Statistical method evaluation for differentially methylated CpGs in base resolution next-generation DNA sequencing data.

PubMed

Zhang, Yun; Baheti, Saurabh; Sun, Zhifu

2018-05-01

High-throughput bisulfite methylation sequencing such as reduced representation bisulfite sequencing (RRBS), Agilent SureSelect Human Methyl-Seq (Methyl-seq) or whole-genome bisulfite sequencing is commonly used for base resolution methylome research. These data are represented either by the ratio of methylated cytosine versus total coverage at a CpG site or numbers of methylated and unmethylated cytosines. Multiple statistical methods can be used to detect differentially methylated CpGs (DMCs) between conditions, and these methods are often the base for the next step of differentially methylated region identification. The ratio data have a flexibility of fitting to many linear models, but the raw count data take consideration of coverage information. There is an array of options in each datatype for DMC detection; however, it is not clear which is an optimal statistical method. In this study, we systematically evaluated four statistic methods on methylation ratio data and four methods on count-based data and compared their performances with regard to type I error control, sensitivity and specificity of DMC detection and computational resource demands using real RRBS data along with simulation. Our results show that the ratio-based tests are generally more conservative (less sensitive) than the count-based tests. However, some count-based methods have high false-positive rates and should be avoided. The beta-binomial model gives a good balance between sensitivity and specificity and is preferred method. Selection of methods in different settings, signal versus noise and sample size estimation are also discussed.

Highly labeled methylene blue-ds DNA silica nanoparticles for signal enhancement of immunoassays: application to the sensitive detection of bacteria in human platelet concentrates.

PubMed

Bonnet, Romaric; Farre, Carole; Valera, Lionel; Vossier, Ludivine; Léon, Fanny; Dagland, Typhaine; Pouzet, Agnès; Jaffrézic-Renault, Nicole; Fareh, Jeannette; Fournier-Wirth, Chantal; Chaix, Carole

2018-05-15

A nanoparticle-based electrochemical sandwich immunoassay was developed for bacteria detection in platelet concentrates. For the assay, magnetic beads were functionalized with antibodies to allow the specific capture of bacteria from the complex matrix, and innovative methylene blue-DNA/nanoparticle assemblies provided the electrochemical response for amplified detection. This nanoparticular system was designed as a temperature-sensitive nano-tool for electrochemical detection. First, oligonucleotide-functionalized nanoparticles were obtained by direct synthesis of the DNA strands on the nanoparticle surface using an automated oligonucleotide synthesizer. Densely packed DNA coverage was thus obtained. Then, DNA duplexes were constructed on the NP surface with a complementary strand bearing a 3 methylene blue tag. This strategy ultimately produced highly functionalized nanoparticles with electrochemical markers. These assemblies enabled amplification of the electrochemical signal, resulting in a very good sensitivity. A proof-of-concept was carried out for E. coli detection in human platelet concentrates. Bacterial contamination of this complex biological matrix is the highest residual infectious risk in blood transfusion. The development of a rapid assay that could reach 10-102 CFU mL-1 sensitivity is a great challenge. The nanoparticle-based electrochemical sandwich immunoassay carried out on a boron doped diamond electrode proved to be sensitive for E. coli detection in human platelets. Two antibody pairs were used to develop either a generic assay against certain Gram negative strains or a specific assay for E. coli. The methylene blue-DNA/nanoparticles amplify sensitivity ×1000 compared with the assay run without NPs for electrochemical detection. A limit of detection of 10 CFU mL-1 in a biological matrix was achieved for E. coli using the highly specific antibody pair.

Broadband pump-probe spectroscopy at 20-MHz modulation frequency.

PubMed

Preda, Fabrizio; Kumar, Vikas; Crisafi, Francesco; Figueroa Del Valle, Diana Gisell; Cerullo, Giulio; Polli, Dario

2016-07-01

We introduce an innovative high-sensitivity broadband pump-probe spectroscopy system, based on Fourier-transform detection, operating at 20-MHz modulation frequency. A common-mode interferometer employing birefringent wedges creates two phase-locked delayed replicas of the broadband probe pulse, interfering at a single photodetector. A single-channel lock-in amplifier demodulates the interferogram, whose Fourier transform provides the differential transmission spectrum. Our approach combines broad spectral coverage with high sensitivity, due to high-frequency modulation and detection. We demonstrate its performances by measuring two-dimensional differential transmission maps of a carbon nanotubes sample, simultaneously acquiring the signal over the entire 950-1350 nm range with 2.7·10^-6  rms noise over 1.5 s integration time.

Zwitterion functionalized gold nanoclusters for multimodal near infrared fluorescence and photoacoustic imaging

NASA Astrophysics Data System (ADS)

Shen, Danjin; Henry, Maxime; Trouillet, Vanessa; Comby-Zerbino, Clothilde; Bertorelle, Franck; Sancey, Lucie; Antoine, Rodolphe; Coll, Jean-Luc; Josserand, Véronique; Le Guével, Xavier

2017-05-01

Gold nanoclusters (Au NCs) are an emerging type of theranostic agents combining therapeutic and imaging features with reduced toxicity. Au NCs stabilized by a zwitterion ligand with a fine control of the metal core size and the ligand coverage were synthesized by wet chemistry. Intense fluorescence signal is reported for the highest ligand coverage, whereas photoacoustic signal is stronger for the largest metal core. The best Au NC candidate with an average molecular weight of 17 kDa could be detected with high sensitivity on a 2D-near-infrared imaging instrument (limit of detection (LOD) = 2.3 μ M ) and by photoacoustic imaging. In vitro and in vivo experiments demonstrate an efficient cell uptake in U87 cell lines, a fast renal clearance (t1 /2 α = 6.5 ± 1.3 min), and a good correlation between near infrared fluorescence and photoacoustic measurements to follow the early uptake of Au NCs in liver.

Validation of a next-generation sequencing assay for clinical molecular oncology.

PubMed

Cottrell, Catherine E; Al-Kateb, Hussam; Bredemeyer, Andrew J; Duncavage, Eric J; Spencer, David H; Abel, Haley J; Lockwood, Christina M; Hagemann, Ian S; O'Guin, Stephanie M; Burcea, Lauren C; Sawyer, Christopher S; Oschwald, Dayna M; Stratman, Jennifer L; Sher, Dorie A; Johnson, Mark R; Brown, Justin T; Cliften, Paul F; George, Bijoy; McIntosh, Leslie D; Shrivastava, Savita; Nguyen, Tudung T; Payton, Jacqueline E; Watson, Mark A; Crosby, Seth D; Head, Richard D; Mitra, Robi D; Nagarajan, Rakesh; Kulkarni, Shashikant; Seibert, Karen; Virgin, Herbert W; Milbrandt, Jeffrey; Pfeifer, John D

2014-01-01

Currently, oncology testing includes molecular studies and cytogenetic analysis to detect genetic aberrations of clinical significance. Next-generation sequencing (NGS) allows rapid analysis of multiple genes for clinically actionable somatic variants. The WUCaMP assay uses targeted capture for NGS analysis of 25 cancer-associated genes to detect mutations at actionable loci. We present clinical validation of the assay and a detailed framework for design and validation of similar clinical assays. Deep sequencing of 78 tumor specimens (≥ 1000× average unique coverage across the capture region) achieved high sensitivity for detecting somatic variants at low allele fraction (AF). Validation revealed sensitivities and specificities of 100% for detection of single-nucleotide variants (SNVs) within coding regions, compared with SNP array sequence data (95% CI = 83.4-100.0 for sensitivity and 94.2-100.0 for specificity) or whole-genome sequencing (95% CI = 89.1-100.0 for sensitivity and 99.9-100.0 for specificity) of HapMap samples. Sensitivity for detecting variants at an observed 10% AF was 100% (95% CI = 93.2-100.0) in HapMap mixes. Analysis of 15 masked specimens harboring clinically reported variants yielded concordant calls for 13/13 variants at AF of ≥ 15%. The WUCaMP assay is a robust and sensitive method to detect somatic variants of clinical significance in molecular oncology laboratories, with reduced time and cost of genetic analysis allowing for strategic patient management. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

SNM detection with an optimized water Cherenkov neutron detector

NASA Astrophysics Data System (ADS)

Dazeley, S.; Sweany, M.; Bernstein, A.

2012-11-01

Special Nuclear Material (SNM) can either spontaneously fission or be induced to do so: either case results in neutron emission. For this reason, neutron detection performs a crucial role in the functionality of Radiation Portal Monitoring (RPM) devices. Since neutrons are highly penetrating and difficult to shield, they could potentially be detected escaping even a well-shielded cargo container. If the shielding were sophisticated, detecting escaping neutrons would require a highly efficient detector with close to full solid angle coverage. In 2008, we reported the successful detection of neutrons with a 250 liter (l) gadolinium doped water Cherenkov prototype [1]—a technology that could potentially be employed cost effectively with full solid angle coverage. More recently we have built and tested both 1-kl and 3.5-kl versions [2], demonstrating that very large, cost effective, non-flammable and environmentally benign neutron detectors can be operated efficiently without being overwhelmed by background. In this paper, we present a new design for a modular system of water-based neutron detectors that could be deployed as a real RPM. The modules contain a number of optimizations that have not previously been combined within a single system. We present simulations of the new system, based on the performance of our previous detectors. Our simulations indicate that an optimized system such as is presented here could achieve SNM sensitivity competitive with a large 3He-based system. Moreover, the realization of large, cost effective neutron detectors could, for the first time, enable the detection of multiple neutrons per fission from within a large object such as a cargo container. Such a signal would provide a robust indication of the presence of fissioning material, reducing the frequency of false alarms while increasing sensitivity.

SNM Detection with an Optimized Water Cherenkov Neutron Detector

DOE PAGES

Dazeley, S.; Sweany, M.; Bernstein, A.

