xiaoling; Tang, Shaohua

2014-01-01

Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping. Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions. Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs.

The Space Infrared Interferometric Telescope (SPIRIT): The Mission Design Solution Space and the Art of the Possible

NASA Technical Reports Server (NTRS)

Leisawitz, David; Hyde, T. Tupper; Rinehart, Stephen A.; Weiss, Michael

2008-01-01

Although the Space Infrared Interferometric Telescope (SPIRIT) was studied as a candidate NASA Origins Probe mission, the real world presents a broader set of options, pressures, and constraints. Fundamentally, SPIRIT is a far-IR observatory for high-resolution imaging and spectroscopy designed to address a variety of compelling scientific questions. How do planetary systems form from protostellar disks, dousing some planets in water while leaving others dry? Where do planets form, and why are some ice giants while others are rocky? How did high-redshift galaxies form and merge to form the present-day population of galaxies? This paper takes a pragmatic look at the mission design solution space for SPIRIT, presents Probe-class and facility-class mission scenarios, and describes optional design changes. The costs and benefits of various mission design alternatives are roughly evaluated, giving a basis for further study and to serve as guidance to policy makers.

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.

PROcess Based Diagnostics PROBE

NASA Technical Reports Server (NTRS)

Clune, T.; Schmidt, G.; Kuo, K.; Bauer, M.; Oloso, H.

2013-01-01

Many of the aspects of the climate system that are of the greatest interest (e.g., the sensitivity of the system to external forcings) are emergent properties that arise via the complex interplay between disparate processes. This is also true for climate models most diagnostics are not a function of an isolated portion of source code, but rather are affected by multiple components and procedures. Thus any model-observation mismatch is hard to attribute to any specific piece of code or imperfection in a specific model assumption. An alternative approach is to identify diagnostics that are more closely tied to specific processes -- implying that if a mismatch is found, it should be much easier to identify and address specific algorithmic choices that will improve the simulation. However, this approach requires looking at model output and observational data in a more sophisticated way than the more traditional production of monthly or annual mean quantities. The data must instead be filtered in time and space for examples of the specific process being targeted.We are developing a data analysis environment called PROcess-Based Explorer (PROBE) that seeks to enable efficient and systematic computation of process-based diagnostics on very large sets of data. In this environment, investigators can define arbitrarily complex filters and then seamlessly perform computations in parallel on the filtered output from their model. The same analysis can be performed on additional related data sets (e.g., reanalyses) thereby enabling routine comparisons between model and observational data. PROBE also incorporates workflow technology to automatically update computed diagnostics for subsequent executions of a model. In this presentation, we will discuss the design and current status of PROBE as well as share results from some preliminary use cases.

Cosmological constraints from a joint analysis of cosmic growth and expansion

NASA Astrophysics Data System (ADS)

Moresco, M.; Marulli, F.

2017-10-01

Combining measurements on the expansion history of the Universe and on the growth rate of cosmic structures is key to discriminate between alternative cosmological frameworks and to test gravity. Recently, Linder proposed a new diagram to investigate the joint evolutionary track of these two quantities. In this letter, we collect the most recent cosmic growth and expansion rate data sets to provide the state-of-the-art observational constraints on this diagram. By performing a joint statistical analysis of both probes, we test the standard Λcold dark matter model, confirming a mild tension between cosmic microwave background predictions from Planck mission and cosmic growth measurements at low redshift (z < 2). Then we test alternative models allowing the variation of one single cosmological parameter at a time. In particular, we find a larger growth index than the one predicted by general relativity γ =0.65^{+0.05}_{-0.04}. However, also a standard model with total neutrino mass of 0.26 ± 0.10 eV provides a similarly accurate description of the current data. By simulating an additional data set consistent with next-generation dark-energy mission forecasts, we show that growth rate constraints at z > 1 will be crucial to discriminate between alternative models.

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 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.

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.

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.

Is Grey Level a Suitable Alternative to Low-Contrast Penetration as a Serial Measure of Sensitivity in Computerised Ultrasound Quality Assurance?

PubMed

Dudley, Nicholas J; Gibson, Nicholas M

2017-02-01

The aim of this study was to test the hypothesis that grey levels are a suitable alternative measure of sensitivity in ultrasound imaging quality assurance, as there are several caveats in the use of penetration depth. In a primary cohort of nine probes, where measurements had been made for 6 to 34 mo, both penetration depth and mean grey level fell below tolerance for six probes; both penetration depth and mean grey level remained within tolerance for three probes. In a secondary cohort where a measurement programme had been in place for a shorter period, grey level and/or penetration depth fell below tolerance in 15 of 66 probes; the sensitivity and specificity of at least 10% loss of grey level in predicting >5% loss in penetration depth were 91% and 93%, respectively. A loss of grey level accompanies a loss of penetration and provides a suitable alternative measure of sensitivity. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Cognitive caching promotes flexibility in task switching: evidence from event-related potentials.

PubMed

Lange, Florian; Seer, Caroline; Müller, Dorothea; Kopp, Bruno

2015-12-08

Time-consuming processes of task-set reconfiguration have been shown to contribute to the costs of switching between cognitive tasks. We describe and probe a novel mechanism serving to reduce the costs of task-set reconfiguration. We propose that when individuals are uncertain about the currently valid task, one task set is activated for execution while other task sets are maintained at a pre-active state in cognitive cache. We tested this idea by assessing an event-related potential (ERP) index of task-set reconfiguration in a three-rule task-switching paradigm involving varying degrees of task uncertainty. In high-uncertainty conditions, two viable tasks were equally likely to be correct whereas in low-uncertainty conditions, one task was more likely than the other. ERP and performance measures indicated substantial costs of task-set reconfiguration when participants were required to switch away from a task that had been likely to be correct. In contrast, task-set-reconfiguration costs were markedly reduced when the previous task set was chosen under high task uncertainty. These results suggest that cognitive caching of alternative task sets adds to human cognitive flexibility under high task uncertainty.

Cognitive caching promotes flexibility in task switching: evidence from event-related potentials

PubMed Central

Lange, Florian; Seer, Caroline; Müller, Dorothea; Kopp, Bruno

2015-01-01

Time-consuming processes of task-set reconfiguration have been shown to contribute to the costs of switching between cognitive tasks. We describe and probe a novel mechanism serving to reduce the costs of task-set reconfiguration. We propose that when individuals are uncertain about the currently valid task, one task set is activated for execution while other task sets are maintained at a pre-active state in cognitive cache. We tested this idea by assessing an event-related potential (ERP) index of task-set reconfiguration in a three-rule task-switching paradigm involving varying degrees of task uncertainty. In high-uncertainty conditions, two viable tasks were equally likely to be correct whereas in low-uncertainty conditions, one task was more likely than the other. ERP and performance measures indicated substantial costs of task-set reconfiguration when participants were required to switch away from a task that had been likely to be correct. In contrast, task-set-reconfiguration costs were markedly reduced when the previous task set was chosen under high task uncertainty. These results suggest that cognitive caching of alternative task sets adds to human cognitive flexibility under high task uncertainty. PMID:26643146

Advanced control of neutral beam injected power in DIII-D

DOE PAGES

Pawley, Carl J.; Crowley, Brendan J.; Pace, David C.; ...

2017-03-23

In the DIII-D tokamak, one of the most powerful techniques to control the density, temperature and plasma rotation is by eight independently modulated neutral beam sources with a total power of 20 MW. The rapid modulation requires a high degree of reproducibility and precise control of the ion source plasma and beam acceleration voltage. Recent changes have been made to the controls to provide a new capability to smoothly vary the beam current and beam voltage during a discharge, while maintaining the modulation capability. The ion source plasma inside the arc chamber is controlled through feedback from the Langmuir probesmore » measuring plasma density near the extraction end. To provide the new capability, the plasma control system (PCS) has been enabled to change the Langmuir probe set point and the beam voltage set point in real time. When the PCS varies the Langmuir set point, the plasma density is directly controlled in the arc chamber, thus changing the beam current (perveance) and power going into the tokamak. Alternately, the PCS can sweep the beam voltage set point by 20 kV or more and adjust the Langmuir probe setting to match, keeping the perveance constant and beam divergence at a minimum. This changes the beam power and average neutral particle energy, which changes deposition in the tokamak plasma. The ion separating magnetic field must accurately match the beam voltage to protect the beam line. To do this, the magnet current control accurately tracks the beam voltage set point. In conclusion, these new capabilities allow continuous in-shot variation of neutral beam ion energy to complement« less

Commercial-Off-The-Shelf Microelectromechanical Systems (MEMS) Flow-Measurement Probes Fabricated And Assembled

NASA Technical Reports Server (NTRS)

Redding, Chip

2002-01-01

As an alternative to conventional tubing instrumentation for measuring airflow, designers and technicians at the NASA Glenn Research Center have been fabricating packaging components and assembling a set of unique probes using commercial-off-the-shelf microelectromechanical systems (MEMS) integrated circuits (computer chips). Using MEMS as an alternative has some compelling advantages over standard measurement devices. Sensor technologies have matured through high-production usage in industries such as automotive and aircraft manufacturers. Currently, MEMS are the choice in applications such as tire pressure monitors, altimeters, pneumatic controls, cable leak detectors, and consumer appliances. Conventional instrumentation uses tubing buried in the model aerodynamic surfaces or wind tunnel walls. The measurements are made when pressure is introduced at the tube opening. The pressure then must travel the tubing for lengths ranging from 20 to hundreds of feet before reaching an electronic signal conditioner. This condition causes a considerable amount of damping and requires measurements to be made only after the test rig has reached steady-state operation. The electronic MEMS pressure sensor is able to take readings continuously under dynamic states in nearly real time. The use of stainless steel tubing for pressure measurements requires many tubes to be cleaned, cut to length, carefully installed, and delicately deburred and spliced for use. A cluster of a few hundred 1/16-in.- (0.0625-in.-) diameter tubes (not uncommon in research testing facilities) can be several inches in diameter and may weigh enough to require two men to handle. Replacing hard tubing with electronic chips can eliminate much of the bulk. Each sensor would fit on the tip of the 1/16-in. tubing with room to spare. The P592 piezoresistive silicon pressure sensor (Lucas NovaSensor, Fremont, CA) was chosen for this project because of its cost, availability, and tolerance to extreme ambient conditions. The chip is 1 mm square by 0.6 mm thick (0.039 by 0.023 in.) with 0.12-mm (0.005-in.) wire connection tabs. Three MEMS chips were used to build the first type of flow-angularity probe. This MEMS probe will be demonstrated as an alternative to a standard tube type "Cobra Probe" now used routinely in wind tunnel and aeronautical hardware applications. The response time and accuracy would allow the probe to be translated on an actuator across a flow field, yielding precision dynamic measurements not possible with conventional instrumentation. The low profile, the minimal power requirement, the rugged construction, and the moderate cost all contribute to making MEMS sensors the enticing choice instrument in future research measurement needs. The MEMS probe efforts are a continuation of work initiated by Brian Willis, without whose foresight and efforts this project would never have been realized. This task was funded through cooperation with the NASA Electronic Parts and Packaging (NEPP) program at the Jet Propulsion Laboratory.

Test probe for surface mounted leadless chip carrier

DOEpatents

Meyer, Kerry L.; Topolewski, John

1989-05-23

A test probe for a surface mounted leadless chip carrier is disclosed. The probed includes specially designed connector pins which allow size reductions in the probe. A thermoplastic housing provides spring action to ensure good mechanical and electrical contact between the pins and the contact strips of a leadless chip carrier. Other features include flexible wires molded into the housing and two different types of pins alternately placed in the housing. These features allow fabrication of a smaller and simpler test probe.

Test probe for surface mounted leadless chip carrier

DOEpatents

Meyer, K.L.; Topolewski, J.

1987-10-02

A test probe for a surface mounted leadless chip carrier is disclosed. The probe includes specially designed connector pins which allow size reductions in the probe. A thermoplastic housing provides spring action to ensure good mechanical and electrical contact between the pins and the contact strips of a leadless chip carrier. Other features include flexible wires molded into the housing and two different types of pins alternately placed in the housing. These features allow fabrication of a smaller and simpler test probe. 1 fig.

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?…

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.

Treatment of vulvar/vaginal condyloma by HPV: developed instrumentation and clinical report

NASA Astrophysics Data System (ADS)

Inada, N. M.; Kurachi, C.; Ferreira, J.; Ribeiro, E. S.; Guimarães, O. C. C.; Quintana, S. M.; Lombardi, W.; Bagnato, V. S.

2009-06-01

Human papillomavirus (HPVs) are a family of sexually viruses with over 100 different genotypes identified till date. They are associated in 99% of cervical cancers, with HPV16 found in about 50% of cases. They are a cause of the second most common female cancer worldwide. PDT may constitute an alternative treatment for condyloma by HPV. In this work we present the development of a PDT device specifically designed for the treatment of vulvar and vaginal lesions induced by HPV. This equipment has been used in a clinical protocol and it is optically based on 640 nm LED (light emitting diodes) arrays. There are three illumination probes available that were anatomically designed for specific site applications: a 30 mm x 115 mm diffuser cylinder for intravaginal illumination and uniform irradiance of 42 mW/cm2; a 36 mm circular probe with 118 mW/cm2 and a 74 mm circular probe with 57 mW/cm2, both for external illumination. The 10% aminolevulinic acid cream is topically placed over the lesions and 4-6 hours after the application the illumination is performed. The illumination time is set depending on the chosen probe and treatment area to achieve a fluence of 200 J/cm2. In this presentation, the preliminary results of this clinical trial will be presented.

Evaluation of a Noncontact, Alternative Mosquito Repellent Assay System.

PubMed

Tisgratog, Rungarun; Kongmee, Monthathip; Sanguanpong, Unchalee; Prabaripai, Atchariya; Bangs, Michael J; Chareonviriyaphap, Theeraphap

2016-09-01

A novel noncontact repellency assay system (NCRAS) was designed and evaluated as a possible alternative method for testing compounds that repel or inhibit mosquitoes from blood feeding. Deet and Aedes aegypti were used in a controlled laboratory setting. Using 2 study designs, a highly significant difference were seen between deet-treated and untreated skin placed behind the protective screens, indicating that deet was detected and was acting as a deterrence to mosquito landing and probing behavior. However, a 2nd study showed significant differences between protected (behind a metal screen barrier) and unprotected (exposed) deet-treated forearms, indicating the screen mesh might restrict the detection of deet and thus influences landing/biting response. These findings indicate the prototype NCRAS shows good promise but requires further evaluation and possible modification in design and testing protocol to achieve more desirable operational attributes in comparison with direct skin-contact repellency mosquito assays.

Comparison of the Nanopulse Lithotripter to the Holmium Laser: Stone Fragmentation Efficiency and Impact on Flexible Ureteroscope Deflection and Flow.

PubMed

Kaplan, Adam G; Chen, Tony T; Sankin, Georgy; Yang, Chen; Dale, Joanne A; Simmons, W Neal; Zhong, Pei; Preminger, Glenn M; Lipkin, Michael Eric

2016-11-01

The Nanopulse Lithotripter (NPL; Lithotech Medical, Israel) is a novel intracorporeal device that uses a nanosecond duration electrical discharge through a reusable flexible coaxial probe to endoscopically fragment urinary stones. This device was compared with a holmium laser lithotripsy (HoL) with regard to stone fragmentation efficiency (SFE) and its impact on flexible ureteroscope (URS) deflection and flow of irrigation. Using a custom bench model, a 6 mm BegoStone cylindrical phantom (mixture 5:2) was confined under 0.9% saline atop sequential mesh sieves. The SFE of two NPL probe sizes (2.0F, 3.6F) and two HoL fibers (200, 365 μm) was evaluated using concordant settings of 1 J and 5 Hz. URS deflection and irrigation flow with NPL probes in the working channel were tested in five new fourth generation flexible URS and compared with other adjunct endourologic instruments. The 2.0F NPL showed improved SFE compared with the 200 μm laser (86 mg/min vs 52 mg/min, p = 0.014) as did the 3.6F NPL vs the 365 μm laser (173 mg/min vs 80 mg/min, p = 0.05). The NPL created more 1 to 2 mm fragments; the laser created more dust. URS deflection reduced by 3.75° with the 2.0 NPL probe. URS irrigation flow reduced from 36.5 to 6.3 mL/min with the 2.0F NPL probe. NPL shows improved SFE compared with HoL. Flow with the 2.0F probe is akin to a stone basket. NPL offers an effective alternative to HoL.

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.

Human Leukocyte Antigen Typing Using a Knowledge Base Coupled with a High-Throughput Oligonucleotide Probe Array Analysis

PubMed Central

Zhang, Guang Lan; Keskin, Derin B.; Lin, Hsin-Nan; Lin, Hong Huang; DeLuca, David S.; Leppanen, Scott; Milford, Edgar L.; Reinherz, Ellis L.; Brusic, Vladimir

2014-01-01

Human leukocyte antigens (HLA) are important biomarkers because multiple diseases, drug toxicity, and vaccine responses reveal strong HLA associations. Current clinical HLA typing is an elimination process requiring serial testing. We present an alternative in situ synthesized DNA-based microarray method that contains hundreds of thousands of probes representing a complete overlapping set covering 1,610 clinically relevant HLA class I alleles accompanied by computational tools for assigning HLA type to 4-digit resolution. Our proof-of-concept experiment included 21 blood samples, 18 cell lines, and multiple controls. The method is accurate, robust, and amenable to automation. Typing errors were restricted to homozygous samples or those with very closely related alleles from the same locus, but readily resolved by targeted DNA sequencing validation of flagged samples. High-throughput HLA typing technologies that are effective, yet inexpensive, can be used to analyze the world’s populations, benefiting both global public health and personalized health care. PMID:25505899

Comparative genomic analysis of the Haloferax volcanii DS2 and Halobacterium salinarium GRB contig maps reveals extensive rearrangement.

PubMed Central

St Jean, A; Charlebois, R L

1996-01-01

Anonymous probes from the genome of Halobacterium salinarium GRB and 12 gene probes were hybridized to the cosmid clones representing the chromosome and plasmids of Halobacterium salinarium GRB and Haloferax volcanii DS2. The order of and pairwise distances between 35 loci uniquely cross-hybridizing to both chromosomes were analyzed in a search for conservation. No conservation between the genomes could be detected at the 15-kbp resolution used in this study. We found distinct sets of low-copy-number repeated sequences in the chromosome and plasmids of Halobacterium salinarium GRB, indicating some degree of partitioning between these replicons. We propose alternative courses for the evolution of the haloarchaeal genome: (i) that the majority of genomic differences that exist between genera came about at the inception of this group or (ii) that the differences have accumulated over the lifetime of the lineage. The strengths and limitations of investigating these models through comparative genomic studies are discussed. PMID:8682791

[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.

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.

An exemplar-familiarity model predicts short-term and long-term probe recognition across diverse forms of memory search.

PubMed

Nosofsky, Robert M; Cox, Gregory E; Cao, Rui; Shiffrin, Richard M

2014-11-01

Experiments were conducted to test a modern exemplar-familiarity model on its ability to account for both short-term and long-term probe recognition within the same memory-search paradigm. Also, making connections to the literature on attention and visual search, the model was used to interpret differences in probe-recognition performance across diverse conditions that manipulated relations between targets and foils across trials. Subjects saw lists of from 1 to 16 items followed by a single item recognition probe. In a varied-mapping condition, targets and foils could switch roles across trials; in a consistent-mapping condition, targets and foils never switched roles; and in an all-new condition, on each trial a completely new set of items formed the memory set. In the varied-mapping and all-new conditions, mean correct response times (RTs) and error proportions were curvilinear increasing functions of memory set size, with the RT results closely resembling ones from hybrid visual-memory search experiments reported by Wolfe (2012). In the consistent-mapping condition, new-probe RTs were invariant with set size, whereas old-probe RTs increased slightly with increasing study-test lag. With appropriate choice of psychologically interpretable free parameters, the model accounted well for the complete set of results. The work provides support for the hypothesis that a common set of processes involving exemplar-based familiarity may govern long-term and short-term probe recognition across wide varieties of memory- search conditions. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Role of Contrastive and Noncontrastive Associates in the Interpretation of Focus Particles

ERIC Educational Resources Information Center

Gotzner, Nicole; Spalek, Katharina

2017-01-01

The present research examines the mechanisms underlying the comprehension of focus alternatives. In particular, we investigate whether listeners determine alternatives based on general semantic priming mechanisms or whether they only consider contrastive alternatives, elements that can replace the expression in focus. In a probe recognition…

Measuring reactive oxygen and nitrogen species with fluorescent probes: challenges and limitations

PubMed Central

Kalyanaraman, Balaraman; Darley-Usmar, Victor; Davies, Kelvin J.A.; Dennery, Phyllis A.; Forman, Henry Jay; Grisham, Matthew B.; Mann, Giovanni E.; Moore, Kevin; Roberts, L. Jackson; Ischiropoulos, Harry

2013-01-01

The purpose of this position paper is to present a critical analysis of the challenges and limitations of the most widely used fluorescent probes for detecting and measuring reactive oxygen and nitrogen species. Where feasible, we have made recommendations for the use of alternate probes and appropriate analytical techniques that measure the specific products formed from the reactions between fluorescent probes and reactive oxygen and nitrogen species. We have proposed guidelines that will help present and future researchers with regard to the optimal use of selected fluorescent probes and interpretation of results. PMID:22027063

The Preignition and Autoignition Oxidation of Alternatives to Petroleum Derived JP-8 and their Surrogate Components in a Pressurized Flow Reactor and Single Cylinder Research Engine

DTIC Science & Technology

2009-09-01

sample probe consisted of TIG welding the 3/8” sample probe shaft to the sample probe tip (Koert, 1990 and Lenhert, 2004b). Silver solder was...was performed in the Drexel University Machine Shop. Conventional TIG welding was sufficient for welding the 3/8” O.D. tube to the sample probe tip...However, to TIG weld the thermocouple and the glass lined tube to the sample probe tip, extreme care had to be taken so as not to damage the

Performance measures for freight & general traffic : investigating similarities and differences using alternate data sources.

DOT National Transportation Integrated Search

2015-06-01

Recent advances in probe vehicle data collection systems have enabled monitoring traffic : conditions at finer temporal and spatial resolution. The primary objective of the current study is : to leverage these probe data sources to understand if ther...

In-Vivo Techniques for Measuring Electrical Properties of Tissues.

DTIC Science & Technology

1980-09-01

probe Electromagnetic energy Dielectric properties Monopole antenna In-situ tissues , Antemortem/Pos tmortem studies Renal blood flow 10 ABSTRACT... mice or rats, which were positioned beneath a fixed measurement probe. Several alternative methods involving the use of semi-rigid or flexible coaxial

Quantitative Probes of Electron-Phonon Coupling in an Organic Charge-Transfer Material

NASA Astrophysics Data System (ADS)

Rury, Aaron; Sorenson, Shayne; Driscoll, Eric; Dawlaty, Jahan

While organic charge transfer (CT) materials may provide alternatives to inorganic materials in electronics and photonics applications, properties central to applications remain understudied in these organic materials. Specifically, electron-phonon coupling plays a pivotal role in electronic applications yet this coupling in CT materials remains difficult to directly characterize. To better understand the suitability of organic CT materials for electronic applications, we have devised an experimental technique that can directly assess electron-phonon coupling in a model organic CT material. Upon non-resonant interaction with an ultrafast laser pulse, we show that coherent excitation of Raman-active lattice vibrations of quinhydrone, a 1:1 co-crystal of the hydroquinone and p-benzoquinone, modulates the energies of electronic transitions probed by a white light pulse. Using a well-established theoretical framework of vibrational quantum beat spectra across the probe bandwidth, we quantitatively extract the parameters describing these electronic transitions to characterize electron-phonon coupling in this material. In conjunction with temperature-dependent resonance Raman measurements, we assess the hypothesis that several sharp transitions in the near-IR correspond to previously unknown excitonic states of this material. These results and their interpretation set the foundation for further elucidation of the one of the most important parameters in the application of organic charge-transfer materials to electronics and photonics.

Immunological Approaches to Biomass Characterization and Utilization

PubMed Central

Pattathil, Sivakumar; Avci, Utku; Zhang, Tiantian; Cardenas, Claudia L.; Hahn, Michael G.

2015-01-01

Plant biomass is the major renewable feedstock resource for sustainable generation of alternative transportation fuels to replace fossil carbon-derived fuels. Lignocellulosic cell walls are the principal component of plant biomass. Hence, a detailed understanding of plant cell wall structure and biosynthesis is an important aspect of bioenergy research. Cell walls are dynamic in their composition and structure, varying considerably among different organs, cells, and developmental stages of plants. Hence, tools are needed that are highly efficient and broadly applicable at various levels of plant biomass-based bioenergy research. The use of plant cell wall glycan-directed probes has seen increasing use over the past decade as an excellent approach for the detailed characterization of cell walls. Large collections of such probes directed against most major cell wall glycans are currently available worldwide. The largest and most diverse set of such probes consists of cell wall glycan-directed monoclonal antibodies (McAbs). These McAbs can be used as immunological probes to comprehensively monitor the overall presence, extractability, and distribution patterns among cell types of most major cell wall glycan epitopes using two mutually complementary immunological approaches, glycome profiling (an in vitro platform) and immunolocalization (an in situ platform). Significant progress has been made recently in the overall understanding of plant biomass structure, composition, and modifications with the application of these immunological approaches. This review focuses on such advances made in plant biomass analyses across diverse areas of bioenergy research. PMID:26579515

Determination of Probe Volume Dimensions in Coherent Measurement Techniques

NASA Technical Reports Server (NTRS)

Tedder, Sarah A.; Weikl, Markus C.; Seeger, Thomas; Leipertz, Alfred

2008-01-01

When investigating combustion phenomena with pump-probe techniques, the spatial resolution is given by the overlapping region of the laser beams and thus defines the probe volume size. The size of this probe volume becomes important when the length scales of interest are on the same order or smaller. In this work, we present a new approach to measure the probe volume in three dimensions (3-D), which can be used to determine the probe volume length, diameter, and shape. The optical arrangement and data evaluation are demonstrated for a dual-pump dual-broadband coherent anti-Stokes Raman scattering (CARS) setup which is used for combustion diagnostics. This new approach offers a simple, quick alternative with more capabilities than formerly used probe volume measurement methods.

Probing dimensionality using a simplified 4-probe method.

PubMed

Kjeldby, Snorre B; Evenstad, Otto M; Cooil, Simon P; Wells, Justin W

2017-10-04

4-probe electrical measurements have been in existence for many decades. One of the most useful aspects of the 4-probe method is that it is not only possible to find the resistivity of a sample (independently of the contact resistances), but that it is also possible to probe the dimensionality of the sample. In theory, this is straightforward to achieve by measuring the 4-probe resistance as a function of probe separation. In practice, it is challenging to move all four probes with sufficient precision over the necessary range. Here, we present an alternative approach. We demonstrate that the dimensionality of the conductive path within a sample can be directly probed using a modified 4-probe method in which an unconventional geometry is exploited; three of the probes are rigidly fixed, and the position of only one probe is changed. This allows 2D and 3D (and other) contributions the to resistivity to be readily disentangled. The required experimental instrumentation can be vastly simplified relative to traditional variable spacing 4-probe instruments.

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.

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.

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).

Signal enhancement in protein NMR using the spin-noise tuning optimum

PubMed Central

Nausner, Martin; Goger, Michael; Bendet-Taicher, Eli; Schlagnitweit, Judith

2010-01-01

We have assessed the potential of an alternative probe tuning strategy based on the spin-noise response for application in common high-resolution multi-dimensional biomolecular NMR experiments with water signal suppression on aqueous and salty samples. The method requires the adjustment of the optimal tuning condition, which may be offset by several 100 kHz from the conventional tuning settings using the noise response of the water protons as an indicator. Although the radio frequency-pulse durations are typically longer under such conditions, signal-to-noise gains of up to 22% were achieved. At salt concentrations up to 100 mM a substantial sensitivity gain was observed. PMID:20924647

Poliovirus serotype-specific VP1 sequencing primers.

PubMed

Kilpatrick, David R; Iber, Jane C; Chen, Qi; Ching, Karen; Yang, Su-Ju; De, Lina; Mandelbaum, Mark D; Emery, Brian; Campagnoli, Ray; Burns, Cara C; Kew, Olen

2011-06-01

The Global Polio Laboratory Network routinely uses poliovirus-specific PCR primers and probes to determine the serotype and genotype of poliovirus isolates obtained as part of global poliovirus surveillance. To provide detailed molecular epidemiologic information, poliovirus isolates are further characterized by sequencing the ~900-nucleotide region encoding the major capsid protein, VP1. It is difficult to obtain quality sequence information when clinical or environmental samples contain poliovirus mixtures. As an alternative to conventional methods for resolving poliovirus mixtures, sets of serotype-specific primers were developed for amplifying and sequencing the VP1 regions of individual components of mixed populations of vaccine-vaccine, vaccine-wild, and wild-wild polioviruses. Published by Elsevier B.V.

Scanning thermal microscopy based on a quartz tuning fork and a micro-thermocouple in active mode (2ω method).

PubMed

Bontempi, Alexia; Nguyen, Tran Phong; Salut, Roland; Thiery, Laurent; Teyssieux, Damien; Vairac, Pascal

2016-06-01

A novel probe for scanning thermal microscope using a micro-thermocouple probe placed on a Quartz Tuning Fork (QTF) is presented. Instead of using an external deflection with a cantilever beam for contact detection, an original combination of piezoelectric resonator and thermal probe is employed. Due to a non-contact photothermal excitation principle, the high quality factor of the QTF allows the probe-to-surface contact detection. Topographic and thermal scanning images obtained on a specific sample points out the interest of our system as an alternative to cantilevered resistive probe systems which are the most spread.

Scanning thermal microscopy based on a quartz tuning fork and a micro-thermocouple in active mode (2ω method)

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

Bontempi, Alexia; Nguyen, Tran Phong; Salut, Roland

A novel probe for scanning thermal microscope using a micro-thermocouple probe placed on a Quartz Tuning Fork (QTF) is presented. Instead of using an external deflection with a cantilever beam for contact detection, an original combination of piezoelectric resonator and thermal probe is employed. Due to a non-contact photothermal excitation principle, the high quality factor of the QTF allows the probe-to-surface contact detection. Topographic and thermal scanning images obtained on a specific sample points out the interest of our system as an alternative to cantilevered resistive probe systems which are the most spread.

Overview of Probe-based Storage Technologies

NASA Astrophysics Data System (ADS)

Wang, Lei; Yang, Ci Hui; Wen, Jing; Gong, Si Di; Peng, Yuan Xiu

2016-07-01

The current world is in the age of big data where the total amount of global digital data is growing up at an incredible rate. This indeed necessitates a drastic enhancement on the capacity of conventional data storage devices that are, however, suffering from their respective physical drawbacks. Under this circumstance, it is essential to aggressively explore and develop alternative promising mass storage devices, leading to the presence of probe-based storage devices. In this paper, the physical principles and the current status of several different probe storage devices, including thermo-mechanical probe memory, magnetic probe memory, ferroelectric probe memory, and phase-change probe memory, are reviewed in details, as well as their respective merits and weakness. This paper provides an overview of the emerging probe memories potentially for next generation storage device so as to motivate the exploration of more innovative technologies to push forward the development of the probe storage devices.

Overview of Probe-based Storage Technologies.

PubMed

Wang, Lei; Yang, Ci Hui; Wen, Jing; Gong, Si Di; Peng, Yuan Xiu

2016-12-01

The current world is in the age of big data where the total amount of global digital data is growing up at an incredible rate. This indeed necessitates a drastic enhancement on the capacity of conventional data storage devices that are, however, suffering from their respective physical drawbacks. Under this circumstance, it is essential to aggressively explore and develop alternative promising mass storage devices, leading to the presence of probe-based storage devices. In this paper, the physical principles and the current status of several different probe storage devices, including thermo-mechanical probe memory, magnetic probe memory, ferroelectric probe memory, and phase-change probe memory, are reviewed in details, as well as their respective merits and weakness. This paper provides an overview of the emerging probe memories potentially for next generation storage device so as to motivate the exploration of more innovative technologies to push forward the development of the probe storage devices.

Detection of viral genomes in the liver by in situ hybridization using 35S-, bromodeoxyuridine-, and biotin-labeled probes

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

Niedobitek, G.; Finn, T.; Herbst, H.

1989-03-01

Methods employing /sup 35/S-, biotin-, and bromodeoxyuridine (BrdUrd)-labeled DNA probes were compared for the detection of hepatitis B virus (HBV) and cytomegalovirus (CMV) in the liver. The results demonstrate that: 1) HBV can be detected reliably only by the use of radiolabeled probes, whereas methods employing nonradioactive probes obviously are not sensitive enough for this virus. The use of /sup 35/S-labeled probes shortens the exposure times considerably in comparison to tritiated probes. 2) Biotin-labeled probes are of limited value for in situ hybridization on liver tissues because the presence of endogenous avidin-binding activity often leads to false positive results. 3)more » Brd-Urd-labeled probes are a useful alternative to biotinylated probes for the detection of CMV. In comparison with biotinylated probes, BrdUrd-labeled probes produce a specific signal of similar staining intensity in the absence of background staining in the liver.« less

Structure-based design, synthesis and crystallization of 2-arylquinazolines as lipid pocket ligands of p38α MAPK

PubMed Central

Bührmann, Mike; Wiedemann, Bianca M.; Müller, Matthias P.; Hardick, Julia; Ecke, Maria

2017-01-01

In protein kinase research, identifying and addressing small molecule binding sites other than the highly conserved ATP-pocket are of intense interest because this line of investigation extends our understanding of kinase function beyond the catalytic phosphotransfer. Such alternative binding sites may be involved in altering the activation state through subtle conformational changes, control cellular enzyme localization, or in mediating and disrupting protein-protein interactions. Small organic molecules that target these less conserved regions might serve as tools for chemical biology research and to probe alternative strategies in targeting protein kinases in disease settings. Here, we present the structure-based design and synthesis of a focused library of 2-arylquinazoline derivatives to target the lipophilic C-terminal binding pocket in p38α MAPK, for which a clear biological function has yet to be identified. The interactions of the ligands with p38α MAPK was analyzed by SPR measurements and validated by protein X-ray crystallography. PMID:28892510

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.

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…

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.

Rapid detection of α-thalassaemia alleles of --(SEA)/, -α(3.7)/ and -α(4.2)/ using a dual labelling, self-quenching hybridization probe/melting curve analysis.

PubMed

Gao, Lan; Liu, Yanhui; Sun, Manna; Zhao, Ying; Xie, Rungui; He, Yi; Xu, Wanfang; Liu, Jianxin; Lin, Yangyang; Lou, Jiwu

2015-12-01

The aim of the study was to set up an alternative automatic molecular diagnostic method for deletional α-thalassaemia mutations without gel electrophoresis. Based on the sequence variation within the two Z boxes and melting curve analysis of dually labelled probes, a real-time PCR assay was developed and validated for the rapid detection of major α-genotypes (--(SEA)/αα, --(SEA)/-α(3.7), --(SEA)/-α(4.2), --(SEA)/--(SEA), -α(3.7)/-α(3.7) and -α(4.2)/-α(4.2)). Samples with the -α(3.7)/-α(3.7), -α(4.2)/-α(4.2), --(SEA)/αα, --(SEA)/-α(3.7), --(SEA)/-α(4.2), and --(SEA)/--(SEA) genotypes could be clearly distinguished. The accuracy of this technique for these samples was 100% sensitivity and specificity. This technique is rapid and reliable, demonstrating feasibility for use in large-scale population screening and prenatal diagnosis of deletional Hb H disease and Hb Bart's hydrops fetalis. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

Fluorescent porous silicon biological probes with high quantum efficiency and stability.

PubMed

Tu, Chang-Ching; Chou, Ying-Nien; Hung, Hsiang-Chieh; Wu, Jingda; Jiang, Shaoyi; Lin, Lih Y

2014-12-01

We demonstrate porous silicon biological probes as a stable and non-toxic alternative to organic dyes or cadmium-containing quantum dots for imaging and sensing applications. The fluorescent silicon quantum dots which are embedded on the porous silicon surface are passivated with carboxyl-terminated ligands through stable Si-C covalent bonds. The porous silicon bio-probes have shown photoluminescence quantum yield around 50% under near-UV excitation, with high photochemical and thermal stability. The bio-probes can be efficiently conjugated with antibodies, which is confirmed by a standard enzyme-linked immunosorbent assay (ELISA) method.

Pump-Probe Noise Spectroscopy of Molecular Junctions.

PubMed

Ochoa, Maicol A; Selzer, Yoram; Peskin, Uri; Galperin, Michael

2015-02-05

The slow response of electronic components in junctions limits the direct applicability of pump-probe type spectroscopy in assessing the intramolecular dynamics. Recently the possibility of getting information on a sub-picosecond time scale from dc current measurements was proposed. We revisit the idea of picosecond resolution by pump-probe spectroscopy from dc measurements and show that any intramolecular dynamics not directly related to charge transfer in the current direction is missed by current measurements. We propose a pump-probe dc shot noise spectroscopy as a suitable alternative. Numerical examples of time-dependent and average responses of junctions are presented for generic models.

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.

Recent Development of Inorganic Nanoparticles for Biomedical Imaging

PubMed Central

2018-01-01

Inorganic nanoparticle-based biomedical imaging probes have been studied extensively as a potential alternative to conventional molecular imaging probes. Not only can they provide better imaging performance but they can also offer greater versatility of multimodal, stimuli-responsive, and targeted imaging. However, inorganic nanoparticle-based probes are still far from practical use in clinics due to safety concerns and less-optimized efficiency. In this context, it would be valuable to look over the underlying issues. This outlook highlights the recent advances in the development of inorganic nanoparticle-based probes for MRI, CT, and anti-Stokes shift-based optical imaging. Various issues and possibilities regarding the construction of imaging probes are discussed, and future research directions are suggested. PMID:29632878

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.

DNA microarrays for identifying fishes.

PubMed

Kochzius, M; Nölte, M; Weber, H; Silkenbeumer, N; Hjörleifsdottir, S; Hreggvidsson, G O; Marteinsson, V; Kappel, K; Planes, S; Tinti, F; Magoulas, A; Garcia Vazquez, E; Turan, C; Hervet, C; Campo Falgueras, D; Antoniou, A; Landi, M; Blohm, D

2008-01-01

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a "Fish Chip" for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.

Kagome fiber based ultrafast laser microsurgery probe delivering micro-Joule pulse energies.

PubMed

Subramanian, Kaushik; Gabay, Ilan; Ferhanoğlu, Onur; Shadfan, Adam; Pawlowski, Michal; Wang, Ye; Tkaczyk, Tomasz; Ben-Yakar, Adela

2016-11-01

We present the development of a 5 mm, piezo-actuated, ultrafast laser scalpel for fast tissue microsurgery. Delivery of micro-Joules level energies to the tissue was made possible by a large, 31 μm, air-cored inhibited-coupling Kagome fiber. We overcome the fiber's low NA by using lenses made of high refractive index ZnS, which produced an optimal focusing condition with 0.23 NA objective. The optical design achieved a focused laser spot size of 4.5 μm diameter covering a 75 × 75 μm 2 scan area in a miniaturized setting. The probe could deliver the maximum available laser power, achieving an average fluence of 7.8 J/cm 2 on the tissue surface at 62% transmission efficiency. Such fluences could produce uninterrupted, 40 μm deep cuts at translational speeds of up to 5 mm/s along the tissue. We predicted that the best combination of speed and coverage exists at 8 mm/s for our conditions. The onset of nonlinear absorption in ZnS, however, limited the probe's energy delivery capabilities to 1.4 μJ for linear operation at 1.5 picosecond pulse-widths of our fiber laser. Alternatives like broadband CaF 2 crystals should mitigate such nonlinear limiting behavior. Improved opto-mechanical design and appropriate material selection should allow substantially higher fluence delivery and propel such Kagome fiber-based scalpels towards clinical translation.

Rhesus monkeys (Macaca mulatta) show robust primacy and recency in memory for lists from small, but not large, image sets.

PubMed

Basile, Benjamin M; Hampton, Robert R

2010-02-01

The combination of primacy and recency produces a U-shaped serial position curve typical of memory for lists. In humans, primacy is often thought to result from rehearsal, but there is little evidence for rehearsal in nonhumans. To further evaluate the possibility that rehearsal contributes to primacy in monkeys, we compared memory for lists of familiar stimuli (which may be easier to rehearse) to memory for unfamiliar stimuli (which are likely difficult to rehearse). Six rhesus monkeys saw lists of five images drawn from either large, medium, or small image sets. After presentation of each list, memory for one item was assessed using a serial probe recognition test. Across four experiments, we found robust primacy and recency with lists drawn from small and medium, but not large, image sets. This finding is consistent with the idea that familiar items are easier to rehearse and that rehearsal contributes to primacy, warranting further study of the possibility of rehearsal in monkeys. However, alternative interpretations are also viable and are discussed. Copyright 2009 Elsevier B.V. All rights reserved.

Nutrition metabolism plays an important role in the alternate bearing of the olive tree (Olea europaea L.).

PubMed

Turktas, Mine; Inal, Behcet; Okay, Sezer; Erkilic, Emine Gulden; Dundar, Ekrem; Hernandez, Pilar; Dorado, Gabriel; Unver, Turgay

2013-01-01

The olive tree (Olea europaea L.) is widely known for its strong tendency for alternate bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between "on year" and "off year" leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree alternate bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the alternate bearing in olive tree.

Nutrition Metabolism Plays an Important Role in the Alternate Bearing of the Olive Tree (Olea europaea L.)

PubMed Central

Turktas, Mine; Inal, Behcet; Okay, Sezer; Erkilic, Emine Gulden; Dundar, Ekrem; Hernandez, Pilar; Dorado, Gabriel; Unver, Turgay

2013-01-01

The olive tree (Olea europaea L.) is widely known for its strong tendency for alternate bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between ”on year” and “off year” leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree alternate bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the alternate bearing in olive tree. PMID:23555820

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).

3D-calibration of three- and four-sensor hot-film probes based on collocated sonic using neural networks

NASA Astrophysics Data System (ADS)

Kit, Eliezer; Liberzon, Dan

2016-09-01

High resolution measurements of turbulence in the atmospheric boundary layer (ABL) are critical to the understanding of physical processes and parameterization of important quantities, such as the turbulent kinetic energy dissipation. Low spatio-temporal resolution of standard atmospheric instruments, sonic anemometers and LIDARs, limits their suitability for fine-scale measurements of ABL. The use of miniature hot-films is an alternative technique, although such probes require frequent calibration, which is logistically untenable in field setups. Accurate and truthful calibration is crucial for the multi-hot-films applications in atmospheric studies, because the ability to conduct calibration in situ ultimately determines the turbulence measurements quality. Kit et al (2010 J. Atmos. Ocean. Technol. 27 23-41) described a novel methodology for calibration of hot-film probes using a collocated sonic anemometer combined with a neural network (NN) approach. An important step in the algorithm is the generation of a calibration set for NN training by an appropriate low-pass filtering of the high resolution voltages, measured by the hot-film-sensors and low resolution velocities acquired by the sonic. In Kit et al (2010 J. Atmos. Ocean. Technol. 27 23-41), Kit and Grits (2011 J. Atmos. Ocean. Technol. 28 104-10) and Vitkin et al (2014 Meas. Sci. Technol. 25 75801), the authors reported on successful use of this approach for in situ calibration, but also on the method’s limitations and restricted range of applicability. In their earlier work, a jet facility and a probe, comprised of two orthogonal x-hot-films, were used for calibration and for full dataset generation. In the current work, a comprehensive laboratory study of 3D-calibration of two multi-hot-film probes (triple- and four-sensor) using a grid flow was conducted. The probes were embedded in a collocated sonic, and their relative pitch and yaw orientation to the mean flow was changed by means of motorized traverses. The study demonstrated that NN-calibration is a powerful tool for calibration of multi-sensor 3D-hot film probes embedded in a collocated sonic, and can be employed in long-lasting field campaigns.

Fast scanning probe for ophthalmic echography using an ultrasound motor.

PubMed

Carotenuto, Riccardo; Caliano, Giosuè; Caronti, Alessandro; Savoia, Alessandro; Pappalardo, Massimo

2005-11-01

High-frequency transducers, up to 35-50 MHz, are widely used in ophthalmic echography to image fine eye structures. Phased-array techniques are not practically applicable at such a high frequency, due to the too small size required for the single transducer element, and mechanical scanning is the only practical alternative. At present, all ophthalmic ultrasound systems use focused single-element, mechanically scanned probes. A good probe positioning and image evaluation feedback requires an image refresh-rate of about 15-30 frames per second, which is achieved in commercial mechanical scanning probes by using electromagnetic motors. In this work, we report the design, construction, and experimental characterization of the first mechanical scanning probe for ophthalmic echography based on a small piezoelectric ultrasound motor. The prototype probe reaches a scanning rate of 15 sectors per second, with very silent operation and little weight. The first high-frequency echographic images obtained with the prototype probe are presented.

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.

An Ultrasonographic Periodontal Probe

NASA Astrophysics Data System (ADS)

Bertoncini, C. A.; Hinders, M. K.

2010-02-01

Periodontal disease, commonly known as gum disease, affects millions of people. The current method of detecting periodontal pocket depth is painful, invasive, and inaccurate. As an alternative to manual probing, an ultrasonographic periodontal probe is being developed to use ultrasound echo waveforms to measure periodontal pocket depth, which is the main measure of periodontal disease. Wavelet transforms and pattern classification techniques are implemented in artificial intelligence routines that can automatically detect pocket depth. The main pattern classification technique used here, called a binary classification algorithm, compares test objects with only two possible pocket depth measurements at a time and relies on dimensionality reduction for the final determination. This method correctly identifies up to 90% of the ultrasonographic probe measurements within the manual probe's tolerance.

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

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.