2012-07-23

Special Nuclear Material (SNM) can either spontaneously fission or be induced to do so: either case results in neutron emission. For this reason, neutron detection performs a crucial role in the functionality of Radiation Portal Monitoring (RPM) devices. Since neutrons are highly penetrating and difficult to shield, they could potentially be detected escaping even a well-shielded cargo container. If the shielding were sophisticated, detecting escaping neutrons would require a highly efficient detector with close to full solid angle coverage. In 2008, we reported the successful detection of neutrons with a 250 liter (l) gadolinium doped water Cherenkov prototype—a technology thatmore » could potentially be employed cost effectively with full solid angle coverage. More recently we have built and tested both 1-kl and 3.5-kl versions, demonstrating that very large, cost effective, non-flammable and environmentally benign neutron detectors can be operated efficiently without being overwhelmed by background. In our paper, we present a new design for a modular system of water-based neutron detectors that could be deployed as a real RPM. The modules contain a number of optimizations that have not previously been combined within a single system. We present simulations of the new system, based on the performance of our previous detectors. These simulations indicate that an optimized system such as is presented here could achieve SNM sensitivity competitive with a large 3He-based system. Moreover, the realization of large, cost effective neutron detectors could, for the first time, enable the detection of multiple neutrons per fission from within a large object such as a cargo container. Such a signal would provide a robust indication of the presence of fissioning material, reducing the frequency of false alarms while increasing sensitivity.« less

Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases is Highly Accurate and Reproducible and More Sensitive for Variant Detection Than Exome Sequencing

PubMed Central

Bujakowska, Kinga M.; Sousa, Maria E.; Fonseca-Kelly, Zoë D.; Taub, Daniel G.; Janessian, Maria; Wang, Dan Yi; Au, Elizabeth D.; Sims, Katherine B.; Sweetser, David A.; Fulton, Anne B.; Liu, Qin; Wiggs, Janey L.; Gai, Xiaowu; Pierce, Eric A.

2015-01-01

Purpose Next-generation sequencing (NGS) based methods are being adopted broadly for genetic diagnostic testing, but the performance characteristics of these techniques have not been fully defined with regard to test accuracy and reproducibility. Methods We developed a targeted enrichment and NGS approach for genetic diagnostic testing of patients with inherited eye disorders, including inherited retinal degenerations, optic atrophy and glaucoma. In preparation for providing this Genetic Eye Disease (GEDi) test on a CLIA-certified basis, we performed experiments to measure the sensitivity, specificity, reproducibility as well as the clinical sensitivity of the test. Results The GEDi test is highly reproducible and accurate, with sensitivity and specificity for single nucleotide variant detection of 97.9% and 100%, respectively. The sensitivity for variant detection was notably better than the 88.3% achieved by whole exome sequencing (WES) using the same metrics, due to better coverage of targeted genes in the GEDi test compared to commercially available exome capture sets. Prospective testing of 192 patients with IRDs indicated that the clinical sensitivity of the GEDi test is high, with a diagnostic rate of 51%. Conclusion The data suggest that based on quantified performance metrics, selective targeted enrichment is preferable to WES for genetic diagnostic testing. PMID:25412400

Circulating vaccine-derived polioviruses: current state of knowledge.

PubMed Central

Kew, Olen M.; Wright, Peter F.; Agol, Vadim I.; Delpeyroux, Francis; Shimizu, Hiroyuki; Nathanson, Neal; Pallansch, Mark A.

2004-01-01

Within the past 4 years, poliomyelitis outbreaks associated with circulating vaccine-derived polioviruses (cVDPVs) have occurred in Hispaniola (2000-01), the Philippines (2001), and Madagascar (2001-02). Retrospective studies have also detected the circulation of endemic cVDPV in Egypt (1988-93) and the likely localized spread of oral poliovirus vaccine (OPV)-derived virus in Belarus (1965-66). Gaps in OPV coverage and the previous eradication of the corresponding serotype of indigenous wild poliovirus were the critical risk factors for all cVDPV outbreaks. The cVDPV outbreaks were stopped by mass immunization campaigns using OPV. To increase sensitivity for detecting vaccine-derived polioviruses (VDPVs), in 2001 the Global Polio Laboratory Network implemented additional testing requirements for all poliovirus isolates under investigation. This approach quickly led to the recognition of the Philippines and Madagascar cVDPV outbreaks, but of no other current outbreaks. The potential risk of cVDPV emergence has increased dramatically in recent years as wild poliovirus circulation has ceased in most of the world. The risk appears highest for the type 2 OPV strain because of its greater tendency to spread to contacts. The emergence of cVDPVs underscores the critical importance of eliminating the last pockets of wild poliovirus circulation, maintaining universally high levels of polio vaccine coverage, stopping OPV use as soon as it is safely possible to do so, and continuing sensitive poliovirus surveillance into the foreseeable future. Particular attention must be given to areas where the risks for wild poliovirus circulation have been highest, and where the highest rates of polio vaccine coverage must be maintained to suppress cVDPV emergence. PMID:15106296

Detection and genotyping of HPV in urine samples from Chilean women attending primary health care centers.

PubMed

Vergara, Nicolás; Balanda, Monserrat; Hidalgo, Wilma; Martín, Héctor San; Aceituno, Alexis; Roldán, Francisco; Villalón, Tania; Hott, Melissa; Espinoza, Gloria; Quiero, Andrea; Valenzuela, María T; Ramírez, Eugenio

2018-04-01

Cervical cancer is the second most common malignant neoplasm in women worldwide representing approximately 10% of all types of cancers. Triage of women through cervical cytology has been an important strategy for the surveillance and control of new cases of cervical cancer. However, in many regions around the world cervical cytology has a low coverage compared to developed countries. The molecular detection of HPV is the most effective method to increase the screening sensitivity of women at risk of developing cervical cancer. There are very few studies about the efficacy of urine testing for detection of HPV in women followed up in primary health care centers. Consequently, the efficacy of using urine HPV screening in these populations has not been addressed yet. Here, we compared the detection of HPV in simultaneous urine and cervical samples of women followed up in primary health care centers. Urine and cervical samples were analyzed in 543 women attending at primary health care centers. HPV was detected by real time PCR, and HPV typing performed by PCR-RLB. A general HPV concordance of 86.2% (κ = 0.72) was determined between urine and cervical samples. The concordance for HPV-16 and 18 was almost perfect (κ = 0.82) and strong (κ = 0.77), respectively. The sensitivity and specificity for all HPV genotypes in urine using cervical samples as reference were 82.1 and 93.7%, respectively. The results showed that urine is a good alternative as clinical sample for HPV screening in women attending primary health care centers. Therefore, urine should be used as an alternative sample for increasing triage coverage either in refractory women participating in Pap surveillance programs or when cervical samples are not available.

Effect of Surface Coverage of Gold Nanoparticles on the Refractive Index Sensitivity in Fiber-Optic Nanoplasmonic Sensing.

PubMed

Wu, Wei-Te; Chen, Chien-Hsing; Chiang, Chang-Yue; Chau, Lai-Kwan

2018-05-31

A simple theoretical model was developed to analyze the extinction spectrum of gold nanoparticles (AuNPs) on the fiber core and glass surfaces in order to aid the determination of the surface coverage and surface distribution of the AuNPs on the fiber core surface for sensitivity optimization of the fiber optic particle plasmon resonance (FOPPR) sensor. The extinction spectrum of AuNPs comprises of the interband absorption of AuNPs, non-interacting plasmon resonance (PR) band due to isolated AuNPs, and coupled PR band of interacting AuNPs. When the surface coverage is smaller than 12.2%, the plasmon coupling effect can almost be ignored. This method is also applied to understand the refractive index sensitivity of the FOPPR sensor with respect to the non-interacting PR band and the coupled PR band. In terms of wavelength sensitivity at a surface coverage of 18.6%, the refractive index sensitivity of the coupled PR band (205.5 nm/RIU) is greater than that of the non-interacting PR band (349.1 nm/RIU). In terms of extinction sensitivity, refractive index sensitivity of the coupled PR band (-3.86/RIU) is similar to that of the non-interacting PR band (-3.93/RIU). Both maximum wavelength and extinction sensitivities were found at a surface coverage of 15.2%.

CNNdel: Calling Structural Variations on Low Coverage Data Based on Convolutional Neural Networks

PubMed Central

2017-01-01

Many structural variations (SVs) detection methods have been proposed due to the popularization of next-generation sequencing (NGS). These SV calling methods use different SV-property-dependent features; however, they all suffer from poor accuracy when running on low coverage sequences. The union of results from these tools achieves fairly high sensitivity but still produces low accuracy on low coverage sequence data. That is, these methods contain many false positives. In this paper, we present CNNdel, an approach for calling deletions from paired-end reads. CNNdel gathers SV candidates reported by multiple tools and then extracts features from aligned BAM files at the positions of candidates. With labeled feature-expressed candidates as a training set, CNNdel trains convolutional neural networks (CNNs) to distinguish true unlabeled candidates from false ones. Results show that CNNdel works well with NGS reads from 26 low coverage genomes of the 1000 Genomes Project. The paper demonstrates that convolutional neural networks can automatically assign the priority of SV features and reduce the false positives efficaciously. PMID:28630866

Cost-Utility Analysis of Extending Public Health Insurance Coverage to Include Diabetic Retinopathy Screening by Optometrists.