Alternative and traditional assessments: Their comparative impact on students' attitudes and science learning outcomes. An exploratory study

NASA Astrophysics Data System (ADS)

Century, Daisy Nelson

This probing study focused on alternative and traditional assessments, their comparative impacts on students' attitudes and science learning outcomes. Four basic questions were asked: What type of science learning stemming from the instruction can best be assessed by the use of traditional paper-and pencil test? What type of science learning stemming from the instruction can best be assessed by the use of alternative assessment? What are the differences in the types of learning outcomes that can be assessed by the use of paper-pencil test and alternative assessment test? Is there a difference in students' attitude towards learning science when assessment of outcomes is by alternative assessment means compared to traditional means compared to traditional means? A mixed methodology involving quantitative and qualitative techniques was utilized. However, the study was essentially a case study. Quantitative data analysis included content achievement and attitude results, to which non-parametric statistics were applied. Analysis of qualitative data was done as a case study utilizing pre-set protocols resulting in a narrative summary style of report. These outcomes were combined in order to produce conclusions. This study revealed that the traditional method yielded more concrete cognitive content learning than did the alternative assessment. The alternative assessment yielded more psychomotor, cooperative learning and critical thinking skills. In both the alternative and the traditional methods the student's attitudes toward science were positive. There was no significant differences favoring either group. The quantitative findings of no statistically significant differences suggest that at a minimum there is no loss in the use of alternative assessment methods, in this instance, performance testing. Adding the results from the qualitative analysis to this suggests (1) that class groups were more satisfied when alternative methods were employed, and (2) that the two assessment methodologies are complementary to each other, and thus should probably be used together to produce maximum benefit.

Combinations of putative virulence markers in typical and variant enteroaggregative Escherichia coli strains from children with and without diarrhoea.

PubMed Central

Elias, W. P.; Uber, A. P.; Tomita, S. K.; Trabulsi, L. R.; Gomes, T. A. T.

2002-01-01

Enteroaggregative Escherichia coli (EAEC) is defined by the ability to produce aggregative adherence (AA) to cultured cells. We analysed 128 EAEC strains, isolated from children with and without diarrhoea, regarding the presence of 11 EAEC virulence genes. Seventy strains carried and 58 lacked the EAEC probe sequence; 17 probe positive and 31 probe negative strains showed variations in the AA pattern. All EAEC probe positive strains carried at least one EAEC marker; aspU (94.3%), irp2 (91.4%), and aggR (74.3%) were the most prevalent. Conversely, among the EAEC probe negative strains, 41.4% were devoid of any marker and astA predominated (44.8%). No significant statistical difference in the prevalence of any marker between cases and controls in both EAEC probe groups or AA variants was found. We suggest that the EAEC probe positive strains may have a higher pathogenic potential or alternatively, EAEC probe negative strains may harbour virulence factors as yet undescribed. PMID:12211596

Surface-enhanced Raman scattering based nonfluorescent probe for multiplex DNA detection.

PubMed

Sun, Lan; Yu, Chenxu; Irudayaraj, Joseph

2007-06-01

To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive, and multiplex format, an alternative surface-enhanced Raman scattering based probe was designed and fabricated to covalently attach both DNA probing sequence and nonfluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the nonfluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). Excellent multiplexing capability of the DNA-AuP-RTag scheme was demonstrated by simultaneous identification of up to eight probes in a mixture. Detection of hybridization of single-stranded DNA to its complementary targets was successfully accomplished with a long-term goal to use nonfluorescent RTags in a Raman-based DNA microarray platform.

Surface-Enhanced Raman Scattering Based Nonfluorescent Probe for Multiplex DNA Detection

PubMed Central

Sun, Lan; Yu, Chenxu; Irudayaraj, Joseph

2008-01-01

To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive and multiplex format, an alternative surface enhanced Raman scattering (SERS) based probe was designed and fabricated to covalently attach both DNA probing sequence and non-fluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the non-fluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). Excellent multiplexing capability of the DNA-AuP-RTag scheme was demonstrated by simultaneous identification of up to eight probes in a mixture. Detection of hybridization of single-stranded DNA (ssDNA) to its complementary targets was successfully accomplished with a long-term goal to use non-fluorescent RTags in a Raman-based DNA microarray platform. PMID:17465531

The possible contamination of Jupiter

NASA Technical Reports Server (NTRS)

Garcia, Joe

1988-01-01

The Galileo probe, though at present its future is uncertain, would, if not sterilized, represent a good chance of contaminating Jupiter. Most scientists opposed to sterilizing the probe argue that to order the probe sterilized would be the death of the project, since sterilization would entail a reconstruction of the probe, and there are not enough funds to accomplish this. These scientists, however, are ignoring a relatively simple and inexpensive alternative to the traditional heat sterilization method. The main threat of contamination comes from Galileo's exterior surfaces: the shell of the probe and its parachute. The probe innermost components would not represent a threat since the probe is sealed. In light of the fact that only the exterior of Galileo would have to be sterilized, heat would not have to be used as a method of sterilization. Instead, various gas mixtures could be sprayed entirely over the probe and its parachute, gases which would kill any and all bacteria. This idea is more thoroughly examined.

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

PubMed Central

Ryan, Michael C; Zeeberg, Barry R; Caplen, Natasha J; Cleland, James A; Kahn, Ari B; Liu, Hongfang; Weinstein, John N

2008-01-01

Background Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays. For example, RT-PCR validation of gene expression microarray results may be unsuccessful if the two technologies target different splice variants. Effective use of sequence-based technologies requires knowledge of the specific splice variant(s) that are targeted. In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant. Results A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript. Conclusion SpliceCenter provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists. PMID:18638396

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

PubMed Central

Galfalvy, Hanga C; Erraji-Benchekroun, Loubna; Smyrniotopoulos, Peggy; Pavlidis, Paul; Ellis, Steven P; Mann, J John; Sibille, Etienne; Arango, Victoria

2003-01-01

Background Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes. Ideally, to assess the accuracy of gene expression analysis methods, one needs a set of genes which are known to be differentially expressed in the samples and which can be used as a "gold standard". We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods. Results Expression of sex-chromosome genes were used as true internal biological controls to compare alternate probe-level data extraction algorithms (Microarray Suite 5.0 [MAS5.0], Model Based Expression Index [MBEI] and Robust Multi-array Average [RMA]), to assess microarray data quality and to establish some statistical guidelines for analyzing large-scale gene expression. These approaches were implemented on a large new dataset of human brain samples. RMA-generated gene expression values were markedly less variable and more reliable than MAS5.0 and MBEI-derived values. A statistical technique controlling the false discovery rate was applied to adjust for multiple testing, as an alternative to the Bonferroni method, and showed no evidence of false negative results. Fourteen probesets, representing nine Y- and two X-chromosome linked genes, displayed significant sex differences in brain prefrontal cortex gene expression. Conclusion In this study, we have demonstrated the use of sex genes as true biological internal controls for genomic analysis of complex tissues, and suggested analytical guidelines for testing alternate oligonucleotide microarray data extraction protocols and for adjusting multiple statistical analysis of differentially expressed genes. Our results also provided evidence for sex differences in gene expression in the brain prefrontal cortex, supporting the notion of a putative direct role of sex-chromosome genes in differentiation and maintenance of sexual dimorphism of the central nervous system. Importantly, these analytical approaches are applicable to all microarray studies that include male and female human or animal subjects. PMID:12962547

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

PubMed

Galfalvy, Hanga C; Erraji-Benchekroun, Loubna; Smyrniotopoulos, Peggy; Pavlidis, Paul; Ellis, Steven P; Mann, J John; Sibille, Etienne; Arango, Victoria

2003-09-08

Genomic studies of complex tissues pose unique analytical challenges for assessment of data quality, performance of statistical methods used for data extraction, and detection of differentially expressed genes. Ideally, to assess the accuracy of gene expression analysis methods, one needs a set of genes which are known to be differentially expressed in the samples and which can be used as a "gold standard". We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods. Expression of sex-chromosome genes were used as true internal biological controls to compare alternate probe-level data extraction algorithms (Microarray Suite 5.0 [MAS5.0], Model Based Expression Index [MBEI] and Robust Multi-array Average [RMA]), to assess microarray data quality and to establish some statistical guidelines for analyzing large-scale gene expression. These approaches were implemented on a large new dataset of human brain samples. RMA-generated gene expression values were markedly less variable and more reliable than MAS5.0 and MBEI-derived values. A statistical technique controlling the false discovery rate was applied to adjust for multiple testing, as an alternative to the Bonferroni method, and showed no evidence of false negative results. Fourteen probesets, representing nine Y- and two X-chromosome linked genes, displayed significant sex differences in brain prefrontal cortex gene expression. In this study, we have demonstrated the use of sex genes as true biological internal controls for genomic analysis of complex tissues, and suggested analytical guidelines for testing alternate oligonucleotide microarray data extraction protocols and for adjusting multiple statistical analysis of differentially expressed genes. Our results also provided evidence for sex differences in gene expression in the brain prefrontal cortex, supporting the notion of a putative direct role of sex-chromosome genes in differentiation and maintenance of sexual dimorphism of the central nervous system. Importantly, these analytical approaches are applicable to all microarray studies that include male and female human or animal subjects.

A Non-Mercury Thermometer Alternative for Use in Older Melting Point Apparatuses

ERIC Educational Resources Information Center

Ongley, Lois K.; Kern, Clayton S.; Woods, Barry W.

2008-01-01

The State of Maine seeks to eliminate most mercury use. This includes removing mercury thermometers from secondary schools and discouraging Hg use in other educational institutions. Alternatives to mercury thermometers in chemical laboratory work include non-mercury thermometers, temperature probes, and thermocouples. In organic chemistry mercury…

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

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

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.

A phenomenological evaluation: using storytelling as a primary teaching method.

PubMed

Davidson, Michele R

2004-09-01

This phenomenological study examines the experiences of students who had been enrolled in an undergraduate women's health issues course where storytelling served as one of the primary teaching and learning tools. Using hermeneutic phenomenology, the investigator explored the perceptions of participants at the conclusion of the course. A purposive sample of 10 students made up the focus group. Themes were explicated and analyzed from interviews until data saturation was reached. Content analysis from focus groups revealed three themes: personalizing learning, participatory learning, and group trust/safe environment. Storytelling provided students with an opportunity to become more actively involved, provided a forum to relate real life examples to concrete didactic data, served as a trigger for information recollection, and made material seem more realistic. The increased discussion and interaction within the classroom setting enabled students to probe alternative views and perspectives in the class room. The use of more diverse teaching tools can enhance the students' experiences in the classroom setting.

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.

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

Objective evaluation of binaural summation through acoustic reflex measures.

PubMed

Rawool, Vishakha W; Parrill, Madaline

2018-02-12

A previous study [Rawool, V. W. (2016). Auditory processing deficits: Assessment and intervention. New York, NY: Thieme Medical Publishers, Inc., pp. 186-187] demonstrated objective assessment of binaural summation through right contralateral acoustic reflex thresholds (ARTs) in women. The current project examined if previous findings could be generalised to men and to the left ear. Cross-sectional. Sixty individuals participated in the study. Left and right contralateral ARTs were obtained in two conditions. In the alternated condition, the probe tone presentation was alternated with the presentation of the reflex activating clicks. In the simultaneous condition, the probe tone and the clicks were presented simultaneously. Binaural summation was calculated by subtracting the ARTs obtained in the simultaneous condition from the ARTs obtained in the alternated condition. MANOVA on ARTs revealed no significant gender or ear effects. The ARTs were significantly lower/better in the simultaneous condition compared to the alternated condition. Binaural summation was 4 dB or higher in 88% of the ears and 6 dB or higher in 76% of ears. Stimulation of six out of the total 120 (0.5%) ears resulted in worse thresholds in the simultaneous condition compared with the alternating condition, suggesting binaural interference.

"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.

CFD evaluation of an advanced thrust vector control concept

NASA Technical Reports Server (NTRS)

Tiarn, Weihnurng; Cavalleri, Robert

1990-01-01

A potential concept that can offer an alternate method for thrust vector control of the Space Shuttle Solid Rocket Booster is the use of a cylindrical probe that is inserted (on demand) through the wall of the rocket nozzle. This Probe Thrust Vector Control (PTVC) concept is an alternate to that of a gimbaled nozzle or a Liquid Injection Thrust Vector (LITVC) system. The viability of the PTVC concept can be assessed either experimentally and/or with the use of CFD. A purely experimental assessment can be time consuming and expensive, whereas a CFD assessment can be very time- and cost-effective. Two key requirements of the proposed concept are PTVC vectoring performance and the active cooling requirements for the probe to maintain its thermal and structural integrity. An active thermal cooling method is the injection of coolant around the pheriphery of the probe. How much coolant is required and how this coolant distributes itself in the flow field is of major concern. The objective of the work reported here is the use of CFD to answer these question and in the design of test hardware to substantiate the results of the CFD predictions.

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...

TaqMan PCR for Detection of Vibrio cholerae O1, O139, Non-O1, and Non-O139 in Pure Cultures, Raw Oysters, and Synthetic Seawater†

PubMed Central

Lyon, W. J.

2001-01-01

Vibrio cholerae is recognized as a leading human waterborne pathogen. Traditional diagnostic testing for Vibrio is not always reliable, because this bacterium can enter a viable but nonculturable state. Therefore, nucleic acid-based tests have emerged as a useful alternative to traditional enrichment testing. In this article, a TaqMan PCR assay is presented for quantitative detection of V. cholerae in pure cultures, oysters, and synthetic seawater. Primers and probe were designed from the nonclassical hemolysin (hlyA) sequence of V. cholerae strains. This probe was applied to DNA from 60 bacterial strains comprising 21 genera. The TaqMan PCR assay was positive for all of the strains of V. cholerae tested and negative for all other species of Vibrio tested. In addition, none of the other genera tested was amplified with the TaqMan primers and probe used in this study. The results of the TaqMan PCR with raw oysters and spiked with V. cholerae serotypes O1 and O139 were comparable to those of pure cultures. The sensitivity of the assay was in the range of 6 to 8 CFU g−1 and 10 CFU ml−1 in spiked raw oyster and synthetic seawater samples, respectively. The total assay could be completed in 3 h. Quantification of the Vibrio cells was linear over at least 6 log units. The TaqMan probe and primer set developed in this study can be used as a rapid screening tool for the presence of V. cholerae in oysters and seawater without prior isolation and characterization of the bacteria by traditional microbiological methods. PMID:11571173

Molecular tools for the selective detection of nine diatom species biomarkers of various water quality levels.

PubMed

Cimarelli, Lucia; Singh, Kumar Saurabh; Mai, Nguyen Thi Nhu; Dhar, Bidhan Chandra; Brandi, Anna; Brandi, Letizia; Spurio, Roberto

2015-05-22

Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

f( R) gravity modifications: from the action to the data

NASA Astrophysics Data System (ADS)

Lazkoz, Ruth; Ortiz-Baños, María; Salzano, Vincenzo

2018-03-01

It is a very well established matter nowadays that many modified gravity models can offer a sound alternative to General Relativity for the description of the accelerated expansion of the universe. But it is also equally well known that no clear and sharp discrimination between any alternative theory and the classical one has been found so far. In this work, we attempt at formulating a different approach starting from the general class of f( R) theories as test probes: we try to reformulate f( R) Lagrangian terms as explicit functions of the redshift, i.e., as f( z). In this context, the f( R) setting to the consensus cosmological model, the Λ CDM model, can be written as a polynomial including just a constant and a third-order term. Starting from this result, we propose various different polynomial parameterizations f( z), including new terms which would allow for deviations from Λ CDM, and we thoroughly compare them with observational data. While on the one hand we have found no statistically preference for our proposals (even if some of them are as good as Λ CDM by using Bayesian Evidence comparison), we think that our novel approach could provide a different perspective for the development of new and observationally reliable alternative models of gravity.

Outer planet atmospheric entry probes - An overview of technology readiness

NASA Technical Reports Server (NTRS)

Vojvodich, N. S.; Reynolds, R. T.; Grant, T. L.; Nachtsheim, P. R.

1975-01-01

Entry probe systems for characterizing, by in situ measurements, the atmospheric properties, chemical composition, and cloud structure of the planets Saturn, Uranus, and Jupiter are examined from the standpoint of unique mission requirements, associated subsystem performance, and degree of commonality of design. Past earth entry vehicles (PAET) and current planetary spacecraft (Pioneer Venus probes and Viking lander) are assessed to identify the extent of potential subsystem inheritance, as well as to establish the significant differences, in both form and function, relative to outer planet requirements. Recent research results are presented and reviewed for the most critical probe technology areas, including: science accommodation, telecommunication, and entry heating and thermal protection. Finally presented is a brief discussion of the use of decision analysis techniques for quantifying various probe heat-shield test alternatives and performance risk.

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...

Lipid biosensor interactions with wild type and matrix deletion HIV-1 Gag proteins.

PubMed

Barklis, Eric; Staubus, August O; Mack, Andrew; Harper, Logan; Barklis, Robin Lid; Alfadhli, Ayna

2018-05-01

The matrix (MA) domain of the HIV-1 precursor Gag protein (PrGag) has been shown interact with the HIV-1 envelope (Env) protein, and to direct PrGag proteins to plasma membrane (PM) assembly sites by virtue of its affinity to phosphatidylinositol-4,5-bisphosphate (PI[4,5]P2). Unexpectedly, HIV-1 viruses with large MA deletions (ΔMA) have been shown to be conditionally infectious as long as they are matched with Env truncation mutant proteins or alternative viral glycoproteins. To characterize the interactions of wild type (WT) and ΔMA Gag proteins with PI(4,5)P2 and other acidic phospholipids, we have employed a set of lipid biosensors as probes. Our investigations showed marked differences in WT and ΔMA Gag colocalization with biosensors, effects on biosensor release, and association of biosensors with virus-like particles. These results demonstrate an alternative approach to the analysis of viral protein-lipid associations, and provide new data as to the lipid compositions of HIV-1 assembly sites. Copyright © 2018 Elsevier Inc. All rights reserved.

METAL RESISTIVITY MEASURING DEVICE

DOEpatents

Renken, J. Jr.; Myers, R.G.

1960-12-20

An eddy current device is offered for detecting discontinuities in metal samples. Alternate short and long duration pulses are inductively applied to a metal sample via the outer coil of a probe. The long pulses give a resultant signal from the metal sample responsive to probe-tosample spacing and discontinuities within the sample and the shont pulses give a resultant signal responsive only to probe -to-sample spacing. The inner coil of the probe detects the two resultant signals and transmits them to a separation network where the two signals are separated. The two separated signals are then transmitted to a compensation network where the detected signals due to the short pulses are used to compensate for variations due to probe-to-sample spacing contained in the detected signals from the long pulses. Thus, a resultant signal is obtained responsive to discontinuities within the sample and independent of probe-to- sample spacing.

Development of a colony hybridization method for the enumeration of total and potentially enteropathogenic Vibrio parahaemolyticus in shellfish.

PubMed

Suffredini, Elisabetta; Cozzi, Loredana; Ciccaglioni, Gianni; Croci, Luciana

2014-09-01

Vibrio parahaemolyticus is a marine microorganism, recognized as cause of gastroenteritis outbreaks associated with seafood consumption. In this study the development and the in-house validation of a colony hybridization method for the enumeration of total and potentially pathogenic V. parahaemolyticus is reported. The method included a set of three controls (process, hybridization and detection control) for the full monitoring of the analytical procedure. Four digoxigenin-labeled probes were designed for pathogenic strains enumeration (tdh1, tdh2, trh1 and trh2 probes) and one for total V. parahaemolyticus count (toxR probe). Probes were tested on a panel of 70 reference strains and 356 environmental, food and clinical isolates, determining the inclusivity (tdh: 96.7%, trh: 97.8%, toxR: 99.4%) and the exclusivity (100% for all probes). Accuracy and linearity of the enumeration were evaluated on pure and mixed cultures: slopes of the regression lines ranged from 0.957 to 1.058 depending on the target gene and R(2) was greater than or equal to 0.989 for all reactions. Evaluation was also carried on using four experimentally contaminated seafood matrices (shellfish, finfish, crustaceans and cephalopods) and the slopes of the curves varied from 0.895 (finfish) to 0.987 (cephalopods) for the counts of potentially pathogenic V. parahaemolyticus (R(2)≥0.965) and from 0.965 to 1.073 for total V. parahaemolyticus enumeration (R(2)≥0.981). Validation was performed on 104 naturally contaminated shellfish samples, analyzed in parallel by colony hybridization, ISO/TS 21872-1 and MPN enumeration. Colony hybridization and ISO method showed a relative accuracy of 86.7%, and a statistically significant correlation was present between colony hybridization enumeration and MPN results (r=0.744, p<0.001). The proposed colony hybridization can be a suitable alternative method for the enumeration of total and potentially pathogenic V. parahaemolyticus in seafood. Copyright © 2014 Elsevier B.V. All rights reserved.

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

Detecting proteins in highly autofluorescent cells using quantum dot antibody conjugates.

PubMed

Orcutt, Karen M; Ren, Shanshan; Gundersen, Kjell

2009-01-01

We have applied quantum dot (Qdot) antibody conjugates as a biomolecular probe for cellular proteins important in biogeochemical cycling in the sea. Conventional immunological methods have been hampered by the strong autofluorescence found in cyanobacteria cells. Qdot conjugates provide an ideal alternative for studies that require long-term imaging of cells such as detection of low abundance cellular antigens by fluorescence microscopy. The advantage of Qdot labeled probes over conventional immunological methods is the photostability of the probe. Phycoerythrin bleaches in cyanobacterial cells under prolonged UV or blue light excitation, which means that the semiconducting nanocrystal probe, the Qdot, can yield a strong fluorescent signal without interference from cellular pigments.

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.

Colorimetric Detection of Ehrlichia Canis via Nucleic Acid Hybridization in Gold Nano-Colloids

PubMed Central

Muangchuen, Ajima; Chaumpluk, Piyasak; Suriyasomboon, Annop; Ekgasit, Sanong

2014-01-01

Canine monocytic ehrlichiosis (CME) is a major thick-bone disease of dog caused by Ehrlichia canis. Detection of this causal agent outside the laboratory using conventional methods is not effective enough. Thus an assay for E. canis detection based on the p30 outer membrane protein gene was developed. It was based on the p30 gene amplification using loop-mediated isothermal DNA amplification (LAMP). The primer set specific to six areas within the target gene were designed and tested for their sensitivity and specificity. Detection of DNA signals was based on modulation of gold nanoparticles' surface properties and performing DNA/DNA hybridization using an oligonucleotide probe. Presence of target DNA affected the gold colloid nanoparticles in terms of particle aggregation with a plasmonic color change of the gold colloids from ruby red to purple, visible by the naked eye. All the assay steps were completed within 90 min including DNA extraction without relying on standard laboratory facilities. This method was very specific to target bacteria. Its sensitivity with probe hybridization was sufficient to detect 50 copies of target DNA. This method should provide an alternative choice for point of care control and management of the disease. PMID:25111239

Colorimetric detection of Ehrlichia canis via nucleic acid hybridization in gold nano-colloids.

PubMed

Muangchuen, Ajima; Chaumpluk, Piyasak; Suriyasomboon, Annop; Ekgasit, Sanong

2014-08-08

Canine monocytic ehrlichiosis (CME) is a major thick-bone disease of dog caused by Ehrlichia canis. Detection of this causal agent outside the laboratory using conventional methods is not effective enough. Thus an assay for E. canis detection based on the p30 outer membrane protein gene was developed. It was based on the p30 gene amplification using loop-mediated isothermal DNA amplification (LAMP). The primer set specific to six areas within the target gene were designed and tested for their sensitivity and specificity. Detection of DNA signals was based on modulation of gold nanoparticles' surface properties and performing DNA/DNA hybridization using an oligonucleotide probe. Presence of target DNA affected the gold colloid nanoparticles in terms of particle aggregation with a plasmonic color change of the gold colloids from ruby red to purple, visible by the naked eye. All the assay steps were completed within 90 min including DNA extraction without relying on standard laboratory facilities. This method was very specific to target bacteria. Its sensitivity with probe hybridization was sufficient to detect 50 copies of target DNA. This method should provide an alternative choice for point of care control and management of the disease.

A Microfluidic Love-Wave Biosensing Device for PSA Detection Based on an Aptamer Beacon Probe.

PubMed

Zhang, Feng; Li, Shuangming; Cao, Kang; Wang, Pengjuan; Su, Yan; Zhu, Xinhua; Wan, Ying

2015-06-11

A label-free and selective aptamer beacon-based Love-wave biosensing device was developed for prostate specific antigen (PSA) detection. The device consists of the following parts: LiTaO3 substrate with SiO2 film as wave guide layer, two set of inter-digital transducers (IDT), gold film for immobilization of the biorecongniton layer and a polydimethylsiloxane (PDMS) microfluidic channels. DNA aptamer, or "artificial antibody", was used as the specific biorecognition probe for PSA capture. Some nucleotides were added to the 3'-end of the aptamer to form a duplex with the 3'-end, turning the aptamer into an aptamer-beacon. Taking advantage of the selective target-induced assembly changes arising from the "aptamer beacon", highly selective and specific detection of PSA was achieved. Furthermore, PDMS microfluidic channels were designed and fabricated to realize automated quantitative sample injection. After optimization of the experimental conditions, the established device showed good performance for PSA detection between 10 ng/mL to 1 μg/mL, with a detection limit of 10 ng/mL. The proposed sensor might be a promising alternative for point of care diagnostics.

Improved fixation quality provided by a Bessel beacon in an adaptive optics system.

PubMed

Lambert, Andrew J; Daly, Elizabeth M; Dainty, Christopher J

2013-07-01

We investigate whether a structured probe beam that creates the beacon for use in a retinal imaging adaptive optics system can provide useful side effects. In particular we investigate whether a Bessel beam that is seen by the subject as a set of concentric rings has a dampening effect on fixation variations of the subject under observation. This calming effect would allow longer periods of observation, particularly for patients with abnormal fixation. An experimental adaptive optics system developed for retinal imaging is used to monitor the fluctuations in aberrations for artificial and human subjects. The probe beam is alternated between a traditional beacon and one provided by a Bessel beam created by SLM. Time-frequency analysis is used to indicate the differences in power and time variation during fixation depending on whether the Bessel beam or the traditional beacon is employed. Comparison is made with the response for an artificial eye to discount systemic variations. Significant evidence is accrued to indicate the reduced fluctuations in fixation when the Bessel beam is employed to create the beacon. © 2013 The Authors Ophthalmic & Physiological Optics © 2013 The College of Optometrists.

Fluorescent probes for the simultaneous detection of multiple analytes in biology.

PubMed

Kolanowski, Jacek L; Liu, Fei; New, Elizabeth J

2018-01-02

Many of the key questions facing cellular biology concern the location and concentration of chemical species, from signalling molecules to metabolites to exogenous toxins. Fluorescent sensors (probes) have revolutionised the understanding of biological systems through their exquisite sensitivity to specific analytes. Probe design has focussed on selective sensors for individual analytes, but many of the most pertinent biological questions are related to the interaction of more than one chemical species. While it is possible to simultaneously use multiple sensors for such applications, data interpretation will be confounded by the fact that sensors will have different uptake, localisation and metabolism profiles. An alternative solution is to instead use a single probe that responds to two analytes, termed a dual-responsive probe. Recent progress in this field has yielded exciting probes, some of which have demonstrated biological application. Here we review work that has been carried out to date, and suggest future research directions that will harness the considerable potential of dual-responsive fluorescent probes.

Sterile working in ultrasonography: the use of dedicated ultrasound covers and sterile ultrasound gel.

PubMed

Marhofer, Peter; Fritsch, Gerhard

2015-01-01

Ultrasound is currently an important tool for diagnostic and interventional procedures. Ultrasound imaging provides significant advantages as compared to other imaging methods. The widespread use of ultrasound also carries the risk of drawbacks such as cross-infections. A large body of literature reports this possibly life-threatening side effect and specific patient populations are particularly at risk (e.g., neonates). Various methods of ultrasound probe disinfection are described; however, none of the mechanical or chemical probe disinfection procedures is optimal and, in particular, disinfection with high concentration of alcohol might be associated with ultrasound probe damage. The preparation of ultrasound probes with dedicated probe covers is a useful alternative for sterile working conditions. One ultrasound probe cover discussed in this paper is directly glued on to the ultrasound probe without the use of ultrasound coupling gel. By the use of sterile ultrasound coupling gel at the outer surface, additional effects on aseptic working conditions can be obtained.

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.

Laparoscopic ablation of endometriosis using the cavitational ultrasonic surgical aspirator.

PubMed

Vasquez, J M; Eisenberg, E; Osteen, K G; Hickerson, D; Diamond, M P

1993-11-01

Surgical modalities such as electrosurgery and lasers have been used for many years to treat endometriosis. They are relatively unselective with wide scatter, however, leading to the potential for significant tissue damage and injury. As an alternative, a technique for performing laparoscopic excision and adhesiolysis using a cavitational ultrasonic surgical aspirator (CUSA) was developed and studied in 15 patients. Endometriosis was removed using a prototype titanium probe developed for a 10-mm laparoscopic port. The ultrasonic laparoscopic probe consisted of an acoustic vibrator, a coupling device, a removable tip, and a protective flue. Vibrations from the acoustic vibrator (magnetostrictive device) were conveyed to the operating tip through a coupling piece. The magnetostrictive device consisted of nickel alloy laminations 10.8 cm in length that transformed electrical energy into mechanical motion at the hollow titanium tip, vibrating at a frequency of 23 kHz. The excursion of the tip (amplitude setting) was arbitrarily set, with a fixed stroke of 200 microm in all cases to remove tissue with a 1- to 2-mm radius of the vibrating tip. The tip was tapered to obtain greater amplitude and ablation efficiency. When placed in contact with the endometriotic implants and adhesions, it destroyed and emulsified the cell membranes, which were irrigated and removed through a built-in suction tube. The resulting debris and irrigating fluid were removed through the hollow central portion of the probe. The vibrating tip was moved over the surgical site in a back-and-forth motion to allow continuous, controlled removal. Vessels larger than 0.5 mm in diameter, nerves, and fibrous tissue capsules rebounded with the ultrasonic vibration waves emitted by the CUSA, and thus were unimpaired by the procedure. The consistency of tissues was sensed accurately when the tip of the device was in contact with them. This tactile feedback was helpful in enabling the surgeon to differentiate target tissues. The future application of this instrument awaits the outcome of research.

Rapid Identification of Pseudallescheria and Scedosporium Strains by Using Rolling Circle Amplification

PubMed Central

Lackner, Michaela; Najafzadeh, Mohammad Javad; Sun, Jiufeng; Lu, Qiaoyun

2012-01-01

The Pseudallescheria boydii complex, comprising environmental pathogens with Scedosporium anamorphs, has recently been subdivided into five main species: Scedosporium dehoogii, S. aurantiacum, Pseudallescheria minutispora, P. apiosperma, and P. boydii, while the validity of some other taxa is being debated. Several Pseudallescheria and Scedosporium species are indicator organisms of pollution in soil and water. Scedosporium dehoogii in particular is enriched in soils contaminated by aliphatic hydrocarbons. In addition, the fungi may cause life-threatening infections involving the central nervous system in severely impaired patients. For screening purposes, rapid and economic tools for species recognition are needed. Our aim is to establish rolling circle amplification (RCA) as a screening tool for species-specific identification of Pseudallescheria and Scedosporium. With this aim, a set of padlock probes was designed on the basis of the internal transcribed spacer (ITS) region, differing by up to 13 fixed mutations. Padlock probes were unique as judged from sequence comparison by BLAST search in GenBank and in dedicated research databases at CBS (Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre). RCA was applied as an in vitro tool, tested with pure DNA amplified from cultures. The species-specific padlock probes designed in this study yielded 100% specificity. The method presented here was found to be an attractive alternative to identification by restriction fragment length polymorphism (RFLP) or sequencing. The rapidity (<1 day), specificity, and low costs make RCA a promising screening tool for environmentally and clinically relevant fungi. PMID:22057865

Rapid identification of Pseudallescheria and Scedosporium strains by using rolling circle amplification.

PubMed

Lackner, Michaela; Najafzadeh, Mohammad Javad; Sun, Jiufeng; Lu, Qiaoyun; Hoog, G Sybren de

2012-01-01

The Pseudallescheria boydii complex, comprising environmental pathogens with Scedosporium anamorphs, has recently been subdivided into five main species: Scedosporium dehoogii, S. aurantiacum, Pseudallescheria minutispora, P. apiosperma, and P. boydii, while the validity of some other taxa is being debated. Several Pseudallescheria and Scedosporium species are indicator organisms of pollution in soil and water. Scedosporium dehoogii in particular is enriched in soils contaminated by aliphatic hydrocarbons. In addition, the fungi may cause life-threatening infections involving the central nervous system in severely impaired patients. For screening purposes, rapid and economic tools for species recognition are needed. Our aim is to establish rolling circle amplification (RCA) as a screening tool for species-specific identification of Pseudallescheria and Scedosporium. With this aim, a set of padlock probes was designed on the basis of the internal transcribed spacer (ITS) region, differing by up to 13 fixed mutations. Padlock probes were unique as judged from sequence comparison by BLAST search in GenBank and in dedicated research databases at CBS (Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre). RCA was applied as an in vitro tool, tested with pure DNA amplified from cultures. The species-specific padlock probes designed in this study yielded 100% specificity. The method presented here was found to be an attractive alternative to identification by restriction fragment length polymorphism (RFLP) or sequencing. The rapidity (<1 day), specificity, and low costs make RCA a promising screening tool for environmentally and clinically relevant fungi.

Study of {Lambda}-{Lambda} oscillation in quantum coherent {Lambda}{Lambda} by using J/{psi}{yields}{Lambda}{Lambda} decay

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

Kang Xianwei; Department of Physics, Henan Normal University, Xinxiang 453007; Li Haibo

2010-03-01

We discuss the possibility of searching for the {Lambda}-{Lambda} oscillations for coherent {Lambda}{Lambda} production in the J/{psi}{yields}{Lambda}{Lambda} decay process. The sensitivity of measurement of {Lambda}-{Lambda} oscillation in the external field at BES-III experiment is considered. These considerations indicate an alternative way to probe the {Delta}B=2 amplitude in addition to neutron oscillation experiments. Both coherent and time-dependent information can be used to extract the {Lambda}-{Lambda} oscillation parameter. With one year's luminosity at BES-III, we can set an upper limit of {delta}m{sub {Lambda}{Lambda}<}10{sup -15} MeV at 90% confidence level, corresponding to about 10{sup -6} s of {Lambda}-{Lambda} oscillation time.

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.

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.

Dynamic Pressure Probes Developed for Supersonic Flow-Field Measurements

NASA Technical Reports Server (NTRS)

Porro, A. Robert

2001-01-01

A series of dynamic flow-field pressure probes were developed for use in large-scale supersonic wind tunnels at the NASA Glenn Research Center. These flow-field probes include pitot and static pressure probes that can capture fast-acting flow-field pressure transients occurring on a millisecond timescale. The pitot and static probes can be used to determine local Mach number time histories during a transient event. The flow-field pressure probe contains four major components: 1) Static pressure aerodynamic tip; 2) Pressure-sensing cartridge assembly; 3) Pitot pressure aerodynamic tip; 4) Mounting stem. This modular design allows for a variety of probe tips to be used for a specific application. Here, the focus is on flow-field pressure measurements in supersonic flows, so we developed a cone-cylinder static pressure tip and a pitot pressure tip. Alternatively, probe tips optimized for subsonic and transonic flows could be used with this design. The pressure-sensing cartridge assembly allows the simultaneous measurement of steady-state and transient pressure which allows continuous calibration of the dynamic pressure transducer.

All-oxide Raman-active traps for light and matter: probing redox homeostasis model reactions in aqueous environment.

PubMed

Alessandri, Ivano; Depero, L E

2014-04-09

Core-shell colloidal crystals can act as very efficient traps for light and analytes. Here it is shown that Raman-active probes can be achieved using SiO2-TiO2 core-shell beads. These systems are successfully tested in monitoring of glutathione redox cycle at physiological concentration in aqueous environment, without need of any interfering enhancers. These materials represent a promising alternative to conventional, metal-based SERS probes for investigating chemical and biochemical reactions under real working conditions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unlabeled probes for the detection and typing of herpes simplex virus.

PubMed

Dames, Shale; Pattison, David C; Bromley, L Kathryn; Wittwer, Carl T; Voelkerding, Karl V

2007-10-01

Unlabeled probe detection with a double-stranded DNA (dsDNA) binding dye is one method to detect and confirm target amplification after PCR. Unlabeled probes and amplicon melting have been used to detect small deletions and single-nucleotide polymorphisms in assays where template is in abundance. Unlabeled probes have not been applied to low-level target detection, however. Herpes simplex virus (HSV) was chosen as a model to compare the unlabeled probe method to an in-house reference assay using dual-labeled, minor groove binding probes. A saturating dsDNA dye (LCGreen Plus) was used for real-time PCR. HSV-1, HSV-2, and an internal control were differentiated by PCR amplicon and unlabeled probe melting analysis after PCR. The unlabeled probe technique displayed 98% concordance with the reference assay for the detection of HSV from a variety of archived clinical samples (n = 182). HSV typing using unlabeled probes was 99% concordant (n = 104) to sequenced clinical samples and allowed for the detection of sequence polymorphisms in the amplicon and under the probe. Unlabeled probes and amplicon melting can be used to detect and genotype as few as 10 copies of target per reaction, restricted only by stochastic limitations. The use of unlabeled probes provides an attractive alternative to conventional fluorescence-labeled, probe-based assays for genotyping and detection of HSV and might be useful for other low-copy targets where typing is informative.

Activity in early visual areas predicts interindividual differences in binocular rivalry dynamics

PubMed Central

Yamashiro, Hiroyuki; Mano, Hiroaki; Umeda, Masahiro; Higuchi, Toshihiro; Saiki, Jun

2013-01-01

When dissimilar images are presented to the two eyes, binocular rivalry (BR) occurs, and perception alternates spontaneously between the images. Although neural correlates of the oscillating perception during BR have been found in multiple sites along the visual pathway, the source of BR dynamics is unclear. Psychophysical and modeling studies suggest that both low- and high-level cortical processes underlie BR dynamics. Previous neuroimaging studies have demonstrated the involvement of high-level regions by showing that frontal and parietal cortices responded time locked to spontaneous perceptual alternation in BR. However, a potential contribution of early visual areas to BR dynamics has been overlooked, because these areas also responded to the physical stimulus alternation mimicking BR. In the present study, instead of focusing on activity during perceptual switches, we highlighted brain activity during suppression periods to investigate a potential link between activity in human early visual areas and BR dynamics. We used a strong interocular suppression paradigm called continuous flash suppression to suppress and fluctuate the visibility of a probe stimulus and measured retinotopic responses to the onset of the invisible probe using functional MRI. There were ∼130-fold differences in the median suppression durations across 12 subjects. The individual differences in suppression durations could be predicted by the amplitudes of the retinotopic activity in extrastriate visual areas (V3 and V4v) evoked by the invisible probe. Weaker responses were associated with longer suppression durations. These results demonstrate that retinotopic representations in early visual areas play a role in the dynamics of perceptual alternations during BR. PMID:24353304

Probe-And-Socket Fasteners For Robotic Assembly

NASA Technical Reports Server (NTRS)

Nyberg, Karen

1995-01-01

Self-alignment and simplicity of actuation make mechanism amenable to robotic assembly. Includes socket, mounted on structure at worksite, and probe, mounted on piece of equipment to be attached to structure at socket. Probe-and-socket mechanism used in conjunction with fixed target aiding in placement of end effector of robot during grasping, and with handle or handles on structure. Intended to enable robot to set up workstation in hostile environment. Workstation then used by astronaut, aquanaut, or other human, spending minimum time in environment. Human concentrates on performing quality work rather than on setting up equipment, with consequent reduction of risk.

COTS MEMS Flow-Measurement Probes

NASA Technical Reports Server (NTRS)

Redding, Chip; Smith, Floyd A.; Blank, Greg; Cruzan, Charles

2004-01-01

As an alternative to conventional tubing instrumentation for measuring airflow, designers and technicians at Glenn Research Center have been fabricating packaging components and assembling a set of unique probes that contain commercial off-the-shelf (COTS) microelectromechanical systems (MEMS) sensor chips. MEMS sensor chips offer some compelling advantages over standard macroscopic measurement devices. MEMS sensor technology has matured through mass production and use in the automotive and aircraft industries. At present, MEMS are the devices of choice for sensors in such applications as tire-pressure monitors, altimeters, pneumatic controls, cable leak detectors, and consumer appliances. Compactness, minimality of power demand, rugged construction, and moderate cost all contribute to making MEMS sensors attractive for instrumentation for future research. Conventional macroscopic flow-measurement instrumentation includes tubes buried beneath the aerodynamic surfaces of wind-tunnel models or in wind-tunnel walls. Pressure is introduced at the opening of each such tube. The pressure must then travel along the tube before reaching a transducer that generates an electronic signal. The lengths of such tubes typically range from 20 ft (approx.= 6 m) to hundreds of feet (of the order of 100 m). The propagation of pressure signals in the tubes damps the signals considerably and makes it necessary to delay measurements until after test rigs have reached steady-state operation. In contrast, a MEMS pressure sensor that generates electronic output can take readings continuously under dynamic conditions in nearly real time. In order to use stainless-steel tubing for pressure measurements, it is necessary to clean many tubes, cut them to length, carefully install them, delicately deburr them, and splice them. A cluster of a few hundred 1/16-in.- (approx.=1.6-mm-) diameter tubes (such clusters are common in research testing facilities) can be several inches (of the order of 10 cm) in diameter and could weigh enough that two technicians are needed to handle it. Replacing hard tubing with electronic chips can eliminate much of the bulk. Each sensor would fit on the tip of a 1/16-in. tube with room to spare. The Lucas NovaSensor P592 piezoresistive silicon pressure sensor was chosen for this project because of its cost, availability, and tolerance to extreme ambient conditions. The sensor chip is 1 mm square by 0.6 mm thick (about 0.039 by 0.039 by 0.024 in.) and includes 0.12-mm (approx.=0.005-in.) wire connection tabs. The figure shows a flow-angularity probe that was built by use of three such MEMS chips. It is planned to demonstrate this MEMS probe as an alternative to a standard tube-type "Cobra" probe now used routinely in wind tunnels and aeronautical hardware. This MEMS probe could be translated across a flow field by use of a suitable actuator, so that its accuracy and the shortness of its response time could be exploited to obtain precise dynamic measurements of a sort that cannot be made by use of conventional tubing-based instrumentation.

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

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.

Uprobe: a genome-wide universal probe resource for comparative physical mapping in vertebrates.

PubMed

Kellner, Wendy A; Sullivan, Robert T; Carlson, Brian H; Thomas, James W

2005-01-01

Interspecies comparisons are important for deciphering the functional content and evolution of genomes. The expansive array of >70 public vertebrate genomic bacterial artificial chromosome (BAC) libraries can provide a means of comparative mapping, sequencing, and functional analysis of targeted chromosomal segments that is independent and complementary to whole-genome sequencing. However, at the present time, no complementary resource exists for the efficient targeted physical mapping of the majority of these BAC libraries. Universal overgo-hybridization probes, designed from regions of sequenced genomes that are highly conserved between species, have been demonstrated to be an effective resource for the isolation of orthologous regions from multiple BAC libraries in parallel. Here we report the application of the universal probe design principal across entire genomes, and the subsequent creation of a complementary probe resource, Uprobe, for screening vertebrate BAC libraries. Uprobe currently consists of whole-genome sets of universal overgo-hybridization probes designed for screening mammalian or avian/reptilian libraries. Retrospective analysis, experimental validation of the probe design process on a panel of representative BAC libraries, and estimates of probe coverage across the genome indicate that the majority of all eutherian and avian/reptilian genes or regions of interest can be isolated using Uprobe. Future implementation of the universal probe design strategy will be used to create an expanded number of whole-genome probe sets that will encompass all vertebrate genomes.

Novel multiregion hybridization assay for the identification of the most prevalent genetic forms of the human immunodeficiency virus type 1 circulating in Portugal.

PubMed

Freitas, Ferdinando B; Esteves, Aida; Piedade, João; Parreira, Ricardo

2013-02-01

The most efficient method for HIV-1 genetic characterization involves full-genome sequencing, but the associated costs, technical features, and low throughput preclude it from being routinely used for the analysis of large numbers of viral strains. Multiregion hybridization assays (MHA) represent an alternative for a consistent genetic analysis of large numbers of viral strains. Classically, MHA rely on the amplification by real-time PCR of several regions scattered along the HIV-1 genome, and on their characterization with clade-specific TaqMan probes (also known as hydrolysis probes). In this context, the aim of our study was the development of a technical variant of an MHA (vMHA(B/G/02)) for genotyping the most prevalent genetic forms of HIV-1 circulating in Portugal. Different sets of primers were designed for universal and clade-specific amplifications of several sections of the viral genome: gag, pol(Pr), pol(RT), vpu, env(gp120), and env(gp41). vMHA(B/G/02) was implemented using a real-time PCR-based approach, with detection dependent on the use of SYBR Green I. As an alternative, a technically less demanding strategy based on conventional PCR and agarose gel analysis of the reaction products was also developed. This method performed with overall good sensitivity and specificity (>91%) when a convenience sample of 45 plasma-derived HIV-1 strains was analyzed. Apart from the detection of subtype B, G, CRF02_AG, and CRF14_BG viruses, several unique B/G recombinant were also detected. Curiously, recombinant viruses including CRF02_AG sequences were not detected in the group of samples analyzed.

Facilitatory effect of AC-iontophoresis of lidocaine hydrochloride on the permeability of human enamel and dentine in extracted teeth.

PubMed

Ikeda, Hideharu; Suda, Hideaki

2013-04-01

The objectives of the present study were to quantitatively evaluate chemical permeability through human enamel/dentine using conductometry and to clarify if alternating current (AC) iontophoresis facilitates such permeability. Electrical impedance of different concentrations of lidocaine hydrochloride was measured using a bipolar platinum impedance probe. A quadratic curve closely fitted to the response functions between conductance and lidocaine hydrochloride. For analysis of the passage of lidocaine hydrochloride through human enamel/dentine, eight premolars that were extracted for orthodontic treatment were sectioned at the cemento-enamel junction. The tooth crowns were held between two chambers with a double O-ring. The enamel-side chamber was filled with lidocaine hydrochloride, and the pulp-side chamber was filled with extrapure water. Two platinum plate electrodes were set at the end of each chamber to pass alternating current. A simulated interstitial pulp pressure was applied to the pulp-side chamber. The change in the concentration of lidocaine hydrochloride in the pulp-side chamber was measured every 2min using a platinum recording probe positioned at the centre of the pulp-side chamber. Passive entry without iontophoresis was used as a control. The level of lidocaine hydrochloride that passed through enamel/dentine against the dentinal fluid flow increased with time. Electrical conductance (G, mho) correlated closely to the concentration (x, mmol/L) of lidocaine hydrochloride (G=2.16x(2)+0.0289x+0.000376, r(2)=0.999). Lidocaine hydrochloride can pass through enamel/dentine. Conductometry showed that the level of lidocaine hydrochloride that passed through enamel/dentine was increased by AC iontophoresis. Copyright © 2012 Elsevier Ltd. All rights reserved.