PubMed

van Katwyk, Sasha; Jin, Ya-Ping; Trope, Graham E; Buys, Yvonne; Masucci, Lisa; Wedge, Richard; Flanagan, John; Brent, Michael H; El-Defrawy, Sherif; Tu, Hong Anh; Thavorn, Kednapa

2017-09-01

Diabetic retinopathy (DR) is one of the leading causes of vision loss and blindness in Canada. Eye examinations play an important role in early detection. However, DR screening by optometrists is not always universally covered by public or private health insurance plans. This study assessed whether expanding public health coverage to include diabetic eye examinations for retinopathy by optometrists is cost-effective from the perspective of the health care system. We conducted a cost-utility analysis of extended coverage for diabetic eye examinations in Prince Edward Island to include examinations by optometrists, not currently publicly covered. We used a Markov chain to simulate disease burden based on eye examination rates and DR progression over a 30-year time horizon. Results were presented as an incremental cost per quality-adjusted life year (QALY) gained. A series of one-way and probabilistic sensitivity analyses were performed. Extending public health coverage to eye examinations by optometrists was associated with higher costs ($9,908,543.32) and improved QALYs (156,862.44), over 30 years, resulting in an incremental cost-effectiveness ratio of $1668.43/QALY gained. Sensitivity analysis showed that the most influential determinants of the results were the cost of optometric screening and selected utility scores. At the commonly used threshold of $50,000/QALY, the probability that the new policy was cost-effective was 99.99%. Extending public health coverage to eye examinations by optometrists is cost-effective based on a commonly used threshold of $50,000/QALY. Findings from this study can inform the decision to expand public-insured optometric services for patients with diabetes. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

A robust hypothesis test for the sensitive detection of constant speed radiation moving sources

NASA Astrophysics Data System (ADS)

Dumazert, Jonathan; Coulon, Romain; Kondrasovs, Vladimir; Boudergui, Karim; Moline, Yoann; Sannié, Guillaume; Gameiro, Jordan; Normand, Stéphane; Méchin, Laurence

2015-09-01

Radiation Portal Monitors are deployed in linear networks to detect radiological material in motion. As a complement to single and multichannel detection algorithms, inefficient under too low signal-to-noise ratios, temporal correlation algorithms have been introduced. Test hypothesis methods based on empirically estimated mean and variance of the signals delivered by the different channels have shown significant gain in terms of a tradeoff between detection sensitivity and false alarm probability. This paper discloses the concept of a new hypothesis test for temporal correlation detection methods, taking advantage of the Poisson nature of the registered counting signals, and establishes a benchmark between this test and its empirical counterpart. The simulation study validates that in the four relevant configurations of a pedestrian source carrier under respectively high and low count rate radioactive backgrounds, and a vehicle source carrier under the same respectively high and low count rate radioactive backgrounds, the newly introduced hypothesis test ensures a significantly improved compromise between sensitivity and false alarm. It also guarantees that the optimal coverage factor for this compromise remains stable regardless of signal-to-noise ratio variations between 2 and 0.8, therefore allowing the final user to parametrize the test with the sole prior knowledge of background amplitude.

A silicon-based peptide biosensor for label-free detection of cancer cells

NASA Astrophysics Data System (ADS)

Martucci, Nicola M.; Rea, Ilaria; Ruggiero, Immacolata; Terracciano, Monica; De Stefano, Luca; Migliaccio, Nunzia; Dardano, Principia; Arcari, Paolo; Rendina, Ivo; Lamberti, Annalisa

2015-05-01

Sensitive and accurate detection of cancer cells plays a crucial role in diagnosis of cancer and minimal residual disease, so being one of the most hopeful approaches to reduce cancer death rates. In this paper, a strategy for highly selective and sensitive detection of lymphoma cells on planar silicon-based biosensor has been evaluated. In this setting an Idiotype peptide, able to specifically bind the B-cell receptor (BCR) of A20 cells in mice engrafted with A20 lymphoma, has been covalently linked to the sensor active surface and used as molecular probe. The biochip here presented showed a coverage efficiency of 85% with a detection efficiency of 8.5×10-3 cells/μm2. The results obtained suggested an efficient way for specific label-free cell detection by using a silicon-based peptide biosensor. In addition, the present recognition strategy, besides being useful for the development of sensing devices capable of monitoring minimal residual disease, could be used to find and characterize new specific receptor-ligand interactions through the screening of a recombinant phage library.

Variation in Empiric Coverage Versus Detection of Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa in Hospitalizations for Community-Onset Pneumonia Across 128 US Veterans Affairs Medical Centers.

PubMed

Jones, Barbara E; Brown, Kevin Antoine; Jones, Makoto M; Huttner, Benedikt D; Greene, Tom; Sauer, Brian C; Madaras-Kelly, Karl; Rubin, Michael A; Bidwell Goetz, Matthew; Samore, Matthew H

2017-08-01

OBJECTIVE To examine variation in antibiotic coverage and detection of resistant pathogens in community-onset pneumonia. DESIGN Cross-sectional study. SETTING A total of 128 hospitals in the Veterans Affairs health system. PARTICIPANTS Hospitalizations with a principal diagnosis of pneumonia from 2009 through 2010. METHODS We examined proportions of hospitalizations with empiric antibiotic coverage for methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa (PAER) and with initial detection in blood or respiratory cultures. We compared lowest- versus highest-decile hospitals, and we estimated adjusted probabilities (AP) for patient- and hospital-level factors predicting coverage and detection using hierarchical regression modeling. RESULTS Among 38,473 hospitalizations, empiric coverage varied widely across hospitals (MRSA lowest vs highest, 8.2% vs 42.0%; PAER lowest vs highest, 13.9% vs 44.4%). Detection rates also varied (MRSA lowest vs highest, 0.5% vs 3.6%; PAER lowest vs highest, 0.6% vs 3.7%). Whereas coverage was greatest among patients with recent hospitalizations (AP for anti-MRSA, 54%; AP for anti-PAER, 59%) and long-term care (AP for anti-MRSA, 60%; AP for anti-PAER, 66%), detection was greatest in patients with a previous history of a positive culture (AP for MRSA, 7.9%; AP for PAER, 11.9%) and in hospitals with a high prevalence of the organism in pneumonia (AP for MRSA, 3.9%; AP for PAER, 3.2%). Low hospital complexity and rural setting were strong negative predictors of coverage but not of detection. CONCLUSIONS Hospitals demonstrated widespread variation in both coverage and detection of MRSA and PAER, but probability of coverage correlated poorly with probability of detection. Factors associated with empiric coverage (eg, healthcare exposure) were different from those associated with detection (eg, microbiology history). Providing microbiology data during empiric antibiotic decision making could better align coverage to risk for resistant pathogens and could promote more judicious use of broad-spectrum antibiotics. Infect Control Hosp Epidemiol 2017;38:937-944.

An Efficient Distributed Coverage Hole Detection Protocol for Wireless Sensor Networks.

PubMed

Sahoo, Prasan Kumar; Chiang, Ming-Jer; Wu, Shih-Lin

2016-03-17

In wireless sensor networks (WSNs), certain areas of the monitoring region may have coverage holes and serious coverage overlapping due to the random deployment of sensors. The failure of electronic components, software bugs and destructive agents could lead to the random death of the nodes. Sensors may be dead due to exhaustion of battery power, which may cause the network to be uncovered and disconnected. Based on the deployment nature of the nodes in remote or hostile environments, such as a battlefield or desert, it is impossible to recharge or replace the battery. However, the data gathered by the sensors are highly essential for the analysis, and therefore, the collaborative detection of coverage holes has strategic importance in WSNs. In this paper, distributed coverage hole detection algorithms are designed, where nodes can collaborate to detect the coverage holes autonomously. The performance evaluation of our protocols suggests that our protocols outperform in terms of hole detection time, limited power consumption and control packet overhead to detect holes as compared to other similar protocols.

Target Coverage in Wireless Sensor Networks with Probabilistic Sensors

PubMed Central

Shan, Anxing; Xu, Xianghua; Cheng, Zongmao

2016-01-01

Sensing coverage is a fundamental problem in wireless sensor networks (WSNs), which has attracted considerable attention. Conventional research on this topic focuses on the 0/1 coverage model, which is only a coarse approximation to the practical sensing model. In this paper, we study the target coverage problem, where the objective is to find the least number of sensor nodes in randomly-deployed WSNs based on the probabilistic sensing model. We analyze the joint detection probability of target with multiple sensors. Based on the theoretical analysis of the detection probability, we formulate the minimum ϵ-detection coverage problem. We prove that the minimum ϵ-detection coverage problem is NP-hard and present an approximation algorithm called the Probabilistic Sensor Coverage Algorithm (PSCA) with provable approximation ratios. To evaluate our design, we analyze the performance of PSCA theoretically and also perform extensive simulations to demonstrate the effectiveness of our proposed algorithm. PMID:27618902

COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

PubMed Central

Krishnan, Neeraja M.; Gaur, Prakhar; Chaudhary, Rakshit; Rao, Arjun A.; Panda, Binay

2012-01-01

Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives), specificity (detection of false positives) and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”. PMID:23110103

Opto-electronic device for frequency standard generation and terahertz-range optical demodulation based on quantum interference

DOEpatents

Georgiades, Nikos P.; Polzik, Eugene S.; Kimble, H. Jeff

1999-02-02

An opto-electronic system and technique for comparing laser frequencies with large frequency separations, establishing new frequency standards, and achieving phase-sensitive detection at ultra high frequencies. Light responsive materials with multiple energy levels suitable for multi-photon excitation are preferably used for nonlinear mixing via quantum interference of different excitation paths affecting a common energy level. Demodulation of a carrier with a demodulation frequency up to 100's THZ can be achieved for frequency comparison and phase-sensitive detection. A large number of materials can be used to cover a wide spectral range including the ultra violet, visible and near infrared regions. In particular, absolute frequency measurement in a spectrum from 1.25 .mu.m to 1.66 .mu.m for fiber optics can be accomplished with a nearly continuous frequency coverage.

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

Ruggles, Kelly V.; Tang, Zuojian; Wang, Xuya

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations and splice variants identified in cancer cells are translated. Herein we therefore describe a proteogenomic data integration tool (QUILTS) and illustrate its application to whole genome, transcriptome and global MS peptide sequence datasets generated from a pair of luminal and basal-like breast cancer patient derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS process replicates. Despite over thirty sample replicates, only about 10% of all SNV (somatic andmore » germline) were detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNV without a detectable mRNA transcript were also observed demonstrating the transcriptome coverage was also incomplete (~80%). In contrast to germ-line variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than the luminal tumor raising the possibility of differential translation or protein degradation effects. In conclusion, the QUILTS program integrates DNA, RNA and peptide sequencing to assess the degree to which somatic mutations are translated and therefore biologically active. By identifying gaps in sequence coverage QUILTS benchmarks current technology and assesses progress towards whole cancer proteome and transcriptome analysis.« less

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

PubMed

Ramos, Enrique; Levinson, Benjamin T; Chasnoff, Sara; Hughes, Andrew; Young, Andrew L; Thornton, Katherine; Li, Allie; Vallania, Francesco L M; Province, Michael; Druley, Todd E

2012-12-06

Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1) create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2) expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence. These results were obtained aligning raw reads against the entire genome using Novoalign followed by variant calling of non-indexed pools using SPLINTER or SAMtools for indexed samples. With these pipelines, we find sensitivity and specificity of 99.4% and 99.7% for pooled exome sequencing. Sensitivity, and to a lesser degree specificity, proved to be a function of coverage. For rare variants (≤2% minor allele frequency), we achieved sensitivity and specificity of ≥94.9% and ≥99.99% for custom capture of 2.5 Mb in multiplexed libraries of 22-48 individuals with only ≥5-fold coverage/chromosome, but these parameters improved to ≥98.7 and 100% with 20-fold coverage/chromosome. This highly scalable methodology enables accurate rare variant detection, with or without individual DNA sample indexing, while reducing the amount of required source DNA and total costs through less hybridization reagent consumption, multi-sample sonication in a standard PCR plate, multiplexed pre-enrichment pooling with a single hybridization and lesser sequencing coverage required to obtain high sensitivity.