Empirical constraints on alternative gravity theories from gravitational lensing

NASA Astrophysics Data System (ADS)

Mortlock, Daniel J.; Turner, Edwin L.

2001-10-01

If it is hypothesized that there is no dark matter, then some alternative gravitational theory must take the place of general relativity (GR) on the largest scales. Dynamical measurements can be used to investigate the nature of such a theory, but only where there is visible matter. Gravitational lensing is potentially a more powerful probe as it can be used to measure deflections far from the lens and, for sufficiently large separations, allow it to be treated as a point-mass. Microlensing within the local group does not yet provide any interesting constraints, as only images formed close to the deflectors are appreciably magnified, but stacking of multiple light-curves and observations of microlensing on cosmological scales may be able to discriminate between GR and non-dark matter theories. Galaxy-galaxy lensing is likely to be a more powerful probe of gravity, with the Sloan Digital Sky Survey (SDSS) commissioning data used here to constrain the deflection law of galaxies to be A(R)~R0.1+/-0.1 for impact parameters in the range 50kpc<~R<~1Mpc. Together with observations of flat rotation curves, these results imply that, in any gravitational theory, photons must experience (close to) twice the deflection of massive particles moving at the speed of light (at least on these physical scales). The full SDSS data set will also be sensitive to asymmetry in the lensing signal and to variation of the deflection law with galaxy type. A detection of either of these effects would represent an independent confirmation that galaxies are dark matter-dominated; conversely, azimuthal symmetry of the shear signal would rule out the typically ellipsoidal haloes predicted by most simulations of structure formation.

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.

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

A Java-based tool for the design of classification microarrays.

PubMed

Meng, Da; Broschat, Shira L; Call, Douglas R

2008-08-04

Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays-and mixed-plasmid microarrays in particular-it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm), several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text), and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff). Weights generated using stepwise discriminant analysis can be stored for analysis of subsequent experimental data. Additionally, PLASMID can be used to construct virtual microarrays with genomes from public databases, which can then be used to identify an optimal set of probes.

Institute for Sustainable Energy

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

Agrawal, Ajay

2016-03-28

Alternate fuels offer unique challenges and opportunities as energy source for power generation, vehicular transportation, and industrial applications. Institute for Sustainable Energy (ISE) at UA conducts innovative research to utilize the complex mix of domestically-produced alternate fuels to achieve low-emissions, high energy-efficiency, and fuel-flexibility. ISE also provides educational and advancement opportunities to students and researchers in the energy field. Basic research probing the physics and chemistry of alternative fuels has generated practical concepts investigated in a burner and engine test platforms.

Development of optical probes for in vivo imaging of polarized macrophages during foreign body reactions

PubMed Central

Tsai, Yi-Ting; Patty, Kaitlen M; Weng, Hong; Tang, Ewin N.; Nair, Ashwin; Hu, Wen-Jing; Tang, Liping

2014-01-01

Plasticity of macrophages (MΦ) phenotypes exist in a spectrum from classically activated (M1) cells, to alternatively activated (M2) cells, contributing to both the normal healing of tissues and the pathogenesis of implant failure. Here, folate- and mannose-based optical probes were fabricated to simultaneously determine the degree of MΦ polarization. In vitro tests show the ability of these probes to specifically target M1 and M2 cells. In an in vivo murine model, they were able to distinguish between M1-dominated inflammatory response to infection and M2-dominated regenerative response to particle implants. Finally, the probes were used to assess the inflammatory/ regenerative property of biomaterial implants. Our results show that these probes can be used to monitor and quantify the dynamic processes of MΦ polarization and their role in cellular responses in real time. PMID:24726956

Simultaneous Optical Measurements of Axial and Tangential Steady-State Blade Deflections

NASA Technical Reports Server (NTRS)

Kurkov, Anatole P.; Dhadwal, Harbans S.

1999-01-01

Currently, the majority of fiber-optic blade instrumentation is being designed and manufactured by aircraft-engine companies for their own use. The most commonly employed probe for optical blade deflection measurements is the spot probe. One of its characteristics is that the incident spot on a blade is not fixed relative to the blade, but changes depending on the blade deformation associated with centrifugal and aerodynamic loading. While there are geometrically more complicated optical probe designs in use by different engine companies, this paper offers an alternate solution derived from a probe-mount design feature that allows one to change the probe axial position until the incident spot contacts either a leading or a trailing edge. By tracing the axial position of either blade edge one is essentially extending the deflection measurement to two dimensions, axial and tangential. The blade deflection measurements were obtained during a wind tunnel test of a fan prototype.

Study of alternative probe technologies

NASA Technical Reports Server (NTRS)

1977-01-01

A number of implied technologies for a deep probe mission was examined; i.e., one that would provide the capability to scientifically examine planetary atmospheres at the 1000 bar level. Conditions imposed by current Jupiter, Saturn, and Uranus atmospheric models were considered. The major thrust of the measurements was to determine lower atmosphere composition, even to trace constituents of one part per billion. Two types of instruments having the necessary accuracy to meet the science objectives were considered and integrated into a deep probe configuration. One deep probe option that resulted was identified as a Minimum Technology Development approach. The significant feature of this option is that only three technology developments are required to enable the mission, i.e., (1) science instrument development, (2) advanced data processing, and (3) external high pressure/thermal insulation. It is concluded that a probe designed for a Jupiter mission could, with minor changes, be used for a Saturn or Uranus mission.

Metal Resistivity Measuring Device

DOEpatents

Renken, Jr, C. J.; Myers, R. G.

1960-12-20

An eddy current device is designed for detecting discontinuities in metal samples. Alternate short and long duration pulses are inductively applied to a metal sample via the outer coil of a probe. The lorg pulses give a resultant signal from the metal sample responsive to probe-tosample spacing and discontinuities with the sample, and the short pulses give a resultant signal responsive only to probe-to-sample spacing. The inner coil of the probe detects the two resultant signals and transmits them to a separation network where the two signals are separated. The two separated signals are then transmitted to a compensation network where the detected signals due to the short pulses are used to compensate for variations due to probeto-sample spacing contained in the detected signals from the long pulses. Thus a resultant signal is obtained responsive to discontinuities within the sample and independent of probe-to- sample spacing.

Modulated microwave microscopy and probes used therewith

DOEpatents

Lai, Keji; Kelly, Michael; Shen, Zhi-Xun

2012-09-11

A microwave microscope including a probe tip electrode vertically positionable over a sample and projecting downwardly from the end of a cantilever. A transmission line connecting the tip electrode to the electronic control system extends along the cantilever and is separated from a ground plane at the bottom of the cantilever by a dielectric layer. The probe tip may be vertically tapped near or at the sample surface at a low frequency and the microwave signal reflected from the tip/sample interaction is demodulated at the low frequency. Alternatively, a low-frequency electrical signal is also a non-linear electrical element associated with the probe tip to non-linearly interact with the applied microwave signal and the reflected non-linear microwave signal is detected at the low frequency. The non-linear element may be semiconductor junction formed near the apex of the probe tip or be an FET formed at the base of a semiconducting tip.

Mixture modeling of multi-component data sets with application to ion-probe zircon ages

NASA Astrophysics Data System (ADS)

Sambridge, M. S.; Compston, W.

1994-12-01

A method is presented for detecting multiple components in a population of analytical observations for zircon and other ages. The procedure uses an approach known as mixture modeling, in order to estimate the most likely ages, proportions and number of distinct components in a given data set. Particular attention is paid to estimating errors in the estimated ages and proportions. At each stage of the procedure several alternative numerical approaches are suggested, each having their own advantages in terms of efficency and accuracy. The methodology is tested on synthetic data sets simulating two or more mixed populations of zircon ages. In this case true ages and proportions of each population are known and compare well with the results of the new procedure. Two examples are presented of its use with sets of SHRIMP U-238 - Pb-206 zircon ages from Palaeozoic rocks. A published data set for altered zircons from bentonite at Meishucun, South China, previously treated as a single-component population after screening for gross alteration effects, can be resolved into two components by the new procedure and their ages, proportions and standard errors estimated. The older component, at 530 +/- 5 Ma (2 sigma), is our best current estimate for the age of the bentonite. Mixture modeling of a data set for unaltered zircons from a tonalite elsewhere defines the magmatic U-238 - Pb-206 age at high precision (2 sigma +/- 1.5 Ma), but one-quarter of the 41 analyses detect hidden and significantly older cores.

High sensitive and direct fluorescence detection of single viral DNA sequences by integration of double strand probes onto microgels particles.

PubMed

Aliberti, A; Cusano, A M; Battista, E; Causa, F; Netti, P A

2016-02-21

A novel class of probes for fluorescence detection was developed and combined to microgel particles for a high sensitive fluorescence detection of nucleic acids. A double strand probe with an optimized fluorescent-quencher couple was designed for the detection of different lengths of nucleic acids (39 nt and 100 nt). Such probe proved efficient in target detection in different contests and specific even in presence of serum proteins. The conjugation of double strand probes onto polymeric microgels allows for a sensitive detection of DNA sequences from HIV, HCV and SARS corona viruses with a LOD of 1.4 fM, 3.7 fM and 1.4 fM, respectively, and with a dynamic range of 10(-9)-10(-15) M. Such combination enhances the sensitivity of the detection of almost five orders of magnitude when compared to the only probe. The proposed platform based on the integration of innovative double strand probe into microgels particles represents an attractive alternative to conventional sensitive DNA detection technologies that rely on amplifications methods.

An alternative view of protein fold space.

PubMed

Shindyalov, I N; Bourne, P E

2000-02-15

Comparing and subsequently classifying protein structures information has received significant attention concurrent with the increase in the number of experimentally derived 3-dimensional structures. Classification schemes have focused on biological function found within protein domains and on structure classification based on topology. Here an alternative view is presented that groups substructures. Substructures are long (50-150 residue) highly repetitive near-contiguous pieces of polypeptide chain that occur frequently in a set of proteins from the PDB defined as structurally non-redundant over the complete polypeptide chain. The substructure classification is based on a previously reported Combinatorial Extension (CE) algorithm that provides a significantly different set of structure alignments than those previously described, having, for example, only a 40% overlap with FSSP. Qualitatively the algorithm provides longer contiguous aligned segments at the price of a slightly higher root-mean-square deviation (rmsd). Clustering these alignments gives a discreet and highly repetitive set of substructures not detectable by sequence similarity alone. In some cases different substructures represent all or different parts of well known folds indicative of the Russian doll effect--the continuity of protein fold space. In other cases they fall into different structure and functional classifications. It is too early to determine whether these newly classified substructures represent new insights into the evolution of a structural framework important to many proteins. What is apparent from on-going work is that these substructures have the potential to be useful probes in finding remote sequence homology and in structure prediction studies. The characteristics of the complete all-by-all comparison of the polypeptide chains present in the PDB and details of the filtering procedure by pair-wise structure alignment that led to the emergent substructure gallery are discussed. Substructure classification, alignments, and tools to analyze them are available at http://cl.sdsc.edu/ce.html.

UCB current detector experiment on Swedish auroral payloads. [ionospheric current and plasma flow measurements

NASA Technical Reports Server (NTRS)

Mozer, F.

1974-01-01

A split Langmuir probe has been developed to make in situ measurements of ionospheric current density and plasma bulk flow. The probe consists of two conducting elements that are separated by a thin insulator that shield each other over a 2 pi solid angle, and that are simultaneously swept from negative to positive with respect to the plasma. By measuring the current to each plate and the difference current between plates, information is obtained on the plasma's current density, bulk flow, electron temperature, and density. The instrument was successfully flown twice on sounding rockets into auroral events. Measurement data indicate that the total auroral current configuration is composed of several alternating east and west electrojets associated with several alternating up and down Birkeland currents.

Influenza Risk Management: Lessons Learned from an A(H1N1) pdm09 Outbreak Investigation in an Operational Military Setting

DTIC Science & Technology

2013-07-10

of the virus in Spain was detected during an outbreak investigation of influenza -like illness (ILI) in soldiers from an engineering military academy...SwInfA primer and probe set) and specific A(H1N1) pdm09 influenza A viruses using SwH1 primer and probe set developed by CDC, Atlanta (WHO...CY062374, CY062375 and CY062376. Viral culture Influenza viruses were isolated from clinical samples by infecting Madin Darby Canine Kidney (MDCK

Local collective motion analysis for multi-probe dynamic imaging and microrheology

NASA Astrophysics Data System (ADS)

Khan, Manas; Mason, Thomas G.

2016-08-01

Dynamical artifacts, such as mechanical drift, advection, and hydrodynamic flow, can adversely affect multi-probe dynamic imaging and passive particle-tracking microrheology experiments. Alternatively, active driving by molecular motors can cause interesting non-Brownian motion of probes in local regions. Existing drift-correction techniques, which require large ensembles of probes or fast temporal sampling, are inadequate for handling complex spatio-temporal drifts and non-Brownian motion of localized domains containing relatively few probes. Here, we report an analytical method based on local collective motion (LCM) analysis of as few as two probes for detecting the presence of non-Brownian motion and for accurately eliminating it to reveal the underlying Brownian motion. By calculating an ensemble-average, time-dependent, LCM mean square displacement (MSD) of two or more localized probes and comparing this MSD to constituent single-probe MSDs, we can identify temporal regimes during which either thermal or athermal motion dominates. Single-probe motion, when referenced relative to the moving frame attached to the multi-probe LCM trajectory, provides a true Brownian MSD after scaling by an appropriate correction factor that depends on the number of probes used in LCM analysis. We show that LCM analysis can be used to correct many different dynamical artifacts, including spatially varying drifts, gradient flows, cell motion, time-dependent drift, and temporally varying oscillatory advection, thereby offering a significant improvement over existing approaches.

Higgs-dilaton cosmology: An inflation-dark-energy connection and forecasts for future galaxy surveys

NASA Astrophysics Data System (ADS)

Casas, Santiago; Pauly, Martin; Rubio, Javier

2018-02-01

The Higgs-dilaton model is a scale-invariant extension of the Standard Model nonminimally coupled to gravity and containing just one additional degree of freedom on top of the Standard Model particle content. This minimalistic scenario predicts a set of measurable consistency relations between the inflationary observables and the dark-energy equation-of-state parameter. We present an alternative derivation of these consistency relations that highlights the connections and differences with the α -attractor scenario. We study how far these constraints allow one to distinguish the Higgs-dilaton model from Λ CDM and w CDM cosmologies. To this end we first analyze existing data sets using a Markov chain Monte Carlo approach. Second, we perform forecasts for future galaxy surveys using a Fisher matrix approach, both for galaxy clustering and weak lensing probes. Assuming that the best fit values in the different models remain comparable to the present ones, we show that both Euclid- and SKA2-like missions will be able to discriminate a Higgs-dilaton cosmology from Λ CDM and w CDM .

European Portuguese adaptation and validation of dilemmas used to assess moral decision-making.

PubMed

Fernandes, Carina; Gonçalves, Ana Ribeiro; Pasion, Rita; Ferreira-Santos, Fernando; Paiva, Tiago Oliveira; Melo E Castro, Joana; Barbosa, Fernando; Martins, Isabel Pavão; Marques-Teixeira, João

2018-03-01

Objective To adapt and validate a widely used set of moral dilemmas to European Portuguese, which can be applied to assess decision-making. Moreover, the classical formulation of the dilemmas was compared with a more focused moral probe. Finally, a shorter version of the moral scenarios was tested. Methods The Portuguese version of the set of moral dilemmas was tested in 53 individuals from several regions of Portugal. In a second study, an alternative way of questioning on moral dilemmas was tested in 41 participants. Finally, the shorter version of the moral dilemmas was tested in 137 individuals. Results Results evidenced no significant differences between English and Portuguese versions. Also, asking whether actions are "morally acceptable" elicited less utilitarian responses than the original question, although without reaching statistical significance. Finally, all tested versions of moral dilemmas exhibited the same pattern of responses, suggesting that the fundamental elements to the moral decision-making were preserved. Conclusions We found evidence of cross-cultural validity for moral dilemmas. However, the moral focus might affect utilitarian/deontological judgments.

Assessing the acquisition and generalization of two mand forms with adults with severe developmental disabilities.

PubMed

Chambers, Mark; Rehfeldt, Ruth Anne

2003-01-01

The purpose of this study was to determine whether manual sign or the Picture Exchange Communication System (P.E.C.S.) (Frost and Bondy, 1994) would be more effective in teaching mand skills to adults with mental retardation in the severe and profound range. Four participants were taught to mand for four reinforcing items using both communication modalities, in an alternating treatments design. Three of four participants demonstrated criterion performance across all four mands using P.E.C.S. first. Two of those three participants later demonstrated criterion performance for the mands using manual sign. The fourth participant was removed from the study during training due to illness, but her progress indicated greater acquisition with P.E.C.S. Generalization probes conducted at participants' respective residences showed that three participants demonstrated generalization across settings using P.E.C.S., and two participants demonstrated generalization across settings using manual sign. Participants were also more likely to mand for reinforcing items not present using P.E.C.S. than using manual sign.

Optical method for distance and displacement measurements of the probe-sample separation in a scanning near-field optical microscope

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

Santamaria, L.; Siller, H. R.; Garcia-Ortiz, C. E., E-mail: cegarcia@cicese.mx

In this work, we present an alternative optical method to determine the probe-sample separation distance in a scanning near-field optical microscope. The experimental method is based in a Lloyd’s mirror interferometer and offers a measurement precision deviation of ∼100 nm using digital image processing and numerical analysis. The technique can also be strategically combined with the characterization of piezoelectric actuators and stability evaluation of the optical system. It also opens the possibility for the development of an automatic approximation control system valid for probe-sample distances from 5 to 500 μm.

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

Hirode, Mitsuhiro; Ono, Atsushi; Miyagishima, Toshikazu

We have constructed a large-scale transcriptome database of rat liver treated with various drugs. In an effort to identify a biomarker for diagnosis of hepatic phospholipidosis, we extracted 78 probe sets of rat hepatic genes from data of 5 drugs, amiodarone, amitriptyline, clomipramine, imipramine, and ketoconazole, which actually induced this phenotype. Principal component analysis (PCA) using these probes clearly separated dose- and time-dependent clusters of treated groups from their controls. Moreover, 6 drugs (chloramphenicol, chlorpromazine, gentamicin, perhexiline, promethazine, and tamoxifen), which were reported to cause phospholipidosis but judged as negative by histopathological examination, were designated as positive by PCA usingmore » these probe sets. Eight drugs (carbon tetrachloride, coumarin, tetracycline, metformin, hydroxyzine, diltiazem, 2-bromoethylamine, and ethionamide), which showed phospholipidosis-like vacuolar formation in the histopathology, could be distinguished from the typical drugs causing phospholipidosis. Moreover, the possible induction of phospholipidosis was predictable by the expression of these genes 24 h after single administration in some of the drugs. We conclude that these identified 78 probe sets could be useful for diagnosis of phospholipidosis, and that toxicogenomics would be a promising approach for prediction of this type of toxicity.« less

Bayesian `hyper-parameters' approach to joint estimation: the Hubble constant from CMB measurements

NASA Astrophysics Data System (ADS)

Lahav, O.; Bridle, S. L.; Hobson, M. P.; Lasenby, A. N.; Sodré, L.

2000-07-01

Recently several studies have jointly analysed data from different cosmological probes with the motivation of estimating cosmological parameters. Here we generalize this procedure to allow freedom in the relative weights of various probes. This is done by including in the joint χ2 function a set of `hyper-parameters', which are dealt with using Bayesian considerations. The resulting algorithm, which assumes uniform priors on the log of the hyper-parameters, is very simple: instead of minimizing \\sum \\chi_j2 (where \\chi_j2 is per data set j) we propose to minimize \\sum Nj (\\chi_j2) (where Nj is the number of data points per data set j). We illustrate the method by estimating the Hubble constant H0 from different sets of recent cosmic microwave background (CMB) experiments (including Saskatoon, Python V, MSAM1, TOCO and Boomerang). The approach can be generalized for combinations of cosmic probes, and for other priors on the hyper-parameters.

Electromagnetic microscope compared with a conventional pulsed eddy-current probe

NASA Astrophysics Data System (ADS)

Podney, Walter N.

1998-03-01

A superconductive probe presently can detect a crack at a rivet hole that is two to three times smaller than the smallest crack detectable by a conventional probe. As the technology matures and noise resolution approaches a limit set by SQUIDS, approximately 1 fH, it will enable detecting submillimeter cracks down to approximately 15 mm.

Using phylogenetic probes for quantification of stable isotope labeling and microbial community analysis

DOEpatents

Brodie, Eoin L; DeSantis, Todd Z; Karaoz, Ulas; Andersen, Gary L

2014-12-09

Herein is described methods for a high-sensitivity means to measure the incorporation of stable isotope labeled substrates into RNA following stable isotope probing experiments (SIP). RNA is hybridized to a set of probes such as phylogenetic microarrays and isotope incorporation is quantified such as by secondary ion mass spectrometer imaging (NanoSIMS).

Probing Cytological and Reproductive Phenomena by Means of Bryophytes.

ERIC Educational Resources Information Center

Newton, M. E.

1985-01-01

Describes procedures (recommended for both secondary and college levels) to study mitosis, Giemsa C-banding, reproductive phenomena (including alternation of generations), and phototropism in mosses and liverworts. (JN)

Sparse sampling and reconstruction for electron and scanning probe microscope imaging

DOEpatents

Anderson, Hyrum; Helms, Jovana; Wheeler, Jason W.; Larson, Kurt W.; Rohrer, Brandon R.

2015-07-28

Systems and methods for conducting electron or scanning probe microscopy are provided herein. In a general embodiment, the systems and methods for conducting electron or scanning probe microscopy with an undersampled data set include: driving an electron beam or probe to scan across a sample and visit a subset of pixel locations of the sample that are randomly or pseudo-randomly designated; determining actual pixel locations on the sample that are visited by the electron beam or probe; and processing data collected by detectors from the visits of the electron beam or probe at the actual pixel locations and recovering a reconstructed image of the sample.

Miniature standoff Raman probe for neurosurgical applications

NASA Astrophysics Data System (ADS)

Stevens, Oliver A. C.; Hutchings, Joanne; Gray, William; Vincent, Rosa Louise; Day, John C.

2016-08-01

Removal of intrinsic brain tumors is a delicate process, where a high degree of specificity is required to remove all of the tumor tissue without damaging healthy brain. The accuracy of this process can be greatly enhanced by intraoperative guidance. Optical biopsies using Raman spectroscopy are a minimally invasive and lower-cost alternative to current guidance methods. A miniature Raman probe for performing optical biopsies of human brain tissue is presented. The probe allows sampling inside a conventional stereotactic brain biopsy system: a needle of length 200 mm and inner diameter of 1.8 mm. By employing a miniature stand-off Raman design, the probe removes the need for any additional components to be inserted into the brain. Additionally, the probe achieves a very low internal silica background while maintaining good collection of Raman signal. To illustrate this, the probe is compared with a Raman probe that uses a pair of optical fibers for collection. The miniature stand-off Raman probe is shown to collect a comparable number of Raman scattered photons, but the Raman signal to background ratio is improved by a factor of five at Raman shifts below ˜500 cm-1. The probe's suitability for use on tissue is demonstrated by discriminating between different types of healthy porcine brain tissue.

Community Analysis of Biofilters Using Fluorescence In Situ Hybridization Including a New Probe for the Xanthomonas Branch of the Class Proteobacteria

PubMed Central

Friedrich, Udo; Naismith, Michèle M.; Altendorf, Karlheinz; Lipski, André

1999-01-01

Domain-, class-, and subclass-specific rRNA-targeted probes were applied to investigate the microbial communities of three industrial and three laboratory-scale biofilters. The set of probes also included a new probe (named XAN818) specific for the Xanthomonas branch of the class Proteobacteria; this probe is described in this study. The members of the Xanthomonas branch do not hybridize with previously developed rRNA-targeted oligonucleotide probes for the α-, β-, and γ-Proteobacteria. Bacteria of the Xanthomonas branch accounted for up to 4.5% of total direct counts obtained with 4′,6-diamidino-2-phenylindole. In biofilter samples, the relative abundance of these bacteria was similar to that of the γ-Proteobacteria. Actinobacteria (gram-positive bacteria with a high G+C DNA content) and α-Proteobacteria were the most dominant groups. Detection rates obtained with probe EUB338 varied between about 40 and 70%. For samples with high contents of gram-positive bacteria, these percentages were substantially improved when the calculations were corrected for the reduced permeability of gram-positive bacteria when formaldehyde was used as a fixative. The set of applied bacterial class- and subclass-specific probes yielded, on average, 58.5% (± a standard deviation of 23.0%) of the corrected eubacterial detection rates, thus indicating the necessity of additional probes for studies of biofilter communities. The Xanthomonas-specific probe presented here may serve as an efficient tool for identifying potential phytopathogens. In situ hybridization proved to be a practical tool for microbiological studies of biofiltration systems. PMID:10427047

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

PubMed

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

2014-04-01

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

Fiber sensors for molecular detection

NASA Astrophysics Data System (ADS)

Gu, Claire; Yang, Xuan; Zhang, Jin; Newhouse, Rebecca; Cao, Liangcai

2010-11-01

The demand on sensors for detecting chemical and biological agents is greater than ever before, including medical, environmental, food safety, military, and security applications. At present, most detection or sensing techniques tend to be either non-molecular specific, bulky, expensive, relatively inaccurate, or unable to provide real time data. Clearly, alternative sensing technologies are urgently needed. Recently, we have been working to develop a compact fiber optic surface enhanced Raman scattering (SERS) sensor system that integrates various novel ideas to achieve compactness, high sensitivity and consistency, molecular specificity, and automatic preliminary identification capabilities. The unique sensor architecture is expected to bring SERS sensors to practical applications due to a combination of 1) novel SERS substrates that provide the high sensitivity and consistency, molecular specificity, and applicability to a wide range of compounds; 2) a unique hollow core optical fiber probe with double SERS substrate structure that provides the compactness, reliability, low cost, and ease of sampling; and 3) an innovative matched spectral filter set that provides automatic preliminary molecule identification. In this paper, we will review the principle of operation and some of the important milestones of fiber SERS sensor development with emphasis on our recent work to integrate photonic crystal fiber SERS probes with a portable Raman spectrometer and to demonstrate a matched spectral filter for molecule identification.

[1,10]Phenanthroline based cyanine dyes as fluorescent probes for ribonucleic acids in live cells

NASA Astrophysics Data System (ADS)

Kovalska, Vladyslava; Kuperman, Marina; Varzatskii, Oleg; Kryvorotenko, Dmytro; Kinski, Elisa; Schikora, Margot; Janko, Christina; Alexiou, Christoph; Yarmoluk, Sergiy; Mokhir, Andriy

2017-12-01

A series of monomethine, trimethine- and styrylcyanine dyes based on a [1,10]phenanthroline moiety was synthesized, characterized and investigated as potential fluorescent probes for nucleic acids in cell free settings and in cells. The dyes were found to be weakly fluorescent in the unbound state, whereas upon the binding to dsDNA or RNA their emission intensity raised up to 50 times (for monomethine benzothiazole derivative FT1 complexed with RNA). The strongest fluorescence intensity in assemblies with dsDNA and RNA was observed for the trimethine benzothiazole derivative FT4. The quantum yield of FT4 fluorescence in its complex with dsDNA was found to be 1.5% and the binding constant (K b) was estimated to be 7.9 × 104 M-1 that is a typical value for intercalating molecules. The FT4 dye was found to be cell membrane permeable. It stains RNA rich components—the nucleoli and most probably the cytoplasmic RNA. FT4 bound to RNAs delivers a very strong fluorescence signal, which makes this easily accessible dye a potentially useful alternative to known RNA stains, e.g. expensive SYTO® 83. The advantage of FT4 is its easy synthetic access including no chromatographic purification steps, which will be reflected in its substantially lower price.

Triboelectrification-Enabled Self-Powered Data Storage.

PubMed

Kuang, Shuang Yang; Zhu, Guang; Wang, Zhong Lin

2018-02-01

Data storage by any means usually requires an electric driving power for writing or reading. A novel approach for self-powered, triboelectrification-enabled data storage (TEDS) is presented. Data are incorporated into a set of metal-based surface patterns. As a probe slides across the patterned surface, triboelectrification between the scanning probe and the patterns produces alternatively varying voltage signal in quasi-square wave. The trough and crest of the quasi-square wave signal are coded as binary bits of "0" and "1," respectively, while the time span of the trough and the crest is associated with the number of bits. The storage of letters and sentences is demonstrated through either square-shaped or disc-shaped surface patterns. Based on experimental data and numerical calculation, the theoretically predicted maximum data storage density could reach as high as 38.2 Gbit in -2 . Demonstration of real-time data retrieval is realized with the assistance of software interface. For the TEDS reported in this work, the measured voltage signal is self-generated as a result of triboelectrification without the reliance on an external power source. This feature brings about not only low power consumption but also a much more simplified structure. Therefore, this work paves a new path to a unique approach of high-density data storage that may have widespread applications.

A comparative study of self-efficacy, outcome expectancy, and retention of beginning urban science teachers

NASA Astrophysics Data System (ADS)

Klein, Nina

The purpose of the multi-tiered study presented is to compare the effect of credentialing route on the self-efficacy, outcome expectancy, and retention of beginning urban science teachers serving students in a large urban school district in Southern California. Candidates from one traditional, university-based teacher education program and from two alternative programs, the Teach for America and District Intern Programs, were surveyed and interviewed during the second semester of their first year of teaching. To determine the potential of a difference in self-efficacy and outcome expectancy, the study gave teachers a modified version of the Science Teachers' Efficacy Belief Instrument (STEBI), developed and validated by Riggs and Enochs (1989). Two representative candidates from each program were then interviewed in order to probe for deeper understanding of possible sources of their efficacy and outcome expectancy. The final part of the study is an evaluation of retention data from the three programs, each to triangulate this information with data collected from the surveys, and comparing these retention rates with published data. The study provides data on unresearched questions about traditionally and alternatively credentialed science teachers in urban settings in California.

Effect of Geometric Parameters on the Performance of Second Throat Annular Steam Ejectors

DTIC Science & Technology

1991-07-01

Cell Pressure versus Rake Average Exit Pitot Pressure . . . . . . . . . . . 42 15. Baseline Wall Pressure Profiles...diffuser exit plane pitot pressure rake . 2.5.2 Alternate Configurations Six alternate ejector diffuser configurations were tested. A summary of...along the walls of the diffusers to help characterize the flow. The ejector diffuser exit pitot pressure was measured with a 6-probe pitot pressure rake

Computer-Based Video Instruction to Teach the Use of Augmentative and Alternative Communication Devices for Ordering at Fast-Food Restaurants

ERIC Educational Resources Information Center

Mechling, Linda C.; Cronin, Beth

2006-01-01

In the study reported on here, the authors used computer-based video instruction (CBVI) to teach 3 high school students with moderate or severe intellectual disabilities how to order in fast-food restaurants by using an augmentative, alternative communication device. The study employed a multiple probe design to institute CBVI as the only…

Are preference and resistance to change convergent expressions of stimulus value?

PubMed

Podlesnik, Christopher A; Jimenez-Gomez, Corina; Shahan, Timothy A

2013-07-01

Behavioral momentum theory asserts that preference and relative resistance to disruption depend on reinforcement rates and provide converging expressions of the conditioned value of discriminative stimuli. However, preference and resistance to disruption diverge when assessing preference during brief extinction probes. We expanded upon this opposing relation by arranging target stimuli signaling equal variable-interval schedules across components of a multiple schedule. We paired one target stimulus with a richer reinforced alternative and the other with a leaner alternative. Furthermore, we varied reinforcement rates for the paired alternatives to assess the effects of manipulating relative conditioned value on preference and resistance to disruption by presession feeding, intercomponent food, and extinction. We replicated the opposing relation between preference and resistance to disruption but varying reinforcement rates for the paired alternatives did not systematically affect preference or resistance to disruption beyond levels observed in our initial condition. Importantly, we found that only preference between the target stimuli was related to relative baseline response rates in the presence of those stimuli. These findings suggest that preference during extinction probes might reveal more about baseline response rates between concurrently available alternatives than relative conditioned value. Resistance to disruption, conversely, appears to better reflect conditioned value because it is less confounded with baseline response rates and is a function of all sources of reinforcement obtained in the presence of a stimulus context. © Society for the Experimental Analysis of Behavior.

Alternative Settings--Alternative Teachers? Reflections on Teaching outside the Mainstream

ERIC Educational Resources Information Center

Dyson, Michael; Plunkett, Margaret

2012-01-01

While alternative educational settings in Australia have expanded over the past two decades, there has been little formal research into teacher perceptions of what it means to teach outside the mainstream. This paper outlines part of a longitudinal study involving the School for Student Leadership (SSL), an alternate educational setting in…

Impact of alternative fuels on emissions characteristics of a gas turbine engine - part 2: volatile and semivolatile particulate matter emissions.

PubMed

Williams, Paul I; Allan, James D; Lobo, Prem; Coe, Hugh; Christie, Simon; Wilson, Christopher; Hagen, Donald; Whitefield, Philip; Raper, David; Rye, Lucas

2012-10-02

The work characterizes the changes in volatile and semivolatile PM emissions from a gas turbine engine resulting from burning alternative fuels, specifically gas-to-liquid (GTL), coal-to-liquid (CTL), a blend of Jet A-1 and GTL, biodiesel, and diesel, to the standard Jet A-1. The data presented here, compares the mass spectral fingerprints of the different fuels as measured by the Aerodyne high resolution time-of-flight aerosol mass spectrometer. There were three sample points, two at the exhaust exit plane with dilution added at different locations and another probe located 10 m downstream. For emissions measured at the downstream probe when the engine was operating at high power, all fuels produced chemically similar organic PM, dominated by C(x)H(y) fragments, suggesting the presence of long chain alkanes. The second largest contribution came from C(x)H(y)O(z) fragments, possibly from carbonyls or alcohols. For the nondiesel fuels, the highest loadings of organic PM were from the downstream probe at high power. Conversely, the diesel based fuels produced more organic material at low power from one of the exit plane probes. Differences in the composition of the PM for certain fuels were observed as the engine power decreased to idle and the measurements were made closer to the exit plane.

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.

Comparison of the structure function F 2 as measured by charged lepton and neutrino scattering from iron targets

DOE PAGES

Kalantarians, N.; Keppel, C.; Christy, M. E.

2017-09-12

A comparison study of world data for the structure function F 2 for Iron, as measured by both charged lepton and neutrino scattering experiments, is presented. Consistency of results for both charged lepton and neutrino scattering is observed for the full global data set in the valence regime. Consistency is also observed at low x for the various neutrino data sets, as well as for the charged lepton data sets, independently. However, data from the two probes exhibit differences on the order of 15% in the shadowing/anti-shadowing transition region where the Bjorken scaling variable x is < 0.15. This observationmore » is indicative that neutrino probes of nucleon structure might be sensitive to different nuclear effects than charged lepton probes. Details and results of the data comparison are here presented.« less

Comparison of the structure function F 2 as measured by charged lepton and neutrino scattering from iron targets

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

Kalantarians, N.; Keppel, C.; Christy, M. E.

A comparison study of world data for the structure function F 2 for Iron, as measured by both charged lepton and neutrino scattering experiments, is presented. Consistency of results for both charged lepton and neutrino scattering is observed for the full global data set in the valence regime. Consistency is also observed at low x for the various neutrino data sets, as well as for the charged lepton data sets, independently. However, data from the two probes exhibit differences on the order of 15% in the shadowing/anti-shadowing transition region where the Bjorken scaling variable x is < 0.15. This observationmore » is indicative that neutrino probes of nucleon structure might be sensitive to different nuclear effects than charged lepton probes. Details and results of the data comparison are here presented.« less

High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis.

PubMed

Friedrich, Torben; Rahmann, Sven; Weigel, Wilfried; Rabsch, Wolfgang; Fruth, Angelika; Ron, Eliora; Gunzer, Florian; Dandekar, Thomas; Hacker, Jörg; Müller, Tobias; Dobrindt, Ulrich

2010-10-21

The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens. We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant Enterobacteriaceae, including the subspecies level, e.g. the reliable distinction of different E. coli pathotypes. Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.

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.

Chemical biology-based approaches on fluorescent labeling of proteins in live cells.

PubMed

Jung, Deokho; Min, Kyoungmi; Jung, Juyeon; Jang, Wonhee; Kwon, Youngeun

2013-05-01

Recently, significant advances have been made in live cell imaging owing to the rapid development of selective labeling of proteins in vivo. Green fluorescent protein (GFP) was the first example of fluorescent reporters genetically introduced to protein of interest (POI). While GFP and various types of engineered fluorescent proteins (FPs) have been actively used for live cell imaging for many years, the size and the limited windows of fluorescent spectra of GFP and its variants set limits on possible applications. In order to complement FP-based labeling methods, alternative approaches that allow incorporation of synthetic fluorescent probes to target POIs were developed. Synthetic fluorescent probes are smaller than fluorescent proteins, often have improved photochemical properties, and offer a larger variety of colors. These synthetic probes can be introduced to POIs selectively by numerous approaches that can be largely categorized into chemical recognition-based labeling, which utilizes metal-chelating peptide tags and fluorophore-carrying metal complexes, and biological recognition-based labeling, such as (1) specific non-covalent binding between an enzyme tag and its fluorophore-carrying substrate, (2) self-modification of protein tags using substrate variants conjugated to fluorophores, (3) enzymatic reaction to generate a covalent binding between a small molecule substrate and a peptide tag, and (4) split-intein-based C-terminal labeling of target proteins. The chemical recognition-based labeling reaction often suffers from compromised selectivity of metal-ligand interaction in the cytosolic environment, consequently producing high background signals. Use of protein-substrate interactions or enzyme-mediated reactions generally shows improved specificity but each method has its limitations. Some examples are the presence of large linker protein, restriction on the choice of introducible probes due to the substrate specificity of enzymes, and competitive reaction mediated by an endogenous analogue of the introduced protein tag. These limitations have been addressed, in part, by the split-intein-based labeling approach, which introduces fluorescent probes with a minimal size (~4 amino acids) peptide tag. In this review, the advantages and the limitations of each labeling method are discussed.

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing.

PubMed

Castle, John; Garrett-Engele, Phil; Armour, Christopher D; Duenwald, Sven J; Loerch, Patrick M; Meyer, Michael R; Schadt, Eric E; Stoughton, Roland; Parrish, Mark L; Shoemaker, Daniel D; Johnson, Jason M

2003-01-01

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing

PubMed Central

Castle, John; Garrett-Engele, Phil; Armour, Christopher D; Duenwald, Sven J; Loerch, Patrick M; Meyer, Michael R; Schadt, Eric E; Stoughton, Roland; Parrish, Mark L; Shoemaker, Daniel D; Johnson, Jason M

2003-01-01

Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing. PMID:14519201

Measurement of locus copy number by hybridisation with amplifiable probes

PubMed Central

Armour, John A. L.; Sismani, Carolina; Patsalis, Philippos C.; Cross, Gareth

2000-01-01

Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicroscopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader–Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications. PMID:10606661

Measurement of locus copy number by hybridisation with amplifiable probes.

PubMed

Armour, J A; Sismani, C; Patsalis, P C; Cross, G

2000-01-15

Despite its fundamental importance in genome analysis, it is only recently that systematic approaches have been developed to assess copy number at specific genetic loci, or to examine genomic DNA for submicro-scopic deletions of unknown location. In this report we show that short probes can be recovered and amplified quantitatively following hybridisation to genomic DNA. This simple observation forms the basis of a new approach to determining locus copy number in complex genomes. The power and specificity of multiplex amplifiable probe hybridisation is demonstrated by the simultaneous assessment of copy number at a set of 40 human loci, including detection of deletions causing Duchenne muscular dystrophy and Prader-Willi/Angelman syndromes. Assembly of other probe sets will allow novel, technically simple approaches to a wide variety of genetic analyses, including the potential for extension to high resolution genome-wide screens for deletions and amplifications.

Surface-enhanced Raman medical probes and system for disease diagnosis and drug testing

DOEpatents

Vo-Dinh, T.

1999-01-26

A probe for a surface-enhanced Raman scattering spectrometer includes a member of optically transmissive material for receiving the excitation radiation from a laser and for carrying the radiation emitted from a specimen to a detector. An end of the member for placing against the specimen has a coating that produces surface enhancement of the specimen during Raman scattering spectroscopic analysis. Specifically the coating is formed by a first layer of microparticles on the member and a metal layer over the first layer. The first layer may form a microstructure surface over which a metal layer is applied. Alternatively the coating may be a material containing microparticles of a metal. An optional layer of a material may be applied to the metal layer to concentrate onto the probe compounds of analytical interest onto the probe. 39 figs.

Surface-enhanced raman medical probes and system for disease diagnosis and drug testing

DOEpatents

Vo-Dinh, Tuan

1999-01-01

A probe for a surface-enhanced Raman scattering spectrometer includes a member of optically transmissive material for receiving the excitation radiation from a laser and for carrying the radiation emitted from a specimen to a detector. An end of the member for placing against the specimen has a coating that produces surface enhancement of the specimen during Raman scattering spectroscopic analysis. Specifically the coating is formed by a first layer of microparticles on the member and a metal layer over the first layer. The first layer may form a microstructure surface over which a metal layer is applied. Alternatively the coating may be a material containing microparticles of a metal. An optional layer of a material may be applied to the metal layer to concentrate onto the probe compounds of analytical interest onto the probe.

How to study picosecond solvation dynamics using fluorescent probes with small Stokes shifts

NASA Astrophysics Data System (ADS)

Silori, Yogita; Dey, Shivalee; De, Arijit K.

2018-02-01

Xanthene dyes have wide ranging applications as fluorescent probes in analytical, biochemical and medical contexts. Being cationic/anionic in nature, the solvation dynamics of xanthene dyes confined within a negatively/positively charged interface are very interesting. Unfortunately, the floppy structure and small Stokes shift render any xanthene dye unsuitable for use as a solvation probe. Using di-sodium fluorescein, we present our work on the picosecond solvation dynamics of bulk and confined water (at pH = 9.2). We also propose a new methodology for studying picosecond solvation dynamics using any fluorescent dye with a small Stokes shift. We discuss how scattering contributions can be effectively removed, and propose an alternative way of defining zero time of solvation. Finally, we demonstrate the tuning location of the probe within confinement.

Self-Nulling Eddy Current Probe for Surface and Subsurface Flaw Detection

NASA Technical Reports Server (NTRS)

Wincheski, B.; Fulton, J. P.; Nath, S.; Namkung, M.; Simpson, J. W.

1994-01-01

An eddy current probe which provides a null-signal in the presence of unflawed material without the need for any balancing circuitry has been developed at NASA Langley Research Center. Such a unique capability of the probe reduces set-up time, eliminates tester configuration errors, and decreases instrumentation requirements. The probe is highly sensitive to surface breaking fatigue cracks, and shows excellent resolution for the measurement of material thickness, including material loss due to corrosion damage. The presence of flaws in the material under test causes an increase in the extremely stable and reproducible output voltage of the probe. The design of the probe and some examples illustrating its flaw detection capabilities are presented.

A practical model for pressure probe system response estimation (with review of existing models)

NASA Astrophysics Data System (ADS)

Hall, B. F.; Povey, T.

2018-04-01

The accurate estimation of the unsteady response (bandwidth) of pneumatic pressure probe systems (probe, line and transducer volume) is a common practical problem encountered in the design of aerodynamic experiments. Understanding the bandwidth of the probe system is necessary to capture unsteady flow features accurately. Where traversing probes are used, the desired traverse speed and spatial gradients in the flow dictate the minimum probe system bandwidth required to resolve the flow. Existing approaches for bandwidth estimation are either complex or inaccurate in implementation, so probes are often designed based on experience. Where probe system bandwidth is characterized, it is often done experimentally, requiring careful experimental set-up and analysis. There is a need for a relatively simple but accurate model for estimation of probe system bandwidth. A new model is presented for the accurate estimation of pressure probe bandwidth for simple probes commonly used in wind tunnel environments; experimental validation is provided. An additional, simple graphical method for air is included for convenience.

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

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

Salomons, Mark; Martins, Bruno V. C.; Zikovsky, Janik

2014-04-15

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

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.

Mapping Rotational Wavepacket Dynamics with Chirped Probe Pulses

NASA Astrophysics Data System (ADS)

Romanov, Dmitri; Odhner, Johanan; Levis, Robert

2014-05-01

We develop an analytical model description of the strong-field pump-probe polarization spectroscopy of rotational transients in molecular gases in a situation when the probe pulse is considerably chirped: the frequency modulation over the pulse duration is comparable with the carrier frequency. In this scenario, a femtosecond pump laser pulse prepares a rotational wavepacket in a gas-phase sample at room temperature. The rotational revivals of the wavepacket are then mapped onto a chirped broadband probe pulse derived from a laser filament. The slow-varying envelope approximation being inapplicable, an alternative approach is proposed which is capable of incorporating the substantial chirp and the related temporal dispersion of refractive indices. Analytical expressions are obtained for the probe signal modulation over the interaction region and for the resulting heterodyned transient birefringence spectra. Dependencies of the outputs on the probe pulse parameters reveal the trade-offs and the ways to optimize the temporal-spectral imaging. The results are in good agreement with the experiments on snapshot imaging of rotational revival patterns in nitrogen gas. We gratefully acknowledge financial support through AFOSR MURI Grant No. FA9550-10-1-0561.

Test module development to detect the flase call probe pins on microeprocessor test equipment

NASA Astrophysics Data System (ADS)

Tang, L. W.; Ong, N. R.; Mohamad, I. S. B.; Alcain, J. B.; Retnasamy, V.

2017-09-01

Probe pins are useful for electrical testing of microelectronic components, printed circuit board assembly (PCBA), microprocessors and other electronic devices due to it provides the conductivity test based on specific device circuit design. During the repeatable test runs, the load of test modules, contact failures and the current conductivity induces layer wear off all the tip of probe pins contact. Contamination will be build-up on probe pins and increased contact resistivity which results of cost loss and time loss for rectifying programs, rectifying testers and exchanging new probe pins. In this study, a resistivity approach will be developed to provide "Testing of Test Probes". The test module based on "Four-wire Ohm measurement" method with two alternative ways of applying power supply, that are 9V from a single power supply and 5V from Arduino UNO power supply were demonstrated to measure the small resistance value of microprocessor probe pin. A microcontroller with VEE Pro software was used to record the measurement data. The accuracy of both test modules were calibrated under different temperature conditions and result shows that 9V from a single power supply test module has higher measurement accuracy.