A New Method for Estimating the Coverage of Mass Vaccination Campaigns Against Poliomyelitis From Surveillance Data

PubMed Central

O'Reilly, K. M.; Cori, A.; Durry, E.; Wadood, M. Z.; Bosan, A.; Aylward, R. B.; Grassly, N. C.

2015-01-01

Mass vaccination campaigns with the oral poliovirus vaccine targeting children aged <5 years are a critical component of the global poliomyelitis eradication effort. Monitoring the coverage of these campaigns is essential to allow corrective action, but current approaches are limited by their cross-sectional nature, nonrandom sampling, reporting biases, and accessibility issues. We describe a new Bayesian framework using data augmentation and Markov chain Monte Carlo methods to estimate variation in vaccination coverage from children's vaccination histories investigated during surveillance for acute flaccid paralysis. We tested the method using simulated data with at least 200 cases and were able to detect undervaccinated groups if they exceeded 10% of all children and temporal changes in coverage of ±10% with greater than 90% sensitivity. Application of the method to data from Pakistan for 2010–2011 identified undervaccinated groups within the Balochistan/Federally Administered Tribal Areas and Khyber Pakhtunkhwa regions, as well as temporal changes in coverage. The sizes of these groups are consistent with the multiple challenges faced by the program in these regions as a result of conflict and insecurity. Application of this new method to routinely collected data can be a useful tool for identifying poorly performing areas and assisting in eradication efforts. PMID:26568569

Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification.

PubMed

Janse, Ingmar; Hamidjaja, Raditijo A; Bok, Jasper M; van Rotterdam, Bart J

2010-12-08

Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum.

Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification

PubMed Central

2010-01-01

Background Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Results Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. Conclusions The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum PMID:21143837

Deep Space Wide Area Search Strategies

NASA Astrophysics Data System (ADS)

Capps, M.; McCafferty, J.

There is an urgent need to expand the space situational awareness (SSA) mission beyond catalog maintenance to providing near real-time indications and warnings of emerging events. While building and maintaining a catalog of space objects is essential to SSA, this does not address the threat of uncatalogued and uncorrelated deep space objects. The Air Force therefore has an interest in transformative technologies to scan the geostationary (GEO) belt for uncorrelated space objects. Traditional ground based electro-optical sensors are challenged in simultaneously detecting dim objects while covering large areas of the sky using current CCD technology. Time delayed integration (TDI) scanning has the potential to enable significantly larger coverage rates while maintaining sensitivity for detecting near-GEO objects. This paper investigates strategies of employing TDI sensing technology from a ground based electro-optical telescope, toward providing tactical indications and warnings of deep space threats. We present results of a notional wide area search TDI sensor that scans the GEO belt from three locations: Maui, New Mexico, and Diego Garcia. Deep space objects in the NASA 2030 debris catalog are propagated over multiple nights as an indicative data set to emulate notional uncatalogued near-GEO orbits which may be encountered by the TDI sensor. Multiple scan patterns are designed and simulated, to compare and contrast performance based on 1) efficiency in coverage, 2) number of objects detected, and 3) rate at which detections occur, to enable follow-up observations by other space surveillance network (SSN) sensors. A step-stare approach is also modeled using a dedicated, co-located sensor notionally similar to the Ground-Based Electro-Optical Deep Space Surveillance (GEODSS) tower. Equivalent sensitivities are assumed. This analysis quantifies the relative benefit of TDI scanning for the wide area search mission.

Monitoring therapy responses at the leukemic subclone level by ultra-deep amplicon resequencing in acute myeloid leukemia.

PubMed

Ojamies, P N; Kontro, M; Edgren, H; Ellonen, P; Lagström, S; Almusa, H; Miettinen, T; Eldfors, S; Tamborero, D; Wennerberg, K; Heckman, C; Porkka, K; Wolf, M; Kallioniemi, O

2017-05-01

In our individualized systems medicine program, personalized treatment options are identified and administered to chemorefractory acute myeloid leukemia (AML) patients based on exome sequencing and ex vivo drug sensitivity and resistance testing data. Here, we analyzed how clonal heterogeneity affects the responses of 13 AML patients to chemotherapy or targeted treatments using ultra-deep (average 68 000 × coverage) amplicon resequencing. Using amplicon resequencing, we identified 16 variants from 4 patients (frequency 0.54-2%) that were not detected previously by exome sequencing. A correlation-based method was developed to detect mutation-specific responses in serial samples across multiple time points. Significant subclone-specific responses were observed for both chemotherapy and targeted therapy. We detected subclonal responses in patients where clinical European LeukemiaNet (ELN) criteria showed no response. Subclonal responses also helped to identify putative mechanisms underlying drug sensitivities, such as sensitivity to azacitidine in DNMT3A mutated cell clones and resistance to cytarabine in a subclone with loss of NF1 gene. In summary, ultra-deep amplicon resequencing method enables sensitive quantification of subclonal variants and their responses to therapies. This approach provides new opportunities for designing combinatorial therapies blocking multiple subclones as well as for real-time assessment of such treatments.

Optimization of microfabricated nanoliter-scale solid-phase extraction device for detection of gel-separated proteins in low abundance by matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Chen, Wenzhang; Shen, Jing; Yin, Xuefeng; Yu, Yingnian

2007-01-01

A nano-scale solid-phase extraction (SPE) device was developed for the detection of gel-separated proteins in low abundance by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) with a simplified microfabrication technology. By using SU-8 photoresist instead of epoxy glue to connect the microchannel and transfer capillary, polymeric contaminant signals in MS analysis were significantly reduced. Micro SPE columns with different capacities and geometric characteristics were investigated in order to increase the detection sensitivity and decrease spot size for MALDI-TOF-MS analysis. It is shown that enhancements in sensitivities for the detection of proteins in low abundance were correlated with the reduction in column capacity and increase in column aspect ratio. Fifty nanoliters of matrix solution were sufficient to elute the sample completely from the optimized micro SPE column with 3.5 nL capacity. The mass spectrum of a 5 fmol in-gel tryptic digest of bovine serum albumin (BSA), processed by the micro SPE column, demonstrated that 29 peptides matched the protein giving a sequence coverage of 51%, which was better than that obtained from analysis of 25 fmol of the same sample prepared by the dried-droplet method. With the micro SPE column treatment of 2 microL of digestion supernatant of a gel spot of the IQGAP1 protein, 15 peptides were detected from the mass spectrum with the highest individual score of 111, while, with a ZipTip procedure, only nine peaks were detected with the highest individual score of 71. Analytical results demonstrated that this approach greatly improved the sequence coverage and identification specificity for the tested protein. It can serve as a very useful tool in proteomics studies, especially for low abundance proteins. Copyright (c) 2006 John Wiley & Sons, Ltd.

An Efficient Distributed Coverage Hole Detection Protocol for Wireless Sensor Networks

PubMed Central

Kumar Sahoo, Prasan; Chiang, Ming-Jer; Wu, Shih-Lin

2016-01-01

In wireless sensor networks (WSNs), certain areas of the monitoring region may have coverage holes and serious coverage overlapping due to the random deployment of sensors. The failure of electronic components, software bugs and destructive agents could lead to the random death of the nodes. Sensors may be dead due to exhaustion of battery power, which may cause the network to be uncovered and disconnected. Based on the deployment nature of the nodes in remote or hostile environments, such as a battlefield or desert, it is impossible to recharge or replace the battery. However, the data gathered by the sensors are highly essential for the analysis, and therefore, the collaborative detection of coverage holes has strategic importance in WSNs. In this paper, distributed coverage hole detection algorithms are designed, where nodes can collaborate to detect the coverage holes autonomously. The performance evaluation of our protocols suggests that our protocols outperform in terms of hole detection time, limited power consumption and control packet overhead to detect holes as compared to other similar protocols. PMID:26999143

Utilization of optical emission endpoint in photomask dry etch processing

NASA Astrophysics Data System (ADS)

Faure, Thomas B.; Huynh, Cuc; Lercel, Michael J.; Smith, Adam; Wagner, Thomas

2002-03-01

Use of accurate and repeatable endpoint detection during dry etch processing of photomask is very important for obtaining good mask mean-to-target and CD uniformity performance. It was found that the typical laser reflectivity endpoint detecting system used on photomask dry etch systems had several key limitations that caused unnecessary scrap and non-optimum image size performance. Consequently, work to develop and implement use of a more robust optical emission endpoint detection system for chrome dry etch processing of photomask was performed. Initial feasibility studies showed that the emission technique was sensitive enough to monitor pattern loadings on contact and via level masks down to 3 percent pattern coverage. Additional work was performed to further improve this to 1 percent pattern coverage by optimizing the endpoint detection parameters. Comparison studies of mask mean-to-target performance and CD uniformity were performed with the use of optical emission endpoint versus laser endpoint for masks built using TOK IP3600 and ZEP 7000 resist systems. It was found that an improvement in mean-to-target performance and CD uniformity was realized on several types of production masks. In addition, part-to-part endpoint time repeatability was found to be significantly improved with the use of optical emission endpoint.

Fragment-based drug design.