Assessing Telomere Length Using Surface Enhanced Raman Scattering

NASA Astrophysics Data System (ADS)

Zong, Shenfei; Wang, Zhuyuan; Chen, Hui; Cui, Yiping

2014-11-01

Telomere length can provide valuable insight into telomeres and telomerase related diseases, including cancer. Here, we present a brand-new optical telomere length measurement protocol using surface enhanced Raman scattering (SERS). In this protocol, two single strand DNA are used as SERS probes. They are labeled with two different Raman molecules and can specifically hybridize with telomeres and centromere, respectively. First, genome DNA is extracted from cells. Then the telomere and centromere SERS probes are added into the genome DNA. After hybridization with genome DNA, excess SERS probes are removed by magnetic capturing nanoparticles. Finally, the genome DNA with SERS probes attached is dropped onto a SERS substrate and subjected to SERS measurement. Longer telomeres result in more attached telomere probes, thus a stronger SERS signal. Consequently, SERS signal can be used as an indicator of telomere length. Centromere is used as the inner control. By calibrating the SERS intensity of telomere probe with that of the centromere probe, SERS based telomere measurement is realized. This protocol does not require polymerase chain reaction (PCR) or electrophoresis procedures, which greatly simplifies the detection process. We anticipate that this easy-operation and cost-effective protocol is a fine alternative for the assessment of telomere length.

Multiwaveguide implantable probe for light delivery to sets of distributed brain targets.

PubMed

Zorzos, Anthony N; Boyden, Edward S; Fonstad, Clifton G

2010-12-15

Optical fibers are commonly inserted into living tissues such as the brain in order to deliver light to deep targets for neuroscientific and neuroengineering applications such as optogenetics, in which light is used to activate or silence neurons expressing specific photosensitive proteins. However, an optical fiber is limited to delivering light to a single target within the three-dimensional structure of the brain. We here demonstrate a multiwaveguide probe capable of independently delivering light to multiple targets along the probe axis, thus enabling versatile optical control of sets of distributed brain targets. The 1.45-cm-long probe is microfabricated in the form of a 360-μm-wide array of 12 parallel silicon oxynitride (SiON) multimode waveguides clad with SiO(2) and coated with aluminum; probes of custom dimensions are easily created as well. The waveguide array accepts light from a set of sources at the input end and guides the light down each waveguide to an aluminum corner mirror that efficiently deflects light away from the probe axis. Light losses at each stage are small (input coupling loss, 0.4 ± 0.3 dB; bend loss, negligible; propagation loss, 3.1 ± 1 dB/cm using the outscattering method and 3.2 ± 0.4 dB/cm using the cutback method; corner mirror loss, 1.5 ± 0.4 dB); a waveguide coupled, for example, to a 5 mW source will deliver over 1.5 mW to a target at a depth of 1 cm.

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.

Dynamic variable selection in SNP genotype autocalling from APEX microarray data.

PubMed

Podder, Mohua; Welch, William J; Zamar, Ruben H; Tebbutt, Scott J

2006-11-30

Single nucleotide polymorphisms (SNPs) are DNA sequence variations, occurring when a single nucleotide--adenine (A), thymine (T), cytosine (C) or guanine (G)--is altered. Arguably, SNPs account for more than 90% of human genetic variation. Our laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension (APEX). This mini-sequencing method is a powerful combination of a highly parallel microarray with distinctive Sanger-based dideoxy terminator sequencing chemistry. Using this microarray platform, our current genotype calling system (known as SNP Chart) is capable of calling single SNP genotypes by manual inspection of the APEX data, which is time-consuming and exposed to user subjectivity bias. Using a set of 32 Coriell DNA samples plus three negative PCR controls as a training data set, we have developed a fully-automated genotyping algorithm based on simple linear discriminant analysis (LDA) using dynamic variable selection. The algorithm combines separate analyses based on the multiple probe sets to give a final posterior probability for each candidate genotype. We have tested our algorithm on a completely independent data set of 270 DNA samples, with validated genotypes, from patients admitted to the intensive care unit (ICU) of St. Paul's Hospital (plus one negative PCR control sample). Our method achieves a concordance rate of 98.9% with a 99.6% call rate for a set of 96 SNPs. By adjusting the threshold value for the final posterior probability of the called genotype, the call rate reduces to 94.9% with a higher concordance rate of 99.6%. We also reversed the two independent data sets in their training and testing roles, achieving a concordance rate up to 99.8%. The strength of this APEX chemistry-based platform is its unique redundancy having multiple probes for a single SNP. Our model-based genotype calling algorithm captures the redundancy in the system considering all the underlying probe features of a particular SNP, automatically down-weighting any 'bad data' corresponding to image artifacts on the microarray slide or failure of a specific chemistry. In this regard, our method is able to automatically select the probes which work well and reduce the effect of other so-called bad performing probes in a sample-specific manner, for any number of SNPs.

Mapping alternating current electroosmotic flow at the dielectrophoresis crossover frequency of a colloidal probe.

PubMed

Wang, Jingyu; Wei, Ming-Tzo; Cohen, Joel A; Ou-Yang, H Daniel

2013-07-01

AC electroosmotic (ACEO) flow above the gap between coplanar electrodes is mapped by the measurement of Stokes forces on an optically trapped polystyrene colloidal particle. E²-dependent forces on the probe particle are selected by amplitude modulation (AM) of the ACEO electric field (E) and lock-in detection at twice the AM frequency. E²-dependent DEP of the probe is eliminated by driving the ACEO at the probe's DEP crossover frequency. The location-independent DEP crossover frequency is determined, in a separate experiment, as the limiting frequency of zero horizontal force as the probe is moved toward the midpoint between the electrodes. The ACEO velocity field, uncoupled from probe DEP effects, was mapped in the region 1-9 μm above a 28 μm gap between the electrodes. By use of variously sized probes, each at its DEP crossover frequency, the frequency dependence of the ACEO flow was determined at a point 3 μm above the electrode gap and 4 μm from an electrode tip. At this location the ACEO flow was maximal at ∼117 kHz for a low salt solution. This optical trapping method, by eliminating DEP forces on the probe, provides unambiguous mapping of the ACEO velocity field. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of optical probes for in vivo imaging of polarized macrophages during foreign body reactions.

PubMed

Baker, David W; Zhou, Jun; Tsai, Yi-Ting; Patty, Kaitlen M; Weng, Hong; Tang, Ewin N; Nair, Ashwin; Hu, Wen-Jing; Tang, Liping

2014-07-01

Plasticity of macrophage (MΦ) phenotypes exist in a spectrum from classically activated (M1) cells, to alternatively activated (M2) cells, contributing to both the normal healing of tissues and the pathogenesis of implant failure. Here, folate- and mannose-based optical probes were fabricated to simultaneously determine the degree of MΦ polarization. In vitro tests show the ability of these probes to specifically target M1 and M2 cells. In an in vivo murine model, they were able to distinguish between the M1-dominated inflammatory response to infection and the M2-dominated regenerative response to particle implants. Finally, the probes were used to assess the inflammatory/regenerative properties of biomaterial implants. Our results show that these probes can be used to monitor and quantify the dynamic processes of MΦ polarization and their role in cellular responses in real time. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Development of a multiplex probe combination-based one-step real-time reverse transcription-PCR for NA subtype typing of avian influenza virus.

PubMed

Sun, Zhihao; Qin, Tao; Meng, Feifei; Chen, Sujuan; Peng, Daxin; Liu, Xiufan

2017-10-18

Nine influenza virus neuraminidase (NA) subtypes have been identified in poultry and wild birds. Few methods are available for rapid and simple NA subtyping. Here we developed a multiplex probe combination-based one-step real-time reverse transcriptase PCR (rRT-PCR) to detect nine avian influenza virus NA subtypes. Nine primer-probe pairs were assigned to three groups based on the different fluorescent dyes of the probes (FAM, HEX, or Texas Red). Each probe detected only one NA subtype, without cross reactivity. The detection limit was less than 100 EID 50 or 100 copies of cDNA per reaction. Data obtained using this method with allantoic fluid samples isolated from live bird markets and H9N2-infected chickens correlated well with data obtained using virus isolation and sequencing, but was more sensitive. This new method provides a specific and sensitive alternative to conventional NA-subtyping methods.

EGR distribution and fluctuation probe based on CO2 measurements

DOEpatents

Parks, II, James E.; Partridge, Jr., William P.; Yoo, Ji Hyung

2015-06-30

A diagnostic system having a laser, an EGR probe, a detector and a processor. The laser may be a swept-.lamda. laser having a sweep range including a significant CO.sub.2 feature and substantially zero absorption regions. The sweep range may extend from about 2.708 .mu.m to about 2.7085 .mu.m. The processor may determine CO.sub.2 concentration as a function of the detector output signal. The processor may normalize the output signal as a function of the zero absorption regions. The system may include a plurality of EGR probes receiving light from a single laser. The system may include a separate detector for each probe. Alternatively, the system may combine the light returning from the different probes into a composite beam that is measured by a single detector. A unique modulation characteristic may be introduced into each light beam before combination so that the processor can discriminate between them in the composite beam.

Experimental validation of an 8 element EMAT phased array probe for longitudinal wave generation

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

Le Bourdais, Florian, E-mail: florian.lebourdais@cea.fr; Marchand, Benoit, E-mail: florian.lebourdais@cea.fr

2015-03-31

Sodium cooled Fast Reactors (SFR) use liquid sodium as a coolant. Liquid sodium being opaque, optical techniques cannot be applied to reactor vessel inspection. This makes it necessary to develop alternative ways of assessing the state of the structures immersed in the medium. Ultrasonic pressure waves are well suited for inspection tasks in this environment, especially using pulsed electromagnetic acoustic transducers (EMAT) that generate the ultrasound directly in the liquid sodium. The work carried out at CEA LIST is aimed at developing phased array EMAT probes conditioned for reactor use. The present work focuses on the experimental validation of amore » newly manufactured 8 element probe which was designed for beam forming imaging in a liquid sodium environment. A parametric study is carried out to determine the optimal setup of the magnetic assembly used in this probe. First laboratory tests on an aluminium block show that the probe has the required beam steering capabilities.« less

Use of a novel FISH assay on paraffin-embedded tissues as an adjunct to diagnosis of alveolar rhabdomyosarcoma.

PubMed

Nishio, Jun; Althof, Pamela A; Bailey, Jacqueline M; Zhou, Ming; Neff, James R; Barr, Frederic G; Parham, David M; Teot, Lisa; Qualman, Stephen J; Bridge, Julia A

2006-06-01

A valuable diagnostic adjunct and important prognostic parameter in alveolar rhabdomyosarcoma (ARMS) is the identification of translocations t(2;13)(q35;q14) and t(1;13)(p36;q14), and the associated PAX3-FKHR and PAX7-FKHR fusion transcripts, respectively. Most RMS fusion gene type studies have been based on reverse transcriptase-polymerase chain reaction (RT-PCR) detection of the fusion transcript, a technique limited by RNA quality and failure of devised primer sets to detect unusual variants. As an alternative approach, we developed a fluorescence in situ hybridization (FISH) assay that can: (1) distinguish between the two most common ARMS-associated fusion genes; (2) identify potential unusual variant translocations; (3) assess histologic components in mixed alveolar/embryonal RMS; and (4) be performed on paraffinized tissue. FISH analyses of 75 specimens (40 ARMS, 16 ERMS, 8 mixed ARMS/ERMS, and 11 non-RMS tumors) using selected cosmid clone, bacterial, P1-derived, and yeast artificial chromosome probe sets were successful in all but two cases. Among specimens with informative results for both FISH and RT-PCR or standard karyotyping, PAX/FKHR classification results were concordant in 94.6% (53/56). The three discordant cases included one exhibiting a t(2;13) by FISH that was subsequently confirmed by repeat RT-PCR, a second showing a rearrangement of the PAX3 locus only (consistent with the presence of a PAX3 variant translocation), and a third revealing a t(2;13) by FISH that lacked this translocation cytogenetically. Both alveolar and embryonal components of the mixed ARMS/ERMS subtype were negative for PAX3, PAX7, and FKHR rearrangements, a surprising finding confirmed by RT-PCR and/or conventional karyotyping. These data demonstrate that FISH with newly designed probe sets is a reliable and highly specific method of detecting t(1;13) and t(2;13) in routinely processed tissue and may be useful in differentiating ARMS from other small round cell tumors. The findings also suggest that FISH may be a more sensitive assay than RT-PCR in some settings, capable of revealing variant translocations.

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.

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

The genomic response of skeletal muscle to methylprednisolone using microarrays: tailoring data mining to the structure of the pharmacogenomic time series

PubMed Central

DuBois, Debra C; Piel, William H; Jusko, William J

2008-01-01

High-throughput data collection using gene microarrays has great potential as a method for addressing the pharmacogenomics of complex biological systems. Similarly, mechanism-based pharmacokinetic/pharmacodynamic modeling provides a tool for formulating quantitative testable hypotheses concerning the responses of complex biological systems. As the response of such systems to drugs generally entails cascades of molecular events in time, a time series design provides the best approach to capturing the full scope of drug effects. A major problem in using microarrays for high-throughput data collection is sorting through the massive amount of data in order to identify probe sets and genes of interest. Due to its inherent redundancy, a rich time series containing many time points and multiple samples per time point allows for the use of less stringent criteria of expression, expression change and data quality for initial filtering of unwanted probe sets. The remaining probe sets can then become the focus of more intense scrutiny by other methods, including temporal clustering, functional clustering and pharmacokinetic/pharmacodynamic modeling, which provide additional ways of identifying the probes and genes of pharmacological interest. PMID:15212590

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.

Generalized alternating stimulation: a novel method to reduce stimulus artifact in electrically evoked compound action potentials.

PubMed

Alvarez, Isaac; de la Torre, Angel; Sainz, Manuel; Roldan, Cristina; Schoesser, Hansjoerg; Spitzer, Philipp

2007-09-15

Stimulus artifact is one of the main limitations when considering electrically evoked compound action potential for clinical applications. Alternating stimulation (average of recordings obtained with anodic-cathodic and cathodic-anodic bipolar stimulation pulses) is an effective method to reduce stimulus artifact when evoked potentials are recorded. In this paper we extend the concept of alternating stimulation by combining anodic-cathodic and cathodic-anodic recordings with a weight in general different to 0.5. We also provide an automatic method to obtain an estimation of the optimal weights. Comparison with conventional alternating, triphasic stimulation and masker-probe paradigm shows that the generalized alternating method improves the quality of electrically evoked compound action potential responses.

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.

Identification of Cannabis sativa L. using the 1-kbTHCA synthase-fluorescence in situ hybridization probe.

PubMed

Jeangkhwoa, Pattraporn; Bandhaya, Achirapa; Umpunjun, Puangpaka; Chuenboonngarm, Ngarmnij; Panvisavas, Nathinee

2017-03-01

This study reports a successful application of fluorescence in situ hybridization (FISH) technique in the identification of Cannabis sativa L. cells recovered from fresh and dried powdered plant materials. Two biotin-16-dUTP-labeled FISH probes were designed from the Cannabis-specific tetrahydrocannabinolic acid synthase (THCAS) gene and the ITS region of the 45S rRNA gene. Specificity of probe-target hybridization was tested against the target and 4 non-target plant species, i.e., Humulus lupulus, Mitragyna speciosa, Papaver sp., and Nicotiana tabacum. The 1-kb THCA synthase hybridization probe gave Cannabis-specific hybridization signals, unlike the 700-bp Cannabis-ITS hybridization probe. Probe-target hybridization was also confirmed against 20 individual Cannabis plant samples. The 1-kb THCA synthase and 700-bp Cannabis-ITS hybridization probes clearly showed 2 hybridization signals per cell with reproducibility. The 1-kb THCA synthase probe did not give any FISH signal when tested against H. lupulus, its closely related member of the Canabaceae family. It was also showed that 1-kb THCA synthase FISH probe can be applied to identify small amount of dried powdered Cannabis material with an addition of rehydration step prior to the experimental process. This study provided an alternative identification method for Cannabis trace. Copyright © 2016. Published by Elsevier B.V.

Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

DOEpatents

Lucas, J.N.; Straume, T.; Bogen, K.T.

1998-03-24

A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

1998-01-01

A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

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

TESTING GRAVITY WITH QUASI-PERIODIC OSCILLATIONS FROM ACCRETING BLACK HOLES: THE CASE OF THE EINSTEIN–DILATON–GAUSS–BONNET THEORY

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

Maselli, Andrea; Gualtieri, Leonardo; Ferrari, Valeria

Quasi-periodic oscillations (QPOs) observed in the X-ray flux emitted by accreting black holes are associated with phenomena occurring near the horizon. Future very large area X-ray instruments will be able to measure QPO frequencies with very high precision, thus probing this strong-field region. Using the relativistic precession model, we show the way in which QPO frequencies could be used to test general relativity (GR) against those alternative theories of gravity which predict deviations from the classical theory in the strong-field and high-curvature regimes. We consider one of the best-motivated high-curvature corrections to GR, namely, the Einstein–Dilaton–Gauss–Bonnet theory, and show thatmore » a detection of QPOs with the expected sensitivity of the proposed ESA M-class mission LOFT would set the most stringent constraints on the parameter space of this theory.« less

Defense on the Move: Ant-Based Cyber Defense

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

Fink, Glenn A.; Haack, Jereme N.; McKinnon, Archibald D.

Many common cyber defenses (like firewalls and IDS) are as static as trench warfare allowing the attacker freedom to probe them at will. The concept of Moving Target Defense (MTD) adds dynamism to the defender side, but puts the systems to be defended themselves in motion, potentially at great cost to the defender. An alternative approach is a mobile resilient defense that removes attackers’ ability to rely on prior experience without requiring motion in the protected infrastructure itself. The defensive technology absorbs most of the cost of motion, is resilient to attack, and is unpredictable to attackers. The Ant-Based Cybermore » Defense (ABCD) is a mobile resilient defense providing a set of roaming, bio-inspired, digital-ant agents working with stationary agents in a hierarchy headed by a human supervisor. The ABCD approach provides a resilient, extensible, and flexible defense that can scale to large, multi-enterprise infrastructures like the smart electric grid.« less

Alternative Setting-Wide Positive Behavior Support

ERIC Educational Resources Information Center

Simonsen, Brandi; Jeffrey-Pearsall, Jennifer; Sugai, George; McCurdy, Barry

2011-01-01

School-wide positive behavior support (SWPBS) has an established evidence base in general education settings, and emerging evidence suggests that SWPBS may be effective in alternative settings (e.g., alternative, residential, or hospital schools; psychiatric hospitals). Given the intense educational and behavioral needs of students typically…

Three-dimensional wide-field pump-probe structured illumination microscopy

PubMed Central

Kim, Yang-Hyo; So, Peter T.C.

2017-01-01

We propose a new structured illumination scheme for achieving depth resolved wide-field pump-probe microscopy with sub-diffraction limit resolution. By acquiring coherent pump-probe images using a set of 3D structured light illumination patterns, a 3D super-resolution pump-probe image can be reconstructed. We derive the theoretical framework to describe the coherent image formation and reconstruction scheme for this structured illumination pump-probe imaging system and carry out numerical simulations to investigate its imaging performance. The results demonstrate a lateral resolution improvement by a factor of three and providing 0.5 µm level axial optical sectioning. PMID:28380860

Improved Detection of HER2 by a Quasi-Targeted Proteomics Approach Using Aptamer-Peptide Probe and Liquid Chromatography-Tandem Mass Spectrometry.

PubMed

Zhou, Weixian; Xu, Feifei; Li, Danni; Chen, Yun

2018-03-01

Human epidermal growth factor receptor 2 (HER2)-positive breast cancer is a particularly aggressive type of the disease. To date, much evidence has indicated that accurate HER2 status detection is crucial for prognosis and treatment strategy selection. Thus, bioanalytical techniques for early and accurate detection of HER2 have the potential to improve patient care. Currently, the widely used immunohistochemical staining normally has problems with reproducibility and lack of standardization, resulting in poor concordance between laboratories. Aptamers are a good alternative, but the extent of their use in quantitative analysis of HER2 is limited because of the lack of effective detection methods. We developed a quasi-targeted proteomics assay and converted the HER2 signal into the mass response of reporter peptide by a combination of aptamer-peptide probe and LC-MS/MS. The selected aptamer-peptide probe consisted of aptamer HB5 and the substrate peptide GDKAVLGVDPFR that contained the reporter peptide AVLGVDPFR. After characterization of this newly synthesized probe (e.g., conjugation efficiency, stability, binding affinity, specificity, and digestion efficiency), probe binding and trypsin shaving conditions were optimized. The resulting limit of quantification for HER2 was 25 pmol/L. Then, the quasi-targeted proteomics assay was applied to determine the HER2 concentrations in the HER2-positive breast cancer cells BT474 and SK-BR-3, the HER2-negative breast cancer cells MDA-MB-231 and MCF-7, and 36 pairs of human breast primary tumors and adjacent normal tissue samples. The results were highly concordant with those obtained by immunohistochemistry with reflex testing by fluorescent in situ hybridization. Quasi-targeted proteomics can be a quantitative alternative for HER2 detection. © 2017 American Association for Clinical Chemistry.

Transcriptomic Analysis of Grape (Vitis vinifera L.) Leaves after Exposure to Ultraviolet C Irradiation

PubMed Central

Xi, Huifen; Ma, Ling; Liu, Guotian; Wang, Nian; Wang, Junfang; Wang, Lina; Dai, Zhanwu; Li, Shaohua; Wang, Lijun

2014-01-01

Background Only a small amount of solar ultraviolet C (UV-C) radiation reaches the Earth's surface. This is because of the filtering effects of the stratospheric ozone layer. Artificial UV-C irradiation is used on leaves and fruits to stimulate different biological processes in plants. Grapes are a major fruit crop and are grown in many parts of the world. Research has shown that UV-C irradiation induces the biosynthesis of phenols in grape leaves. However, few studies have analyzed the overall changes in gene expression in grape leaves exposed to UV-C. Methodology/Principal Findings In the present study, transcriptional responses were investigated in grape (Vitis vinifera L.) leaves before and after exposure to UV-C irradiation (6 W·m−2 for 10 min) using an Affymetrix Vitis vinifera (Grape) Genome Array (15,700 transcripts). A total of 5274 differentially expressed probe sets were defined, including 3564 (67.58%) probe sets that appeared at both 6 and 12 h after exposure to UV-C irradiation but not before exposure. A total of 468 (8.87%) probe sets and 1242 (23.55%) probe sets were specifically expressed at these times. The probe sets were associated with a large number of important traits and biological pathways, including cell rescue (i.e., antioxidant enzymes), protein fate (i.e., HSPs), primary and secondary metabolism, and transcription factors. Interestingly, some of the genes involved in secondary metabolism, such as stilbene synthase, responded intensely to irradiation. Some of the MYB and WRKY family transcription factors, such as VvMYBPA1, VvMYB14, VvMYB4, WRKY57-like, and WRKY 65, were also strongly up-regulated (about 100 to 200 fold). Conclusions UV-C irridiation has an important role in some biology processes, especially cell rescue, protein fate, secondary metabolism, and regulation of transcription.These results opened up ways of exploring the molecular mechanisms underlying the effects of UV-C irradiation on grape leaves and have great implications for further studies. PMID:25464056

Transcriptomic analysis of grape (Vitis vinifera L.) leaves after exposure to ultraviolet C irradiation.

PubMed

Xi, Huifen; Ma, Ling; Liu, Guotian; Wang, Nian; Wang, Junfang; Wang, Lina; Dai, Zhanwu; Li, Shaohua; Wang, Lijun

2014-01-01

Only a small amount of solar ultraviolet C (UV-C) radiation reaches the Earth's surface. This is because of the filtering effects of the stratospheric ozone layer. Artificial UV-C irradiation is used on leaves and fruits to stimulate different biological processes in plants. Grapes are a major fruit crop and are grown in many parts of the world. Research has shown that UV-C irradiation induces the biosynthesis of phenols in grape leaves. However, few studies have analyzed the overall changes in gene expression in grape leaves exposed to UV-C. In the present study, transcriptional responses were investigated in grape (Vitis vinifera L.) leaves before and after exposure to UV-C irradiation (6 W·m-2 for 10 min) using an Affymetrix Vitis vinifera (Grape) Genome Array (15,700 transcripts). A total of 5274 differentially expressed probe sets were defined, including 3564 (67.58%) probe sets that appeared at both 6 and 12 h after exposure to UV-C irradiation but not before exposure. A total of 468 (8.87%) probe sets and 1242 (23.55%) probe sets were specifically expressed at these times. The probe sets were associated with a large number of important traits and biological pathways, including cell rescue (i.e., antioxidant enzymes), protein fate (i.e., HSPs), primary and secondary metabolism, and transcription factors. Interestingly, some of the genes involved in secondary metabolism, such as stilbene synthase, responded intensely to irradiation. Some of the MYB and WRKY family transcription factors, such as VvMYBPA1, VvMYB14, VvMYB4, WRKY57-like, and WRKY 65, were also strongly up-regulated (about 100 to 200 fold). UV-C irridiation has an important role in some biology processes, especially cell rescue, protein fate, secondary metabolism, and regulation of transcription.These results opened up ways of exploring the molecular mechanisms underlying the effects of UV-C irradiation on grape leaves and have great implications for further studies.

High sensitivity, loop-mediated isothermal amplification combined with colorimetric gold-nanoparticle probes for visual detection of high risk human papillomavirus genotypes 16 and 18.

PubMed

Kumvongpin, Ratchanida; Jearanaikool, Patcharee; Wilailuckana, Chotechana; Sae-Ung, Nattaya; Prasongdee, Prinya; Daduang, Sakda; Wongsena, Metee; Boonsiri, Patcharee; Kiatpathomchai, Wansika; Swangvaree, Sukumarn Sanersak; Sandee, Alisa; Daduang, Jureerut

2016-08-01

High-risk human papillomavirus (HR-HPV) causes cervical cancer. HPV16 and HPV18 are the most prevalent strains of the virus reported in women worldwide. Loop-mediated isothermal amplification (LAMP) is an alternative method for DNA detection under isothermal conditions. However, it results in a turbid amplified product which is not easily detected by the naked eye. This study aimed to develop an improved technique by using gold nanoparticles (AuNPs) attached to a single-stranded DNA probe for the detection of HPV16 and HPV18. Detection of the LAMP product by AuNP color change was compared with detection by visual turbidity. The optimal conditions for this new LAMP-AuNP assay were an incubation time of 20min and a temperature of 65°C. After LAMP amplification was complete, its products were hybridized with the AuNP probe for 5min and then detected by the addition of magnesium salt. The color changed from red to blue as a result of aggregation of the AuNP probe under high ionic strength conditions produced by the addition of the salt. The sensitivity of the LAMP-AuNP assay was greater than the LAMP turbidity assay by up to 10-fold for both HPV genotypes. The LAMP-AuNP assay showed higher sensitivity and ease of visualization than did the LAMP turbidity for the detection of HPV16 and HPV18. Additionally, AuNP-HPV16 and AuNP-HPV18 probes were stable for over 1year. The combination of LAMP and the AuNP-probe colorimetric assay offers a simple, rapid and highly sensitive alternative diagnostic tool for the detection of HPV16 and HPV18 in district hospitals or field studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Alternative Fuels Data Center: Los Angeles Sets the Stage for Plug-In

Science.gov Websites

Electric Vehicles Los Angeles Sets the Stage for Plug-In Electric Vehicles to someone by E-mail Share Alternative Fuels Data Center: Los Angeles Sets the Stage for Plug-In Electric Vehicles on Facebook Tweet about Alternative Fuels Data Center: Los Angeles Sets the Stage for Plug-In Electric

Eddy Current Probe for Surface and Sub-Surface Inspection

NASA Technical Reports Server (NTRS)

Wincheski, Russell A. (Inventor); Simpson, John W. (Inventor)

2014-01-01

An eddy current probe includes an excitation coil for coupling to a low-frequency alternating current (AC) source. A magneto-resistive sensor is centrally disposed within and at one end of the excitation coil to thereby define a sensing end of the probe. A tubular flux-focusing lens is disposed between the excitation coil and the magneto-resistive sensor. An excitation wire is spaced apart from the magneto-resistive sensor in a plane that is perpendicular to the sensor's axis of sensitivity and such that, when the sensing end of the eddy current probe is positioned adjacent to the surface of a structure, the excitation wire is disposed between the magneto-resistive sensor and the surface of the structure. The excitation wire is coupled to a high-frequency AC source. The excitation coil and flux-focusing lens can be omitted when only surface inspection is required.

Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach

NASA Technical Reports Server (NTRS)

Liu, W. T.; Mirzabekov, A. D.; Stahl, D. A.

2001-01-01

The utility of a high-density oligonucleotide microarray (microchip) for identifying strains of five closely related bacilli (Bacillus anthracis, Bacillus cereus, Bacillus mycoides, Bacillus medusa and Bacillus subtilis) was demonstrated using an approach that compares the non-equilibrium dissociation rates ('melting curves') of all probe-target duplexes simultaneously. For this study, a hierarchical set of 30 oligonucleotide probes targeting the 16S ribosomal RNA of these bacilli at multiple levels of specificity (approximate taxonomic ranks of domain, kingdom, order, genus and species) was designed and immobilized in a high-density matrix of gel pads on a glass slide. Reproducible melting curves for probes with different levels of specificity were obtained using an optimized salt concentration. Clear discrimination between perfect match (PM) and mismatch (MM) duplexes was achieved. By normalizing the signals to an internal standard (a universal probe), a more than twofold discrimination (> 2.4x) was achieved between PM and 1-MM duplexes at the dissociation temperature at which 50% of the probe-target duplexes remained intact. This provided excellent differentiation among representatives of different Bacillus species, both individually and in mixtures of two or three. The overall pattern of hybridization derived from this hierarchical probe set also provided a clear 'chip fingerprint' for each of these closely related Bacillus species.

The reliability and internal consistency of one-shot and flicker change detection for measuring individual differences in visual working memory capacity.

PubMed

Pailian, Hrag; Halberda, Justin

2015-04-01

We investigated the psychometric properties of the one-shot change detection task for estimating visual working memory (VWM) storage capacity-and also introduced and tested an alternative flicker change detection task for estimating these limits. In three experiments, we found that the one-shot whole-display task returns estimates of VWM storage capacity (K) that are unreliable across set sizes-suggesting that the whole-display task is measuring different things at different set sizes. In two additional experiments, we found that the one-shot single-probe variant shows improvements in the reliability and consistency of K estimates. In another additional experiment, we found that a one-shot whole-display-with-click task (requiring target localization) also showed improvements in reliability and consistency. The latter results suggest that the one-shot task can return reliable and consistent estimates of VWM storage capacity (K), and they highlight the possibility that the requirement to localize the changed target is what engenders this enhancement. Through a final series of four experiments, we introduced and tested an alternative flicker change detection method that also requires the observer to localize the changing target and that generates, from response times, an estimate of VWM storage capacity (K). We found that estimates of K from the flicker task correlated with estimates from the traditional one-shot task and also had high reliability and consistency. We highlight the flicker method's ability to estimate executive functions as well as VWM storage capacity, and discuss the potential for measuring multiple abilities with the one-shot and flicker tasks.

Inclinometer--time-domain reflectometry comparative study : research implementation plan.

DOT National Transportation Integrated Search

2005-10-01

ODOT currently uses slope indicator probing to analyze subsurface conditions at roadway landslide : locations. However, the current method is subject to several limitations, and time domain reflectometry : (TDR) has been proposed as an alternative to...

Alternative Futures for the Education of Students with Severe Disabilities. Proceedings of the Conference on Severe and Multiple Handicaps: Alternative Futures (Edmonton, Canada, May 6-8, 1987).

ERIC Educational Resources Information Center

Baine, David, Ed.; And Others

This book contains 23 papers given at a 1987 Edmonton (Canada) conference. Papers have the following titles and authors: "Current Trends and Future Challenges in the Education of Students with Severe Handicaps" (Dick Sobsey); "How Often Do You Need to Collect Student Performance Data? A Study of the Effects of Frequency of Probe Data Collection…

Tunable biasing magnetic field design of ferrite tuner for ICRF heating system in EAST

NASA Astrophysics Data System (ADS)

Manman, XU; Yuntao, SONG; Gen, CHEN; Yanping, ZHAO; Yuzhou, MAO; Guang, LIU; Zhen, PENG

2017-11-01

Ion cyclotron range of frequency (ICRF) heating has been used in tokamaks as one of the most successful auxiliary heating tools and has been adopted in the EAST. However, the antenna load will fluctuate with the change of plasma parameters in the ICRF heating process. To ensure the steady operation of the ICRF heating system in the EAST, fast ferrite tuner (FFT) has been carried out to achieve real-time impedance matching. For the requirements of the FFT impedance matching system, the magnet system of the ferrite tuner (FT) was designed by numerical simulations and experimental analysis, where the biasing magnetic circuit and alternating magnetic circuit were the key researched parts of the ferrite magnet. The integral design goal of the FT magnetic circuit is that DC bias magnetic field is 2000 Gs and alternating magnetic field is ±400 Gs. In the FTT, E-type magnetic circuit was adopted. Ferrite material is NdFeB with a thickness of 30 mm by setting the working point of NdFeB, and the ampere turn of excitation coil is 25 through the theoretical calculation and simulation analysis. The coil inductance to generate alternating magnetic field is about 7 mH. Eddy-current effect has been analyzed, while the magnetic field distribution has been measured by a Hall probe in the medium plane of the biasing magnet. Finally, the test results show the good performance of the biasing magnet satisfying the design and operating requirements of the FFT.

Restoring Behavior via Inverse Neurocontroller in a Lesioned Cortical Spiking Model Driving a Virtual Arm

PubMed Central

Dura-Bernal, Salvador; Li, Kan; Neymotin, Samuel A.; Francis, Joseph T.; Principe, Jose C.; Lytton, William W.

2016-01-01

Neural stimulation can be used as a tool to elicit natural sensations or behaviors by modulating neural activity. This can be potentially used to mitigate the damage of brain lesions or neural disorders. However, in order to obtain the optimal stimulation sequences, it is necessary to develop neural control methods, for example by constructing an inverse model of the target system. For real brains, this can be very challenging, and often unfeasible, as it requires repeatedly stimulating the neural system to obtain enough probing data, and depends on an unwarranted assumption of stationarity. By contrast, detailed brain simulations may provide an alternative testbed for understanding the interactions between ongoing neural activity and external stimulation. Unlike real brains, the artificial system can be probed extensively and precisely, and detailed output information is readily available. Here we employed a spiking network model of sensorimotor cortex trained to drive a realistic virtual musculoskeletal arm to reach a target. The network was then perturbed, in order to simulate a lesion, by either silencing neurons or removing synaptic connections. All lesions led to significant behvaioral impairments during the reaching task. The remaining cells were then systematically probed with a set of single and multiple-cell stimulations, and results were used to build an inverse model of the neural system. The inverse model was constructed using a kernel adaptive filtering method, and was used to predict the neural stimulation pattern required to recover the pre-lesion neural activity. Applying the derived neurostimulation to the lesioned network improved the reaching behavior performance. This work proposes a novel neurocontrol method, and provides theoretical groundwork on the use biomimetic brain models to develop and evaluate neurocontrollers that restore the function of damaged brain regions and the corresponding motor behaviors. PMID:26903796

Standard Practices for Usage of Inductive Magnetic Field Probes with Application to Electric Propulsion Testing

NASA Technical Reports Server (NTRS)

Polzin, Kurt A.; Hill, Carrie S.; Turchi, Peter J.; Burton, Rodney L.; Messer, Sarah; Lovberg, Ralph H.; Hallock, Ashley K.

2013-01-01

Inductive magnetic field probes (also known as B-dot probes and sometimes as B-probes or magnetic probes) are often employed to perform field measurements in electric propulsion applications where there are time-varying fields. Magnetic field probes provide the means to measure these magnetic fields and can even be used to measure the plasma current density indirectly through the application of Ampere's law. Measurements of this type can yield either global information related to a thruster and its performance or detailed, local data related to the specific physical processes occurring in the plasma. Results of the development of a standard for B-dot probe measurements are presented, condensing the available literature on the subject into an accessible set of rules, guidelines, and techniques to standardize the performance and presentation of future measurements.

Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization.

PubMed

Ibrahim, Tamer M; Bauer, Matthias R; Boeckler, Frank M

2015-01-01

Structure-based virtual screening techniques can help to identify new lead structures and complement other screening approaches in drug discovery. Prior to docking, the data (protein crystal structures and ligands) should be prepared with great attention to molecular and chemical details. Using a subset of 18 diverse targets from the recently introduced DEKOIS 2.0 benchmark set library, we found differences in the virtual screening performance of two popular docking tools (GOLD and Glide) when employing two different commercial packages (e.g. MOE and Maestro) for preparing input data. We systematically investigated the possible factors that can be responsible for the found differences in selected sets. For the Angiotensin-I-converting enzyme dataset, preparation of the bioactive molecules clearly exerted the highest influence on VS performance compared to preparation of the decoys or the target structure. The major contributing factors were different protonation states, molecular flexibility, and differences in the input conformation (particularly for cyclic moieties) of bioactives. In addition, score normalization strategies eliminated the biased docking scores shown by GOLD (ChemPLP) for the larger bioactives and produced a better performance. Generalizing these normalization strategies on the 18 DEKOIS 2.0 sets, improved the performances for the majority of GOLD (ChemPLP) docking, while it showed detrimental performances for the majority of Glide (SP) docking. In conclusion, we exemplify herein possible issues particularly during the preparation stage of molecular data and demonstrate to which extent these issues can cause perturbations in the virtual screening performance. We provide insights into what problems can occur and should be avoided, when generating benchmarks to characterize the virtual screening performance. Particularly, careful selection of an appropriate molecular preparation setup for the bioactive set and the use of score normalization for docking with GOLD (ChemPLP) appear to have a great importance for the screening performance. For virtual screening campaigns, we recommend to invest time and effort into including alternative preparation workflows into the generation of the master library, even at the cost of including multiple representations of each molecule. Graphical AbstractUsing DEKOIS 2.0 benchmark sets in structure-based virtual screening to probe the impact of molecular preparation and score normalization.

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).

Implicit memory for novel figure-ground displays includes a history of cross-border competition.

PubMed

Peterson, Mary A; Lampignano, Daniel W

2003-08-01

When configural cues specify that a figure lies on opposite sides of a repeated border in prime andprobe shapes, probe latencies are longer than when prime and probe borders are unrelated. Do such results reflect negative priming for the shape of the prime ground or cross-border competition from figure memory? The present study tested these alternatives by adding partial closure as a competing cue and reducing the similarity between the prime ground and the shape of the probe. Results supported the cross-border competition interpretation. Additional findings were that partial closure is a configural cue and that response effects can emerge from the potential shape on the ground side of a border. One prior experience was sufficient for these effects.

Indium nanowires at the silicon surface

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

Kozhukhov, A. S., E-mail: antonkozhukhov@yandex.ru; Sheglov, D. V.; Latyshev, A. V.

2016-07-15

Conductive indium nanowires up to 50 nm in width and up to 10 μm in length are fabricated on the surface of silicon by local resputtering from the probe of an atomic-force microscope. The transfer of indium from the probe of the atomic-force microscope onto the silicon surface is initiated by applying a potential between the probe and the surface as they approach each other to spacings, at which the mutual repulsive force is ~10{sup –7} N. The conductivity of the nanowires ranges from 7 × 10{sup –3} to 4 × 10{sup –2} Ω cm, which is several orders ofmore » magnitude lower than that in the case of the alternative technique of heat transfer.« less

Quantized Rabi oscillations and circular dichroism in quantum Hall systems

NASA Astrophysics Data System (ADS)

Tran, D. T.; Cooper, N. R.; Goldman, N.

2018-06-01

The dissipative response of a quantum system upon periodic driving can be exploited as a probe of its topological properties. Here we explore the implications of such phenomena in two-dimensional gases subjected to a uniform magnetic field. It is shown that a filled Landau level exhibits a quantized circular dichroism, which can be traced back to its underlying nontrivial topology. Based on selection rules, we find that this quantized effect can be suitably described in terms of Rabi oscillations, whose frequencies satisfy simple quantization laws. We discuss how quantized dissipative responses can be probed locally, both in the bulk and at the boundaries of the system. This work suggests alternative forms of topological probes based on circular dichroism.

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.

Combination probes with intercalating anchors and proximal fluorophores for DNA and RNA detection

PubMed Central

Qiu, Jieqiong; Wilson, Adam; El-Sagheer, Afaf H.; Brown, Tom

2016-01-01

A new class of modified oligonucleotides (combination probes) has been designed and synthesised for use in genetic analysis and RNA detection. Their chemical structure combines an intercalating anchor with a reporter fluorophore on the same thymine nucleobase. The intercalator (thiazole orange or benzothiazole orange) provides an anchor, which upon hybridisation of the probe to its target becomes fluorescent and simultaneously stabilizes the duplex. The anchor is able to communicate via FRET to a proximal reporter dye (e.g. ROX, HEX, ATTO647N, FAM) whose fluorescence signal can be monitored on a range of analytical devices. Direct excitation of the reporter dye provides an alternative signalling mechanism. In both signalling modes, fluorescence in the unhybridised probe is switched off by collisional quenching between adjacent intercalator and reporter dyes. Single nucleotide polymorphisms in DNA and RNA targets are identified by differences in the duplex melting temperature, and the use of short hybridization probes, made possible by the stabilisation provided by the intercalator, enhances mismatch discrimination. Unlike other fluorogenic probe systems, placing the fluorophore and quencher on the same nucleobase facilitates the design of short probes containing multiple modifications. The ability to detect both DNA and RNA sequences suggests applications in cellular imaging and diagnostics. PMID:27369379

Metabolite profiling with HPLC-ICP-MS as a tool for in vivo characterization of imaging probes.

PubMed

Boros, Eszter; Pinkhasov, Omar R; Caravan, Peter

2018-01-01

Current analytical methods for characterizing pharmacokinetic and metabolic properties of positron emission tomography (PET) and single photon emission computed tomography (SPECT) probes are limited. Alternative methods to study tracer metabolism are needed. The study objective was to assess the potential of high performance liquid chromatography - inductively coupled plasma - mass spectrometry (HPLC-ICP-MS) for quantification of molecular probe metabolism and pharmacokinetics using stable isotopes. Two known peptide-DOTA conjugates were chelated with nat Ga and nat In. Limit of detection of HPLC-ICP-MS for 69 Ga and 115 In was determined. Rats were administered 50-150 nmol of Ga- and/or In-labeled probes, blood was serially sampled, and plasma analyzed by HPLC-ICP-MS using both reverse phase and size exclusion chromatography. The limits of detection were 0.16 pmol for 115 In and 0.53 pmol for 69 Ga. Metabolites as low as 0.001 %ID/g could be detected and transchelation products identified. Simultaneous administration of Ga- and In-labeled probes allowed the determination of pharmacokinetics and metabolism of both probes in a single animal. HPLC-ICP-MS is a robust, sensitive and radiation-free technique to characterize the pharmacokinetics and metabolism of imaging probes.

Hydrophobic interactions in donor-disulphide-acceptor (DSSA) probes looking beyond fluorescence resonance energy transfer theory.

PubMed

Sanjeeva, Shilpa Kammaradi; Korrapati, Swathi; Nair, Chandrasekhar B; Rao, P V Subba; Pullela, Phani Kumar; Vijayalakshmi, U; Siva, Ramamoorthy

2014-07-01

Donor-linker-acceptor (DSSA) is a concept in fluorescence chemistry with acceptor being a fluorescent compound (FRET) or quencher. The DSSA probes used to measure thiol levels in vitro and in vivo. The reduction potential of these dyes are in the range of -0.60 V, much lower than the best thiol reductant reported in literature, the DTT (-0.33 V). DSSA disulphide having an unusually low reduction potential compared to the typical thiol reductants is a puzzle. Secondly, DSSA probes have a cyclized rhodamine ring as acceptor which does not have any spectral overlap with fluorescein, but quenches its absorbance and fluorescence. To understand the structural features of DSSA probes, we have synthesized DSSANa and DSSAOr. The calculated reduction potential of these dyes suggest that DSSA probes have an alternate mechanism from the FRET based quenching, namely hydrophobic interaction or dye to dye quenching. The standard reduction potential change with increasing complexity and steric hindrance of the molecule is small, suggesting that ultra- low Eo' has no contribution from the disulphide linker and is based on structural interactions between fluorescein and cyclized rhodamine. Our results help to understand the DSSA probe quenching mechanism and provide ways to design fluorescent probes.

RCP: a novel probe design bias correction method for Illumina Methylation BeadChip.

PubMed

Niu, Liang; Xu, Zongli; Taylor, Jack A

2016-09-01

The Illumina HumanMethylation450 BeadChip has been extensively utilized in epigenome-wide association studies. This array and its successor, the MethylationEPIC array, use two types of probes-Infinium I (type I) and Infinium II (type II)-in order to increase genome coverage but differences in probe chemistries result in different type I and II distributions of methylation values. Ignoring the difference in distributions between the two probe types may bias downstream analysis. Here, we developed a novel method, called Regression on Correlated Probes (RCP), which uses the existing correlation between pairs of nearby type I and II probes to adjust the beta values of all type II probes. We evaluate the effect of this adjustment on reducing probe design type bias, reducing technical variation in duplicate samples, improving accuracy of measurements against known standards, and retention of biological signal. We find that RCP is statistically significantly better than unadjusted data or adjustment with alternative methods including SWAN and BMIQ. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html). niulg@ucmail.uc.edu Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

Prognostic significance of equivocal human epidermal growth factor receptor 2 results and clinical utility of alternative chromosome 17 genes in patients with invasive breast cancer: A cohort study.

PubMed

Sneige, Nour; Hess, Kenneth R; Multani, Asha S; Gong, Yun; Ibrahim, Nuhad K

2017-04-01

The 2013 testing guidelines for determining the human epidermal growth factor receptor 2 (HER2) status include new cutoff points for the HER2/chromosome enumeration probe 17 (CEP17) ratio and the average HER2 copy number per cell, and they recommend using a reflex test with alternative chromosome 17 probes (Ch17Ps) to resolve equivocal HER2 results. This study sought to determine the clinical utility of alternative Ch17Ps in equivocal cases and the effects of equivocal results and/or a change in the HER2 status on patients' outcomes. The University of Texas MD Anderson Cancer Center database of HER2 dual-probe fluorescence in situ hybridization results from 2000 to 2010 was searched for cases of invasive breast cancer with HER2/CEP17 ratios < 2 and average HER2 copy numbers < 6 per cell. Cases with HER2 copy numbers of 4 to < 6 (the definition of equivocal HER2 results) were analyzed with alternative Ch17Ps for Smith-Magenis syndrome and retinoic acid receptor α genes. Disease-free survival (DFS) and overall survival (OS) were evaluated with respect to the HER2 copy number with multivariate Cox proportional hazards regression. Among the 3630 patients meeting the inclusion criteria, 137 (4%) had equivocal HER2 results. With alternative Ch17Ps, 35 of 57 equivocal HER2 cases (61%) were upgraded to a positive HER2 status, and 22 cases (39%) remained unchanged. The 5-year DFS and OS adjusted hazard ratios (HRs) for copy numbers of 4 to < 6 versus < 4 were 0.6 (95% confidence interval [CI], 0.3-1.2) and 0.5 (95% CI, 0.2-1.0) with P values of .16 and .66, respectively. In comparison with HER2-negative cases, these CIs indicated that equivocal HER2 results were associated with either a protective effect (HR, < 0.5) or no effect (HR, 1.0). These findings rule out a significant deleterious effect of equivocal HER2 results. Alternative Ch17Ps may erroneously upgrade the HER2 status; therefore, they cannot be considered reliable in clinical practice. Cancer 2017;123:1115-1123. © 2016 American Cancer Society. © 2016 American Cancer Society.

Design and modeling of a planar probe for power measurements in a capacitive plasma sheath

NASA Astrophysics Data System (ADS)

Gahan, D.; Hopkins, M. B.; Ellingboe, A. R.

2004-09-01

The design and modeling of a planar probe for power measurement in a capacitive RF sheath is described. The probe is to be biased negatively, using a DC power supply, while simultaneously being driven with an RF voltage. A simple model has been developed which describes the voltage, current and impedance from the generator to the probe surface incorporating the transmission line. A conventional method to determine the power through such a probe would be to measure the voltage, current and their phase relationship very close to the probe surface. This can be very difficult to do with much accuracy since the load is almost purely reactive. An alternative method is discussed. The model shows that for certain lengths of transmission line there exists a point on that transmission line where the imaginary impedance goes to zero. If the power is measured at this point where the current and voltage are almost in phase the result should be more accurate. A brief description of the model is given along with some results for its validation. The operation of the power sensor used is also explained.

Mechanistic Study of the Validity of Using Hydroxyl Radical Probes To Characterize Electrochemical Advanced Oxidation Processes.

PubMed

Jing, Yin; Chaplin, Brian P

2017-02-21

The detection of hydroxyl radicals (OH • ) is typically accomplished by using reactive probe molecules, but prior studies have not thoroughly investigated the suitability of these probes for use in electrochemical advanced oxidation processes (EAOPs), due to the neglect of alternative reaction mechanisms. In this study, we investigated the suitability of four OH • probes (coumarin, p-chlorobenzoic acid, terephthalic acid, and p-benzoquinone) for use in EAOPs. Experimental results indicated that both coumarin and p-chlorobenzoic acid are oxidized via direct electron transfer reactions, while p-benzoquinone and terephthalic acid are not. Coumarin oxidation to form the OH • adduct product 7-hydroxycoumarin was found at anodic potentials lower than that necessary for OH • formation. Density functional theory (DFT) simulations found a thermodynamically favorable and non-OH • mediated pathway for 7-hydroxycoumarin formation, which is activationless at anodic potentials > 2.10 V/SHE. DFT simulations also provided estimates of E° values for a series of OH • probe compounds, which agreed with voltammetry results. Results from this study indicated that terephthalic acid is the most appropriate OH • probe compound for the characterization of electrochemical and catalytic systems.

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.

Effects of dynamic text in an AAC app on sight word reading for individuals with autism spectrum disorder.

PubMed

Caron, Jessica; Light, Janice; Holyfield, Christine; McNaughton, David

2018-06-01

The purpose of this study was to investigate the effects of Transition to Literacy (T2L) software features (i.e., dynamic text and speech output upon selection of a graphic symbol) within a grid display in an augmentative and alternative communication (AAC) app, on the sight word reading skills of individuals with autism spectrum disorders (ASD) and complex communication needs. The study implemented a single-subject multiple probe research design across one set of three participants. The same design was utilized with an additional set of two participants. As part of the intervention, the participants were exposed to an AAC app with the T2L features during a highly structured matching task. With only limited exposure to the features, the five participants all demonstrated increased accuracy of identification of 12 targeted sight words. This study provides preliminary evidence that redesigning AAC apps to include the provision of dynamic text combined with speech output, can positively impact the sight-word reading of participants during a structured task. This adaptation in AAC system design could be used to complement literacy instruction and to potentially infuse components of literacy learning into daily communication.

Arrays of probes for positional sequencing by hybridization

DOEpatents

Cantor, Charles R [Boston, MA; Prezetakiewiczr, Marek [East Boston, MA; Smith, Cassandra L [Boston, MA; Sano, Takeshi [Waltham, MA

2008-01-15

This invention is directed to methods and reagents useful for sequencing nucleic acid targets utilizing sequencing by hybridization technology comprising probes, arrays of probes and methods whereby sequence information is obtained rapidly and efficiently in discrete packages. That information can be used for the detection, identification, purification and complete or partial sequencing of a particular target nucleic acid. When coupled with a ligation step, these methods can be performed under a single set of hybridization conditions. The invention also relates to the replication of probe arrays and methods for making and replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5'- and/or 3'-overhangs.

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.

Cryptic Translocation Identification in Human and Mouse using Several Telomeric Multiplex FISH (TM-FISH) Strategies

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

Henegariu, O; Artan, S; Greally, J M

2003-08-19

Experimental data published in recent years showed that up to 10% of all cases with mild to severe idiopathic mental retardation may result from small rearrangements of the subtelomeric regions of human chromosomes. To detect such cryptic translocations, we developed a ''telomeric'' multiplex FISH assay, using a set of previously published and commercially available subtelomeric probes. This set of probes includes 41 cosmid/PAC/P1 clones located from less than 100kb to about 1 Mb from the end of the chromosomes. Similarly, a published mouse probe set, comprised of BACs hybridizing to the closest known marker toward the centromere and telomere ofmore » each mouse chromosome, was used to develop a mouse-specific ''telomeric'' M-FISH. Three different combinatorial labeling strategies were used to simultaneously detect all human sub-telomeric regions on one slide. The simplest approach uses only three fluors, and can be performed in laboratories lacking sophisticated imaging equipment or personnel highly trained in cytogenetics. A standard fluorescence microscope equipped with only three filters is sufficient. Fluor-dUTPs and labeled probes can be custom-made, thus dramatically reducing costs. Images can be prepared using generic imaging software (Adobe Photoshop), and analysis performed by simple visual inspection.« less

Task probability and report of feature information: what you know about what you 'see' depends on what you expect to need.

PubMed

Pilling, Michael; Gellatly, Angus

2013-07-01

We investigated the influence of dimensional set on report of object feature information using an immediate memory probe task. Participants viewed displays containing up to 36 coloured geometric shapes which were presented for several hundred milliseconds before one item was abruptly occluded by a probe. A cue presented simultaneously with the probe instructed participants to report either about the colour or shape of the probe item. A dimensional set towards the colour or shape of the presented items was induced by manipulating task probability - the relative probability with which the two feature dimensions required report. This was done across two participant groups: One group was given trials where there was a higher report probability of colour, the other a higher report probability of shape. Two experiments showed that features were reported most accurately when they were of high task probability, though in both cases the effect was largely driven by the colour dimension. Importantly the task probability effect did not interact with display set size. This is interpreted as tentative evidence that this manipulation influences feature processing in a global manner and at a stage prior to visual short term memory. Copyright © 2013 Elsevier B.V. All rights reserved.

Estimating three-demensional energy transfer in isotropic turbulence

NASA Technical Reports Server (NTRS)

Li, K. S.; Helland, K. N.; Rosenblatt, M.

1980-01-01

To obtain an estimate of the spectral transfer function that indicates the rate of decay of energy, an x-wire probe was set at a fixed position, and two single wire probes were set at a number of locations in the same plane perpendicular to the mean flow in the wind tunnel. The locations of the single wire probes are determined by pseudo-random numbers (Monte Carlo). Second order spectra and cross spectra are estimated. The assumption of isotropy relative to second order spectra is examined. Third order spectra are also estimated corresponding to the positions specified. A Monte Carlo Fourier transformation of the downstream bispectra corresponding to integration across the plane perpendicular to the flow is carried out assuming isotropy. Further integration is carried out over spherical energy shells.

Improved Safety for Molecular Diagnosis of Classical Rabies Viruses by Use of a TaqMan Real-Time Reverse Transcription-PCR “Double Check” Strategy▿ †

PubMed Central

Hoffmann, B.; Freuling, C. M.; Wakeley, P. R.; Rasmussen, T. B.; Leech, S.; Fooks, A. R.; Beer, M.; Müller, T.

2010-01-01

To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany), the Veterinary Laboratories Agency (VLA; United Kingdom), and the DTU National Veterinary Institute (Lindholm, Denmark), covering the global diversity of rabies virus lineages, it was shown that both the newly developed assay and a previously described one had some detection failures. This was overcome by a combined assay that detected all samples as positive. In addition, the introduction of labeled positive controls (LPC) increased the diagnostic safety of the single as well as the combined assay. Based on the newly developed, alternative assay for the detection of rabies virus and the application of LPCs, an improved diagnostic sensitivity and reliability can be ascertained for postmortem and intra vitam real-time RT-PCR analyses in rabies reference laboratories. PMID:20739489

Improved safety for molecular diagnosis of classical rabies viruses by use of a TaqMan real-time reverse transcription-PCR "double check" strategy.

PubMed

Hoffmann, B; Freuling, C M; Wakeley, P R; Rasmussen, T B; Leech, S; Fooks, A R; Beer, M; Müller, T

2010-11-01

To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany), the Veterinary Laboratories Agency (VLA; United Kingdom), and the DTU National Veterinary Institute (Lindholm, Denmark), covering the global diversity of rabies virus lineages, it was shown that both the newly developed assay and a previously described one had some detection failures. This was overcome by a combined assay that detected all samples as positive. In addition, the introduction of labeled positive controls (LPC) increased the diagnostic safety of the single as well as the combined assay. Based on the newly developed, alternative assay for the detection of rabies virus and the application of LPCs, an improved diagnostic sensitivity and reliability can be ascertained for postmortem and intra vitam real-time RT-PCR analyses in rabies reference laboratories.

Structure-based design and profiling of novel 17β-HSD14 inhibitors.

PubMed

Braun, Florian; Bertoletti, Nicole; Möller, Gabriele; Adamski, Jerzy; Frotscher, Martin; Guragossian, Nathalie; Madeira Gírio, Patrícia Alexandra; Le Borgne, Marc; Ettouati, Laurent; Falson, Pierre; Müller, Sebastian; Vollmer, Günther; Heine, Andreas; Klebe, Gerhard; Marchais-Oberwinkler, Sandrine

2018-05-22

The human enzyme 17β-hydroxysteroid dehydrogenase 14 (17β-HSD14) oxidizes the hydroxyl group at position 17 of estradiol and 5-androstenediol using NAD + as cofactor. However, the physiological role of the enzyme remains unclear. We recently described the first class of nonsteroidal inhibitors for this enzyme with compound 1 showing a high 17β-HSD14 inhibitory activity. Its crystal structure was used as starting point for a structure-based optimization in this study. The goal was to develop a promising chemical probe to further investigate the enzyme. The newly designed compounds revealed mostly very high inhibition of the enzyme and for seven of them the crystal structures of the corresponding inhibitor-enzyme complexes were resolved. The crystal structures disclosed that a small change in the substitution pattern of the compounds resulted in an alternative binding mode for one inhibitor. The profiling of a set of the most potent inhibitors identified 13 (K i  = 9 nM) with a good selectivity profile toward three 17β-HSDs and the estrogen receptor alpha. This inhibitor displayed no cytotoxicity, good solubility, and auspicious predicted bioavailability. Overall, 13 is a highly interesting 17β-HSD14 inhibitor, which might be used as chemical probe for further investigation of the target enzyme. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Note: Circuit design for direct current and alternating current electrochemical etching of scanning probe microscopy tips.

PubMed

Jobbins, Matthew M; Raigoza, Annette F; Kandel, S Alex

2012-03-01

We present control circuits designed for electrochemically etching, reproducibly sharp STM probes. The design uses an Arduino UNO microcontroller to allow for both ac and dc operation, as well as a comparator driven shut-off that allows for etching to be stopped in 0.5-1 μs. The Arduino allows the instrument to be customized to suit a wide variety of potential applications without significant changes to hardware. Data is presented for coarse chemical etching of 80:20 platinum-iridium, tungsten, and nickel tips.

Tracing Cosmic Dawn

NASA Astrophysics Data System (ADS)

Fialkov, Anastasia

2018-05-01

Observational effort is on the way to probe the 21-cm of neutral hydrogen from the epochs of Reionization and Cosmic Dawn. Our current poor knowledge of high redshift astrophysics results in a large uncertainty in the theoretically predicted 21-cm signal. A recent parameter study that is highlighted here explores the variety of 21-cm signals resulting from viable astrophysical scenarios. Model-independent relations between the shape of the signal and the underlying astrophysics are discussed. Finally, I briefly note on possible alternative probes of the high redshift Universe, specifically Fast Radio Bursts.

Near-Field Spectroscopy with Nanoparticles Deposited by AFM

NASA Technical Reports Server (NTRS)

Anderson, Mark S.

2008-01-01

An alternative approach to apertureless near-field optical spectroscopy involving an atomic-force microscope (AFM) entails less complexity of equipment than does a prior approach. The alternative approach has been demonstrated to be applicable to apertureless near-field optical spectroscopy of the type using an AFM and surface enhanced Raman scattering (SERS), and is expected to be equally applicable in cases in which infrared or fluorescence spectroscopy is used. Apertureless near-field optical spectroscopy is a means of performing spatially resolved analyses of chemical compositions of surface regions of nanostructured materials. In apertureless near-field spectroscopy, it is common practice to utilize nanostructured probe tips or nanoparticles (usually of gold) having shapes and dimensions chosen to exploit plasmon resonances so as to increase spectroscopic-signal strengths. To implement the particular prior approach to which the present approach is an alternative, it is necessary to integrate a Raman spectrometer with an AFM and to utilize a special SERS-active probe tip. The resulting instrumentation system is complex, and the tasks of designing and constructing the system and using the system to acquire spectro-chemical information from nanometer-scale regions on a surface are correspondingly demanding.

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.

A systematic quality review of high-tech AAC interventions as an evidence-based practice.

PubMed

Morin, Kristi L; Ganz, Jennifer B; Gregori, Emily V; Foster, Margaret J; Gerow, Stephanie L; Genç-Tosun, Derya; Hong, Ee Rea

2018-06-01

Although high-tech augmentative and alternative communication (AAC) is commonly used to teach social-communication skills to people with autism spectrum disorder or intellectual disabilities who have complex communication needs, there is a critical need to evaluate the efficacy of this approach. The aim of this systematic review was to evaluate the quality of single-case experimental design research on the use of high-tech AAC to teach social-communication skills to individuals with autism spectrum disorder or intellectual disabilities who have complex communication needs, to determine if this intervention approach meets the criteria for evidence-based practices as outlined by the What Works Clearinghouse. Additionally, information on the following extended methodological standards is reported on all included studies: participant description, description of setting and materials, interventionist description, baseline and intervention description, maintenance, generalization, procedural integrity, and social validity. The results from 18 multiple-baseline or multiple-probe experiments across 17 studies indicate that using high-tech AAC to teach social-communication skills to individuals with autism spectrum disorder or intellectual disabilities and complex communication needs can be considered an evidence-based practice, although the review of comparison (i.e., alternating treatment) design studies did not indicate that high-tech AAC is significantly better than low-tech AAC.

When do letter features migrate? A boundary condition for feature-integration theory.

PubMed

Butler, B E; Mewhort, D J; Browse, R A

1991-01-01

Feature-integration theory postulates that a lapse of attention will allow letter features to change position and to recombine as illusory conjunctions (Treisman & Paterson, 1984). To study such errors, we used a set of uppercase letters known to yield illusory conjunctions in each of three tasks. The first, a bar-probe task, showed whole-character mislocations but not errors based on feature migration and recombination. The second, a two-alternative forced-choice detection task, allowed subjects to focus on the presence or absence of subletter features and showed illusory conjunctions based on feature migration and recombination. The third was also a two-alternative forced-choice detection task, but we manipulated the subjects' knowledge of the shape of the stimuli: In the case-certain condition, the stimuli were always in uppercase, but in the case-uncertain condition, the stimuli could appear in either upper- or lowercase. Subjects in the case-certain condition produced illusory conjunctions based on feature recombination, whereas subjects in the case-uncertain condition did not. The results suggest that when subjects can view the stimuli as feature groups, letter features regroup as illusory conjunctions; when subjects encode the stimuli as letters, whole items may be mislocated, but subletter features are not. Thus, illusory conjunctions reflect the subject's processing strategy, rather than the architecture of the visual system.

Clustering and group selection of multiple criteria alternatives with application to space-based networks.

PubMed

Malakooti, Behnam; Yang, Ziyong

2004-02-01

In many real-world problems, the range of consequences of different alternatives are considerably different. In addition, sometimes, selection of a group of alternatives (instead of only one best alternative) is necessary. Traditional decision making approaches treat the set of alternatives with the same method of analysis and selection. In this paper, we propose clustering alternatives into different groups so that different methods of analysis, selection, and implementation for each group can be applied. As an example, consider the selection of a group of functions (or tasks) to be processed by a group of processors. The set of tasks can be grouped according to their similar criteria, and hence, each cluster of tasks to be processed by a processor. The selection of the best alternative for each clustered group can be performed using existing methods; however, the process of selecting groups is different than the process of selecting alternatives within a group. We develop theories and procedures for clustering discrete multiple criteria alternatives. We also demonstrate how the set of alternatives is clustered into mutually exclusive groups based on 1) similar features among alternatives; 2) ideal (or most representative) alternatives given by the decision maker; and 3) other preferential information of the decision maker. The clustering of multiple criteria alternatives also has the following advantages. 1) It decreases the set of alternatives to be considered by the decision maker (for example, different decision makers are assigned to different groups of alternatives). 2) It decreases the number of criteria. 3) It may provide a different approach for analyzing multiple decision makers problems. Each decision maker may cluster alternatives differently, and hence, clustering of alternatives may provide a basis for negotiation. The developed approach is applicable for solving a class of telecommunication networks problems where a set of objects (such as routers, processors, or intelligent autonomous vehicles) are to be clustered into similar groups. Objects are clustered based on several criteria and the decision maker's preferences.

Tabletop Imaging of Structural Evolutions in Chemical Reactions

NASA Astrophysics Data System (ADS)

Ibrahim, Heide; Wales, Benji; Beaulieu, Samuel; Schmidt, Bruno E.; Thiré, Nicolas; Fowe, Emmanuel P.; Bisson, Éric; Hebeisen, Christoph T.; Wanie, Vincent; Giguére, Mathieu; Kieffer, Jean-Claude; Spanner, Michael; Bandrauk, André D.; Sanderson, Joseph; Schuurman, Michael S.; Légaré, François

The first high-resolution molecular movie of proton migration in the acetylene cation is obtained using a tabletop multiphoton pump-probe approach—an alternative to demanding free-electron-lasers and other VUV light sources when ionizing from the HOMO-1.

SPRUCE S1 Bog Peat Depth Determined by Push Probe and GPR: 2009-2010

DOE Data Explorer

Slater, L. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hanson, P. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hook, L. A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2012-01-01

This data set reports the thickness of peat for the S1 Bog measured directly with manual push probes on September 21 and 22, 2009, and measured by ground penetrating radar (GPR) across transects from January 26 to February 2, 2010 and June 2 to June 9, 2010. Also included are interpolated values of peat depth from both probe and GPR data for the S1 Bog at 1 meter square horizontal resolution.

Self-calibrated active pyrometer for furnace temperature measurements

DOEpatents

Woskov, Paul P.; Cohn, Daniel R.; Titus, Charles H.; Surma, Jeffrey E.

1998-01-01

Pyrometer with a probe beam superimposed on its field-of-view for furnace temperature measurements. The pyrometer includes a heterodyne millimeter/sub-millimeter-wave or microwave receiver including a millimeter/sub-millimeter-wave or microwave source for probing. The receiver is adapted to receive radiation from a surface whose temperature is to be measured. The radiation includes a surface emission portion and a surface reflection portion which includes the probe beam energy reflected from the surface. The surface emission portion is related to the surface temperature and the surface reflection portion is related to the emissivity of the surface. The simultaneous measurement of surface emissivity serves as a real time calibration of the temperature measurement. In an alternative embodiment, a translatable base plate and a visible laser beam allow slow mapping out of interference patterns and obtaining peak values therefor. The invention also includes a waveguide having a replaceable end portion, an insulating refractory sleeve and/or a source of inert gas flow. The pyrometer may be used in conjunction with a waveguide to form a system for temperature measurements in a furnace. The system may employ a chopper or alternatively, be constructed without a chopper. The system may also include an auxiliary reflector for surface emissivity measurements.

Probe for high resolution NMR with sample reorientation

DOEpatents

Pines, Alexander; Samoson, Ago

1990-01-01

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero.

Acoustics of the piezo-electric pressure probe

NASA Technical Reports Server (NTRS)

Dutt, G. S.

1974-01-01

Acoustical properties of a piezoelectric device are reported for measuring the pressure in the plasma flow from an MPD arc. A description and analysis of the acoustical behavior in a piezoelectric probe is presented for impedance matching and damping. The experimental results are presented in a set of oscillographic records.

Evolution and Persistence of 5-um Hot Spots at the Galileo Probe entry Latitude

NASA Technical Reports Server (NTRS)

Fisher, B. M.

1997-01-01

We present a study on the longtudinal locations, morphology and evolution of the 5-um hot spots at 6.5 deg. N latitude (planetocentric), from an extensive IRTF-NSFCAM data set spanning more that 3 years, which includes the date of the Galileo Probe entry.

Expanding probe repertoire and improving reproducibility in human genomic hybridization

PubMed Central

Dorman, Stephanie N.; Shirley, Ben C.; Knoll, Joan H. M.; Rogan, Peter K.

2013-01-01

Diagnostic DNA hybridization relies on probes composed of single copy (sc) genomic sequences. Sc sequences in probe design ensure high specificity and avoid cross-hybridization to other regions of the genome, which could lead to ambiguous results that are difficult to interpret. We examine how the distribution and composition of repetitive sequences in the genome affects sc probe performance. A divide and conquer algorithm was implemented to design sc probes. With this approach, sc probes can include divergent repetitive elements, which hybridize to unique genomic targets under higher stringency experimental conditions. Genome-wide custom probe sets were created for fluorescent in situ hybridization (FISH) and microarray genomic hybridization. The scFISH probes were developed for detection of copy number changes within small tumour suppressor genes and oncogenes. The microarrays demonstrated increased reproducibility by eliminating cross-hybridization to repetitive sequences adjacent to probe targets. The genome-wide microarrays exhibited lower median coefficients of variation (17.8%) for two HapMap family trios. The coefficients of variations of commercial probes within 300 nt of a repetitive element were 48.3% higher than the nearest custom probe. Furthermore, the custom microarray called a chromosome 15q11.2q13 deletion more consistently. This method for sc probe design increases probe coverage for FISH and lowers variability in genomic microarrays. PMID:23376933

Galactic Abundance Patterns via Peimbert Types I & II Planetary Nebulae

NASA Astrophysics Data System (ADS)

Milingo, J. B.; Barnes, K. L.; Kwitter, K. B.; Souza, S. P.; Henry, R. B. C.; Skinner, J. N.

2005-12-01

Planetary Nebulae (PNe) are well known fonts of information about both stellar evolution and galactic chemical evolution. Abundance patterns in PNe are used to note signatures and constraints of nuclear processing, and as tracers of the distribution of metals throughout galaxies. In this poster abundance gradients and heavy element ratios are presented based upon newly acquired spectrophotometry of a sample of Galactic Peimbert Type I PNe. This new data set is extracted from spectra that extend from λ 3600 - 9600Å allowing the use of [S III] features at λ 9069 and 9532Å. Since a significant portion of S in PNe resides in S+2 and higher ionization stages, including these features improves the extrapolation from observed ion abundances to total element abundance. An alternate metallicity tracer, Sulfur is precluded from enhancement and depletion across the range of PNe progenitor masses. Its stability in intermediate mass stars makes it a useful tool to probe the natal conditions as well as the evolution of PNe progenitors. This is a continuation of our Type II PNe work, the impetus being to compile a relatively large set of line strengths and abundances with internally consistent observation, reduction, calibration, and abundance determination, minimizing systematic affects that come from compiling various data sets. This research is supported by the AAS Small Research Grants program, the Franklin & Marshall Committee on Grants, and NSF grant AST-0307118.

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

An alternative method for processing northern blots after capillary transfer.

PubMed

Nilsen, Timothy W

2015-03-02

Different laboratories use different methods for the prehybridization, hybridization, and washing steps of the northern blotting procedure. In this protocol, a northern blot is pretreated with Church and Gilbert hybridization buffer to block nonspecific probe-binding sites. The immobilized RNA is then hybridized to a DNA probe specific for the RNA of interest. Finally, the membrane is washed and subjected to autoradiography or phosphorimaging. The solutions and conditions described here may be ideal for those who prefer to use fewer ingredients in their solutions. This protocol is designed to achieve the same goals as other northern blotting approaches. It minimizes background (nonspecific adherence of probe to membrane and nonspecific hybridization) and maximizes specific hybridization to RNAs immobilized on a membrane. © 2015 Cold Spring Harbor Laboratory Press.

Probing Aircraft Flight Test Hazard Mitigation for the Alternative Fuel Effects on Contrails & Cruise Emissions (ACCESS) Research Team

NASA Technical Reports Server (NTRS)

Kelly, Michael J.

2013-01-01

The Alternative Fuel Effects on Contrails & Cruise Emissions (ACCESS) Project Integration Manager requested in July 2012 that the NASA Engineering and Safety Center (NESC) form a team to independently assess aircraft structural failure hazards associated with the ACCESS experiment and to identify potential flight test hazard mitigations to ensure flight safety. The ACCESS Project Integration Manager subsequently requested that the assessment scope be focused predominantly on structural failure risks to the aircraft empennage raft empennage.

Cosmological Parameters and Hyper-Parameters: The Hubble Constant from Boomerang and Maxima

NASA Astrophysics Data System (ADS)

Lahav, Ofer

Recently several studies have jointly analysed data from different cosmological probes with the motivation of estimating cosmological parameters. Here we generalise this procedure to allow freedom in the relative weights of various probes. This is done by including in the joint likelihood function a set of `Hyper-Parameters', which are dealt with using Bayesian considerations. The resulting algorithm, which assumes uniform priors on the log of the Hyper-Parameters, is very simple to implement. We illustrate the method by estimating the Hubble constant H0 from different sets of recent CMB experiments (including Saskatoon, Python V, MSAM1, TOCO, Boomerang and Maxima). The approach can be generalised for a combination of cosmic probes, and for other priors on the Hyper-Parameters. Reference: Lahav, Bridle, Hobson, Lasenby & Sodre, 2000, MNRAS, in press (astro-ph/9912105)

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

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.

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.

Probing gravity theory and cosmic acceleration using (in)consistency tests between cosmological data sets

NASA Astrophysics Data System (ADS)

Ishak-Boushaki, Mustapha B.

2018-06-01

Testing general relativity at cosmological scales and probing the cause of cosmic acceleration are among important objectives targeted by incoming and future astronomical surveys and experiments. I present our recent results on (in)consistency tests that can provide insights about the underlying gravity theory and cosmic acceleration using cosmological data sets. We use new statistical measures that can detect discordances between data sets when present. We use an algorithmic procedure based on these new measures that is able to identify in some cases whether an inconsistency is due to problems related to systematic effects in the data or to the underlying model. Some recent published tensions between data sets are also examined using our formalism, including the Hubble constant measurements, Planck and Large-Scale-Structure. (Work supported in part by NSF under Grant No. AST-1517768).

A Critical Evaluation of Studies Employing Alkenyl Halide ’Mechanistic Probe’ as Indicators of Single Electron Transfer Processes.

DTIC Science & Technology

1987-07-07

College Station, TX 77843 Pittsburgh, PA 15260 Introduction: Chemical reactions come about through the reorganization of valence electrons. The notion...Contmnue on reverie of necessary and odentify 0)’ Wooc ,7umor r) Recently it has been suggested that many reaction traditionally classed in polar terms may...evaluates the utility of these alkenyl halide probes as mechanistic probes for SET. Reactions which interfere with the standard analysis ~ include the

Observations of mesospheric turbulence by rocket probe and VHF radar, part 2.4A

NASA Astrophysics Data System (ADS)

Royrvik, O.; Smith, L. G.

1984-12-01

Data from the Jicamarca VHF radar and from a Languir probe fine-structure on a Nike Orion rocket launched from Punto Lobos, Peru, have been compared. A single mesospheric scattering layer was observed by the radar. The Langmuir probe detected irregularities in the electron-density profile in a narrow region between 85.2 and 86.6 km. It appears from a comparison between these two data sets that turbulence in the neutral atmosphere is the mechanism generating the refractive index irregularities.

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

Observations of Mesospheric Turbulence by Rocket Probe and VHF Radar, Part 2.4A

NASA Technical Reports Server (NTRS)

Royrvik, O.; Smith, L. G.

1984-01-01

Data from the Jicamarca VHF radar and from a Languir probe fine-structure on a Nike Orion rocket launched from Punto Lobos, Peru, have been compared. A single mesospheric scattering layer was observed by the radar. The Langmuir probe detected irregularities in the electron-density profile in a narrow region between 85.2 and 86.6 km. It appears from a comparison between these two data sets that turbulence in the neutral atmosphere is the mechanism generating the refractive index irregularities.

Effect of AEM energy applicator configuration on magnetic nanoparticle mediated hyperthermia for breast cancer.

PubMed

Sanapala, Krishna K; Hewaparakrama, Kapila; Kang, Kyung A

2011-01-01

Magnetic nanoparticle mediated low heat hyperthermia (42~45( o )C) via alternating electromagnetic (AEM) energy is a promising, cancer specific and minimally-invasive cancer therapy. Iron oxide particles frequently used for this therapy are non-toxic and already used as a contrast agent for magnetic resonance imaging. One important issue in the hyperthermia is applying an appropriate amount of energy to the tumor at various sizes and depths, with a minimal damage to normal tissue. For the therapy to be desirable, the AEM energy applicator needs to be non-invasive and user-friendly. To better understand the effect of the probe on the magnetic field distribution, computer simulation was performed for the field distribution by probes with various configurations. In a solenoid-type probe, the field is mainly inside the probe and, therefore, is difficult to use on body. A pancake-shaped probe is easy to use but the field penetration is shallow and, thus, may better serve surface tumor treatment. A sandwich probe, composed of two pancake probes, has a penetration depth deeper than a pancake probe. The results also showed that the spacing between two adjacent coils and the number of coil turns are very important for controlling the field penetration depth and strength. Experiments were also performed to study the effects of the size and concentration of iron oxide nanoparticles on heating. Among the tested particle sizes of 10~50 nm, 30 nm particles showed the best heating for the same mass.

Interpretation of discrepancies in mass spectroscopy data obtained from different experimental configurations

NASA Technical Reports Server (NTRS)

Russell, John M.

1993-01-01

Many helium mass spectrometer leak detectors at KSC employ sampling systems that feature hand held sniffer probes. Authors of general leakage-testing literature recommend sniffer probes for leak location but not for quantitative leakage measurement. Their use in the latter application at KSC involves assumptions that may be subtle. The purpose of the research effort reported herein was to establish the significance of indicated leak rates displayed by sniffer-probe equipped leak detectors and to determine whether the use of alternative hardware or testing procedures may reduce the uncertainty of leakage measurements made with them. The report classifies probe-type sampling systems for helium leak detectors according to their internal plumbing (direct or branched), presents a basic analysis of the fluid dynamics in the sampling system in the branched-conduit case, describes the usual test method for measuring the internal supply-to-sample flowrate ratio (a.k.a permeation ratio), and describes a concept for a sponge-tipped probe whose external supply-to-sample flowrate ratio promises to be lower than that of a simple-ended probe. One conclusion is that the main source of uncertainty in the use of probe-type sampling systems for leakage measurement is uncertainty in the external supply-to-sample flowrate ratio. In contrast, the present method for measuring the internal supply-to-sample flowrate ratio is quantitative and satisfactory. The implication is that probes of lower external supply-to-sample flowrate ratio must be developed before this uncertainty may be reduced significantly.

Langmuir probe diagnostic suite in the C-2 field-reversed configuration

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

Roche, T., E-mail: troche@trialphaenergy.com; Armstrong, S.; Knapp, K.

2014-11-15

Several in situ probes have been designed and implemented into the diagnostic array of the C-2 field-reversed configuration (FRC) at Tri Alpha Energy [M. Tuszewski et al. (the TAE Team), Phys. Rev. Lett. 108, 255008 (2012)]. The probes are all variations on the traditional Langmuir probe. They include linear arrays of triple probes, linear arrays of single-tipped swept probes, a multi-faced Gundestrup probe, and an ion-sensitive probe. The probes vary from 5 to 7 mm diameter in size to minimize plasma perturbations. They also have boron nitride outer casings that prevent unwanted electrical breakdown and reduce the introduction of impurities.more » The probes are mounted on motorized linear-actuators allowing for programmatic scans of the various plasma parameters over the course of several shots. Each probe has a custom set of electronics that allows for measurement of the desired signals. High frequency ( > 5MHz) analog optical-isolators ensure that plasma parameters can be measured at sub-microsecond time scales while providing electrical isolation between machine and data acquisition systems. With these probes time-resolved plasma parameters (temperature, density, spatial potential, flow, and electric field) can be directly/locally measured in the FRC jet and edge/scrape-off layer.« less

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.

What Can States Learn about College and Career Readiness Accountability Measures from Alternative Education? Ask the CCRS Center

ERIC Educational Resources Information Center

Deeds, Carinne; Malter, Zachary

2016-01-01

This "Ask the CCRS Center Brief" provides an overview of the accountability measures used by states and districts to assess the college and career readiness of students who are educated in alternative programs and schools (defined hereafter as "alternative settings"). Alternative settings are designed to serve at-risk students…

Achieving Student Success in a Regional Public Alternative School Setting through a Consequence-Based Model

ERIC Educational Resources Information Center

Burkholder, Sue M.; Merritt, Marti

2007-01-01

Genesis Alternative School is a regional, public alternative school setting for middle and high school students from four participating school divisions. It serves 1 rural county school division and 3 small city school divisions. Students are placed at Genesis for disciplinary reasons. Genesis is unique among alternative schools in Virginia…

[In vitro and in vivo recoveries of cutaneous micro-dialysis probe of paeonol, eugenol and piperine].

PubMed

Yang, Chang; Bai, Jie; Du, Shou-Ying; Cui, Ya-Hua; Zhang, Qin-Shuai; Ma, Jun-Ming

2016-11-01

To establish a method for detecting micro-dialysis recovery of paeonol, eugenol and piperine in Huoxue Zhitong patch, in order to provide the basis for further percutaneous pharmacokinetics studies. The concentrations of paeonol, eugenol and piperine in dialysates were determined by HPLC, and probe deliveries were calculated respectively. The effects of concentration and calibration approaches on the micro-dialysis probe deliveries of the three components were investigated, and their probe absorbability, in vitro and in vivo probe stability and repeatability were also studied.The results indicated that little paeonol, eugenol and piperine were observed in probes with 30% alcohol as the perfusate, and could be cleaned from probe in a short time. And the in vivo and in vitro probe deliveries of three components were stable within 8 h, drug-containing solution and blank perfusate were alternatively used for three times, and the in vivo and in vitro probe deliveries of three components were basically unchanged. The in vitro recoveries of paeonol, eugenol and piperine with a range of concentration were respectively (45.7±4.66)%, (27.82±2.95)%, (41.3±3.96)%, which indicated no concentration independent. Under the same conditions, the similar delivery was observed by dialysis, retrodialysis and no-net flux. Therefore, the concentrations of analyses of the collected fraction could be calibrated by in vitro or in vivo recoveries. Meanwhile, this also proved that the micro-dialysis method built by this study is applicable to the study on percutaneous pharmacokinetics of Huoxue Zhitong patch. Copyright© by the Chinese Pharmaceutical Association.

Enabling technologies for robot assisted ultrasound tomography.

PubMed

Aalamifar, Fereshteh; Khurana, Rishabh; Cheng, Alexis; Guo, Xiaoyu; Iordachita, Iulian; Boctor, Emad M

2017-03-01

Currently available ultrasound (US) tomography systems suggest utilizing cylindrical transducers that can be used for a specific organ. In this paper, our focus is on an alternative way of creating US tomographic images that could be used for other anatomies and more general applications. This system consists of two conventional US probes facing each other while one or several of the transducers in one probe can act as the transmitter and the rest as the receiver. Aligning the two US probes is a challenging task. To address this issue, we propose a robot assisted US tomography system in which one probe is operated freehanded and another by a robotic arm. In this paper, enabling technologies for this system are described. With the current prototype, a reconstruction precision of 4.12, 1.73, and 2.23 mm for the three calibrations, and an overall alignment repeatability in the range of 5-9 mm were achieved. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

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

Probe for high resolution NMR with sample reorientation

DOEpatents

Pines, A.; Samoson, A.

1990-02-06

An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero. 8 figs.

Teaching Special Education Teachers How to Conduct Functional Analysis in Natural Settings

ERIC Educational Resources Information Center

Erbas, Dilek; Tekin-Iftar, Elif; Yucesoy, Serife

2006-01-01

Effects of a training program utilized to teach how to conduct functional analysis process to teachers of children with developmental disabilities was examined. Furthermore, teachers' opinions regarding this process were investigated. A multiple probe design across subjects with probe conditions was used. Teacher training was in two phases. In the…

Fluorescent signatures for variable DNA sequences

PubMed Central

Rice, John E.; Reis, Arthur H.; Rice, Lisa M.; Carver-Brown, Rachel K.; Wangh, Lawrence J.

2012-01-01

Life abounds with genetic variations writ in sequences that are often only a few hundred nucleotides long. Rapid detection of these variations for identification of genetic diseases, pathogens and organisms has become the mainstay of molecular science and medicine. This report describes a new, highly informative closed-tube polymerase chain reaction (PCR) strategy for analysis of both known and unknown sequence variations. It combines efficient quantitative amplification of single-stranded DNA targets through LATE-PCR with sets of Lights-On/Lights-Off probes that hybridize to their target sequences over a broad temperature range. Contiguous pairs of Lights-On/Lights-Off probes of the same fluorescent color are used to scan hundreds of nucleotides for the presence of mutations. Sets of probes in different colors can be combined in the same tube to analyze even longer single-stranded targets. Each set of hybridized Lights-On/Lights-Off probes generates a composite fluorescent contour, which is mathematically converted to a sequence-specific fluorescent signature. The versatility and broad utility of this new technology is illustrated in this report by characterization of variant sequences in three different DNA targets: the rpoB gene of Mycobacterium tuberculosis, a sequence in the mitochondrial cytochrome C oxidase subunit 1 gene of nematodes and the V3 hypervariable region of the bacterial 16 s ribosomal RNA gene. We anticipate widespread use of these technologies for diagnostics, species identification and basic research. PMID:22879378

Label-Free, LC-MS-Based Assays to Quantitate Small-Molecule Antagonist Binding to the Mammalian BLT1 Receptor.

PubMed

Chen, Xun; Stout, Steven; Mueller, Uwe; Boykow, George; Visconti, Richard; Siliphaivanh, Phieng; Spencer, Kerrie; Presland, Jeremy; Kavana, Michael; Basso, Andrea D; McLaren, David G; Myers, Robert W

2017-08-01

We have developed and validated label-free, liquid chromatography-mass spectrometry (LC-MS)-based equilibrium direct and competition binding assays to quantitate small-molecule antagonist binding to recombinant human and mouse BLT1 receptors expressed in HEK 293 cell membranes. Procedurally, these binding assays involve (1) equilibration of the BLT1 receptor and probe ligand, with or without a competitor; (2) vacuum filtration through cationic glass fiber filters to separate receptor-bound from free probe ligand; and (3) LC-MS analysis in selected reaction monitoring mode for bound probe ligand quantitation. Two novel, optimized probe ligands, compounds 1 and 2, were identified by screening 20 unlabeled BLT1 antagonists for direct binding. Saturation direct binding studies confirmed the high affinity, and dissociation studies established the rapid binding kinetics of probe ligands 1 and 2. Competition binding assays were established using both probe ligands, and the affinities of structurally diverse BLT1 antagonists were measured. Both binding assay formats can be executed with high specificity and sensitivity and moderate throughput (96-well plate format) using these approaches. This highly versatile, label-free method for studying ligand binding to membrane-associated receptors should find broad application as an alternative to traditional methods using labeled ligands.

Cyclic coding for Brillouin optical time-domain analyzers using probe dithering.

PubMed

Iribas, Haritz; Loayssa, Alayn; Sauser, Florian; Llera, Miguel; Le Floch, Sébastien

2017-04-17

We study the performance limits of mono-color cyclic coding applied to Brillouin optical time-domain analysis (BOTDA) sensors that use probe wave dithering. BOTDA analyzers with dithering of the probe use a dual-probe-sideband setup in which an optical frequency modulation of the probe waves along the fiber is introduced. This avoids non-local effects while keeping the Brillouin threshold at its highest level, thus preventing the spontaneous Brillouin scattering from generating noise in the deployed sensing fiber. In these conditions, it is possible to introduce an unprecedented high probe power into the sensing fiber, which leads to an enhancement of the signal-to-noise ratio (SNR) and consequently to a performance improvement of the analyzer. The addition of cyclic coding in these set-ups can further increase the SNR and accordingly enhance the performance. However, this unprecedented probe power levels that can be employed result in the appearance of detrimental effects in the measurement that had not previously been observed in other BOTDA set-ups. In this work, we analyze the distortion in the decoding process and the errors in the measurement that this distortion causes, due to three factors: the power difference of the successive pulses of a code sequence, the appearance of first-order non-local effects and the non-linear amplification of the probe wave that results when using mono-color cyclic coding of the pump pulses. We apply the results of this study to demonstrate the performance enhancement that can be achieved in a long-range dithered dual-probe BOTDA. A 164-km fiber-loop is measured with 1-m spatial resolution, obtaining 3-MHz Brillouin frequency shift measurement precision at the worst contrast location. To the best of our knowledge, this is the longest sensing distance achieved with a BOTDA sensor using mono-color cyclic coding.

Usability evaluation of a medication reconciliation tool: Embedding safety probes to assess users' detection of medication discrepancies.

PubMed

Russ, Alissa L; Jahn, Michelle A; Patel, Himalaya; Porter, Brian W; Nguyen, Khoa A; Zillich, Alan J; Linsky, Amy; Simon, Steven R

2018-06-01

An electronic medication reconciliation tool was previously developed by another research team to aid provider-patient communication for medication reconciliation. To evaluate the usability of this tool, we integrated artificial safety probes into standard usability methods. The objective of this article is to describe this method of using safety probes, which enabled us to evaluate how well the tool supports users' detection of medication discrepancies. We completed a mixed-method usability evaluation in a simulated setting with 30 participants: 20 healthcare professionals (HCPs) and 10 patients. We used factual scenarios but embedded three artificial safety probes: (1) a missing medication (i.e., omission); (2) an extraneous medication (i.e., commission); and (3) an inaccurate dose (i.e., dose discrepancy). We measured users' detection of each probe to estimate the probability that a HCP or patient would detect these discrepancies. Additionally, we recorded participants' detection of naturally occurring discrepancies. Each safety probe was detected by ≤50% of HCPs. Patients' detection rates were generally higher. Estimates indicate that a HCP and patient, together, would detect 44.8% of these medication discrepancies. Additionally, HCPs and patients detected 25 and 45 naturally-occurring discrepancies, respectively. Overall, detection of medication discrepancies was low. Findings indicate that more advanced interface designs are warranted. Future research is needed on how technologies can be designed to better aid HCPs' and patients' detection of medication discrepancies. This is one of the first studies to evaluate the usability of a collaborative medication reconciliation tool and assess HCPs' and patients' detection of medication discrepancies. Results demonstrate that embedded safety probes can enhance standard usability methods by measuring additional, clinically-focused usability outcomes. The novel safety probes we used may serve as an initial, standard set for future medication reconciliation research. More prevalent use of safety probes could strengthen usability research for a variety of health information technologies. Published by Elsevier Inc.

APPLICATION OF FISH AND MICROAUTORADIOGRAPHY TO DETERMINE MICROBIAL COMMUNITY STRUCTURE AND ACTIVITY IN SOIL

EPA Science Inventory

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a well established technique for identifying populations of microorganisms at various taxonomic levels in natural and engineered systems. The strength of this technique over alternative nuclei...

Development, fabrication and test of a high purity silica heat shield

NASA Technical Reports Server (NTRS)

Rusert, E. L.; Drennan, D. N.; Biggs, M. S.

1978-01-01

A highly reflective hyperpure ( 25 ppm ion impurities) slip cast fused silica heat shield material developed for planetary entry probes was successfully scaled up. Process development activities for slip casting large parts included green strength improvements, casting slip preparation, aggregate casting, strength, reflectance, and subscale fabrication. Successful fabrication of a one-half scale Saturn probe (shape and size) heat shield was accomplished while maintaining the silica high purity and reflectance through the scale-up process. However, stress analysis of this original aggregate slip cast material indicated a small margin of safety (MS. = +4%) using a factor of safety of 1.25. An alternate hyperpure material formulation to increase the strength and toughness for a greater safety margin was evaluated. The alternate material incorporates short hyperpure silica fibers into the casting slip. The best formulation evaluated has a 50% by weight fiber addition resulting in an 80% increase in flexural strength and a 170% increase in toughness over the original aggregate slip cast materials with comparable reflectance.