PubMed

Feyfant, Eric; Cross, Jason B; Paris, Kevin; Tsao, Désirée H H

2011-01-01

Fragment-based drug design (FBDD), which is comprised of both fragment screening and the use of fragment hits to design leads, began more than 15 years ago and has been steadily gaining in popularity and utility. Its origin lies on the fact that the coverage of chemical space and the binding efficiency of hits are directly related to the size of the compounds screened. Nevertheless, FBDD still faces challenges, among them developing fragment screening libraries that ensure optimal coverage of chemical space, physical properties and chemical tractability. Fragment screening also requires sensitive assays, often biophysical in nature, to detect weak binders. In this chapter we will introduce the technologies used to address these challenges and outline the experimental advantages that make FBDD one of the most popular new hit-to-lead process.

Root coverage with Emdogain/AlloDerm: a new way to treat gingival recessions.

PubMed

Saadoun, André P

2008-01-01

The recession of the gingival margin is becoming a more prominent condition in the oral situation of many patients and should be treated at its earliest detection. The multifactorial etiology, decision modality, and current trends in the treatment of gingival recession are discussed in this article. The surgical technique of choice depends on several factors, but among the different surgical protocols available, the clinician should select one that will minimize surgical trauma and achieve predictable esthetic results. All of the approaches described in this article can effectively treat deep and shallow Class I or II buccal recessions. Recently, as an alternative to autogenous gingival grafts in root coverage procedures, enamel matrix derivative (Emdogain) and acellular dermal matrix allograft (AlloDerm) were utilized to correct these gingival defects, negating the morbidity and the requirement for a second palatal surgical procedure. Emdogain or AlloDerm materials used alone or in combination are a predictable treatment for root coverage, are relatively easy to perform (although they are technique sensitive), present low patient morbidity, offer a significant increase in the percentage of root coverage and amount of keratinized tissue, and should be part of the periodontal plastic surgery armamentarium.

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis

PubMed Central

Gan, Mingyu; Liu, Qingyun; Yang, Chongguang; Gao, Qian; Luo, Tao

2016-01-01

Mixed infection by multiple Mycobacterium tuberculosis (MTB) strains is associated with poor treatment outcome of tuberculosis (TB). Traditional genotyping methods have been used to detect mixed infections of MTB, however, their sensitivity and resolution are limited. Deep whole-genome sequencing (WGS) has been proved highly sensitive and discriminative for studying population heterogeneity of MTB. Here, we developed a phylogenetic-based method to detect MTB mixed infections using WGS data. We collected published WGS data of 782 global MTB strains from public database. We called homogeneous and heterogeneous single nucleotide variations (SNVs) of individual strains by mapping short reads to the ancestral MTB reference genome. We constructed a phylogenomic database based on 68,639 homogeneous SNVs of 652 MTB strains. Mixed infections were determined if multiple evolutionary paths were identified by mapping the SNVs of individual samples to the phylogenomic database. By simulation, our method could specifically detect mixed infections when the sequencing depth of minor strains was as low as 1× coverage, and when the genomic distance of two mixed strains was as small as 16 SNVs. By applying our methods to all 782 samples, we detected 47 mixed infections and 45 of them were caused by locally endemic strains. The results indicate that our method is highly sensitive and discriminative for identifying mixed infections from deep WGS data of MTB isolates. PMID:27391214

A statistical assessment of pesticide pollution in surface waters using environmental monitoring data: Chlorpyrifos in Central Valley, California.

PubMed

Wang, Dan; Singhasemanon, Nan; Goh, Kean S

2016-11-15

Pesticides are routinely monitored in surface waters and resultant data are analyzed to assess whether their uses will damage aquatic eco-systems. However, the utility of the monitoring data is limited because of the insufficiency in the temporal and spatial sampling coverage and the inability to detect and quantify trace concentrations. This study developed a novel assessment procedure that addresses those limitations by combining 1) statistical methods capable of extracting information from concentrations below changing detection limits, 2) statistical resampling techniques that account for uncertainties rooted in the non-detects and insufficient/irregular sampling coverage, and 3) multiple lines of evidence that improve confidence in the final conclusion. This procedure was demonstrated by an assessment on chlorpyrifos monitoring data in surface waters of California's Central Valley (2005-2013). We detected a significant downward trend in the concentrations, which cannot be observed by commonly-used statistical approaches. We assessed that the aquatic risk was low using a probabilistic method that works with non-detects and has the ability to differentiate indicator groups with varying sensitivity. In addition, we showed that the frequency of exceedance over ambient aquatic life water quality criteria was affected by pesticide use, precipitation and irrigation demand in certain periods anteceding the water sampling events. Copyright © 2016 Elsevier B.V. All rights reserved.

Constellations of elliptical inclined lunar orbits providing polar and global coverage

NASA Technical Reports Server (NTRS)

Ely, Todd A.; Lieb, Erica

2005-01-01

Prior results have developed a methodology for selecting a long-lived constellation of 3 satellites that provide persistent, stable coverage to either the North or South Pole with no requirement for stationkeeping under the influence of only gravitational perturbations. In the present study, the sensitivity of this coverage in the presence of non-gravitational forces is determined, and a design strategy is formulated that minimizes any potential sensitivity to these accelerations.

Direct patterning of gold nanoparticles using flexographic printing for biosensing applications

NASA Astrophysics Data System (ADS)

Benson, Jamie; Fung, Chung Man; Lloyd, Jonathan Stephen; Deganello, Davide; Smith, Nathan Andrew; Teng, Kar Seng

2015-03-01

In this paper, we have presented the use of flexographic printing techniques in the selective patterning of gold nanoparticles (AuNPs) onto a substrate. Highly uniform coverage of AuNPs was selectively patterned on the substrate surface, which was subsequently used in the development of a glucose sensor. These AuNPs provide a biocompatible site for the attachment of enzymes and offer high sensitivity in the detection of glucose due to their large surface to volume ratio. The average size of the printed AuNPs is less than 60 nm. Glucose sensing tests were performed using printed carbon-AuNP electrodes functionalized with glucose oxidase (GOx). The results showed a high sensitivity of 5.52 μA mM-1 cm-2 with a detection limit of 26 μM. We have demonstrated the fabrication of AuNP-based biosensors using flexographic printing, which is ideal for low-cost, high-volume production of the devices.

Broad-Spectrum Molecular Detection of Fungal Nucleic Acids by PCR-Based Amplification Techniques.

PubMed

Czurda, Stefan; Lion, Thomas

2017-01-01

Over the past decade, the incidence of life-threatening invasive fungal infections has dramatically increased. Infections caused by hitherto rare and emerging fungal pathogens are associated with significant morbidity and mortality among immunocompromised patients. These observations render the coverage of a broad range of clinically relevant fungal pathogens highly important. The so-called panfungal or, perhaps more correctly, broad-range nucleic acid amplification techniques do not only facilitate sensitive detection of all clinically relevant fungal species but are also rapid and can be applied to analyses of any patient specimens. They have therefore become valuable diagnostic tools for sensitive screening of patients at risk of invasive fungal infections. This chapter summarizes the currently available molecular technologies employed in testing of a wide range of fungal pathogens, and provides a detailed workflow for patient screening by broad-spectrum nucleic acid amplification techniques.

Opto-electronic device for frequency standard generation and terahertz-range optical demodulation based on quantum interference

DOEpatents

Georgiades, N.P.; Polzik, E.S.; Kimble, H.J.

1999-02-02

An opto-electronic system and technique for comparing laser frequencies with large frequency separations, establishing new frequency standards, and achieving phase-sensitive detection at ultra high frequencies are disclosed. Light responsive materials with multiple energy levels suitable for multi-photon excitation are preferably used for nonlinear mixing via quantum interference of different excitation paths affecting a common energy level. Demodulation of a carrier with a demodulation frequency up to 100`s THZ can be achieved for frequency comparison and phase-sensitive detection. A large number of materials can be used to cover a wide spectral range including the ultra violet, visible and near infrared regions. In particular, absolute frequency measurement in a spectrum from 1.25 {micro}m to 1.66 {micro}m for fiber optics can be accomplished with a nearly continuous frequency coverage. 7 figs.

Identification of copy number variants in whole-genome data using Reference Coverage Profiles

PubMed Central

Glusman, Gustavo; Severson, Alissa; Dhankani, Varsha; Robinson, Max; Farrah, Terry; Mauldin, Denise E.; Stittrich, Anna B.; Ament, Seth A.; Roach, Jared C.; Brunkow, Mary E.; Bodian, Dale L.; Vockley, Joseph G.; Shmulevich, Ilya; Niederhuber, John E.; Hood, Leroy

2015-01-01

The identification of DNA copy numbers from short-read sequencing data remains a challenge for both technical and algorithmic reasons. The raw data for these analyses are measured in tens to hundreds of gigabytes per genome; transmitting, storing, and analyzing such large files is cumbersome, particularly for methods that analyze several samples simultaneously. We developed a very efficient representation of depth of coverage (150–1000× compression) that enables such analyses. Current methods for analyzing variants in whole-genome sequencing (WGS) data frequently miss copy number variants (CNVs), particularly hemizygous deletions in the 1–100 kb range. To fill this gap, we developed a method to identify CNVs in individual genomes, based on comparison to joint profiles pre-computed from a large set of genomes. We analyzed depth of coverage in over 6000 high quality (>40×) genomes. The depth of coverage has strong sequence-specific fluctuations only partially explained by global parameters like %GC. To account for these fluctuations, we constructed multi-genome profiles representing the observed or inferred diploid depth of coverage at each position along the genome. These Reference Coverage Profiles (RCPs) take into account the diverse technologies and pipeline versions used. Normalization of the scaled coverage to the RCP followed by hidden Markov model (HMM) segmentation enables efficient detection of CNVs and large deletions in individual genomes. Use of pre-computed multi-genome coverage profiles improves our ability to analyze each individual genome. We make available RCPs and tools for performing these analyses on personal genomes. We expect the increased sensitivity and specificity for individual genome analysis to be critical for achieving clinical-grade genome interpretation. PMID:25741365

A New Method for Estimating the Coverage of Mass Vaccination Campaigns Against Poliomyelitis From Surveillance Data.