Biomedical device prototype based on small scale hydrodynamic cavitation

NASA Astrophysics Data System (ADS)

Ghorbani, Morteza; Sozer, Canberk; Alcan, Gokhan; Unel, Mustafa; Ekici, Sinan; Uvet, Huseyin; Koşar, Ali

2018-03-01

This study presents a biomedical device prototype based on small scale hydrodynamic cavitation. The application of small scale hydrodynamic cavitation and its integration to a biomedical device prototype is offered as an important alternative to other techniques, such as ultrasound therapy, and thus constitutes a local, cheap, and energy-efficient solution, for urinary stone therapy and abnormal tissue ablation (e.g., benign prostate hyperplasia (BPH)). The destructive nature of bubbly, cavitating, flows was exploited, and the potential of the prototype was assessed and characterized. Bubbles generated in a small flow restrictive element (micro-orifice) based on hydrodynamic cavitation were utilized for this purpose. The small bubbly, cavitating, flow generator (micro-orifice) was fitted to a small flexible probe, which was actuated with a micromanipulator using fine control. This probe also houses an imaging device for visualization so that the emerging cavitating flow could be locally targeted to the desired spot. In this study, the feasibility of this alternative treatment method and its integration to a device prototype were successfully accomplished.

Eddy-Current Monitoring Of Composite Layups

NASA Technical Reports Server (NTRS)

Fox, Robert L.; Buckley, John D.

1993-01-01

Eddy-current-probe apparatus used to determine predominant orientations of fibers in fiber/matrix composite materials. Apparatus nondestructive, noninvasive means for monitoring composite prepregs and layups during fabrication to ensure predictable and repeatable mechanical properties of finished composite panels. Consists essentially of electromagnet coil wrapped around horseshoe-shaped powdered-iron or ferrite ore. Optionally, capacitor included in series or parallel with coil to form resonant circuit. Impedance monitor excites radio-frequency current in coil and measures impedance of probe circuit. Affected by whatever material placed near ends of core, where material intercepts alternating magnetic field excited in core by current in coil.

Method and apparatus for optical temperature measurements

DOEpatents

Angel, S.M.; Hirschfeld, T.B.

1986-04-22

A method and apparatus are provided for remotely monitoring temperature. Both method and apparatus employ a temperature probe material having an excitation-dependent emission line whose fluorescence intensity varies directly with temperature whenever excited by light having a first wavelength and whose fluorescence intensity varies inversely with temperature whenever excited by light having a second wavelength. Temperature is measured by alternatively illiminating the temperature probe material with light having the first wavelength and light having the second wavelength, monitoring the intensity of the successive emissions of the excitation-dependent emission line, and relating the intensity ratio of successive emissions to temperature. 3 figs.

Method and apparatus for optical temperature measurements

DOEpatents

Angel, S. Michael; Hirschfeld, Tomas B.

1988-01-01

A method and apparatus are provided for remotely monitoring temperature. Both method and apparatus employ a temperature probe material having an excitation-dependent emission line whose fluorescence intensity varies directly with temperature whenever excited by light having a first wavelength and whose fluorescence intensity varies inversely with temperature whenever excited by light having a second wavelength. Temperature is measured by alternatively illuminating the temperature probe material with light having the first wavelength and light having the second wavelength, monitoring the intensity of the successive emissions of the excitation-dependent emission line, and relating the intensity ratio of successive emissions to temperature.

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.

Solid phase sequencing of biopolymers

DOEpatents

Cantor, Charles; Koster, Hubert

2010-09-28

This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

Comparison of CpG island methylator phenotype (CIMP) frequency in colon cancer using different probe- and gene-specific scoring alternatives on recommended multi-gene panels.

PubMed

Berg, Marianne; Hagland, Hanne R; Søreide, Kjetil

2014-01-01

In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP). However, a consensus of how to score CIMP is not reached, and variation in definition may influence the reported CIMP prevalence in tumours. Thus, we sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), with subsequent fragment analysis, was used to investigate methylation of tumour samples. In total, 31 CpG sites, located in 8 different genes (RUNX3, MLH1, NEUROG1, CDKN2A, IGF2, CRABP1, SOCS1 and CACNA1G) were investigated in 64 distinct colon cancers and 2 colon cancer cell lines. The Ogino gene panel includes all 8 genes, in addition to the Weisenberger panel of which only 5 of the 8 genes included were investigated. In total, 18 alternative combinations of scoring of CIMP positivity on probe-, gene-, and panel-level were analysed and compared. For 47 samples (71%), the CIMP status was constant and independent of criteria used for scoring; 34 samples were constantly scored as CIMP negative, and 13 (20%) consistently scored as CIMP positive. Only four of 31 probes (13%) investigated showed no difference in the numbers of positive samples using the different cut-offs. Within the panels a trend was observed that increasing the gene-level stringency resulted in a larger difference in CIMP positive samples than increasing the probe-level stringency. A significant difference between positive samples using 'the most stringent' as compared to 'the least stringent' criteria (20% vs 46%, respectively; p<0.005) was demonstrated. A statistical significant variation in the frequency of CIMP depending on the cut-offs and genes included in a panel was found, with twice as many positives samples by least compared to most stringent definition used.

A modified multiplex ligation-dependent probe amplification method for the detection of 22q11.2 copy number variations in patients with congenital heart disease.

PubMed

Zhang, Xiaoqing; Xu, Yuejuan; Liu, Deyuan; Geng, Juan; Chen, Sun; Jiang, Zhengwen; Fu, Qihua; Sun, Kun

2015-05-08

Copy number variations (CNVs) of chromosomal region 22q11.2 are associated with a subset of patients with congenital heart disease (CHD). Accurate and efficient detection of CNV is important for genetic analysis of CHD. The aim of the study was to introduce a novel approach named CNVplex®, a high-throughput analysis technique designed for efficient detection of chromosomal CNVs, and to explore the prevalence of sub-chromosomal imbalances in 22q11.2 loci in patients with CHD from a single institute. We developed a novel technique, CNVplex®, for high-throughput detection of sub-chromosomal copy number aberrations. Modified from the multiplex ligation-dependent probe amplification (MLPA) method, it introduced a lengthening ligation system and four universal primer sets, which simplified the synthesis of probes and significantly improved the flexibility of the experiment. We used 110 samples, which were extensively characterized with chromosomal microarray analysis and MLPA, to validate the performance of the newly developed method. Furthermore, CNVplex® was used to screen for sub-chromosomal imbalances in 22q11.2 loci in 818 CHD patients consecutively enrolled from Shanghai Children's Medical Center. In the methodology development phase, CNVplex® detected all copy number aberrations that were previously identified with both chromosomal microarray analysis and MLPA, demonstrating 100% sensitivity and specificity. In the validation phase, 22q11.2 deletion and 22q11.2 duplication were detected in 39 and 1 of 818 patients with CHD by CNVplex®, respectively. Our data demonstrated that the frequency of 22q11.2 deletion varied among sub-groups of CHD patients. Notably, 22q11.2 deletion was more commonly observed in cases with conotruncal defect (CTD) than in cases with non-CTD (P<0.001). With higher resolution and more probes against selected chromosomal loci, CNVplex® also identified several individuals with small CNVs and alterations in other chromosomes. CNVplex® is sensitive and specific in its detection of CNVs, and it is an alternative to MLPA for batch screening of pathogenetic CNVs in known genomic loci.

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.

Gaussian interferometric power and Black box estimation of Unruh temperature

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

Wang, Jieci, E-mail: jcwang@hunnu.edu.cn; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190; Cao, Haixin

2016-10-15

We present a black box estimation paradigm of Unruh temperature in a relativistic bosonic continuous-variable setting. It is shown that the guaranteed precision for the estimation of Unruh temperature can be evaluated by the Gaussian interferometric power for a given probe state. We demonstrate that the amount of interferometric power is always beyond the entanglement type quantum correlations in a relativistic setting. It is found that due to the fact that Unruh radiation acts as a thermal bath on the probe system, it destroys available resources of the probe system and reduces the guaranteed precision of the estimation of Unruhmore » temperature. We also find that the thermal noise induced by Unruh effect will generate interferometric power between accelerated Bob and his auxiliary partner anti-Bob, while it does not generate any correlation between inertial Alice and anti-Bob.« less

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.

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.

Compensation of the sheath effects in cylindrical floating probes

NASA Astrophysics Data System (ADS)

Park, Ji-Hwan; Chung, Chin-Wook

2018-05-01

In cylindrical floating probe measurements, the plasma density and electron temperature are overestimated due to sheath expansion and oscillation. To reduce these sheath effects, a compensation method based on well-developed floating sheath theories is proposed and applied to the floating harmonic method. The iterative calculation of the Allen-Boyd-Reynolds equation can derive the floating sheath thickness, which can be used to calculate the effective ion collection area; in this way, an accurate ion density is obtained. The Child-Langmuir law is used to calculate the ion harmonic currents caused by sheath oscillation of the alternating-voltage-biased probe tip. Accurate plasma parameters can be obtained by subtracting these ion harmonic currents from the total measured harmonic currents. Herein, the measurement principles and compensation method are discussed in detail and an experimental demonstration is presented.

Transpiring purging access probe for particulate laden or hazardous environments

DOEpatents

VanOsdol, John G

2013-12-03

An access probe for remote-sensing access through a viewing port, viewing volume, and access port into a vessel. The physical boundary around the viewing volume is partially formed by a porous sleeve lying between the viewing volume and a fluid conduit. In a first mode of operation, a fluid supplied to the fluid conduit encounters the porous sleeve and flows through the porous material to maintain the viewing volume free of ash or other matter. When additional fluid force is needed to clear the viewing volume, the pressure of the fluid flow is increased sufficiently to slidably translate the porous sleeve, greatly increasing the flow into the viewing volume. The porous sleeve is returned to position by an actuating spring. The access probe thereby provides for alternate modes of operation based on the pressure of an actuating fluid.

A measurement of perpendicular current density in an aurora

NASA Technical Reports Server (NTRS)

Bering, E. A.; Mozer, F. S.

1975-01-01

A Nike Tomahawk sounding rocket was launched into a 400-gamma auroral substorm from Esrange, Kiruna, Sweden. The rocket instrumentation included a split Langmuir-probe plasma-velocity detector and a double-probe electric-field detector. Above 140-km altitude, the electric field deduced from the ion-flow velocity measurement and the electric field measured by the double probe agree to an accuracy within the uncertainties of the two measurements. The difference between the two measurements at altitudes below 140 km provides an in situ measurement of current density and conductivity. Alternatively, if values for the conductivity are assumed, the neutral-wind velocity can be deduced. The height-integrated current was 0.11 A/m flowing at an azimuth angle of 276 deg. The neutral winds were strong, exhibited substantial altitude variation in the east-west component, and were predominantly southward.

Nanoplasmonic probes of RNA folding and assembly during pre-mRNA splicing

NASA Astrophysics Data System (ADS)

Nguyen, Anh H.; Lee, Jong Uk; Sim, Sang Jun

2016-02-01

RNA splicing plays important roles in transcriptome and proteome diversity. Herein, we describe the use of a nanoplasmonic system that unveils RNA folding and assembly during pre-mRNA splicing wherein the quantification of mRNA splice variants is not taken into account. With a couple of SERS-probes and plasmonic probes binding at the boundary sites of exon-2/intron-2 and intron-2/exon-3 of the pre-mature RNA of the β-globin gene, the splicing process brings the probes into the plasmonic bands. For plasmonic probes, a plasmon shift increase of ~29 nm, corresponding to intron removal and exon-2 and exon-3 connection to form the mRNA molecule, is measured by plasmonic coupling. The increased scattering intensity and surface-enhanced Raman scattering (SERS) fingerprinting reveal the clear dynamics of pre-mRNA splicing. Moreover, a time-resolved experiment of individual RNA molecules exhibited a successful splicing and an inhibited splicing event by 33 μM biflavonoid isoginkgetin, a general inhibitor of RNA splicing. The results suggest that the RNA splicing is successfully monitored with the nanoplasmonic system. Thus, this platform can be useful for studying RNA nanotechnology, biomolecular folding, alternative splicing, and maturation of microRNA.

Development and Beam-Shape Analysis of an Integrated Fiber-Optic Confocal Probe for High-Precision Central Thickness Measurement of Small-Radius Lenses

PubMed Central

Sutapun, Boonsong; Somboonkaew, Armote; Amarit, Ratthasart; Chanhorm, Sataporn

2015-01-01

This work describes a new design of a fiber-optic confocal probe suitable for measuring the central thicknesses of small-radius optical lenses or similar objects. The proposed confocal probe utilizes an integrated camera that functions as a shape-encoded position-sensing device. The confocal signal for thickness measurement and beam-shape data for off-axis measurement can be simultaneously acquired using the proposed probe. Placing the probe’s focal point off-center relative to a sample’s vertex produces a non-circular image at the camera’s image plane that closely resembles an ellipse for small displacements. We were able to precisely position the confocal probe’s focal point relative to the vertex point of a ball lens with a radius of 2.5 mm, with a lateral resolution of 1.2 µm. The reflected beam shape based on partial blocking by an aperture was analyzed and verified experimentally. The proposed confocal probe offers a low-cost, high-precision technique, an alternative to a high-cost three-dimensional surface profiler, for tight quality control of small optical lenses during the manufacturing process. PMID:25871720

Ultrasound-guided Subclavian Vein Cannulation Using a Micro-Convex Ultrasound Probe

PubMed Central

Fair, James; Hirshberg, Eliotte L.; Grissom, Colin K.; Brown, Samuel M.

2014-01-01

Background: The subclavian vein is the preferred site for central venous catheter placement due to infection risk and patient comfort. Ultrasound guidance is useful in cannulation of other veins, but for the subclavian vein, current ultrasound-guided techniques using high-frequency linear array probes are generally limited to axillary vein cannulation. Methods: We report a series of patients who underwent clinically indicated subclavian venous catheter placement using a micro-convex pediatric probe for real-time guidance in the vein’s longitudinal axis. We identified rates of successful placement and complications by chart review. Results: Twenty-four catheters were placed using the micro-convex pediatric probe with confirmation of placement of the needle medial to the lateral border of the first rib. Sixteen of the catheters were placed by trainee physicians. In 23 patients, the catheter was placed without complication (hematoma, pneumothorax, infection). In one patient, the vein could not be safely cannulated without risk of arterial puncture, so an alternative site was selected. Conclusions: Infraclavicular subclavian vein cannulation using real-time ultrasound with a micro-convex pediatric probe appears to be a safe and effective method of placing subclavian vascular catheters. This technique merits further study to confirm safety and efficacy. PMID:24611628

Accuracy of non-operative identification of the sentinel lymph node using combined gamma and ultrasound scanning.

PubMed

Whelehan, P; Vinnicombe, S J; Brown, D C; McLean, D; Evans, A

2014-08-01

To assess how accurately the sentinel lymph node (SLN) can be identified percutaneously, using gamma probe and ultrasound technology. Women with breast cancer, scheduled for wide local excision or mastectomy with SLN biopsy (SLNB), were included. Peri-areolar intradermal injection of technetium-99 nanocolloid was performed on the morning of surgery and 1-2 ml of blue dye was injected in the peri-areolar region once the patient was anaesthetized. Prior to surgery, a gamma probe was used over the skin to identify any hot spot that could represent a SLN. Ultrasound, guided by the hot spot, was then used to visualize potential SLNs and guide the insertion of a localizing wire. The accuracy in localizing the SLN by preoperative gamma-probe guided ultrasonography was assessed by comparison to SLNB. A SLN was correctly identified and marked using gamma-probe guided ultrasonography in 44 of 59 cases (75%; 95% CI: 63-86%). This study supports the case for investigating percutaneous gamma probe and ultrasound guided interventions in the axilla in women with breast cancer, as a potential alternative to surgical SLNB. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Pump-Flow-Probe X-Ray Absorption Spectroscopy as a Tool for Studying Intermediate States of Photocatalytic Systems.

PubMed

Smolentsev, Grigory; Guda, Alexander; Zhang, Xiaoyi; Haldrup, Kristoffer; Andreiadis, Eugen; Chavarot-Kerlidou, Murielle; Canton, Sophie E; Nachtegaal, Maarten; Artero, Vincent; Sundstrom, Villy

2013-08-29

A new setup for pump-flow-probe X-ray absorption spectroscopy has been implemented at the SuperXAS beamline of the Swiss Light Source. It allows recording X-ray absorption spectra with a time resolution of tens of microseconds and high detection efficiency for samples with sub-mM concentrations. A continuous wave laser is used for the photoexcitation, with the distance between laser and X-ray beams and velocity of liquid flow determining the time delay, while the focusing of both beams and the flow speed define the time resolution. This method is compared with the alternative measurement technique that utilizes a 1 kHz repetition rate laser and multiple X-ray probe pulses. Such an experiment was performed at beamline 11ID-D of the Advanced Photon Source. Advantages, limitations and potential for improvement of the pump-flow-probe setup are discussed by analyzing the photon statistics. Both methods, with Co K-edge probing were applied to the investigation of a cobaloxime-based photo-catalytic reaction. The interplay between optimizing for efficient photoexcitation and time resolution as well as the effect of sample degradation for these two setups are discussed.

Pump-Flow-Probe X-Ray Absorption Spectroscopy as a Tool for Studying Intermediate States of Photocatalytic Systems

PubMed Central

Smolentsev, Grigory; Guda, Alexander; Zhang, XIaoyi; Haldrup, Kristoffer; Andreiadis, Eugen; Chavarot-Kerlidou, Murielle; Canton, Sophie E.; Nachtegaal, Maarten; Artero, Vincent; Sundstrom, Villy

2014-01-01

A new setup for pump-flow-probe X-ray absorption spectroscopy has been implemented at the SuperXAS beamline of the Swiss Light Source. It allows recording X-ray absorption spectra with a time resolution of tens of microseconds and high detection efficiency for samples with sub-mM concentrations. A continuous wave laser is used for the photoexcitation, with the distance between laser and X-ray beams and velocity of liquid flow determining the time delay, while the focusing of both beams and the flow speed define the time resolution. This method is compared with the alternative measurement technique that utilizes a 1 kHz repetition rate laser and multiple X-ray probe pulses. Such an experiment was performed at beamline 11ID-D of the Advanced Photon Source. Advantages, limitations and potential for improvement of the pump-flow-probe setup are discussed by analyzing the photon statistics. Both methods, with Co K-edge probing were applied to the investigation of a cobaloxime-based photo-catalytic reaction. The interplay between optimizing for efficient photoexcitation and time resolution as well as the effect of sample degradation for these two setups are discussed. PMID:24443663

Reply to "Comment on `Particle path through a nested Mach-Zehnder interferometer' "

NASA Astrophysics Data System (ADS)

Griffiths, Robert B.

2017-06-01

The correctness of the consistent histories analysis of weakly interacting probes, related to the path of a particle, is maintained against the criticisms in the Comment, and against the alternative approach described there, which receives no support from standard (textbook) quantum mechanics.

Kerr hysteresis loop tracer with alternate driving magnetic field up to 10 kHz

NASA Astrophysics Data System (ADS)

Callegaro, Luca; Fiorini, Carlo; Triggiani, Giacomo; Puppin, Ezio

1997-07-01

A magneto-optical Kerr loop tracer for hysteresis loop measurements in thin films with field excitation frequency f0 from 10 mHz to 10 kHz is described. A very high sensitivity is obtained by using an ultrabright light-emitting diode as a low-noise light source and a novel acquisition process. The field is generated with a coil driven by an audio amplifier connected to a free-running oscillator. The conditioned detector output constitutes the magnetization signal (M); the magnetic field (H) is measured with a fast Hall probe. The acquisition electronics are based on a set of sample-and-hold amplifiers which allow the simultaneous sampling of M, H, and dH/dt. Acquisition is driven by a personal computer equipped with a multifunction I/O board. Test results on a 120 nm Fe film on Si substrate are shown. The coercive field of the film increases with frequency and nearly doubles at 10 kHz with respect to dc.

Advanced yellow fever virus genome detection in point-of-care facilities and reference laboratories.

PubMed

Domingo, Cristina; Patel, Pranav; Yillah, Jasmin; Weidmann, Manfred; Méndez, Jairo A; Nakouné, Emmanuel Rivalyn; Niedrig, Matthias

2012-12-01

Reported methods for the detection of the yellow fever viral genome are beset by limitations in sensitivity, specificity, strain detection spectra, and suitability to laboratories with simple infrastructure in areas of endemicity. We describe the development of two different approaches affording sensitive and specific detection of the yellow fever genome: a real-time reverse transcription-quantitative PCR (RT-qPCR) and an isothermal protocol employing the same primer-probe set but based on helicase-dependent amplification technology (RT-tHDA). Both assays were evaluated using yellow fever cell culture supernatants as well as spiked and clinical samples. We demonstrate reliable detection by both assays of different strains of yellow fever virus with improved sensitivity and specificity. The RT-qPCR assay is a powerful tool for reference or diagnostic laboratories with real-time PCR capability, while the isothermal RT-tHDA assay represents a useful alternative to earlier amplification techniques for the molecular diagnosis of yellow fever by field or point-of-care laboratories.

Phage protein-targeted cancer nanomedicines

PubMed Central

Petrenko, V.A.; Jayanna, P.K.

2015-01-01

Nanoencapsulation of anticancer drugs improves their therapeutic indices by virtue of the enhanced permeation and retention effect which achieves passive targeting of nanoparticles in tumors. This effect can be significantly enhanced by active targeting of nanovehicles to tumors. Numerous ligands have been proposed and used in various studies with peptides being considered attractive alternatives to antibodies. This is further reinforced by the availability of peptide phage display libraries which offer an unlimited reservoir of target-specific probes. In particular landscape phages with multivalent display of target-specific peptides which enable the phage particle itself to become a nanoplatform creates a paradigm for high throughput selection of nanoprobes setting the stage for personalized cancer management. Despite its promise, this conjugate of combinatorial chemistry and nanotechnology has not made a significant clinical impact in cancer management due to a lack of using robust processes that facilitate scale-up and manufacturing. To this end we proposed the use of phage fusion protein as the navigating modules of novel targeted nanomedicine platforms which are described in this review. PMID:24269681

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

PubMed Central

2012-01-01

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings. PMID:16964229

Magnetic resonance fingerprinting.

PubMed

Ma, Dan; Gulani, Vikas; Seiberlich, Nicole; Liu, Kecheng; Sunshine, Jeffrey L; Duerk, Jeffrey L; Griswold, Mark A

2013-03-14

Magnetic resonance is an exceptionally powerful and versatile measurement technique. The basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50 years, being mainly restricted to the qualitative probing of only a limited set of the properties that can in principle be accessed by this technique. Here we introduce an approach to data acquisition, post-processing and visualization--which we term 'magnetic resonance fingerprinting' (MRF)--that permits the simultaneous non-invasive quantification of multiple important properties of a material or tissue. MRF thus provides an alternative way to quantitatively detect and analyse complex changes that can represent physical alterations of a substance or early indicators of disease. MRF can also be used to identify the presence of a specific target material or tissue, which will increase the sensitivity, specificity and speed of a magnetic resonance study, and potentially lead to new diagnostic testing methodologies. When paired with an appropriate pattern-recognition algorithm, MRF inherently suppresses measurement errors and can thus improve measurement accuracy.

The Influence of Motivating Operations on Generalization Probes of Specific Mands by Children with Autism

ERIC Educational Resources Information Center

Fragale, Christina L.; O'Reilly, Mark F.; Aguilar, Jeannie; Pierce, Nigel; Lang, Russell; Sigafoos, Jeff; Lancioni, Giulio

2012-01-01

We investigated the influence of motivating operations on the generalization of newly taught mands across settings and communication partners for 3 children with autism. Two conditions were implemented prior to generalization probes. In the first condition, participants were given access to a preferred item until they rejected the item (i.e.,…

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

ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.

PubMed

Sahoo, Sudhakar; Świtnicki, Michał P; Pedersen, Jakob Skou

2016-09-01

Recently, new RNA secondary structure probing techniques have been developed, including Next Generation Sequencing based methods capable of probing transcriptome-wide. These techniques hold great promise for improving structure prediction accuracy. However, each new data type comes with its own signal properties and biases, which may even be experiment specific. There is therefore a growing need for RNA structure prediction methods that can be automatically trained on new data types and readily extended to integrate and fully exploit multiple types of data. Here, we develop and explore a modular probabilistic approach for integrating probing data in RNA structure prediction. It can be automatically trained given a set of known structures with probing data. The approach is demonstrated on SHAPE datasets, where we evaluate and selectively model specific correlations. The approach often makes superior use of the probing data signal compared to other methods. We illustrate the use of ProbFold on multiple data types using both simulations and a small set of structures with both SHAPE, DMS and CMCT data. Technically, the approach combines stochastic context-free grammars (SCFGs) with probabilistic graphical models. This approach allows rapid adaptation and integration of new probing data types. ProbFold is implemented in C ++. Models are specified using simple textual formats. Data reformatting is done using separate C ++ programs. Source code, statically compiled binaries for x86 Linux machines, C ++ programs, example datasets and a tutorial is available from http://moma.ki.au.dk/prj/probfold/ : jakob.skou@clin.au.dk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Parallel gene analysis with allele-specific padlock probes and tag microarrays

PubMed Central

Banér, Johan; Isaksson, Anders; Waldenström, Erik; Jarvius, Jonas; Landegren, Ulf; Nilsson, Mats

2003-01-01

Parallel, highly specific analysis methods are required to take advantage of the extensive information about DNA sequence variation and of expressed sequences. We present a scalable laboratory technique suitable to analyze numerous target sequences in multiplexed assays. Sets of padlock probes were applied to analyze single nucleotide variation directly in total genomic DNA or cDNA for parallel genotyping or gene expression analysis. All reacted probes were then co-amplified and identified by hybridization to a standard tag oligonucleotide array. The technique was illustrated by analyzing normal and pathogenic variation within the Wilson disease-related ATP7B gene, both at the level of DNA and RNA, using allele-specific padlock probes. PMID:12930977

Termination of atrial spiral waves by traction into peripheral non 1:1 conducting regions - A numerical study.

PubMed

Rozner, Amit; Zlochiver, Sharon

2016-11-01

Atrial ablation has been recently utilized to treat atrial fibrillation (AF) by isolation or destruction of arrhythmia drivers. In chronic or persistent AF patients these drivers often consist of one or few rotors at unknown locations, and several ablations are commonly conducted before arrhythmia is terminated. However, the irreversible damage done to the tissue may lead to AF recurrence. We propose an alternative strategy to terminate rotor activity by its attraction into a non 1:1 conducting region. The feasibility of the method was numerically tested in 2D models of chronic AF human atrial tissue. Left-to-right gradients of either acetylcholine (ACh) or potassium conductance were employed to generate regions of 1:1 and non 1:1 conduction, characterized by their dominant frequency (DF) ratios. Spiral waves were established in the 1:1 conducting region and raster scanning was employed using a stimulating probe to attract the spiral wave tip. The probe was then linearly moved towards the boundary between the two regions. Successful attraction of spiral waves to the probe was demonstrated when the probe was <8mm from the spiral wave tip. Maximal traction velocity without loss of anchoring increased in a non-linear way with increasing values of ACh. Success rate of spiral wave termination was over 90% for regional DF ratios of as low as 1:1.2. Given that normally much higher ratios are measured in physiological atrial tissues, we envision this technique to provide a feasible, safer alternative to ablation procedures performed in persistent AF patients. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

The influence of probe level on the tuning of stimulus frequency otoacoustic emissions and behavioral test in human.

PubMed

Wang, Yao; Gong, Qin; Zhang, Tao

2016-05-10

Frequency selectivity (FS) of the auditory system is established at the level of the cochlea and it is important for the perception of complex sounds. Although direct measurements of cochlear FS require surgical preparation, it can also be estimated with the measurements of otoacoustic emissions or behavioral tests, including stimulus frequency otoacoustic emission suppression tuning curves (SFOAE STCs) or psychophysical tuning curves (PTCs). These two methods result in similar estimates of FS at low probe levels. As the compressive nonlinearity of cochlea is strongly dependent on the stimulus intensity, the sharpness of tuning curves which is relevant to the cochlear nonlinearity will change as a function of probe level. The present study aims to investigate the influence of different probe levels on the relationship between SFOAE STCs and PTCs. The study included 15 young subjects with normal hearing. SFOAE STCs and PTCs were recorded at low and moderate probe levels for frequencies centred at 1, 2, and 4 kHz. The ratio or the difference of the characteristic parameters between the two methods was calculated at each probe level. The effect of probe level on the ratio or the difference between the parameters of SFOAE STCs and PTCs was then statistically analysed. The tuning of SFOAE STCs was significantly positively correlated with the tuning of the PTCs at both low and moderate probe levels; yet, at the moderate probe level, the SFOAE STCs were consistently broader than the PTCs. The mean ratio of sharpness of tuning at low probe levels was constantly around 1 while around 1.5 at moderate probe levels. Probe level had a significant effect on the sharpness of tuning between the two methods of estimating FS. SFOAE STC seems a good alternative measurement of PTC for FS assessment at low probe levels. At moderate probe levels, SFOAE STC and PTC were not equivalent measures of the FS in terms of their bandwidths. Because SFOAE STCs are not biased by higher levels auditory processing, they may represent cochlear FS better than PTCs.

Factors Associated with Student Resilience: Perspectives of Graduates of Alternative Education Programs

ERIC Educational Resources Information Center

Zolkoski, Staci M.; Bullock, Lyndal M.; Gable, Robert A.

2016-01-01

Many students with emotional and behavioral disorders placed in alternative education settings lack resilience and are likely to experience failure in school and beyond without carefully designed intervention programs. Although researchers have examined both resilience in children and youth and their placement in alternative education settings,…

Vulnerable Youth: Identifying Their Need for Alternative Educational Settings.

ERIC Educational Resources Information Center

Zweig, Janine M.

This paper examines the extent to which alternative education can meet the needs of disconnected youth who are at risk of economic and social hardship. It summarizes characteristics of disconnected youth, risk factors associated with disconnection, and characteristics of students in selected alternative education settings. The most common factors…

Discovery of a novel calcium-sensitive fluorescent probe for α-ketoglutarate.

PubMed

Gan, Lin-Lin; Chen, Lin-Hai; Nan, Fa-Jun

2017-12-01

α-Ketoglutarate (α-KG), a pivotal metabolite in energy metabolism, has been implicated in nonalcoholic fatty liver disease (NAFLD) and several cancers. It is recently proposed that plasma α-KG is a surrogate biomarker of NAFLD. Here, we report the development of a novel "turn-on" chemosensor for α-KG that contains a coumarin moiety as a fluorophore. Using benzothiazole-coumarin (BTC) as inspiration, we designed a probe for calcium ion recognition that possesses a unique fluorophore compared with previously reported probes for α-KG measurement. This chemosensor is based on the specific Schiff base reaction and the calcium ion recognition property of the widely used calcium indicator BTC. The probe was synthesized, and a series of parallel experiments were conducted to optimize the chemical recognition process. Compared to the initial weak fluorescence, a remarkable 7.6-fold enhancement in fluorescence intensity (I/I 0 at 495 nm) was observed for the conditions in which the probe (1 μmol/L), α-KG (50 μmol/L), and Ca 2+ (100 μmol/L) were incubated at 30 °C in EtOH. The probe displayed good selectivity for α-KG even in an environment with an abundance of amino acids and other interfering species such as glutaric acid. We determined that the quantitative detection range of α-KG in EtOH was between 5 and 50 μmol/L. Finally, probe in serum loaded with α-KG (10 mmol/L) showed a 7.4-fold fluorescence enhancement. In summary, a novel probe for detecting the biomarker α-KG through a typical Schiff base reaction has been discovered. With further optimization, this probe may be a good alternative for detecting the physiological metabolite α-KG.

A Coaxial Dielectric Probe Technique for Distinguishing Tooth Enamel from Dental Resin

PubMed Central

Williams, Benjamin B.; Geimer, Shireen D.; Flood, Ann B.; Swartz, Harold M.

2016-01-01

For purposes of biodosimetry in the event of a large scale radiation disaster, one major and very promising point-of contact device is assessing dose using tooth enamel. This technique utilizes the capabilities of electron paramagnetic resonance to measure free radicals and other unpaired electron species, and the fact that the deposition of energy from ionizing radiation produces free radicals in most materials. An important stipulation for this strategy is that the measurements, need to be performed on a central incisor that is basically intact, i.e. which has an area of enamel surface that is as large as the probing tip of the resonator that is without decay or restorative care that replaces the enamel. Therefore, an important consideration is how to quickly assess whether the tooth has sufficient enamel to be measured for dose and whether there is resin present on the tooth being measured and to be able to characterize the amount of surface that is impacted. While there is a relatively small commercially available dielectric probe which could be used in this context, it has several disadvantages for the intended use. Therefore, a smaller, 1.19mm diameter 50 ohm, open-ended, coaxial dielectric probe has been developed as an alternative. The performance of the custom probe was validated against measurement results of known standards. Measurements were taken of multiple teeth enamel and dental resin samples using both probes. While the probe contact with the teeth samples was imperfect and added to measurement variability, the inherent dielectric contrast between the enamel and resin was sufficient that the probe measurements could be used as a robust means of distinguishing the two material types. The smaller diameter probe produced markedly more definitive results in terms of distinguishing the two materials. PMID:27182531

Accelerated Photobleaching of a Cyanine Dye in the Presence of a Ternary Target DNA, PNA Probe, Dye Catalytic Complex: A Molecular Diagnostic

PubMed Central

Wang, M.; Holmes-Davis, R.; Rafinski, Z.; Jedrzejewska, B.; Choi, K. Y.; Zwick, M.; Bupp, C.; Izmailov, A.; Paczkowski, J.; Warner, B.; Koshinsky, H.

2009-01-01

In many settings, molecular testing is needed but unavailable due to complexity and cost. Simple, rapid, and specific DNA detection technologies would provide important alternatives to existing detection methods. Here we report a novel, rapid nucleic acid detection method based on the accelerated photobleaching of the light-sensitive cyanine dye, 3,3′-diethylthiacarbocyanine iodide (DiSC2(3) I−), in the presence of a target genomic DNA and a complementary peptide nucleic acid (PNA) probe. On the basis of the UV–vis, circular dichroism, and fluorescence spectra of DiSC2(3) with PNA–DNA oligomer duplexes and on characterization of a product of photolysis of DiSC2(3) I−, a possible reaction mechanism is proposed. We propose that (1) a novel complex forms between dye, PNA, and DNA, (2) this complex functions as a photosensitizer producing 1O2, and (3) the 1O2 produced promotes photobleaching of dye molecules in the mixture. Similar cyanine dyes (DiSC3(3), DiSC4(3), DiSC5(3), and DiSCpy(3)) interact with preformed PNA–DNA oligomer duplexes but do not demonstrate an equivalent accelerated photobleaching effect in the presence of PNA and target genomic DNA. The feasibility of developing molecular diagnostic assays based on the accelerated photobleaching (the smartDNA assay) that results from the novel complex formed between DiSC2(3) and PNA–DNA is under way. PMID:19231844

Kagome fiber based ultrafast laser microsurgery probe delivering micro-Joule pulse energies

PubMed Central

Subramanian, Kaushik; Gabay, Ilan; Ferhanoğlu, Onur; Shadfan, Adam; Pawlowski, Michal; Wang, Ye; Tkaczyk, Tomasz; Ben-Yakar, Adela

2016-01-01

We present the development of a 5 mm, piezo-actuated, ultrafast laser scalpel for fast tissue microsurgery. Delivery of micro-Joules level energies to the tissue was made possible by a large, 31 μm, air-cored inhibited-coupling Kagome fiber. We overcome the fiber’s low NA by using lenses made of high refractive index ZnS, which produced an optimal focusing condition with 0.23 NA objective. The optical design achieved a focused laser spot size of 4.5 μm diameter covering a 75 × 75 μm2 scan area in a miniaturized setting. The probe could deliver the maximum available laser power, achieving an average fluence of 7.8 J/cm2 on the tissue surface at 62% transmission efficiency. Such fluences could produce uninterrupted, 40 μm deep cuts at translational speeds of up to 5 mm/s along the tissue. We predicted that the best combination of speed and coverage exists at 8 mm/s for our conditions. The onset of nonlinear absorption in ZnS, however, limited the probe’s energy delivery capabilities to 1.4 μJ for linear operation at 1.5 picosecond pulse-widths of our fiber laser. Alternatives like broadband CaF2 crystals should mitigate such nonlinear limiting behavior. Improved opto-mechanical design and appropriate material selection should allow substantially higher fluence delivery and propel such Kagome fiber-based scalpels towards clinical translation. PMID:27896003

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

NeuroMEMS: Neural Probe Microtechnologies

PubMed Central

HajjHassan, Mohamad; Chodavarapu, Vamsy; Musallam, Sam

2008-01-01

Neural probe technologies have already had a significant positive effect on our understanding of the brain by revealing the functioning of networks of biological neurons. Probes are implanted in different areas of the brain to record and/or stimulate specific sites in the brain. Neural probes are currently used in many clinical settings for diagnosis of brain diseases such as seizers, epilepsy, migraine, Alzheimer's, and dementia. We find these devices assisting paralyzed patients by allowing them to operate computers or robots using their neural activity. In recent years, probe technologies were assisted by rapid advancements in microfabrication and microelectronic technologies and thus are enabling highly functional and robust neural probes which are opening new and exciting avenues in neural sciences and brain machine interfaces. With a wide variety of probes that have been designed, fabricated, and tested to date, this review aims to provide an overview of the advances and recent progress in the microfabrication techniques of neural probes. In addition, we aim to highlight the challenges faced in developing and implementing ultra-long multi-site recording probes that are needed to monitor neural activity from deeper regions in the brain. Finally, we review techniques that can improve the biocompatibility of the neural probes to minimize the immune response and encourage neural growth around the electrodes for long term implantation studies. PMID:27873894

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.

Design and validation of the ball-pen probe for measurements in a low-temperature magnetized plasma

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

Bousselin, G.; Cavalier, J.; Pautex, J. F.

Ball-pen probes have been used in fusion devices for direct measurements of the plasma potential. Their application in low-temperature magnetized plasma devices is still subject to studies. In this context, a ball-pen probe has been recently implemented on the linear plasma device Mirabelle. Produced by a thermionic discharge, the plasma is characterized by a low electron temperature and a low density. Plasma confinement is provided by an axial magnetic field that goes up to 100 mT. The principle of the ball-pen probe is to adjust the saturation current ratio to 1 by reducing the electron current contribution. In that case,more » the floating potential of the probe is close to the plasma potential. A thorough study of the ball-pen probe operation is performed for different designs of the probe over a large set of plasma conditions. Comparisons between ball-pen, Langmuir, and emissive probes are conducted in the same plasma conditions. The ball-pen probe is successfully measuring the plasma potential in these specific plasma conditions only if an adapted electronics and an adapted probe size to the plasma characteristic lengths ({lambda}{sub D}, {rho}{sub ce}) are used.« less

Preassembled Fluorescent Multivalent Probes for the Imaging of Anionic Membranes.

PubMed

Roland, Felicia M; Peck, Evan M; Rice, Douglas R; Smith, Bradley D

2017-04-19

A new self-assembly process known as Synthavidin (synthetic avidin) technology was used to prepare targeted probes for near-infrared fluorescence imaging of anionic membranes and cell surfaces, a hallmark of many different types of disease. The probes were preassembled by threading a tetralactam macrocycle with six appended zinc-dipicolylamine (ZnDPA) targeting units onto a linear scaffold with one or two squaraine docking stations to produce hexavalent or dodecavalent fluorescent probes. A series of liposome titration experiments showed that multivalency promoted stronger membrane binding by the dodecavalent probe. In addition, the dodecavalent probe exhibited turn-on fluorescence due to probe unfolding during fluorescence microscopy at the membrane surface. However, the dodecavalent probe also had a higher tendency to self-aggregate after membrane binding, leading to probe self-quenching under certain conditions. This self-quenching effect was apparent during fluorescence microscopy experiments that recorded low fluorescence intensity from anionic dead and dying mammalian cells that were saturated with the dodecavalent probe. Conversely, probe self-quenching was not a factor with anionic microbial surfaces, where there was intense fluorescence staining by the dodecavalent probe. A successful set of rat tumor imaging experiments confirmed that the preassembled probes have sufficient mechanical stability for effective in vivo imaging. The results demonstrate the feasibility of this general class of preassembled fluorescent probes for multivalent targeting, but fluorescence imaging performance depends on the specific physical attributes of the biomarker target, such as the spatial distance between different copies of the biomarker and the propensity of the probe-biomarker complex to self-aggregate.

Methods, compounds and systems for detecting a microorganism in a sample

DOEpatents

Colston, Jr, Bill W.; Fitch, J. Patrick; Gardner, Shea N.; Williams, Peter L.; Wagner, Mark C.

2016-09-06

Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.

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].

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.

Mind-Sets for a Happier Life.

ERIC Educational Resources Information Center

Webber, Jo

1997-01-01

Discusses how irrational beliefs can be disputed and replaced with alternative, healthier mind-sets. Focuses on cognitive restructuring theory, changing unhealthy thoughts, disputation, semantics, and adopting alternative mind-sets, such as life is bizarre and funny. Claims that using words that indicate preferences and possibilities can help…

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.

An alternative method to quantify 2-MIB producing cyanobacteria in drinking water reservoirs: Method development and field applications.

PubMed

Chiu, Yi-Ting; Yen, Hung-Kai; Lin, Tsair-Fuh

2016-11-01

2-Methylisoborneol (2-MIB) is a commonly detected cyanobacterial odorant in drinking water sources in many countries. To provide safe and high-quality water, development of a monitoring method for the detection of 2-MIB-synthesis (mibC) genes is very important. In this study, new primers MIBS02F/R intended specifically for the mibC gene were developed and tested. Experimental results show that the MIBS02F/R primer set was able to capture 13 2-MIB producing cyanobacterial strains grown in the laboratory, and to effectively amplify the targeted DNA region from 17 2-MIB-producing cyanobacterial strains listed in the literature. The primers were further coupled with a TaqMan probe to detect 2-MIB producers in 29 drinking water reservoirs (DWRs). The results showed statistically significant correlations between mibC genes and 2-MIB concentrations for the data from each reservoir (R 2 =0.413-0.998; p<0.05), from all reservoirs in each of the three islands (R 2 =0.302-0.796; p<0.01), and from all data of the three islands (R 2 =0.473-0.479; p<0.01). The results demonstrate that the real-time PCR can be an alternative method to provide information to managers of reservoirs and water utilities facing 2-MIB-related incidents. Copyright © 2016 Elsevier Inc. All rights reserved.

Methodologies for Salmonella enterica subsp. enterica Subtyping: Gold Standards and Alternatives▿

PubMed Central

Wattiau, Pierre; Boland, Cécile; Bertrand, Sophie

2011-01-01

For more than 80 years, subtyping of Salmonella enterica has been routinely performed by serotyping, a method in which surface antigens are identified based on agglutination reactions with specific antibodies. The serotyping scheme, which is continuously updated as new serovars are discovered, has generated over time a data set of the utmost significance, allowing long-term epidemiological surveillance of Salmonella in the food chain and in public health control. Conceptually, serotyping provides no information regarding the phyletic relationships inside the different Salmonella enterica subspecies. In epidemiological investigations, identification and tracking of salmonellosis outbreaks require the use of methods that can fingerprint the causative strains at a taxonomic level far more specific than the one achieved by serotyping. During the last 2 decades, alternative methods that could successfully identify the serovar of a given strain by probing its DNA have emerged, and molecular biology-based methods have been made available to address phylogeny and fingerprinting issues. At the same time, accredited diagnostics have become increasingly generalized, imposing stringent methodological requirements in terms of traceability and measurability. In these new contexts, the hand-crafted character of classical serotyping is being challenged, although it is widely accepted that classification into serovars should be maintained. This review summarizes and discusses modern typing methods, with a particular focus on those having potential as alternatives for classical serotyping or for subtyping Salmonella strains at a deeper level. PMID:21856826

Variability sensitivity of dynamic texture based recognition in clinical CT data

NASA Astrophysics Data System (ADS)

Kwitt, Roland; Razzaque, Sharif; Lowell, Jeffrey; Aylward, Stephen

2014-03-01

Dynamic texture recognition using a database of template models has recently shown promising results for the task of localizing anatomical structures in Ultrasound video. In order to understand its clinical value, it is imperative to study the sensitivity with respect to inter-patient variability as well as sensitivity to acquisition parameters such as Ultrasound probe angle. Fully addressing patient and acquisition variability issues, however, would require a large database of clinical Ultrasound from many patients, acquired in a multitude of controlled conditions, e.g., using a tracked transducer. Since such data is not readily attainable, we advocate an alternative evaluation strategy using abdominal CT data as a surrogate. In this paper, we describe how to replicate Ultrasound variabilities by extracting subvolumes from CT and interpreting the image material as an ordered sequence of video frames. Utilizing this technique, and based on a database of abdominal CT from 45 patients, we report recognition results on an organ (kidney) recognition task, where we try to discriminate kidney subvolumes/videos from a collection of randomly sampled negative instances. We demonstrate that (1) dynamic texture recognition is relatively insensitive to inter-patient variation while (2) viewing angle variability needs to be accounted for in the template database. Since naively extending the template database to counteract variability issues can lead to impractical database sizes, we propose an alternative strategy based on automated identification of a small set of representative models.

Experimental evaluation of the resolution improvement provided by a silicon PET probe.

PubMed

Brzeziński, K; Oliver, J F; Gillam, J; Rafecas, M; Studen, A; Grkovski, M; Kagan, H; Smith, S; Llosá, G; Lacasta, C; Clinthorne, N H

2016-09-01

A high-resolution PET system, which incorporates a silicon detector probe into a conventional PET scanner, has been proposed to obtain increased image quality in a limited region of interest. Detailed simulation studies have previously shown that the additional probe information improves the spatial resolution of the reconstructed image and increases lesion detectability, with no cost to other image quality measures. The current study expands on the previous work by using a laboratory prototype of the silicon PET-probe system to examine the resolution improvement in an experimental setting. Two different versions of the probe prototype were assessed, both consisting of a back-to-back pair of 1-mm thick silicon pad detectors, one arranged in 32 × 16 arrays of 1.4 mm × 1.4 mm pixels and the other in 40 × 26 arrays of 1.0 mm × 1.0 mm pixels. Each detector was read out by a set of VATAGP7 ASICs and a custom-designed data acquisition board which allowed trigger and data interfacing with the PET scanner, itself consisting of BGO block detectors segmented into 8 × 6 arrays of 6 mm × 12 mm × 30 mm crystals. Limited-angle probe data was acquired from a group of Na-22 point-like sources in order to observe the maximum resolution achievable using the probe system. Data from a Derenzo-like resolution phantom was acquired, then scaled to obtain similar statistical quality as that of previous simulation studies. In this case, images were reconstructed using measurements of the PET ring alone and with the inclusion of the probe data. Images of the Na-22 source demonstrated a resolution of 1.5 mm FWHM in the probe data, the PET ring resolution being approximately 6 mm. Profiles taken through the image of the Derenzo-like phantom showed a clear increase in spatial resolution. Improvements in peak-to-valley ratios of 50% and 38%, in the 4.8 mm and 4.0 mm phantom features respectively, were observed, while previously unresolvable 3.2 mm features were brought to light by the addition of the probe. These results support the possibility of improving the image resolution of a clinical PET scanner using the silicon PET-probe.

Alternative Placements in Initial Teacher Education: An Evaluation

ERIC Educational Resources Information Center

Purdy, Noel; Gibson, Ken

2008-01-01

The paper evaluates a programme of short alternative placements for final-year B.Ed. students in Northern Ireland, which aims to broaden student teachers' experience and develop their transferable skills. The alternative placement programme is set first in an international context of evolving pre-service field placements and then set in a local…

Comparing Panelists' Understanding of Standard Setting across Multiple Levels of an Alternate Science Assessment

ERIC Educational Resources Information Center

Hansen, Mary A.; Lyon, Steven R.; Heh, Peter; Zigmond, Naomi

2013-01-01

Large-scale assessment programs, including alternate assessments based on alternate achievement standards (AA-AAS), must provide evidence of technical quality and validity. This study provides information about the technical quality of one AA-AAS by evaluating the standard setting for the science component. The assessment was designed to have…

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. I. Covalent immobilization of oligonucleotide probes onto the nylon].

PubMed

Dmitrienko, E V; Pyshnaia, I A; Pyshnyĭ, D V

2010-01-01

The features of UV-induced immobilization of oligonucleotides on a nylon membranes and the effectiveness of enzymatic labeling of immobilized probes at heterophase detection of nucleic acids are studied. Short terminal oligothymidilate (up to 10 nt) sequences are suggested to attach to the probe via a flexible ethylene glycol based linker. The presence of such fragment enhances the intensity of immobilization and reduces UV-dependent degradation of the targeted (sequence-specific) part of the probe by reducing the dose needed for the immobilization of DNA. The optimum dose of UV-irradiation is determined to be ~0.4 J/cm(2) at the wavelength 254 nm. This dose provides high level of hybridization signal for immobilized probes with various nucleotide composition of the sequence specific moiety. The amide groups of the polyamide are shown to play the key role in the photoinduced immobilization of nucleic acids, whereas the primary amino groups in the structure of PA is not the center responsible for the covalent binding of DNA by UV-irradiation, as previously believed. Various additives in the soaking solution during the membrane of UV-dependent immobilization of probes are shown to influence its effectiveness. The use of alternative to UV-irradiation system of radical generation are shown to provide the immobilization of oligonucleotides onto the nylon membrane.

Homogeneous real-time detection of single-nucleotide polymorphisms by strand displacement amplification on the BD ProbeTec ET system.

PubMed

Wang, Sha-Sha; Thornton, Keith; Kuhn, Andrew M; Nadeau, James G; Hellyer, Tobin J

2003-10-01

The BD ProbeTec ET System is based on isothermal strand displacement amplification (SDA) of target nucleic acid coupled with homogeneous real-time detection using fluorescent probes. We have developed a novel, rapid method using this platform that incorporates a universal detection format for identification of single-nucleotide polymorphisms (SNPs) and other genotypic variations. The system uses a common pair of fluorescent Detector Probes in conjunction with unlabeled allele-specific Adapter Primers and a universal buffer chemistry to permit analysis of multiple SNP loci under generic assay conditions. We used Detector Probes labeled with different dyes to facilitate differentiation of two alternative alleles in a single reaction with no postamplification manipulation. We analyzed six SNPs within the human beta(2)-adrenergic receptor (beta(2)AR) gene, using whole blood, buccal swabs, and urine samples, and compared results with those obtained by DNA sequencing. Unprocessed whole blood was successfully genotyped with as little as 0.1-1 micro L of sample per reaction. All six beta(2)AR assays were able to accommodate >/==" BORDER="0">20 micro L of unprocessed whole blood. For the 14 individuals tested, genotypes determined with the six beta(2)AR assays agreed with DNA sequencing results. SDA-based allelic differentiation on the BD ProbeTec ET System can detect SNPs rapidly, using whole blood, buccal swabs, or urine.

Comparison of marginal bleeding using a periodontal probe or an interdental brush as indicators of gingivitis.

PubMed

Hofer, D; Sahrmann, P; Attin, T; Schmidlin, P R

2011-08-01

To compare the use of interdental brushes to a periodontal probe in assessing marginal bleeding, in natural gingivitis. Sixty-four consecutive volunteers presenting with gingival inflammation were recruited at their semi-annual recall appointments for this study. All had ≥50% papillary height and no pocketing that exceeded 4 mm. Contra-lateral quadrants (1 & 3 or 2 & 4) were randomly tested for bleeding with one pass-through with an interdental brush or with a periodontal probe inserted 2 mm into the gingival sulcus. The presence or absence of both bleeding and plaque were then recorded. Correlation coefficients were calculated for the interdental brushes and the periodontal probe, and the plaque and bleeding scores. The periodontal probe and the interdental brushes showed mean average bleeding scores of 47.39% and 45.74% respectively. The correlation coefficient for the two methods was 0.73 (P < 0.0001). No correlation between plaque and bleeding was found. Interdental brushes can be considered a valid alternative to a periodontal probe in assessing marginal bleeding in gingivitis patients. An interdental brush, sized correctly for each interdental space, is easy to handle, atraumatic to the papillae and will allow gingivitis patients to monitor their own progress, while at the same time performing a beneficial oral hygiene procedure and removing any interdental plaque present. © 2010 John Wiley & Sons A/S.

A new multimodality system for quantitative in vivo studies in small animals: combination of nuclear magnetic resonance and the radiosensitive /spl beta/-MicroProbe

NASA Astrophysics Data System (ADS)

Desbree, A.; Pain, F.; Gurden, H.; Pinot, L.; Grenier, D.; Zimmer, L.; Mastrippolito, R.; Laniece, P.

2005-10-01

Elucidating complex physiological mechanisms in small animal in vivo requires the development of new investigatory techniques including imaging with multiple modalities. Combining exploratory techniques has the tremendous advantage to record simultaneously complementary parameters on the same animal. In this field, an exciting challenge remains in the combination of nuclear magnetic resonance (NMR) and positron emission tomography (PET) since small animals studies are limited by strict technical constraints in vivo. Coupling NMR with a radiosensitive /spl beta/-MicroProbe offers therefore an interesting technical alternative. To assess the feasibility of this new dual-modality system, we designed theoretical and experimental approaches to test the ability of the /spl beta/-Microprobe to quantify radioactivity concentration in an intense magnetic field. In an initial step, simulations were carried out using Geant4. First, we evaluated the influence of a magnetic field on the probe detection volume. Then, the detection sensitivity and energy response of the probe were quantified. In a second step, experiments were run within a 7-T magnet to confirm our simulations results. We showed that using the probe in magnetic fields leads to a slight attenuation in sensitivity and an increase of the scintillation light yield. These data demonstrate the feasibility of combining NMR to the /spl beta/-MicroProbe.

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

Application of Time Domain Reflectometers to Urban Settings

EPA Science Inventory

Time domain reflectometers (TDRs) are in-situ monitoring probes that produce a temperature-compensated signal proportional to soil moisture content of the surrounding material when calibrated to a particular media. Typically used in agricultural settings, TDRs may also be applied...

Molecular mapping of chromosomes 17 and X

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

Barker, D.F.

1991-01-15

Progress toward the construction of high density genetic maps of chromosomes 17 and X has been made by isolating and characterizing a relatively large set of polymorphic probes for each chromosome and using these probes to construct genetic maps. We have mapped the same polymorphic probes against a series of chromosome breakpoints on X and 17. The probes could be assigned to over 30 physical intervals on the X chromosome and 7 intervals on 17. In many cases, this process resulted in improved characterization of the relative locations of the breakpoints with respect to each other and the definition ofmore » new physical intervals. The strategy for isolation of the polymorphic clones utilized chromosome specific libraries of 1--15 kb segments from each of the two chromosomes. From these libraries, clones were screened for those detecting restriction fragment length polymorphisms. The markers were further characterized, the chromosomal assignments confirmed and in most cases segments of the original probes were subcloned into plasmids to produce probes with improved signal to noise ratios for use in the genetic marker studies. The linkage studies utilize the CEPH reference families and other well-characterized families in our collection which have been used for genetic disease linkage work. Preliminary maps and maps of portions of specific regions of 17 and X are provided. We have nearly completed a map of the 1 megabase Mycoplasma arthritidis genome by applying these techniques to a lambda phage library of its genome. We have found bit mapping to be an efficient means to organize a contiguous set of overlapping clones from a larger genome.« less

Molecular mapping of chromosomes 17 and X. Progress report

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

Barker, D.F.

1991-01-15

Progress toward the construction of high density genetic maps of chromosomes 17 and X has been made by isolating and characterizing a relatively large set of polymorphic probes for each chromosome and using these probes to construct genetic maps. We have mapped the same polymorphic probes against a series of chromosome breakpoints on X and 17. The probes could be assigned to over 30 physical intervals on the X chromosome and 7 intervals on 17. In many cases, this process resulted in improved characterization of the relative locations of the breakpoints with respect to each other and the definition ofmore » new physical intervals. The strategy for isolation of the polymorphic clones utilized chromosome specific libraries of 1--15 kb segments from each of the two chromosomes. From these libraries, clones were screened for those detecting restriction fragment length polymorphisms. The markers were further characterized, the chromosomal assignments confirmed and in most cases segments of the original probes were subcloned into plasmids to produce probes with improved signal to noise ratios for use in the genetic marker studies. The linkage studies utilize the CEPH reference families and other well-characterized families in our collection which have been used for genetic disease linkage work. Preliminary maps and maps of portions of specific regions of 17 and X are provided. We have nearly completed a map of the 1 megabase Mycoplasma arthritidis genome by applying these techniques to a lambda phage library of its genome. We have found bit mapping to be an efficient means to organize a contiguous set of overlapping@ clones from a larger genome.« less

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 Exploration of Indigenous Knowledge Related to Physics Concepts Held by Senior Citizens in Chókwé, Mozambique

NASA Astrophysics Data System (ADS)

Muambalane Baquete, Aguiar; Grayson, Diane; Vasco Mutimucuio, Inocente

2016-01-01

Indigenous knowledge is at risk of being lost in many parts of the world. It is important to find ways to preserve it for both cultural and practical reasons, since it is often well-suited to addressing local needs using available resources. If indigenous knowledge can be incorporated into school science curricula, it can also provide familiar contexts within which to learn scientific concepts, as well as helping the younger generation to recognise its value. The purpose of this study was to identify indigenous knowledge that could be related to physics concepts, with a view to integrating it into school curricula. Twenty-nine senior citizens from Chókwé, a rural village in Mozambique, volunteered to participate in two sets of in-depth interviews. The first set of interviews was individual and unstructured in order to explore which aspects of indigenous knowledge might be related to physics concepts. The second set was semi-structured and conducted in small groups in order to probe participants' understanding and application of the identified physics concepts. The results showed that participants had indigenous knowledge that was useful to them in their daily lives and that were applications of thermal physics, static electricity and mechanics concepts. In some cases participants' explanations were aligned to physics explanations, in some cases they were similar to students' alternative conceptions identified in the literature, and in other cases they referred to supernatural phenomena.

A Literature Review of Research Quality and Effective Practices in Alternative Education Settings

ERIC Educational Resources Information Center

Flower, Andrea; McDaniel, Sara C.; Jolivette, Kristine

2011-01-01

Effective behavioral practices for students with emotional/behavioral disorders (E/BD) are critical. Students with E/BD are often served in alternative education (AE) settings due to behavior that cannot be supported in a typical school setting or due to court adjudication based on delinquent activity. Like other settings for students with E/BD,…

An ergonomic handheld ultrasound probe providing contact forces and pose information.

PubMed

Yohan Noh; Housden, R James; Gomez, Alberto; Knight, Caroline; Garcia, Francesca; Hongbin Liu; Razavi, Reza; Rhode, Kawal; Althoefer, Kaspar

2015-08-01

This paper presents a handheld ultrasound probe which is integrated with sensors to measure force and pose (position/orientation) information. Using an integrated probe like this, one can relate ultrasound images to spatial location and create 3D ultrasound maps. The handheld device can be used by sonographers and also easily be integrated with robot arms for automated sonography. The handheld device is ergonomically designed; rapid attachment and removal of the ultrasound transducer itself is possible using easy-to-operate clip mechanisms. A cable locking mechanism reduces the impact that gravitational and other external forces have (originating from data and power supply cables connected to the probe) on our measurements. Gravitational errors introduced by the housing of the probe are compensated for using knowledge of the housing geometry and the integrated pose sensor that provides us with accurate orientation information. In this paper, we describe the handheld probe with its integrated force/pose sensors and our approach to gravity compensation. We carried out a set of experiments to verify the feasibility of our approach to obtain accurate spatial information of the handheld probe.

EXTASE - An Experimental Thermal Probe For Applications In Snow Research And Earth Sciences

NASA Astrophysics Data System (ADS)

Schröer, K.; Seiferlin, K.; Marczewski, W.; Spohn, T.

EXTASE is a spin-off project from the Rosetta Lander (MUPUS) thermal probe, both funded by DLR. The application of this probe is to be tested in different fields e.g. in snow research, agriculture, permafrost etc. The probe penetrates the surface ca. 32 cm and provides a temperature profile (16 sensors) and thermal conductivity profile of the penetrated layer. The main advantages of the probe in comparison to common temperature profile measurement methods are: -no need to excavate material -minimized influence of the probe on the temperature field -minimized modification of the microstructure of the studied medium. Presently we are concentrating on agriculture (soil humidity) and snow research. Fur- ther applications could be: monitoring waste deposits and the heat set free by decom- position, volcanology and ground truth for remote sensing. We present the general concept of the probe, some temperature profiles measured during a field measurement campaign to demonstrate the capability of this new technique and first experiments made in the laboratory. First attempts to calculate thermal diffusivity and conductivity from the data are also given.

Measuring the lateral charge-carrier mobility in metal-insulator-semiconductor capacitors via Kelvin-probe.

PubMed

Milotti, Valeria; Pietsch, Manuel; Strunk, Karl-Philipp; Melzer, Christian

2018-01-01

We report a Kelvin-probe method to investigate the lateral charge-transport properties of semiconductors, most notably the charge-carrier mobility. The method is based on successive charging and discharging of a pre-biased metal-insulator-semiconductor stack by an alternating voltage applied to one edge of a laterally confined semiconductor layer. The charge carriers spreading along the insulator-semiconductor interface are directly measured by a Kelvin-probe, following the time evolution of the surface potential. A model is presented, describing the device response for arbitrary applied biases allowing the extraction of the lateral charge-carrier mobility from experimentally measured surface potentials. The method is tested using the organic semiconductor poly(3-hexylthiophene), and the extracted mobilities are validated through current voltage measurements on respective field-effect transistors. Our widely applicable approach enables robust measurements of the lateral charge-carrier mobility in semiconductors with weak impact from the utilized contact materials.

Measuring the lateral charge-carrier mobility in metal-insulator-semiconductor capacitors via Kelvin-probe

NASA Astrophysics Data System (ADS)

Milotti, Valeria; Pietsch, Manuel; Strunk, Karl-Philipp; Melzer, Christian

2018-01-01

We report a Kelvin-probe method to investigate the lateral charge-transport properties of semiconductors, most notably the charge-carrier mobility. The method is based on successive charging and discharging of a pre-biased metal-insulator-semiconductor stack by an alternating voltage applied to one edge of a laterally confined semiconductor layer. The charge carriers spreading along the insulator-semiconductor interface are directly measured by a Kelvin-probe, following the time evolution of the surface potential. A model is presented, describing the device response for arbitrary applied biases allowing the extraction of the lateral charge-carrier mobility from experimentally measured surface potentials. The method is tested using the organic semiconductor poly(3-hexylthiophene), and the extracted mobilities are validated through current voltage measurements on respective field-effect transistors. Our widely applicable approach enables robust measurements of the lateral charge-carrier mobility in semiconductors with weak impact from the utilized contact materials.

Measuring the mechanical properties of molecular conformers

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

Results of an investigation to determine local flow characteristics at the air data probe locations using an 0.030-scale model (45-0) of the space shuttle vehicle orbiter configuration 140A/B (modified) in the NASA Ames Research Center unitary plan wind tunnel (OA161, A, B, C), volume 1

NASA Technical Reports Server (NTRS)

Nichols, M. E.

1976-01-01

Results are presented of wind tunnel test 0A161 of a 0.030-scale model 45-0 of the configuration 140A/B (modified) space shuttle vehicle orbiter in the NASA Ames Research Center Unitary Plan Wind Tunnel facilities. The purpose of this test was to determine local total and static pressure environments for the air data probe locations and relative effectiveness of alternate flight-test probe configurations. Testing was done in the Mach number range from 0.30 to 3.5. Angle of attack was varied from -8 to 25 degrees while sideslip varied between -8 and 8 degrees.

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

Hauer, John F.; Mittelstadt, William; Martin, Kenneth E.

During 2005 and 2006 the Western Electricity Coordinating Council (WECC) performed three major tests of western system dynamics. These tests used a Wide Area Measurement System (WAMS) based primarily on Phasor Measurement Units (PMUs) to determine response to events including the insertion of the 1400-MW Chief Joseph braking resistor, probing signals, and ambient events. Test security was reinforced through real-time analysis of wide area effects, and high-quality data provided dynamic profiles for interarea modes across the entire western interconnection. The tests established that low-level optimized pseudo-random ±20-MW probing with the Pacific DC Intertie (PDCI) roughly doubles the apparent noise thatmore » is natural to the power system, providing sharp dynamic information with negligible interference to system operations. Such probing is an effective alternative to use of the 1400-MW Chief Joseph dynamic brake, and it is under consideration as a standard means for assessing dynamic security.« less

Subsurface Ice Probe

NASA Technical Reports Server (NTRS)

Hecht, Michael; Carsey, Frank

2005-01-01

The subsurface ice probe (SIPR) is a proposed apparatus that would bore into ice to depths as great as hundreds of meters by melting the ice and pumping the samples of meltwater to the surface. Originally intended for use in exploration of subsurface ice on Mars and other remote planets, the SIPR could also be used on Earth as an alternative to coring, drilling, and melting apparatuses heretofore used to sample Arctic and Antarctic ice sheets. The SIPR would include an assembly of instrumentation and electronic control equipment at the surface, connected via a tether to a compact assembly of boring, sampling, and sensor equipment in the borehole (see figure). Placing as much equipment as possible at the surface would help to attain primary objectives of minimizing power consumption, sampling with high depth resolution, and unobstructed imaging of the borehole wall. To the degree to which these requirements would be satisfied, the SIPR would offer advantages over the aforementioned ice-probing systems.

Periodically modulated dark states

NASA Astrophysics Data System (ADS)

Han, Yingying; Zhang, Jun; Zhang, Wenxian

2018-04-01

Phenomena of electromagnetically induced transparency (PEIT) may be interpreted by the Autler-Townes Splitting (ATS), where the coupled states are split by the coupling laser field, or by the quantum destructive interference (QDI), where the atomic phases caused by the coupling laser and the probe laser field cancel. We propose modulated experiments to explore the PEIT in an alternative way by periodically modulating the coupling and the probe fields in a Λ-type three-level system initially in a dark state. Our analytical and numerical results rule out the ATS interpretation and show that the QDI interpretation is more appropriate for the modulated experiments. Interestingly, dark state persists in the double-modulation situation where control and probe fields never occur simultaneously, which is significant difference from the traditional dark state condition. The proposed experiments are readily implemented in atomic gases, artificial atoms in superconducting quantum devices, or three-level meta-atoms in meta-materials.

A highly selective and sensitive photoswitchable fluorescent probe for Hg2+ based on bisthienylethene-rhodamine 6G dyad and for live cells imaging

NASA Astrophysics Data System (ADS)

Xu, Li; Wang, Sheng; Lv, Yingnian; Son, Young-A.; Cao, Derong

2014-07-01

A new photochromic diarylethene derivative bearing rhodamine 6G dimmer as a fluorescent molecular probe is designed and synthesized successfully. All the compounds are characterized by nuclear magnetic resonance and mass spectrometry. The bisthienylethene-rhodamine 6G dyad exhibit excellent phtochromism with reversibly color and fluorescence changes alternating irradiation with ultraviolet and visible light. Upon addition of Hg2+, its color changes from colorless to red and its fluorescence is remarkably enhanced. Whereas other ions including K+, Na+, Ca2+, Mg2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Mn2+, Pb2+, Ni2+, Fe3+, Al3+, Cr3+ and so on induce basically no spectral changes, which constitute a highly selective and sensitive photoswitchable fluorescent probe toward Hg2+. Furthermore, by means of laser confocal scanning microscopy experiments, it is demonstrated that this probe can be applied for live cell imaging and monitoring Hg2+ in living lung cancer cells with satisfying results, which shows its value of potential application in environmental and biological systems.

Line Intensity Mapping during the Epoch of Reionization

NASA Astrophysics Data System (ADS)

Silva, Marta B.; Zaroubi, Saleem

2018-05-01

Characterizing the properties and the evolution of the first stars and galaxies is a challenging task for traditional galaxy surveys since they are sensitivity limited and can only detect the brightest light sources. Three-dimensional intensity mapping (IM) of transition lines can be a valuable alternative to study the high redshift Universe given that this technique avoids sensitivity limitation problems by measuring the overall emission of a line, with a low resolution, without resolving its sources. While 21cm line IM surveys probe neutral hydrogen gas and can, therefore, be used to probe the state of the IGM and the evolution of the ionization field during the Epoch of Reionization (EoR). IM surveys of other lines, such as CO, CII, Ly-alpha or H-alpha, can be used to probe the galaxies which emitted most of the ionizing radiation responsible for the EoR. These lines will trace the different ISM gas phases, the excitation state of this gas, its metallicity, etc. This study addresses IM of multiple transition lines and how it can be used to probe the EoR and to constrain the redshift evolution of galaxy properties.

Gravitational-wave localization alone can probe origin of stellar-mass black hole mergers.

PubMed

Bartos, I; Haiman, Z; Marka, Z; Metzger, B D; Stone, N C; Marka, S

2017-10-10

The recent discovery of gravitational waves from stellar-mass binary black hole mergers by the Laser Interferometer Gravitational-wave Observatory opened the door to alternative probes of stellar and galactic evolution, cosmology and fundamental physics. Probing the origin of binary black hole mergers will be difficult due to the expected lack of electromagnetic emission and limited localization accuracy. Associations with rare host galaxy types-such as active galactic nuclei-can nevertheless be identified statistically through spatial correlation. Here we establish the feasibility of statistically proving the connection between binary black hole mergers and active galactic nuclei as hosts, even if only a sub-population of mergers originate from active galactic nuclei. Our results are the demonstration that the limited localization of gravitational waves, previously written off as not useful to distinguish progenitor channels, can in fact contribute key information, broadening the range of astrophysical questions probed by binary black hole observations.Binary black hole mergers have recently been observed through the detection of gravitational wave signatures. The authors demonstrate that their association with active galactic nuclei can be made through a statistical spatial correlation.

A "signal on" protection-displacement-hybridization-based electrochemical hepatitis B virus gene sequence sensor with high sensitivity and peculiar adjustable specificity.

PubMed

Li, Fengqin; Xu, Yanmei; Yu, Xiang; Yu, Zhigang; He, Xunjun; Ji, Hongrui; Dong, Jinghao; Song, Yongbin; Yan, Hong; Zhang, Guiling

2016-08-15

One "signal on" electrochemical sensing strategy was constructed for the detection of a specific hepatitis B virus (HBV) gene sequence based on the protection-displacement-hybridization-based (PDHB) signaling mechanism. This sensing system is composed of three probes, one capturing probe (CP) and one assistant probe (AP) which are co-immobilized on the Au electrode surface, and one 3-methylene blue (MB) modified signaling probe (SP) free in the detection solution. One duplex are formed between AP and SP with the target, a specific HBV gene sequence, hybridizing with CP. This structure can drive the MB labels close to the electrode surface, thereby producing a large detection current. Two electrochemical testing techniques, alternating current voltammetry (ACV) and cyclic voltammetry (CV), were used for characterizing the sensor. Under the optimized conditions, the proposed sensor exhibits a high sensitivity with the detection limit of ∼5fM for the target. When used for the discrimination of point mutation, the sensor also features an outstanding ability and its peculiar high adjustability. Copyright © 2016 Elsevier B.V. All rights reserved.

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 versatile technique for fabrication of SiC SPM probes

NASA Astrophysics Data System (ADS)

Therrien, Joel; Schmidt, Daniel; Barrot, Sheetal; Patel, Bhavin

2008-03-01

To date SPM probes have largely been fabricated via methods borrowed from the semiconductor industry for fabricating Micro Electro Mechanical Systems. Although these techniques have enabled SPM to see widespread use, the processes put significant limitations on what structures can be made. We report our progress on fabricating SPM cantilevers composed of Silicon Carbide using polymer molding techniques. A pre-ceramic polymer is molded into the desired probe shape and then converted to SiC via pyrolisys. We will also report on progress in using photo-sterolithography for fabrication of even more complex geometries. In addition to opening up a much larger set of probe structures, the use of SiC leads to improved wear resistance of the resulting probes. Among the potential applications, this method enables the fabrication of low spring constant, high resonant frequency cantilevers via cross sectional geometries not accessible to standard fabrication techniques. Such probes are required for high speed tapping and non-contact imaging.

Solid phase sequencing of double-stranded nucleic acids

DOEpatents

Fu, Dong-Jing; Cantor, Charles R.; Koster, Hubert; Smith, Cassandra L.

2002-01-01

This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

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.

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.

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.

Character Sets for PLATO/NovaNET: An Expository Catalog.

ERIC Educational Resources Information Center

Gilpin, John B.

The PLATO and NovaNET computer-based instructional systems use a fixed system character set ("normal font") and an author-definable character set ("alternate font"). The alternate font lets the author construct his own symbols and bitmapped pictures. This expository catalog allows users to determine quickly (1) whether there is…

Robotic end effector

DOEpatents

Minichan, Richard L.

1993-01-01

An end effector for use in probing a surface with a robotic arm. The end effector has a first portion that carries a gimbal with a probe, the gimbal holding the probe normal to the surface, and a second portion with a set of three shafts within a housing for urging the gimbal and probe against the surface. The second portion contains a potentiometer connected by another shaft to the first portion to measure the position of the first portion with respect to the second so that the second portion can be moved to place and maintain the shafts at the midpoint of their travel. Then, as irregularities in the surface are encountered, the first portion can respond by moving closer to or farther from the second portion.

Robotic end effector

DOEpatents

Minichan, R.L.

1993-10-05

An end effector is described for use in probing a surface with a robotic arm. The end effector has a first portion that carries a gimbal with a probe, the gimbal holding the probe normal to the surface, and a second portion with a set of three shafts within a housing for urging the gimbal and probe against the surface. The second portion contains a potentiometer connected by another shaft to the first portion to measure the position of the first portion with respect to the second so that the second portion can be moved to place and maintain the shafts at the midpoint of their travel. Then, as irregularities in the surface are encountered, the first portion can respond by moving closer to or farther from the second portion. 7 figures.

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton

PubMed Central

Muller, Jean; Mehlen, André; Vetter, Guillaume; Yatskou, Mikalai; Muller, Arnaud; Chalmel, Frédéric; Poch, Olivier; Friederich, Evelyne; Vallar, Laurent

2007-01-01

Background The actin cytoskeleton plays a crucial role in supporting and regulating numerous cellular processes. Mutations or alterations in the expression levels affecting the actin cytoskeleton system or related regulatory mechanisms are often associated with complex diseases such as cancer. Understanding how qualitative or quantitative changes in expression of the set of actin cytoskeleton genes are integrated to control actin dynamics and organisation is currently a challenge and should provide insights in identifying potential targets for drug discovery. Here we report the development of a dedicated microarray, the Actichip, containing 60-mer oligonucleotide probes for 327 genes selected for transcriptome analysis of the human actin cytoskeleton. Results Genomic data and sequence analysis features were retrieved from GenBank and stored in an integrative database called Actinome. From these data, probes were designed using a home-made program (CADO4MI) allowing sequence refinement and improved probe specificity by combining the complementary information recovered from the UniGene and RefSeq databases. Actichip performance was analysed by hybridisation with RNAs extracted from epithelial MCF-7 cells and human skeletal muscle. Using thoroughly standardised procedures, we obtained microarray images with excellent quality resulting in high data reproducibility. Actichip displayed a large dynamic range extending over three logs with a limit of sensitivity between one and ten copies of transcript per cell. The array allowed accurate detection of small changes in gene expression and reliable classification of samples based on the expression profiles of tissue-specific genes. When compared to two other oligonucleotide microarray platforms, Actichip showed similar sensitivity and concordant expression ratios. Moreover, Actichip was able to discriminate the highly similar actin isoforms whereas the two other platforms did not. Conclusion Our data demonstrate that Actichip is a powerful alternative to commercial high density microarrays for cytoskeleton gene profiling in normal or pathological samples. Actichip is available upon request. PMID:17727702

Improved Multiplex Ligation-dependent Probe Amplification (i-MLPA) for rapid copy number variant (CNV) detection.

PubMed

Saxena, Sonal; Gowdhaman, Kavitha; Kkani, Poornima; Vennapusa, Bhavyasri; Rama Subramanian, Chellamuthu; Ganesh Kumar, S; Mohan, Kommu Naga

2015-10-23

In Multiplex Ligation-dependent Probe Amplification (MLPA), copy number variants (CNVs) for specific genes are identified after normalization of the amounts of PCR products from ligated reference probes hybridized to genomic regions that are ideally free from normal variation. However, we observed ambiguous calls for two reference probes in an investigation of the human 15q11.2 region by MLPA among 20 controls, due to the presence of single nucleotide polymorphisms (SNPs) in the probe-binding regions. Further in silico analysis revealed that 18 out of 19 reference probes hybridize to regions subject to variation, underlining the requirement for designing new reference probes against variation-free regions. An improved MLPA (i-MLPA) method was developed by generating a new set of reference probes to reduce the chances of ambiguous calls and new reagents that reduce hybridization times to 30 min from 16h to obtain MLPA ratio data within 6h. Using i-MLPA, we screened 240 schizophrenia patients for CNVs in 15q11.2 region. Three deletions and two duplications were identified among the 240 schizophrenia patients. No variation was observed for the new reference probes. Taken together, i-MLPA procedure helps obtaining non-ambiguous CNV calls within 6h without compromising accuracy. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Parallels, How Many? Geometry Module for Use in a Mathematics Laboratory Setting.

ERIC Educational Resources Information Center

Brotherton, Sheila; And Others

This is one of a series of geometry modules developed for use by secondary students in a laboratory setting. This module was conceived as an alternative approach to the usual practice of giving Euclid's parallel postulate and then mentioning that alternate postulates would lead to an alternate geometry or geometries. Instead, the student is led…

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

Hiser, C.; McIntosh, L.

Mitochondria from 24-hour-aged potato slices possess an alternative path capacity and a 36kD protein not present in fresh potato mitochondria. This 36kD protein was identified by a monoclonal antibody against the Sauromatum guttatum alternative oxidase. These results suggest de novo synthesis of the 36kD protein during the aging process. To investigate this phenomenon, a clone containing a potato alternative oxidase gene was isolated from a cDNA library using the S. guttatum gene as a probe. This clone shows areas of high homology to the S. guttatum gene. Norther blots of RNA from fresh and 24-hour-aged potato slices are being probedmore » with the potato gene to examine its expression in relation to the appearance of the 36kD protein.« less

A 'Quad-Disc' static pressure probe for measurement in adverse atmospheres - With a comparative review of static pressure probe designs

NASA Astrophysics Data System (ADS)

Nishiyama, Randall T.; Bedard, Alfred J., Jr.

1991-09-01

There are many areas of need for accurate measurements of atmospheric static pressure. These include observations of surface meteorology, airport altimeter settings, pressure distributions around buildings, moving measurement platforms, as well as basic measurements of fluctuating pressures in turbulence. Most of these observations require long-term observations in adverse environments (e.g., rain, dust, or snow). Currently, many pressure measurements are made, of necessity, within buildings, thus involving potential errors of several millibars in mean pressure during moderate winds, accompanied by large fluctuating pressures induced by the structure. In response to these needs, a 'Quad-Disk' pressure probe for continuous, outdoor monitoring purposes was designed which is inherently weather-protected. This Quad-Disk probe has the desirable features of omnidirectional response and small error in pitch. A review of past static pressure probes contrasts design approaches and capabilities.

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.

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

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.

Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences

PubMed Central

Gibbs, Mark J; Armstrong, John S; Gibbs, Adrian J

2005-01-01

Background Most current DNA diagnostic tests for identifying organisms use specific oligonucleotide probes that are complementary in sequence to, and hence only hybridise with the DNA of one target species. By contrast, in traditional taxonomy, specimens are usually identified by 'dichotomous keys' that use combinations of characters shared by different members of the target set. Using one specific character for each target is the least efficient strategy for identification. Using combinations of shared bisectionally-distributed characters is much more efficient, and this strategy is most efficient when they separate the targets in a progressively binary way. Results We have developed a practical method for finding minimal sets of sub-sequences that identify individual sequences, and could be targeted by combinations of probes, so that the efficient strategy of traditional taxonomic identification could be used in DNA diagnosis. The sizes of minimal sub-sequence sets depended mostly on sequence diversity and sub-sequence length and interactions between these parameters. We found that 201 distinct cytochrome oxidase subunit-1 (CO1) genes from moths (Lepidoptera) were distinguished using only 15 sub-sequences 20 nucleotides long, whereas only 8–10 sub-sequences 6–10 nucleotides long were required to distinguish the CO1 genes of 92 species from the 9 largest orders of insects. Conclusion The presence/absence of sub-sequences in a set of gene sequences can be used like the questions in a traditional dichotomous taxonomic key; hybridisation probes complementary to such sub-sequences should provide a very efficient means for identifying individual species, subtypes or genotypes. Sequence diversity and sub-sequence length are the major factors that determine the numbers of distinguishing sub-sequences in any set of sequences. PMID:15817134

American Alcohol Photo Stimuli (AAPS): A standardized set of alcohol and matched non-alcohol images.

PubMed

Stauffer, Christopher S; Dobberteen, Lily; Woolley, Joshua D

2017-11-01

Photographic stimuli are commonly used to assess cue reactivity in the research and treatment of alcohol use disorder. The stimuli used are often non-standardized, not properly validated, and poorly controlled. There are no previously published, validated, American-relevant sets of alcohol images created in a standardized fashion. We aimed to: 1) make available a standardized, matched set of photographic alcohol and non-alcohol beverage stimuli, 2) establish face validity, the extent to which the stimuli are subjectively viewed as what they are purported to be, and 3) establish construct validity, the degree to which a test measures what it claims to be measuring. We produced a standardized set of 36 images consisting of American alcohol and non-alcohol beverages matched for basic color, form, and complexity. A total of 178 participants (95 male, 82 female, 1 genderqueer) rated each image for appetitiveness. An arrow-probe task, in which matched pairs were categorized after being presented for 200 ms, assessed face validity. Criteria for construct validity were met if variation in AUDIT scores were associated with variation in performance on tasks during alcohol image presentation. Overall, images were categorized with >90% accuracy. Participants' AUDIT scores correlated significantly with alcohol "want" and "like" ratings [r(176) = 0.27, p = <0.001; r(176) = 0.36, p = <0.001] and arrow-probe latency [r(176) = -0.22, p = 0.004], but not with non-alcohol outcomes. Furthermore, appetitive ratings and arrow-probe latency for alcohol, but not non-alcohol, differed significantly for heavy versus light drinkers. Our image set provides valid and reliable alcohol stimuli for both explicit and implicit tests of cue reactivity. The use of standardized, validated, reliable image sets may improve consistency across research and treatment paradigms.

Characteristics of Ferromagnetic Flux Focusing Lens in the Development of Surface/Subsurface Flaw Detector

NASA Technical Reports Server (NTRS)

Wincheski, Buzz; Fulton, Jim; Nath, Shridhar; Namkung, Min; Simpson, John

1993-01-01

Electromagnetic NDE techniques have in the past steered away from the use of ferromagnetic materials. Although their high permeabilities lead to increased field levels, the properties of ferrous elements in the presence of alternating magnetic fields are difficult to determine. In addition, their use leads to losses which can be minimized through the use of low conductivity ferrites. In fact, the eddy current probes which do incorporate ferromagnetic materials have focused on these losses and the shielding which can be obtained by surrounding a probe with a high permeability, conducting material. Eddy current probes enclosed in conducting and magnetic shields have been used to prevent the generated fields from interacting with materials in the vicinity of the probe, such as when testing near material boundaries. A recent invention has used ferromagnetic shielding to magnetically separate individual concentric eddy current probes in order to eliminate cross-talk between the probes so that simultaneous detection of different types of flaws at different depths can be achieved. In contrast to the previous uses of ferromagnetic materials purely as magnetic shields, an electromagnetic flaw detector recently developed at NASA Langley Research Center takes advantage of the flux focusing properties of a ferromagnetic mild steel in order to produce a simple, effective device for the non-destructive evaluation of conducting materials. The Flux Focusing Eddy Current Probe has been shown to accurately measure material thickness and fatigue damage. The straight forward flaw response of the probe makes the device ideal for rapid inspection of large structures, and has lead to its incorporation in a computer controlled search routine to locate fatigue crack tips and monitor experimental fatigue crack growth experiments.

Propionate stimulates pyruvate oxidation in the presence of acetate.

PubMed

Purmal, Colin; Kucejova, Blanka; Sherry, A Dean; Burgess, Shawn C; Malloy, Craig R; Merritt, Matthew E

2014-10-15

Flux through pyruvate dehydrogenase (PDH) in the heart may be reduced by various forms of injury to the myocardium, or by oxidation of alternative substrates in normal heart tissue. It is important to distinguish these two mechanisms because imaging of flux through PDH based on the appearance of hyperpolarized (HP) [(13)C]bicarbonate derived from HP [1-(13)C]pyruvate has been proposed as a method for identifying viable myocardium. The efficacy of propionate for increasing PDH flux in the setting of PDH inhibition by an alternative substrate was studied using isotopomer analysis paired with exams using HP [1-(13)C]pyruvate. Hearts from C57/bl6 mice were supplied with acetate (2 mM) and glucose (8.25 mM). (13)C NMR spectra were acquired in a cryogenically cooled probe at 14.1 Tesla. After addition of hyperpolarized [1-(13)C]pyruvate, (13)C NMR signals from lactate, alanine, malate, and aspartate were easily detected, in addition to small signals from bicarbonate and CO2. The addition of propionate (2 mM) increased appearance of HP [(13)C]bicarbonate >30-fold without change in O2 consumption. Isotopomer analysis of extracts from the freeze-clamped hearts indicated that acetate was the preferred substrate for energy production, glucose contribution to energy production was minimal, and anaplerosis was stimulated in the presence of propionate. Under conditions where production of acetyl-CoA is dominated by the availability of an alternative substrate, acetate, propionate markedly stimulated PDH flux as detected by the appearance of hyperpolarized [(13)C]bicarbonate from metabolism of hyperpolarized [1-(13)C]pyruvate. Copyright © 2014 the American Physiological Society.

Probe Oscillation Shear Wave Elastography: Initial In Vivo Results in Liver.

PubMed

Mellema, Daniel C; Song, Pengfei; Kinnick, Randall R; Trzasko, Joshua D; Urban, Matthew W; Greenleaf, James F; Manduca, Armando; Chen, Shigao

2018-05-01

Shear wave elastography methods are able to accurately measure tissue stiffness, allowing these techniques to monitor the progression of hepatic fibrosis. While many methods rely on acoustic radiation force to generate shear waves for 2-D imaging, probe oscillation shear wave elastography (PROSE) provides an alternative approach by generating shear waves through continuous vibration of the ultrasound probe while simultaneously detecting the resulting motion. The generated shear wave field in in vivo liver is complicated, and the amplitude and quality of these shear waves can be influenced by the placement of the vibrating probe. To address these challenges, a real-time shear wave visualization tool was implemented to provide instantaneous visual feedback to optimize probe placement. Even with the real-time display, it was not possible to fully suppress residual motion with established filtering methods. To solve this problem, the shear wave signal in each frame was decoupled from motion and other sources through the use of a parameter-free empirical mode decomposition before calculating shear wave speeds. This method was evaluated in a phantom as well as in in vivo livers from five volunteers. PROSE results in the phantom as well as in vivo liver correlated well with independent measurements using the commercial General Electric Logiq E9 scanner.

The vector homology problem in diagnostic nucleic acid hybridization of clinical specimens.

PubMed Central

Ambinder, R F; Charache, P; Staal, S; Wright, P; Forman, M; Hayward, S D; Hayward, G S

1986-01-01

Nucleic acid hybridization techniques using cloned probes are finding application in assays of clinical specimens in research and diagnostic laboratories. The probes that we and others have used are recombinant plasmids composed of viral inserts and bacterial plasmid vectors such as pBR322. We suspected that there was material homologous to pBR322 present in many clinical samples. because hybridization occurred in samples which lacked evidence of virus by other techniques. If the presence of this vector-homologous material was unrecognized, hybridization in the test sample might erroneously be interpreted as indicating the presence of viral sequences. In this paper we demonstrate specific hybridization of labeled pBR322 DNA with DNA from various clinical samples. Evidence is presented that nonspecific probe trapping could not account for this phenomenon. In mixing experiments, it is shown that contamination of clinical samples with bacteria would explain such a result. Approaches tested to circumvent this problem included the use of isolated insert probes, alternate cloning vectors, and cold competitor pBR322 DNA in prehybridization and hybridization mixes. None proved entirely satisfactory. We therefore emphasize that it is essential that all hybridization detection systems use a control probe of the vector alone in order to demonstrate the absence of material with vector homology in the specimen tested. Images PMID:3013928

Recombinant phage probes for Listeria monocytogenes

NASA Astrophysics Data System (ADS)

Carnazza, S.; Gioffrè, G.; Felici, F.; Guglielmino, S.

2007-10-01

Monitoring of food and environmental samples for biological threats, such as Listeria monocytogenes, requires probes that specifically bind biological agents and ensure their immediate and efficient detection. There is a need for robust and inexpensive affinity probes as an alternative to antibodies. These probes may be recruited from random peptide libraries displayed on filamentous phage. In this study, we selected from two phage peptide libraries phage clones displaying peptides capable of specific and strong binding to the L. monocytogenes cell surface. The ability of isolated phage clones to interact specifically with L. monocytogenes was demonstrated using enzyme-linked immunosorbent assay (ELISA) and confirmed by co-precipitation assay. We also assessed the sensitivity of phage-bacteria binding by PCR on phage-captured Listeria cells, which could be detected at a concentration of 104 cells ml-1. In addition, as proof-of-concept, we tested the possibility of immobilizing the affinity-selected phages to a putative biosensor surface. The quality of phage deposition was monitored by ELISA and fluorescent microscopy. Phage-bacterial binding was confirmed by high power optical phase contrast microscopy. Overall, the results of this work validate the concept of affinity-selected recombinant filamentous phages as probes for detecting and monitoring bacterial agents under any conditions that warrant their recognition, including in food products.

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

PubMed

Dong, F; Allawi, H T; Anderson, T; Neri, B P; Lyamichev, V I

2001-08-01

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

Fluorogenic PNA probes

PubMed Central

2018-01-01

Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years. PMID:29507634

Impact of Context and Representation on Year 10 Students' Expression of Conceptions of Rate

ERIC Educational Resources Information Center

Herbert, Sandra

2010-01-01

Rate is an important, but difficult mathematical concept. More than twenty years of research, especially with calculus students, report difficulties with this concept. This paper reports on an alternative analysis, from the perspective of multiple representations and context, of interviews probing twenty Victorian Year 10 students' conceptions of…

An Independent Evaluation of the Technical Features of the Basic Reading Inventory

ERIC Educational Resources Information Center

Bieber, Gregg; Hulac, David M.; Schweinle, William

2015-01-01

The present study investigated some psychometric properties of the Basic Reading Inventory (BRI), a widely used informal reading inventory. The BRI and Dynamic Indicators of Basic Early Literacy Skills (DIBELS) probes were administered to 149 third, fourth, and fifth graders. Test--retest and alternate forms reliability analyses indicated adequate…

A Comparison of Simultaneous Prompting and Constant Time Delay Procedures in Teaching State Capitals

ERIC Educational Resources Information Center

Head, Kenneth David; Collins, Belva C.; Schuster, John W.; Ault, Melinda Jones

2011-01-01

This investigation compared the effectiveness and efficiency of constant time delay (CTD) and simultaneous prompting (SP) procedures in teaching discrete social studies facts to 4 high school students with learning and behavior disorders using an adapted alternating treatments design nested within a multiple probe design. The results indicated…

Lessons for Teaching Botany: What Middle School Students Know about Plants.

ERIC Educational Resources Information Center

Natarajan, Chitra; Chunawala, Sugra; Apte, Swapna; Ramadas, Jayashree

Students' alternative conceptions arise out of an interconnected system of beliefs: about the nature of science, of learning, of the natural and social world. Cross-cultural perspectives on these world views are therefore essential. This study probed middle school students' conceptions about plants. Tribal students were found to have a richer and…

Antifouling strategies and corrosion control in cooling circuits.

PubMed

Cristiani, P; Perboni, G

2014-06-01

Biofouling and corrosion phenomena dramatically reduce the functionality of industrial cooling circuits, especially in marine environments. This study underlines the effectiveness of a low level chlorination treatment of seawater to prevent biological fouling and biocorrosion. Reported examples emphasize the reaction of chlorine with bromide, ammonia and organic compounds in seawater and the effectiveness of a treatment performed in such a way to guarantee a residual concentration lower than 3μM at the outlet of the condensers. In a brief review of antifouling strategies, alternatives to chlorination and the monitoring approach able to optimize the treatments are also reported. An integrated, on-line system based on electrochemical probes (Biox system and a linear polarization resistance probe) demonstrated to be sufficient to monitor in real time: corrosion, biofilm growth and chemical treatments based on chlorine or alternative oxidant products (chlorine dioxide, etc.). A careful electrochemical monitoring and the optimized treatments help the plant operators of industrial cooling circuits prevent the decay of the equipment performance, allowing at the same time the control of the halogenated by-products formation. Copyright © 2014 Elsevier B.V. All rights reserved.