PubMed

O'Reilly, K M; Cori, A; Durry, E; Wadood, M Z; Bosan, A; Aylward, R B; Grassly, N C

2015-12-01

Mass vaccination campaigns with the oral poliovirus vaccine targeting children aged <5 years are a critical component of the global poliomyelitis eradication effort. Monitoring the coverage of these campaigns is essential to allow corrective action, but current approaches are limited by their cross-sectional nature, nonrandom sampling, reporting biases, and accessibility issues. We describe a new Bayesian framework using data augmentation and Markov chain Monte Carlo methods to estimate variation in vaccination coverage from children's vaccination histories investigated during surveillance for acute flaccid paralysis. We tested the method using simulated data with at least 200 cases and were able to detect undervaccinated groups if they exceeded 10% of all children and temporal changes in coverage of ±10% with greater than 90% sensitivity. Application of the method to data from Pakistan for 2010-2011 identified undervaccinated groups within the Balochistan/Federally Administered Tribal Areas and Khyber Pakhtunkhwa regions, as well as temporal changes in coverage. The sizes of these groups are consistent with the multiple challenges faced by the program in these regions as a result of conflict and insecurity. Application of this new method to routinely collected data can be a useful tool for identifying poorly performing areas and assisting in eradication efforts. © The Author 2015. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health.

Constrained motion model of mobile robots and its applications.

PubMed

Zhang, Fei; Xi, Yugeng; Lin, Zongli; Chen, Weidong

2009-06-01

Target detecting and dynamic coverage are fundamental tasks in mobile robotics and represent two important features of mobile robots: mobility and perceptivity. This paper establishes the constrained motion model and sensor model of a mobile robot to represent these two features and defines the k -step reachable region to describe the states that the robot may reach. We show that the calculation of the k-step reachable region can be reduced from that of 2(k) reachable regions with the fixed motion styles to k + 1 such regions and provide an algorithm for its calculation. Based on the constrained motion model and the k -step reachable region, the problems associated with target detecting and dynamic coverage are formulated and solved. For target detecting, the k-step detectable region is used to describe the area that the robot may detect, and an algorithm for detecting a target and planning the optimal path is proposed. For dynamic coverage, the k-step detected region is used to represent the area that the robot has detected during its motion, and the dynamic-coverage strategy and algorithm are proposed. Simulation results demonstrate the efficiency of the coverage algorithm in both convex and concave environments.

Responses of aquatic macrophytes to anthropogenic pressures: comparison between macrophyte metrics and indices.

PubMed

Camargo, Julio A

2018-02-26

Macrophyte responses to anthropogenic pressures in two rivers of Central Spain were assessed to check if simple metrics can exhibit a greater discriminatory and explanatory power than complex indices at small spatial scales. Field surveys were undertaken during the summer of 2014 (Duraton River) and the spring of 2015 (Tajuña River). Aquatic macrophytes were sampled using a sampling square (45 × 45 cm). In the middle Duraton River, macrophytes responded positively to the presence of a hydropower dam and a small weir, with Myriophyllum spicatum and Potamogeton pectinatus being relatively favored. Index of Macrophytes (IM) was better than Macroscopic Aquatic Vegetation Index (MAVI) and Fluvial Macrophyte Index (FMI) in detecting these responses, showing positive and significant correlations with total coverage, species richness, and species diversity. In the upper Tajuña River, macrophytes responded both negatively and positively to the occurrence of a trout farm effluent and a small weir, with Leptodictyum riparium and Veronica anagallis-aquatica being relatively favored. Although IM, MAVI, and FMI detected both negative and positive responses, correlations of IM with total coverage, species richness, and species diversity were higher. Species evenness was not sensitive enough to detect either positive or negative responses of aquatic macrophytes along the study areas. Overall, traditional and simple metrics (species composition, total coverage, species richness, species diversity) exhibited a greater discriminatory and explanatory power than more recent and complex indices (IM, MAVI, FMI) when assessing responses of aquatic macrophytes to anthropogenic pressures at impacted specific sites.

Detection limits of 405 nm and 633 nm excited PpIX fluorescence for brain tumor detection during stereotactic biopsy

NASA Astrophysics Data System (ADS)

Markwardt, Niklas; Götz, Marcus; Haj-Hosseini, Neda; Hollnburger, Bastian; Sroka, Ronald; Stepp, Herbert; Zelenkov, Petr; Rühm, Adrian

2016-04-01

5-aminolevulinic-acid-(5-ALA)-induced protoporphyrin IX (PpIX) fluorescence may be used to improve stereotactic brain tumor biopsies. In this study, the sensitivity of PpIX-based tumor detection has been investigated for two potential excitation wavelengths (405 nm, 633 nm). Using a 200 μm fiber in contact with semi-infinite optical phantoms containing ink and Lipovenös, PpIX detection limits of 4.0 nM and 200 nM (relating to 1 mW excitation power) were determined for 405 nm and 633 nm excitation, respectively. Hence, typical PpIX concentrations in glioblastomas of a few μM should be well detectable with both wavelengths. Additionally, blood layers of selected thicknesses were placed between fiber and phantom. Red excitation was shown to be considerably less affected by blood interference: A 50 μm blood layer, for instance, blocked the 405- nm-excited fluorescence completely, but reduced the 633-nm-excited signal by less than 50%. Ray tracing simulations demonstrated that - without blood layer - the sensitivity advantage of 405 nm rises for decreasing fluorescent volume from 50-fold to a maximum of 100-fold. However, at a tumor volume of 1 mm3, which is a typical biopsy sample size, the 633-nm-excited fluorescence signal is only reduced by about 10%. Further simulations revealed that with increasing fiber-tumor distance, the signal drops faster for 405 nm. This reduces the risk of detecting tumor tissue outside the needle's coverage, but diminishes the overlap between optically and mechanically sampled volumes. While 405 nm generally offers a higher sensitivity, 633 nm is more sensitive to distant tumors and considerably superior in case of blood-covered tumor tissue.

Determining water sensitive card spread factors for real world tank mixes

USDA-ARS?s Scientific Manuscript database

The use of water sensitive cards provides a quick and easy method to sample the coverage and deposition from spray applications. Typically, this measure is limited to percent coverage as measures of droplet size, and thus deposition rate, are highly influenced by the stain diameter resulting from t...

Point Source Polarimetry with the Gemini Planet Imager: Sensitivity Characterization with T5.5 Dwarf Companion HD 19467 B

NASA Technical Reports Server (NTRS)

Jensen-Clem, Rebecca; Millar-Blanchaer, Max; Mawet, Dimitri; Graham, James R.; Wallace, J. Kent; Macintosh, Bruce; Hinkley, Sasha; Wiktorowicz, Sloane J.; Perrin, Marshall D.; Marley, Mark S.;

Point source polarimetry with the Gemini planet imager: Sensitivity characterization with T5.5 dwarf companion HD 19467 B

DOE PAGES

Jensen-Clem, Rebecca; Millar-Blanchaer, Max; Mawet, Dimitri; ...

2016-03-29

Detecting polarized light from self-luminous exoplanets has the potential to provide key information about rotation, surface gravity, cloud grain size, and cloud coverage. While field brown dwarfs with detected polarized emission are common, no exoplanet or substellar companion has yet been detected in polarized light. With the advent of high contrast imaging spectro-polarimeters such as GPI and SPHERE, such a detection may now be possible with careful treatment of instrumental polarization. In this paper, we present 28 minutes of H-band GPI polarimetric observations of the benchmark T5.5 companion HD 19467 B. We detect no polarization signal from the target, and place an upper limit on the degree of linear polarization ofmore » $${p}_{\\mathrm{CL}99.73\\%}\\leqslant 2.4\\%$$. In conclusion, we discuss our results in the context of T dwarf cloud models and photometric variability.« less

Genotyping of 25 leukemia-associated genes in a single work flow by next-generation sequencing technology with low amounts of input template DNA.

PubMed

Rinke, Jenny; Schäfer, Vivien; Schmidt, Mathias; Ziermann, Janine; Kohlmann, Alexander; Hochhaus, Andreas; Ernst, Thomas

2013-08-01

We sought to establish a convenient, sensitive next-generation sequencing (NGS) method for genotyping the 26 most commonly mutated leukemia-associated genes in a single work flow and to optimize this method for low amounts of input template DNA. We designed 184 PCR amplicons that cover all of the candidate genes. NGS was performed with genomic DNA (gDNA) from a cohort of 10 individuals with chronic myelomonocytic leukemia. The results were compared with NGS data obtained from sequencing of DNA generated by whole-genome amplification (WGA) of 20 ng template gDNA. Differences between gDNA and WGA samples in variant frequencies were determined for 2 different WGA kits. For gDNA samples, 25 of 26 genes were successfully sequenced with a sensitivity of 5%, which was achieved by a median coverage of 492 reads (range, 308-636 reads) per amplicon. We identified 24 distinct mutations in 11 genes. With WGA samples, we reliably detected all mutations above 5% sensitivity with a median coverage of 506 reads (range, 256-653 reads) per amplicon. With all variants included in the analysis, WGA amplification by the 2 kits tested yielded differences in variant frequencies that ranged from -28.19% to +9.94% [mean (SD) difference, -0.2% (4.08%)] and from -35.03% to +18.67% [mean difference, -0.75% (5.12%)]. Our method permits simultaneous analysis of a wide range of leukemia-associated target genes in a single sequencing run. NGS can be performed after WGA of template DNA for reliable detection of variants without introducing appreciable bias.

Study and comparison of different sensitivity models for a two-plane Compton camera.

PubMed

Muñoz, Enrique; Barrio, John; Bernabéu, José; Etxebeste, Ane; Lacasta, Carlos; Llosá, Gabriela; Ros, Ana; Roser, Jorge; Oliver, Josep F

2018-06-25

Given the strong variations in the sensitivity of Compton cameras for the detection of events originating from different points in the field of view (FoV), sensitivity correction is often necessary in Compton image reconstruction. Several approaches for the calculation of the sensitivity matrix have been proposed in the literature. While most of these models are easily implemented and can be useful in many cases, they usually assume high angular coverage over the scattered photon, which is not the case for our prototype. In this work, we have derived an analytical model that allows us to calculate a detailed sensitivity matrix, which has been compared to other sensitivity models in the literature. Specifically, the proposed model describes the probability of measuring a useful event in a two-plane Compton camera, including the most relevant physical processes involved. The model has been used to obtain an expression for the system and sensitivity matrices for iterative image reconstruction. These matrices have been validated taking Monte Carlo simulations as a reference. In order to study the impact of the sensitivity, images reconstructed with our sensitivity model and with other models have been compared. Images have been reconstructed from several simulated sources, including point-like sources and extended distributions of activity, and also from experimental data measured with 22 Na sources. Results show that our sensitivity model is the best suited for our prototype. Although other models in the literature perform successfully in many scenarios, they are not applicable in all the geometrical configurations of interest for our system. In general, our model allows to effectively recover the intensity of point-like sources at different positions in the FoV and to reconstruct regions of homogeneous activity with minimal variance. Moreover, it can be employed for all Compton camera configurations, including those with low angular coverage over the scatterer.

Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

PubMed

Li, Jonathan Z; Chapman, Brad; Charlebois, Patrick; Hofmann, Oliver; Weiner, Brian; Porter, Alyssa J; Samuel, Reshmi; Vardhanabhuti, Saran; Zheng, Lu; Eron, Joseph; Taiwo, Babafemi; Zody, Michael C; Henn, Matthew R; Kuritzkes, Daniel R; Hide, Winston; Wilson, Cara C; Berzins, Baiba I; Acosta, Edward P; Bastow, Barbara; Kim, Peter S; Read, Sarah W; Janik, Jennifer; Meres, Debra S; Lederman, Michael M; Mong-Kryspin, Lori; Shaw, Karl E; Zimmerman, Louis G; Leavitt, Randi; De La Rosa, Guy; Jennings, Amy

2014-01-01

The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs. A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with Illumina and 454 platforms at comparable costs. Illumina sequence analysis was performed with the novel snp-assess tool and 454 sequencing was analyzed with V-Phaser. Illumina sequencing resulted in significantly higher sequence coverage and a 0.095% limit of detection. Illumina accurately detected all MVs in the control library at ≥0.5% and 7/10 MVs expected at 0.1%. 454 sequencing failed to detect any MVs at 0.1% with 5 false positive calls. For MVs detected in the patient samples by both 454 and Illumina, the correlation in the detected variant frequencies was high (R2 = 0.92, P<0.001). Illumina sequencing detected 2.4-fold greater nucleotide MVs and 2.9-fold greater amino acid MVs compared to 454. The only raltegravir-resistant MV detected was an E138K mutation in one participant by Illumina sequencing, but not by 454. In participants of A5262 with raltegravir resistance at virologic failure, baseline raltegravir-resistant MVs were rarely detected. At comparable costs to 454 sequencing, Illumina demonstrated greater depth of coverage, increased sensitivity for detecting HIV MVs, and fewer false positive variant calls.

Feasibility study of a new RF coil design for prostate MRI

NASA Astrophysics Data System (ADS)

Ha, Seunghoon; Roeck, Werner W.; Cho, Jaedu; Nalcioglu, Orhan

2014-09-01

The combined use of a torso-pelvic RF array coil and endorectal RF coil is the current state-of-the-art in prostate MRI. The endorectal coil provides high detection sensitivity to acquire high-spatial resolution images and spectroscopic data, while the torso-pelvic coil provides large coverage to assess pelvic lymph nodes and pelvic bones for metastatic disease. However, the use of an endorectal coil is an invasive procedure that presents difficulties for both patients and technicians. In this study, we propose a novel non-invasive RF coil design that can provide both image signal to noise ratio and field of view coverage comparable to the combined torso-pelvic and endorectal coil configuration. A prototype coil was constructed and tested using a pelvic phantom. The results demonstrate that this new design is a viable alternative for prostate MRI

Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM.

PubMed

Zhang, Suhua; Bian, Yingnan; Chen, Anqi; Zheng, Hancheng; Gao, Yuzhen; Hou, Yiping; Li, Chengtao

2017-03-01

Utilizing massively parallel sequencing (MPS) technology for SNP testing in forensic genetics is becoming attractive because of the shortcomings of STR markers, such as their high mutation rates and disadvantages associated with the current PCR-CE method as well as its limitations regarding multiplex capabilities. MPS offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. In this study, we designed a customized SNP panel that includes 273 forensically relevant identity SNPs chosen from SNPforID, IISNP, and the HapMap database as well as previously related studies and evaluated the levels of genotyping precision, sequence coverage, sensitivity and SNP performance using the Ion Torrent PGM. In a concordant study of the custom MPS-SNP panel, only four MPS callings were missing due to coverage reads that were too low (<20), whereas the others were fully concordant with Sanger's sequencing results across the two control samples, that is, 9947A and 9948. The analyses indicated a balanced coverage among the included loci, with the exception of the 16 SNPs that were used to detect an inconsistent allele balance and/or lower coverage reads among 50 tested individuals from the Chinese HAN population and the above controls. With the exception of the 16 poorly performing SNPs, the sequence coverage obtained was extensive for the bulk of the SNPs, and only three Y-SNPs (rs16980601, rs11096432, rs3900) showed a mean coverage below 1000. Analyses of the dilution series of control DNA 9948 yielded reproducible results down to 1ng of DNA input. In addition, we provide an analysis tool for automated data quality control and genotyping checks, and we conclude that the SNP targets are polymorphic and independent in the Chinese HAN population. In summary, the evaluation of the sensitivity, accuracy and genotyping performance provides strong support for the application of MPS technology in forensic SNP analysis, and the assay offers a straightforward sample-to-genotype workflow that could be beneficial in forensic casework with respect to both individual identification and complex kinship issues. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Measuring and Specifying Combinatorial Coverage of Test Input Configurations

PubMed Central

Kuhn, D. Richard; Kacker, Raghu N.; Lei, Yu

2015-01-01

A key issue in testing is how many tests are needed for a required level of coverage or fault detection. Estimates are often based on error rates in initial testing, or on code coverage. For example, tests may be run until a desired level of statement or branch coverage is achieved. Combinatorial methods present an opportunity for a different approach to estimating required test set size, using characteristics of the test set. This paper describes methods for estimating the coverage of, and ability to detect, t-way interaction faults of a test set based on a covering array. We also develop a connection between (static) combinatorial coverage and (dynamic) code coverage, such that if a specific condition is satisfied, 100% branch coverage is assured. Using these results, we propose practical recommendations for using combinatorial coverage in specifying test requirements. PMID:28133442

Measles in Mexico, 1941-2001: interruption of endemic transmission and lessons learned.

PubMed

Santos, Jose Ignacio; Nakamura, Miguel Angel; Godoy, Miriam Veras; Kuri, Pablo; Lucas, Carlos Alvarez; Conyer, Roberto Tapia

2004-05-01

In Mexico, measles occurred in a cyclical endemic-epidemic pattern until the early 1970s. Beginning in 1973, routine vaccination augmented by mass vaccination campaigns led to a decrease in the incidence of measles until the 1989-1990 regional pandemic, when the measles attack rate rose to 80 cases per 100000, resulting in 5899 deaths. Since the pandemic, measles elimination efforts in Mexico have resulted in increasing coverage to >95% among children aged 1-6 years with 2 doses of either measles or measles-mumps-rubella vaccine since 1996 and in coverage of 97.6% among children aged 6-10 since 1999. Surveillance data suggest that the transmission of indigenous measles virus was interrupted in 1997. After almost 4 years without measles cases, in April 2000, measles virus was reintroduced into Mexico and 30 laboratory-confirmed cases were reported. Detection of relatively few cases in nonprogrammatic age groups affirms the high immunization coverage and the sensitivity of measles surveillance in Mexico. We conclude that the specific strategies adopted for measles elimination have enabled Mexico to eliminate the endemic transmission of measles.

Biolayer modeling and optimization for the SPARROW biosensor

NASA Astrophysics Data System (ADS)

Feng, Ke

2007-12-01

Biosensor direct detection of molecular binding events is of significant interest in applications from molecular screening for cancer drug design to bioagent detection for homeland security and defense. The Stacked Planar Affinity Regulated Resonant Optical Waveguide (SPARROW) structure based on coupled waveguides was recently developed to achieve increased sensitivity within a fieldable biosensor device configuration. Under ideal operating conditions, modification of the effective propagation constant of the structure's sensing waveguide through selective attachment of specific targets to probes on the waveguide surface results in a change in the coupling characteristics of the guide over a specifically designed interaction length with the analyte. Monitoring the relative power in each waveguide after interaction enables 'recognition' of those targets which have selectively bound to the surface. However, fabrication tolerances, waveguide interface roughness, biolayer surface roughness and biolayer partial coverage have an effect on biosensor behavior and achievable limit of detection (LOD). In addition to these influences which play a role in device optimization, the influence of the spatially random surface loading of molecular binding events has to be considered, especially for low surface coverage. In this dissertation an analytic model is established for the SPARROW biosensor which accounts for these nonidealities with which the design of the biosensor can be guided and optimized. For the idealized case of uniform waveguide transducer layers and biolayer, both theoretical simulation (analytical expression) and computer simulation (numerical calculation) are completed. For the nonideal case of an inhomogeneous transducer with nonideal waveguide and biolayer surfaces, device output power is affected by such physical influences as surface scattering, coupling length, absorption, and percent coverage of binding events. Using grating and perturbation techniques we explore the influence of imperfect surfaces and random surface loading on scattering loss and coupling length. Results provide a range of achievable limits of detection in the SPARROW device for a given target size, surface loading, and detectable optical power.

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells

PubMed Central

Han, Lin; Wu, Hua-Jun; Zhu, Haiying; Kim, Kun-Yong; Marjani, Sadie L.; Riester, Markus; Euskirchen, Ghia; Zi, Xiaoyuan; Yang, Jennifer; Han, Jasper; Snyder, Michael; Park, In-Hyun; Irizarry, Rafael; Weissman, Sherman M.