An exo probe-based recombinase polymerase amplification assay for the rapid detection of porcine parvovirus.

PubMed

Wang, Jian-Chang; Liu, Li-Bing; Han, Qing-An; Wang, Jin-Feng; Yuan, Wan-Zhe

2017-10-01

Recombinase polymerase amplification (RPA), an isothermal amplification technology, has been developed as an alternative to PCR in pathogen detection. A real-time RPA assay (rt-RPA) was developed to detect the porcine parvovirus (PPV) using primers and exo probe specific for the VP2 gene. The amplification was performed at 39°C for 20min. There was no cross-reaction with other pathogens tested. Using the recombinant plasmid pPPV-VP2 as template, the analytical sensitivity was 103 copies. The assay performance was evaluated by testing 115 field samples by rt-RPA and a real-time PCR assay. The diagnostic agreement between assays was 100%, and PPV DNA was detected in 94 samples. The R 2 value of rt-RPA and real-time PCR was 0.909 by linear regression analysis. The developed rt-RPA assay provides a useful alternative tool for rapid, simple and reliable detection of PPV in diagnostic laboratories and at point-of-care, especially in remote and rural areas. Copyright © 2017 Elsevier B.V. All rights reserved.

Ease of Access to List Items in Short-Term Memory Depends on the Order of the Recognition Probes

ERIC Educational Resources Information Center

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

2011-01-01

We report data from 4 experiments using a recognition design with multiple probes to be matched to specific study positions. Items could be accessed rapidly, independent of set size, when the test order matched the study order (forward condition). When the order of testing was random, backward, or in a prelearned irregular sequence (reordered…

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

Coppens, Philip; Makal, Anna; Fournier, Bertrand

In picosecond and slower pump–probe diffraction experiments, collection of response–ratio correlation sets prior to full data collection provides an invaluable confirmation of the existence of a light-induced signal prior to full data collection. If a response to light exposure is observed, the quality of the data being collected can be assessed. We present a number of such correlation plots both for synchrotron and in-house pump–probe data collection.

Tertiary-Tier PBIS in Alternative, Residential and Correctional School Settings: Considering Intensity in the Delivery of Evidence-Based Practice

ERIC Educational Resources Information Center

Scott, Terrance M.; Cooper, Justin

2013-01-01

Students in alternative, residential, and correctional settings present challenges in the classroom and facility due to the complexity and intensity of their behaviors. In addition, the factors typically associated with these settings including crowding, inconsistency, and conflicting staff perspectives on education and discipline present…

Controlled soil warming powered by alternative energy for remote field sites.

PubMed

Johnstone, Jill F; Henkelman, Jonathan; Allen, Kirsten; Helgason, Warren; Bedard-Haughn, Angela

2013-01-01

Experiments using controlled manipulation of climate variables in the field are critical for developing and testing mechanistic models of ecosystem responses to climate change. Despite rapid changes in climate observed in many high latitude and high altitude environments, controlled manipulations in these remote regions have largely been limited to passive experimental methods with variable effects on environmental factors. In this study, we tested a method of controlled soil warming suitable for remote field locations that can be powered using alternative energy sources. The design was tested in high latitude, alpine tundra of southern Yukon Territory, Canada, in 2010 and 2011. Electrical warming probes were inserted vertically in the near-surface soil and powered with photovoltaics attached to a monitoring and control system. The warming manipulation achieved a stable target warming of 1.3 to 2 °C in 1 m(2) plots while minimizing disturbance to soil and vegetation. Active control of power output in the warming plots allowed the treatment to closely match spatial and temporal variations in soil temperature while optimizing system performance during periods of low power supply. Active soil heating with vertical electric probes powered by alternative energy is a viable option for remote sites and presents a low-disturbance option for soil warming experiments. This active heating design provides a valuable tool for examining the impacts of soil warming on ecosystem processes.

Probing the surface profile and friction behavior of heterogeneous polymers: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Dai, L.; Sorkin, V.; Zhang, Y. W.

2017-04-01

We perform molecular dynamics simulations to investigate molecular structure alternation and friction behavior of heterogeneous polymer (perfluoropolyether) surfaces using a nanoscale probing tip (tetrahedral amorphous carbon). It is found that depending on the magnitude of the applied normal force, three regimes exist: the shallow depth-sensing (SDS), deep depth-sensing (DDS), and transitional depth-sensing (TDS) regimes; TDS is between SDS and DDS. In SDS, the tip is floating on the polymer surface and there is insignificant permanent alternation in the polymer structure due to largely recoverable atomic deformations, and the surface roughness profile can be accurately measured. In DDS, the tip is plowing through the polymer surface and there is significant permanent alternation in the molecular structure. In this regime, the lateral friction force rises sharply and fluctuates violently when overcoming surface pile-ups. In SDS, the friction can be described by a modified Amonton’s law including the adhesion effect; meanwhile, in DDS, the adhesion effect is negligible but the friction coefficient is significantly higher. The underlying reason for the difference in these regimes rests upon different contributions by the repulsion and attraction forces between the tip and polymer surfaces to the friction force. Our findings here reveal important insights into lateral depth-sensing on heterogeneous polymer surfaces and may help improve the precision of depth-sensing devices.

Fluorescence In Situ Hybridization Probe Validation for Clinical Use.

PubMed

Gu, Jun; Smith, Janice L; Dowling, Patricia K

2017-01-01

In this chapter, we provide a systematic overview of the published guidelines and validation procedures for fluorescence in situ hybridization (FISH) probes for clinical diagnostic use. FISH probes-which are classified as molecular probes or analyte-specific reagents (ASRs)-have been extensively used in vitro for both clinical diagnosis and research. Most commercially available FISH probes in the United States are strictly regulated by the U.S. Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), the Centers for Medicare & Medicaid Services (CMS) the Clinical Laboratory Improvement Amendments (CLIA), and the College of American Pathologists (CAP). Although home-brewed FISH probes-defined as probes made in-house or acquired from a source that does not supply them to other laboratories-are not regulated by these agencies, they too must undergo the same individual validation process prior to clinical use as their commercial counterparts. Validation of a FISH probe involves initial validation and ongoing verification of the test system. Initial validation includes assessment of a probe's technical specifications, establishment of its standard operational procedure (SOP), determination of its clinical sensitivity and specificity, development of its cutoff, baseline, and normal reference ranges, gathering of analytics, confirmation of its applicability to a specific research or clinical setting, testing of samples with or without the abnormalities that the probe is meant to detect, staff training, and report building. Ongoing verification of the test system involves testing additional normal and abnormal samples using the same method employed during the initial validation of the probe.

Probing Majorana bound states via counting statistics of a single electron transistor

NASA Astrophysics Data System (ADS)

Li, Zeng-Zhao; Lam, Chi-Hang; You, J. Q.

2015-06-01

We propose an approach for probing Majorana bound states (MBSs) in a nanowire via counting statistics of a nearby charge detector in the form of a single-electron transistor (SET). We consider the impacts on the counting statistics by both the local coupling between the detector and an adjacent MBS at one end of a nanowire and the nonlocal coupling to the MBS at the other end. We show that the Fano factor and the skewness of the SET current are minimized for a symmetric SET configuration in the absence of the MBSs or when coupled to a fermionic state. However, the minimum points of operation are shifted appreciably in the presence of the MBSs to asymmetric SET configurations with a higher tunnel rate at the drain than at the source. This feature persists even when varying the nonlocal coupling and the pairing energy between the two MBSs. We expect that these MBS-induced shifts can be measured experimentally with available technologies and can serve as important signatures of the MBSs.

Biased predecisional processing of leading and nonleading alternatives.

PubMed

Blanchard, Simon J; Carlson, Kurt A; Meloy, Margaret G

2014-03-01

When people obtain information about choice alternatives in a set one attribute at a time, they rapidly identify a leading alternative. Although previous research has established that people then distort incoming information, it is unclear whether distortion occurs through favoring of the leading alternative, disfavoring of the trailing alternative, or both. Prior examinations have not explored the predecisional treatment of the nonleading alternative (or alternatives) because they conceptualized distortion as a singular construct in binary choice and measured it using a relative item comparing the evaluation of both alternatives simultaneously. In this article, we introduce a measure of distortion at the level of the alternative, which allows for measuring whether predecisional distortion favors or disfavors every alternative being considered in choice sets of various sizes. We report that both proleader and antitrailer distortion occur and that the use of antitrailer processing differs between binary choices and multiple-options choices.

Target capture enrichment of nuclear SNP markers for massively parallel sequencing of degraded and mixed samples.

PubMed

Bose, Nikhil; Carlberg, Katie; Sensabaugh, George; Erlich, Henry; Calloway, Cassandra

2018-05-01

DNA from biological forensic samples can be highly fragmented and present in limited quantity. When DNA is highly fragmented, conventional PCR based Short Tandem Repeat (STR) analysis may fail as primer binding sites may not be present on a single template molecule. Single Nucleotide Polymorphisms (SNPs) can serve as an alternative type of genetic marker for analysis of degraded samples because the targeted variation is a single base. However, conventional PCR based SNP analysis methods still require intact primer binding sites for target amplification. Recently, probe capture methods for targeted enrichment have shown success in recovering degraded DNA as well as DNA from ancient bone samples using next-generation sequencing (NGS) technologies. The goal of this study was to design and test a probe capture assay targeting forensically relevant nuclear SNP markers for clonal and massively parallel sequencing (MPS) of degraded and limited DNA samples as well as mixtures. A set of 411 polymorphic markers totaling 451 nuclear SNPs (375 SNPs and 36 microhaplotype markers) was selected for the custom probe capture panel. The SNP markers were selected for a broad range of forensic applications including human individual identification, kinship, and lineage analysis as well as for mixture analysis. Performance of the custom SNP probe capture NGS assay was characterized by analyzing read depth and heterozygote allele balance across 15 samples at 25 ng input DNA. Performance thresholds were established based on read depth ≥500X and heterozygote allele balance within ±10% deviation from 50:50, which was observed for 426 out of 451 SNPs. These 426 SNPs were analyzed in size selected samples (at ≤75 bp, ≤100 bp, ≤150 bp, ≤200 bp, and ≤250 bp) as well as mock degraded samples fragmented to an average of 150 bp. Samples selected for ≤75 bp exhibited 99-100% reportable SNPs across varied DNA amounts and as low as 0.5 ng. Mock degraded samples at 1 ng and 10 ng exhibited >90% reportable SNPs. Finally, two-person male-male mixtures were tested at 10 ng in contributor varying ratios. Overall, 85-100% of alleles unique to the minor contributor were observed at all mixture ratios. Results from these studies using the SNP probe capture NGS system demonstrates proof of concept for application to forensically relevant degraded and mixed DNA samples. Copyright © 2018 Elsevier B.V. All rights reserved.

Addressing the Social, Academic, and Behavioral Needs of Students with Challenging Behavior in Inclusive and Alternative Settings. Highlights from the Forum on Comprehensive Programming for a Diverse Population of Children and Youth with Challenging Behavior: Addressing Social, Academic, and Behavioral Needs within Inclusive and Alternative Settings (Las Vegas, Nevada, February 9-10, 2001).

ERIC Educational Resources Information Center

Bullock, Lyndal M., Ed.; Gable, Robert A., Ed.

This document presents the texts of 11 major presentations and conference highlights from a February 2001 conference on the social, academic, and behavioral needs of students with challenging behavior in inclusive and alternative settings as required under the 1997 amendments to the Individuals with Disabilities Education Act. The presentations…

Distinctive gene expression profiles characterize donor biopsies from HCV-positive kidney donors.

PubMed

Mas, Valeria R; Archer, Kellie J; Suh, Lacey; Scian, Mariano; Posner, Marc P; Maluf, Daniel G

2010-12-15

Because of the shortage of organs for transplantation, procurement of kidneys from extended criteria donors is inevitable. Frequently, donors infected with hepatitis C virus (HCV) are used. To elucidate an initial compromise of molecular pathways in HCV graft, gene expression profiles were evaluated. Twenty-four donor allograft biopsies (n=12 HCV positive (+) and n=12 HCV negative (-)) were collected at preimplantation time and profiled using microarrays. Donors were age, race, gender, and cold and warm ischemia time matched between groups. Probe level data were read into the R programming environment using the affy Bioconductor package, and the robust multiarray average method was used to obtain probe set expression summaries. To identify probe sets exhibiting differential expression, a two sample t test was performed. Molecular and biologic functions were analyzed using Interaction Networks and Functional Analysis. Fifty-eight probe sets were differentially expressed between HCV (+) versus HCV (-) donors (P<0.001). The molecular functions associated with the two top scored networks from the analysis of the differentially expressed genes were connective tissue development and function and tissue morphology (score 34), cell death, cell signaling, cellular assembly, and organization (score 32). Among the differentially affected top canonical pathways, we found the role of RIG1-like receptors in antiviral innate immunity (P<0.001), natural killer cell signaling (P=0.007), interleukin-8 signaling (P=0.048), interferon signaling (P=0.0 11; INFA21, INFGR1, and MED14), ILK signaling (P=0.001), and apoptosis signaling. A unique gene expression pattern was identified in HCV (+) kidney grafts. Innate immune system and inflammatory pathways were the most affected.

Genome-wide comparative chromosome maps of Arvicola amphibius, Dicrostonyx torquatus, and Myodes rutilus.

PubMed

Romanenko, Svetlana A; Lemskaya, Natalya A; Trifonov, Vladimir A; Serdyukova, Natalya A; O'Brien, Patricia C M; Bulatova, Nina Sh; Golenishchev, Feodor N; Ferguson-Smith, Malcolm A; Yang, Fengtang; Graphodatsky, Alexander S

2016-05-01

The subfamily Arvicolinae consists of a great number of species with highly diversified karyotypes. In spite of the wide use of arvicolines in biological and medicine studies, the data on their karyotype structures are limited. Here, we made a set of painting probes from flow-sorted chromosomes of a male Palearctic collared lemming (Dicrostonyx torquatus, DTO). Together with the sets of painting probes made previously from the field vole (Microtus agrestis, MAG) and golden hamster (Mesocricetus auratus, MAU), we carried out a reciprocal chromosome painting between these three species. The three sets of probes were further hybridized onto the chromosomes of the Eurasian water vole (Arvicola amphibius) and northern red-backed vole (Myodes rutilus). We defined the diploid chromosome number in D. torquatus karyotype as 2n = 45 + Bs and showed that the system of sex chromosomes is X1X2Y1. The probes developed here provide a genomic tool-kit, which will help to investigate the evolutionary biology of the Arvicolinae rodents. Our results show that the syntenic association MAG1/17 is present not only in Arvicolinae but also in some species of Cricetinae; and thus, should not be considered as a cytogenetic signature for Arvicolinae. Although cytogenetic signature markers for the genera have not yet been found, our data provides insight into the likely ancestral karyotype of Arvicolinae. We conclude that the karyotypes of modern voles could have evolved from a common ancestral arvicoline karyotype (AAK) with 2n = 56 mainly by centric fusions and fissions.

Probing Aircraft Flight Test Hazard Mitigation for the Alternative Fuel Effects on Contrails and Cruise Emissions (ACCESS) Research Team . Volume 2; Appendices

NASA Technical Reports Server (NTRS)

Kelly, Michael J.

2013-01-01

The Alternative Fuel Effects on Contrails and Cruise Emissions (ACCESS) Project Integration Manager requested in July 2012 that the NASA Engineering and Safety Center (NESC) form a team to independently assess aircraft structural failure hazards associated with the ACCESS experiment and to identify potential flight test hazard mitigations to ensure flight safety. The ACCESS Project Integration Manager subsequently requested that the assessment scope be focused predominantly on structural failure risks to the aircraft empennage (horizontal and vertical tail). This report contains the Appendices to Volume I.

Optimizing results of lithotripsy using robust electromagnetic probe.

PubMed

Keeley, F X; Pye, S D; Smith, G; Tolley, D A

1999-05-01

A significant impediment to the measurement of the pressures and forces created by lithotripter shockwaves has been their destructive properties, which have rendered most measuring devices impractical. We have developed and tested a robust electromagnetic probe to measure cavitational forces in vitro in the focal zones of extracorporeal lithotripters. The probe responds to the pressure gradient generated by the radial motion of cavitation bubbles. The effects of shockwaves from the Dornier MPL 9000 electrohydraulic lithotripter were measured over the lifetime of multiple electrodes. The pulse energy from the electrodes dropped off rapidly after approximately 50% of the lifetime quoted by the manufacturer. The electrodes were more efficient at higher power settings. As a result, we altered our protocol for the treatment of ureteral stones to use a higher kilovoltage and a second electrode whenever necessary. Stone-free rates after shockwave lithotripsy (SWL) in situ for stones < 11 mm have increased from 68.2% to 83.3%, and the retreatment rate has dropped from 23% to 15%. Despite significantly higher power settings (23.7 kV v 18.7 kV; P < 0.0001), the need for sedoanalgesia has remained relatively constant (26% v 31%). Measurement of cavitational forces from lithotripters using a robust electromagnetic probe is useful in planning treatment strategy. We have demonstrated a clinically measurable improvement since implementing our new treatment protocol. Because the probe responds directly to cavitational forces, it should also prove useful for the objective comparison of different SWL machines.

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.

The role of phonological alternation in speech production: evidence from Mandarin tone sandhi

PubMed Central

Politzer-Ahles, Stephen; Zhang, Jie

2014-01-01

We investigate the role of phonological alternation during speech production in Mandarin using implicit priming, a paradigm in which participants respond faster to words in sets that are phonologically homogeneous than in sets that are phonologically heterogeneous. We test whether priming is obtained when words in a set share the same tones at the underlying level but have different tones at the surface level-i.e., when the set includes a word that undergoes a phonological alternation which changes the tone. Sets that are heterogeneous at the surface level (in which the heterogeneity is due to a phonological operation) failed to elicit priming, as did sets that are heterogeneous at the underlying and surface levels (in which the heterogeneity is due to the lexical representations). This finding suggests that the phonological alternation was computed before the initiation of articulation, offering evidence that the progression from underlying phonological representations to articulatory execution may be mediated online by phonological input-to-output mapping. Furthermore, sets of words that are heterogeneous only at the surface level showed a different trend than sets of words that are heterogeneous at both levels, suggesting that both the surface and underlying levels of representation play a role during speech production. PMID:24967001

Disinfection of transvaginal ultrasound probes in a clinical setting: comparative performance of automated and manual reprocessing methods.

PubMed

Buescher, D L; Möllers, M; Falkenberg, M K; Amler, S; Kipp, F; Burdach, J; Klockenbusch, W; Schmitz, R

2016-05-01

Transvaginal and intracavitary ultrasound probes are a possible source of cross-contamination with microorganisms and thus a risk to patients' health. Therefore appropriate methods for reprocessing are needed. This study was designed to compare the standard disinfection method for transvaginal ultrasound probes in Germany with an automated disinfection method in a clinical setting. This was a prospective randomized controlled clinical study of two groups. In each group, 120 microbial samples were collected from ultrasound transducers before and after disinfection with either an automated method (Trophon EPR®) or a manual method (Mikrozid Sensitive® wipes). Samples were then analyzed for microbial growth and isolates were identified to species level. Automated disinfection had a statistically significantly higher success rate of 91.4% (106/116) compared with 78.8% (89/113) for manual disinfection (P = 0.009). The risk of contamination was increased by 2.9-fold when disinfection was performed manually (odds ratio, 2.9 (95% CI, 1.3-6.3)). Before disinfection, bacterial contamination was observed on 98.8% of probes. Microbial analysis revealed 36 different species of bacteria, including skin and environmental bacteria as well as pathogenic bacteria such as Staphylococcus aureus, enterobacteriaceae and Pseudomonas spp. Considering the high number of contaminated probes and bacterial species found, disinfection of the ultrasound probe's body and handle should be performed after each use to decrease the risk of cross-contamination. This study favored automated disinfection owing to its significantly higher efficacy compared with a manual method. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd. Copyright © 2015 ISUOG. Published by John Wiley & Sons Ltd.

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

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.

The Implementation of an Alternative School Setting for High Risk Handicapped Adjudicated Juveniles Aged Nine to Sixteen Years.

ERIC Educational Resources Information Center

LaCoste, Linda D.

This practicum was designed to provide an alternative setting for those handicapped adjudicated youths (ages 9-16) who, because of antisocial acts, behavioral/emotional problems, learning disabilities, attendance problems, and other reasons, were excluded from the mainstreamed setting. The practicum sought to enhance the cooperative efforts of the…

Universal fluorescent tri-probe ligation equipped with capillary electrophoresis for targeting SMN1 and SMN2 genes in diagnosis of spinal muscular atrophy.

PubMed

Wang, Chun-Chi; Shih, Chi-Jen; Jong, Yuh-Jyh; Wu, Shou-Mei

2014-06-23

This is the first ligase chain reaction used for diagnosis of spinal muscular atrophy (SMA). Universal fluorescent tri-probe ligation (UFTPL), a novel strategy used for distinguishing the multi-nucleotide alternations at single base, is developed to quantitatively analyze the SMN1/SMN2 genes in diagnosis of SMA. Ligase chain reaction was performed by adding three probes including universal fluorescent probe, connecting probe and recognizing probe to differentiate single nucleotide polymorphisms in UFTPL. Our approach was based on the two UFTPL products of survival motor neuron 1 (SMN1) and SMN2 genes (the difference of 9 mer) and analyzed by capillary electrophoresis (CE). We successfully determined various gene dosages of SMN1 and SMN2 genes in homologous or heterologous subjects. By using the UFTPL-CE method, the SMN1 and SMN2 genes were fully resolved with the resolution of 2.16±0.37 (n=3). The r values of SMN1 and SMN2 regression curves over a range of 1-4 copies were above 0.9944. Of the 48 DNA samples, the data of gene dosages were corresponding to that analyzed by conformation sensitive CE and denatured high-performance liquid chromatography (DHPLC). This technique was found to be a good methodology for quantification or determination of the relative genes having multi-nucleotide variants at single base. Copyright © 2014 Elsevier B.V. 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

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.

Allele-specific HLA-DR typing by mass spectrometry: an alternative to hybridization-based typing methods.

PubMed

Worrall, T A; Schmeckpeper, B J; Corvera, J S; Cotter, R J

2000-11-01

The primer oligomer base extension (PROBE) reaction, combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, is used to characterize HLA-DR2 polymorphism. Alleles are distinguished rapidly and accurately by measuring the mass of primer extension products at every known variable region of HLA-DR2 alleles. Since differentiation of alleles by PROBE relies on measuring differences in extension product mass rather than differences in hybridization properties, mistyped alleles resulting from nonspecific hybridization are absent. The method shows considerable potential for high-throughput screening of HLA-DR polymorphism in a chip-based format, including rapid tissue typing of unrelated volunteer donors.

Probing Modified Gravity with Double Pulsars

NASA Astrophysics Data System (ADS)

Deng, Xue-Mei; Xie, Yi; Huang, Tian-Yi

2015-01-01

Although Einstein's general relativity has passed all the tests so far, alternative theories are still required for deeper understanding of the nature of gravity. Double pulsars provide us a significant opportunity to test them. In order to probe some modified gravities which try to explain some astrophysical phenomena without dark matter, we use periastron advance dot ω of four binary pulsars (PSR B1913+16, PSR B1534+12, PSR J0737-3039 and PSR B2127+11C) to constrain their Yukawa parameters: λ = (3.97 ± 0.01) × 108m and α = (2.40 ± 0.02) × 10-8. It might help us to distinguish different gravity theories and get closer to the new physics.

Structure of the Iconic Vega Debris Disk

NASA Astrophysics Data System (ADS)

Su, Kate

2015-10-01

Debris structures provide the best means to explore planets down to ice-giant masses in the outer (>5 AU) parts of extrasolar planetary systems. It is thought that the iconic Vega debris disk composes of two separate belts shepherded by unseen planets, similar to the Solar System. We will probe this possibility with SOFIA at 35 microns by: 1.) documenting the structure of the debris with sufficient resolution to distinguish a separate warm belt from the alternative model of dust flowing inward from the outer debris ring; and 2.) testing for traces of dust in its 15-60 AU zone and thus probing the possibility that ice giant planets may be shepherding the debris belts.

The Mars Microprobe Mission: Advanced Micro-Avionics for Exploration Surface

NASA Astrophysics Data System (ADS)

Blue, Randel

2000-01-01

The Mars Microprobe Mission is the second spacecraft developed as part of the New Millennium Program deep space missions. The objective of the Microprobe Project is to demonstrate the applicability of key technologies for future planetary missions by developing two probes for deployment on Mars. The probes are designed with a single stage entry, descent, and landing system and impact the Martian surface at speeds of approximately 200 meters per second. The microprobes are composed of two main sections, a forebody section that penetrates to a depth below the Martian surface of 0.5 to 2 meters, and an aftbody section that remains on the surface. Each probe system consists of a number of advanced technology components developed specifically for this mission. These include a non-erosive aeroshell for entry into. the atmosphere, a set of low temperature batteries to supply probe power, an advanced microcontroller to execute the mission sequence, collect the science data, and react to possible system fault conditions, a telecommunications subsystem implemented on a set of custom integrated circuits, and instruments designed to provide science measurements from above and below the Martian surface. All of the electronic components have been designed and fabricated to withstand the severe impact shock environment and to operate correctly at predicted temperatures below -100 C.

Fiber optic probe for light scattering measurements

DOEpatents

Nave, Stanley E.; Livingston, Ronald R.; Prather, William S.

1995-01-01

A fiber optic probe and a method for using the probe for light scattering analyses of a sample. The probe includes a probe body with an inlet for admitting a sample into an interior sample chamber, a first optical fiber for transmitting light from a source into the chamber, and a second optical fiber for transmitting light to a detector such as a spectrophotometer. The interior surface of the probe carries a coating that substantially prevents non-scattered light from reaching the second fiber. The probe is placed in a region where the presence and concentration of an analyte of interest are to be detected, and a sample is admitted into the chamber. Exciting light is transmitted into the sample chamber by the first fiber, where the light interacts with the sample to produce Raman-scattered light. At least some of the Raman-scattered light is received by the second fiber and transmitted to the detector for analysis. Two Raman spectra are measured, at different pressures. The first spectrum is subtracted from the second to remove background effects, and the resulting sample Raman spectrum is compared to a set of stored library spectra to determine the presence and concentration of the analyte.

Building versatile bipartite probes for quantum metrology

NASA Astrophysics Data System (ADS)

Farace, Alessandro; De Pasquale, Antonella; Adesso, Gerardo; Giovannetti, Vittorio

2016-01-01

We consider bipartite systems as versatile probes for the estimation of transformations acting locally on one of the subsystems. We investigate what resources are required for the probes to offer a guaranteed level of metrological performance, when the latter is averaged over specific sets of local transformations. We quantify such a performance via the average skew information (AvSk), a convex quantity which we compute in closed form for bipartite states of arbitrary dimensions, and which is shown to be strongly dependent on the degree of local purity of the probes. Our analysis contrasts and complements the recent series of studies focused on the minimum, rather than the average, performance of bipartite probes in local estimation tasks, which was instead determined by quantum correlations other than entanglement. We provide explicit prescriptions to characterize the most reliable states maximizing the AvSk, and elucidate the role of state purity, separability and correlations in the classification of optimal probes. Our results can help in the identification of useful resources for sensing, estimation and discrimination applications when complete knowledge of the interaction mechanism realizing the local transformation is unavailable, and access to pure entangled probes is technologically limited.

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

PubMed

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

2017-12-01

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

Fiber optic probe for light scattering measurements

DOEpatents

Nave, S.E.; Livingston, R.R.; Prather, W.S.

1993-01-01

This invention is comprised of a fiber optic probe and a method for using the probe for light scattering analyses of a sample. The probe includes a probe body with an inlet for admitting a sample into an interior sample chamber, a first optical fiber for transmitting light from a source into the chamber, and a second optical fiber for transmitting light to a detector such as a spectrophotometer. The interior surface of the probe carries a coating that substantially prevents non-scattered light from reaching the second fiber. The probe is placed in a region where the presence and concentration of an analyte of interest are to be detected, and a sample is admitted into the chamber. Exciting light is transmitted into the sample chamber by the first fiber, where the light interacts with the sample to produce Raman-scattered light. At least some of the Raman- scattered light is received by the second fiber and transmitted to the detector for analysis. Two Raman spectra are measured, at different pressures. The first spectrum is subtracted from the second to remove background effects, and the resulting sample Raman spectrum is compared to a set of stored library spectra to determine the presence and concentration of the analyte.

Tracer diffusion in active suspensions

NASA Astrophysics Data System (ADS)

Burkholder, Eric W.; Brady, John F.

2017-05-01

We study the diffusion of a Brownian probe particle of size R in a dilute dispersion of active Brownian particles of size a , characteristic swim speed U0, reorientation time τR, and mechanical energy ksTs=ζaU02τR/6 , where ζa is the Stokes drag coefficient of a swimmer. The probe has a thermal diffusivity DP=kBT /ζP , where kBT is the thermal energy of the solvent and ζP is the Stokes drag coefficient for the probe. When the swimmers are inactive, collisions between the probe and the swimmers sterically hinder the probe's diffusive motion. In competition with this steric hindrance is an enhancement driven by the activity of the swimmers. The strength of swimming relative to thermal diffusion is set by Pes=U0a /DP . The active contribution to the diffusivity scales as Pes2 for weak swimming and Pes for strong swimming, but the transition between these two regimes is nonmonotonic. When fluctuations in the probe motion decay on the time scale τR, the active diffusivity scales as ksTs/ζP : the probe moves as if it were immersed in a solvent with energy ksTs rather than kBT .

Probing the coagulation pathway with aptamers identifies combinations that synergistically inhibit blood clot formation

PubMed Central

Bompiani, Kristin M; Lohrmann, Jens L; Pitoc, George A; Frederiksen, James W; Mackensen, George B; Sullenger, Bruce A

2014-01-01

SUMMARY Coordinated enzymatic reactions regulate blood clot generation. To explore the contributions of various coagulation enzymes in this process, we utilized a panel of aptamers against factors VIIa, IXa, Xa, and prothrombin. Each aptamer dose-dependently inhibited clot formation, yet none was able to completely impede this process in highly procoagulant settings. However several combinations of two aptamers synergistically impaired clot formation. One extremely potent aptamer combination was able to maintain human blood fluidity even during extracorporeal circulation, a highly procoagulant setting encountered during cardiopulmonary bypass surgery. Moreover, this aptamer cocktail could be rapidly reversed with antidotes to restore normal hemostasis, indicating that even highly potent aptamer combinations can be rapidly controlled. These studies highlight the potential utility of using sets of aptamers to probe the functions of proteins in molecular pathways for research and therapeutic ends. PMID:25065530

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.

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.

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

Design and validation of a real-time RT-PCR for the simultaneous detection of enteroviruses and parechoviruses in clinical samples.

PubMed

Cabrerizo, María; Calvo, Cristina; Rabella, Nuria; Muñoz-Almagro, Carmen; del Amo, Eva; Pérez-Ruiz, Mercedes; Sanbonmatsu-Gámez, Sara; Moreno-Docón, Antonio; Otero, Almudena; Trallero, Gloria

2014-11-01

Human enteroviruses (EVs) and parechoviruses (HPeVs) are important etiological agents causing infections such as meningitis, encephalitis and sepsis-like disease in neonates and young children. We have developed a real-time RT-PCR for simultaneous detection of EV and HPeV in clinical samples. Primers and probe sets were designed from the conserved 5'-noncoding region of the genomes. The sensitivity, specificity and reproducibility of the technique were measured using a set of 25 EV and 6 HPeV types. All EVs but no HPeVs were detected with the EV primers-probe set. The HPeV primers-probe set detected only the 6 HPeV types. The lower detection limit was found to be 4 and 40CCID50/ml for HPeV and EV respectively, demonstrating high sensitivity of the technique for both viruses. The threshold cycle values were highly reproducible on repeat testing of positive controls among assay runs. The assay was evaluated in 53 clinical samples of suspected meningitis, sepsis or febrile syndromes from children under 3 years. In 11 of these (21%) EVs were detected, while 4, i.e. 7.5%, were HPeV positive. Molecular typing was carried out for 73% of the viruses. In summary, the RT-PCR method developed demonstrated effectively both EV and HPeV detection, which can cause similar clinical symptoms in infants. Copyright © 2014 Elsevier B.V. All rights reserved.

Morpholine Derivative-Functionalized Carbon Dots-Based Fluorescent Probe for Highly Selective Lysosomal Imaging in Living Cells.

PubMed

Wu, Luling; Li, Xiaolin; Ling, Yifei; Huang, Chusen; Jia, Nengqin

2017-08-30

The development of a suitable fluorescent probe for the specific labeling and imaging of lysosomes through the direct visual fluorescent signal is extremely important for understanding the dysfunction of lysosomes, which might induce various pathologies, including neurodegenerative diseases, cancer, and Alzheimer's disease. Herein, a new carbon dot-based fluorescent probe (CDs-PEI-ML) was designed and synthesized for highly selective imaging of lysosomes in live cells. In this probe, PEI (polyethylenimine) is introduced to improve water solubility and provide abundant amine groups for the as-prepared CDs-PEI, and the morpholine group (ML) serves as a targeting unit for lysosomes. More importantly, passivation with PEI could dramatically increase the fluorescence quantum yield of CDs-PEI-ML as well as their stability in fluorescence emission under different excitation wavelength. Consequently, experimental data demonstrated that the target probe CDs-PEI-ML has low cytotoxicity and excellent photostability. Additionally, further live cell imaging experiment indicated that CDs-PEI-ML is a highly selective fluorescent probe for lysosomes. We speculate the mechanism for selective staining of lysosomes that CDs-PEI-ML was initially taken up by lysosomes through the endocytic pathway and then accumulated in acidic lysosomes. It is notable that there was less diffusion of CDs-PEI-ML into cytoplasm, which could be ascribed to the presence of lysosome target group morpholine on surface of CDs-PEI-ML. The blue emission wavelength combined with the high photo stability and ability of long-lasting cell imaging makes CDs-PEI-ML become an alternative fluorescent probe for multicolor labeling and long-term tracking of lysosomes in live cells and the potential application in super-resolution imaging. To best of our knowledge, there are still limited carbon dots-based fluorescent probes that have been studied for specific lysosomal imaging in live cells. The concept of surface functionality of carbon dots will also pave a new avenue for developing carbon dots-based fluorescent probes for subcellular labeling.

Magnetic and Langmuir Probe Measurements on the Plasmoid Thruster Experiment (PTX)

NASA Technical Reports Server (NTRS)

Koelfgen, Syri J.; Eskridge, Richard; Lee, Michael H.; Martin, Adam; Hawk, Clark W.; Fimognan, Peter

2004-01-01

The Plasmoid Thruster Experiment (PTX) operates by inductively producing plasmoids in a conical theta-pinch coil and ejecting them at high velocity. A plasmoid is a plasma with an imbedded closed magnetic field structure. The shape and magnetic field structure of the translating plasmoids have been measured with of an array of magnetic field probes. Six sets of two B-dot probes were constructed for measuring B(sub z) and B(sub theta), the axial and azimuthal components of the magnetic field. The probes are wound on a square G10 form, and have an average (calibrated) NA of 9.37 x l0(exp -5) square meters, where N is the number of turns and A is the cross-sectional area. The probes were calibrated with a Helmholtz coil, driven by a high-voltage pulser to measure NA, and by a signal generator to determine the probe's frequency response. The plasmoid electron number density n(sub e) electron temperature T(sub e), and velocity ratio v/c(sub m), (where v is the bulk plasma flow velocity and c(sub m), is the ion thermal speed) have also been measured with a quadruple Langmuir probe. The Langmuir probe tips are 10 mm long, 20-mil diameter stainless steel wire, housed in a 6-inch long 4-bore aluminum rod. Measurements on PTX with argon and hydrogen from the magnetic field probes and quadruple Langmuir probe will be presented in this paper.

Proton Probing using the T-Cubed Laser

NASA Astrophysics Data System (ADS)

Kordell, Peter; Campbell, Paul; Willingale, Louise; Maksimchuk, Anatoly; Krushelnick, Karl; Tubman, Eleanor; Woolsey, Nigel

2015-11-01

The University of Michigan's 20 TW, 400 fs pulse T-cubed laser can produce proton beams of up to 7.2 MeV through target normal sheeth acceleration. The proton flux at 4 MeV produces sufficient signal on Radiochromic Film for use as an ultrafast, electromagnetic field diagnostic. A two beam experiment has been set-up to enable co-timed, pump-probe relativistic intensity interactions. We present an evaluation of the flux, uniformity, energy and laminar flow of the proton probe for future use in imaging of a simple wire target interaction. This work was supported by the DOE (Grant No. DE-SC0012327).

Evaluation of the UFXC32k photon-counting detector for pump-probe experiments using synchrotron radiation.

PubMed

Koziol, Anna; Bordessoule, Michel; Ciavardini, Alessandra; Dawiec, Arkadiusz; Da Silva, Paulo; Desjardins, Kewin; Grybos, Pawel; Kanoute, Brahim; Laulhe, Claire; Maj, Piotr; Menneglier, Claude; Mercere, Pascal; Orsini, Fabienne; Szczygiel, Robert

2018-03-01

This paper presents the performance of a single-photon-counting hybrid pixel X-ray detector with synchrotron radiation. The camera was evaluated with respect to time-resolved experiments, namely pump-probe-probe experiments held at SOLEIL. The UFXC camera shows very good energy resolution of around 1.5 keV and allows the minimum threshold setting to be as low as 3 keV keeping the high-count-rate capabilities. Measurements of a synchrotron characteristic filling mode prove the proper separation of an isolated bunch of photons and the usability of the detector in time-resolved experiments.

Analysis of multicrystal pump–probe data sets. I. Expressions for the RATIO model

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

Fournier, Bertrand; Coppens, Philip

2014-08-30

The RATIO method in time-resolved crystallography [Coppenset al.(2009).J. Synchrotron Rad.16, 226–230] was developed for use with Laue pump–probe diffraction data to avoid complex corrections due to wavelength dependence of the intensities. The application of the RATIO method in processing/analysis prior to structure refinement requires an appropriate ratio model for modeling the light response. The assessment of the accuracy of pump–probe time-resolved structure refinements based on the observed ratios was discussed in a previous paper. In the current paper, a detailed ratio model is discussed, taking into account both geometric and thermal light-induced changes.

Majority Teachers' Perceptions of Urban Adolescents and Their Abilities: Probes from Self-Reflection and Teacher Autobiographies

ERIC Educational Resources Information Center

Harushimana, Immaculee

2010-01-01

This article presents a small scale, qualitative study of nine majority alternate-route teachers and the perceptions they hold about themselves as urban educators and their urban students' academic abilities. Data for this study was collected through self-reflective, written interviews and meta-reflective responses to two published teacher…

Model Analysis of Fine Structures of Student Models: An Example with Newton's Third Law.

ERIC Educational Resources Information Center

Bao, Lei; Hogg, Kirsten; Zollman, Dean

2002-01-01

Studies the role of context in students' uses of alternative conceptual models by using Newton's third law. Identifies four contextual features that are frequently used by students in their reasoning. Probes the effects of specific contextual features on student reasoning using a multiple-choice survey. (Contains 39 references.) (Author/YDS)

European Scientific Notes. Volume 37, Numbers 12.

DTIC Science & Technology

1983-12-01

Hamburg during August. This article highlights some of the papers dealing with oceano- graphy, geology, and geophysics. ENERGY Egypt’s Energy Crisis...little progress in developing alternative sources of energy . ENGINEERING Leeds-Lyon Tribology Conference ................................. Harold’G...probe the structure of the electric field in collective ion acceleration experiments. Energy -Transfer Processes in Condensed Matter

Flexible Staffing and Scheduling in U.S. Corporations. Research Bulletin No. 240.

ERIC Educational Resources Information Center

Christensen, Kathleen

A national survey in 1988 probed the use of flexible staffing and scheduling alternatives in 521 of the largest U.S. corporations. Company executives indicated they expected their companies to decrease their rate of growth of contingent staffing and increase their use of flextime, job sharing, and home-based work. Several specifics stood out…

Structure Determination of Cisplatin-Amino Acid Analogues by Infrared Multiple Photon Dissociation Action Spectroscopy

NASA Astrophysics Data System (ADS)

He, Chenchen; Bao, Xun; Zhu, Yanlong; Strobehn, Stephen; Kimutai, Bett; Nei, Y.-W.; Chow, C. S.; Rodgers, M. T.; Gao, Juehan; Oomens, J.

2015-06-01

To gain a better understanding of the binding mechanism and assist in the optimization of relevant drug and chemical probe design, both experimental and theoretical studies were performed on a series of amino acid-linked cisplatin derivatives, including glycine-, lysine-, and ornithine-linked cisplatin, Gplatin, Kplatin, and Oplatin, respectively. Cisplatin, the first FDA-approved platinum-based anticancer drug, has been widely used in cancer chemotherapy. Its pharmacological mechanism has been identified as its ability to coordinate to genomic DNA, and guanine is its major target. In previous reports, cisplatin was successfully utilized as a chemical probe to detect solvent accessible sites in ribosomal RNA (rRNA). Among the amino-acid-linked cisplatin derivatives, Oplatin exhibits preference for adenine over guanine. The mechanism behind its different selectivity compared to cisplatin may relate to its potential of forming a hydrogen bond between the carboxylate group in Pt (II) complex and the 6-amino moiety of adenosine stabilizes A-Oplatin products. Tandem mass spectrometry analysis also indicates that different coordination sites of Oplatin on adenosine affect glycosidic bond stability. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments were performed on all three amino acid-linked cisplatin to characterize their structures. An extensive theoretical study has been performed on Gplatin to guide the selection of the most effective theory and basis set based on its geometric information. The results for Gplatin provide the foundation for characterization of the more complex amino acid-linked cisplatin derivatives, Oplatin and Kplatin. Structural and energetic information elucidated for these compounds, particularly Oplatin reveal the reason for its alternative selectivity compared to cisplatin.

Alternative medicine in the workplace.

PubMed

Lippin, R A

1996-01-01

Workplace settings are ripe for the application of alternative medical interventions for a variety of reasons. Included among them are a shared interest in prevention by both the occupational and alternative medicine communities, economic incentives by corporations as major purchasers of healthcare to reduce healthcare costs and improve employee productivity, and the willingness of corporations to be differentially creative in their approach to delivering and purchasing healthcare. This paper describes the US workforce in transition, provides an overview of occupational medicine including current programs and emerging issues, describes the current applications of alternative medicine interventions in the workplace, and argues for future expanded application of alternative medicine in workplace settings.

Providing Behavioral Feedback to Students in an Alternative High School Setting

ERIC Educational Resources Information Center

Whitcomb, Sara A.; Hefter, Sheera; Barker, Elizabeth

2016-01-01

This column provides an example method for improving the consistency and quality of daily behavioral feedback provided to students in an alternative high school setting. Often, homeroom or advisory periods are prime points in the day for students to review their behavior from the previous day and set goals for a successful day to come. The method…

An Interactive Microcomputer Program for Teaching the Impacts of Alternative Policy Sets in the Market for a Single Commodity.

ERIC Educational Resources Information Center

Li, Elton; Stoecker, Arthur

1995-01-01

Describes a computer software program where students define alternative policy sets and compare their effects on the welfare of consumers, producers, and the public sector. Policy sets may be a single tax or quota or a mix of taxes, subsidies, and/or price supports implemented in the marketing chain. (MJP)

A Quantitative Approach to Determine Analogous Areas Using Environmental Parameters

DTIC Science & Technology

2008-03-01

degrees Celsius COADS Comprehensive Ocean - Atmosphere Data Set CONUS Continental United States CTD Conductivity/Temperature/Depth probe...consolidation of a marine database. Out of this effort came the Comprehensive Ocean - Atmosphere Data Set (COADS). The original 17 data sets were...National Oceanic and Atmospheric Administration (NOAA) has compiled a database of total sediment thickness of the global oceans and seas. These data are

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions.

PubMed

Singh, Anuradha; Mantri, Shrikant; Sharma, Monica; Chaudhury, Ashok; Tuli, Rakesh; Roy, Joy

2014-01-16

The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study identified several quality related key genes including many other genes, their interactions (quality x development) and temporal and spatial distributions. The candidate genes identified for processing quality and information on temporal and spatial distributions of their expressions would be useful for designing wheat improvement programs for processing quality either by changing their expression or development of single nucleotide polymorphisms (SNPs) markers.

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

PubMed Central

2014-01-01

Background The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Results Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study identified several quality related key genes including many other genes, their interactions (quality x development) and temporal and spatial distributions. Conclusions The candidate genes identified for processing quality and information on temporal and spatial distributions of their expressions would be useful for designing wheat improvement programs for processing quality either by changing their expression or development of single nucleotide polymorphisms (SNPs) markers. PMID:24433256

Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns.

PubMed

Peng, Tao; Bonamy, Ghislain M C; Glory-Afshar, Estelle; Rines, Daniel R; Chanda, Sumit K; Murphy, Robert F

2010-02-16

Many proteins or other biological macromolecules are localized to more than one subcellular structure. The fraction of a protein in different cellular compartments is often measured by colocalization with organelle-specific fluorescent markers, requiring availability of fluorescent probes for each compartment and acquisition of images for each in conjunction with the macromolecule of interest. Alternatively, tailored algorithms allow finding particular regions in images and quantifying the amount of fluorescence they contain. Unfortunately, this approach requires extensive hand-tuning of algorithms and is often cell type-dependent. Here we describe a machine-learning approach for estimating the amount of fluorescent signal in different subcellular compartments without hand tuning, requiring only the acquisition of separate training images of markers for each compartment. In testing on images of cells stained with mixtures of probes for different organelles, we achieved a 93% correlation between estimated and expected amounts of probes in each compartment. We also demonstrated that the method can be used to quantify drug-dependent protein translocations. The method enables automated and unbiased determination of the distributions of protein across cellular compartments, and will significantly improve imaging-based high-throughput assays and facilitate proteome-scale localization efforts.