2017-01-01

Abstract Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population. PMID:28126923

Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality

PubMed Central

Lee, Elvina; Khurana, Maninder S.; Whiteley, Andrew S.; Monis, Paul T.; Bath, Andrew; Gordon, Cameron; Ryan, Una M.; Paparini, Andrea

2017-01-01

Next generation sequencing (NGS) has rapidly become an invaluable tool for the detection, identification and relative quantification of environmental microorganisms. Here, we demonstrate two new 16S rDNA primer sets, which are compatible with NGS approaches and are primarily for use in water quality studies. Compared to 16S rRNA gene based universal primers, in silico and experimental analyses demonstrated that the new primers showed increased specificity for the Cyanobacteria and Proteobacteria phyla, allowing increased sensitivity for the detection, identification and relative quantification of toxic bloom-forming microalgae, microbial water quality bioindicators and common pathogens. Significantly, Cyanobacterial and Proteobacterial sequences accounted for ca. 95% of all sequences obtained within NGS runs (when compared to ca. 50% with standard universal NGS primers), providing higher sensitivity and greater phylogenetic resolution of key water quality microbial groups. The increased selectivity of the new primers allow the parallel sequencing of more samples through reduced sequence retrieval levels required to detect target groups, potentially reducing NGS costs by 50% but still guaranteeing optimal coverage and species discrimination. PMID:28118368

Surface sensitization mechanism on negative electron affinity p-GaN nanowires

NASA Astrophysics Data System (ADS)

Diao, Yu; Liu, Lei; Xia, Sihao; Feng, Shu; Lu, Feifei

2018-03-01

The surface sensitization is the key to prepare negative electron affinity photocathode. The thesis emphasizes on the study of surface sensitization mechanism of p-type doping GaN nanowires utilizing first principles based on density function theory. The adsorption energy, work function, dipole moment, geometry structure, electronic structure and optical properties of Mg-doped GaN nanowires surfaces with various coverages of Cs atoms are investigated. The GaN nanowire with Mg doped in core position is taken as the sensitization base. At the initial stage of sensitization, the best adsorption site for Cs atom on GaN nanowire surface is BN, the bridge site of two adjacent N atoms. Surface sensitization generates a p-type internal surface with an n-type surface state, introducing a band bending region which can help reduce surface barrier and work function. With increasing Cs coverage, work functions decrease monotonously and the "Cs-kill" phenomenon disappears. For Cs coverage of 0.75 ML and 1 ML, the corresponding sensitization systems reach negative electron affinity state. Through surface sensitization, the absorption curves are red shifted and the absorption coefficient is cut down. All theoretical calculations can guide the design of negative electron affinity Mg doped GaN nanowires photocathode.

OBIST methodology incorporating modified sensitivity of pulses for active analogue filter components

NASA Astrophysics Data System (ADS)

Khade, R. H.; Chaudhari, D. S.

2018-03-01

In this paper, oscillation-based built-in self-test method is used to diagnose catastrophic and parametric faults in integrated circuits. Sallen-Key low pass filter and high pass filter circuits with different gains are used to investigate defects. Variation in seven parameters of operational amplifier (OP-AMP) like gain, input impedance, output impedance, slew rate, input bias current, input offset current, input offset voltage and catastrophic as well as parametric defects in components outside OP-AMP are introduced in the circuit and simulation results are analysed. Oscillator output signal is converted to pulses which are used to generate a signature of the circuit. The signature and pulse count changes with the type of fault present in the circuit under test (CUT). The change in oscillation frequency is observed for fault detection. Designer has flexibility to predefine tolerance band of cut-off frequency and range of pulses for which circuit should be accepted. The fault coverage depends upon the required tolerance band of the CUT. We propose a modification of sensitivity of parameter (pulses) to avoid test escape and enhance yield. Result shows that the method provides 100% fault coverage for catastrophic faults.

The Swift/BAT Hard X-ray Transient Monitor

NASA Technical Reports Server (NTRS)

Krimm, H. A.; Holland, S. T.; Corbet, R.H.D.; Pearlman, A. B.; Romano, P.; Kennea, J. A.; Bloom, J. S.; Barthelmy, S. D.; Baumgartner, W. H.; Cummings, J. R.;

Using Optically Stimulated Electron Emission as an Inspection Method to Monitor Surface Contamination

NASA Technical Reports Server (NTRS)

Lingbloom, Mike S.

2008-01-01

During redesign of the Space Shuttle reusable solid rocket motor (RSRM), NASA amended the contract with ATK Launch Systems (then Morton Thiokol Inc.) with Change Order 966 to implement a contamination control and cleanliness verification method. The change order required: (1) A quantitative inspection method (2) A written record of actual contamination levels versus a known reject level (3) A method that is more sensitive than existing methods of visual and black light inspection. Black light inspection is only useful for inspection of contaminants that fluoresce near the 365 nm spectral line and is not useful for inspection of most silicones that will not produce strong fluorescence. Black light inspection conducted by a qualified inspector under controlled light is capable of detecting Conoco HD-2 grease in gross amounts and is very subjective due to operator sensitivity. Optically stimulated electron emission (OSEE), developed at the Materials and Process Laboratory at Marshall Space Flight Center (MSFC), was selected to satisfy Change Order 966. OSEE offers several important advantages over existing laboratory methods with similar sensitivity, e.g., spectroscopy and nonvolatile residue sampling, which provide turn around time, real time capability, and full coverage inspection capability. Laboratory methods require sample gathering and in-lab analysis, which sometimes takes several days to get results. This is not practical in a production environment. In addition, these methods do not offer full coverage inspection of the large components

Cross-platform comparison for the detection of RAS mutations in cfDNA (ddPCR Biorad detection assay, BEAMing assay, and NGS strategy).

PubMed

Garcia, Jessica; Forestier, Julien; Dusserre, Eric; Wozny, Anne-Sophie; Geiguer, Florence; Merle, Patrick; Tissot, Claire; Ferraro-Peyret, Carole; Jones, Frederick S; Edelstein, Daniel L; Cheynet, Valérie; Bardel, Claire; Vilchez, Gaelle; Xu, Zhenyu; Bringuier, Pierre Paul; Barritault, Marc; Brengle-Pesce, Karen; Guillet, Marielle; Chauvenet, Marion; Manship, Brigitte; Brevet, Marie; Rodriguez-Lafrasse, Claire; Hervieu, Valérie; Couraud, Sébastien; Walter, Thomas; Payen, Léa

2018-04-20

CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed. Detection thresholds were between 0.5-1% for cfDNA samples examined using ddPCR and NGS, and 0.03% with BEAMing. This high level of sensitivity enabled the detection of KRAS mutations in 5/19 CRC patients with negative FFPE profiles. In the mCRC cohort, comparison of mutation results obtained by testing FFPE to those obtained by testing cfDNA by ddPCR resulted in 47% sensitivity, 77% specificity, 70% positive predictive value (PPV) and 55% negative predictive value (NPV). For BEAMing, we observed 93% sensitivity, 69% specificity, 78% PPV and 90% NPV. Finally, sensitivity of NGS was 73%, specificity was 77%, PPV 79% and NPV 71%. Our study highlights the complementarity of different diagnostic approaches and variability of results between OncoBEAM™-RAS-CRC and NGS assays. While the NGS assay provided a larger breadth of coverage of the major targetable alterations of 56 genes in one run, its performance for specific alterations was frequently confirmed by ddPCR results.

Cross-platform comparison for the detection of RAS mutations in cfDNA (ddPCR Biorad detection assay, BEAMing assay, and NGS strategy)

PubMed Central

Garcia, Jessica; Forestier, Julien; Dusserre, Eric; Wozny, Anne-Sophie; Geiguer, Florence; Merle, Patrick; Tissot, Claire; Ferraro-Peyret, Carole; Jones, Frederick S.; Edelstein, Daniel L.; Cheynet, Valérie; Bardel, Claire; Vilchez, Gaelle; Xu, Zhenyu; Bringuier, Pierre Paul; Barritault, Marc; Brengle-Pesce, Karen; Guillet, Marielle; Chauvenet, Marion; Manship, Brigitte; Brevet, Marie; Rodriguez-Lafrasse, Claire; Hervieu, Valérie; Couraud, Sébastien; Walter, Thomas; Payen, Léa

2018-01-01

CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed. Detection thresholds were between 0.5–1% for cfDNA samples examined using ddPCR and NGS, and 0.03% with BEAMing. This high level of sensitivity enabled the detection of KRAS mutations in 5/19 CRC patients with negative FFPE profiles. In the mCRC cohort, comparison of mutation results obtained by testing FFPE to those obtained by testing cfDNA by ddPCR resulted in 47% sensitivity, 77% specificity, 70% positive predictive value (PPV) and 55% negative predictive value (NPV). For BEAMing, we observed 93% sensitivity, 69% specificity, 78% PPV and 90% NPV. Finally, sensitivity of NGS was 73%, specificity was 77%, PPV 79% and NPV 71%. Our study highlights the complementarity of different diagnostic approaches and variability of results between OncoBEAM™-RAS-CRC and NGS assays. While the NGS assay provided a larger breadth of coverage of the major targetable alterations of 56 genes in one run, its performance for specific alterations was frequently confirmed by ddPCR results. PMID:29765524

Bi-functional ion exchangers for enhanced performance of dye-sensitized solar cells.

PubMed

Kong, Eui-Hyun; Chang, Yong-June; Lim, Jongchul; Kim, Back-Hyun; Lee, Jung-Hoon; Kwon, Do-Kyun; Park, Taiho; Jang, Hyun Myung

2013-07-28

Ion exchange using aerosol OT (AOT) offers dye adsorption twice as fast as known methods. Moreover, it suppresses the dye-agglomeration that may cause insufficient dye-coverage on the photoelectrode surface. Consequently, its dual function of fast dye-loading and higher dye-coverage significantly improves the power conversion efficiency of dye-sensitized solar cells.

Hospitalizations owing to ambulatory care sensitive conditions in Florianopolis, Santa Catarina - an ecological study, 2001-2011.

PubMed

Brasil, Vinicius Paim; Costa, Juvenal Soares Dias da

2016-01-01

to evaluate trends in rates of hospitalizations owing to ambulatory care sensitive conditions in the municipality of Florianópolis, Santa Catarina, Brazil, from 2001 to 2011, and to assess correlation with the public health expendutures Family Health Strategy (FHS) population coverage. this was an ecological study using Ministry of Health secondary data; data were analyzed using Poisson Regression. the regression coefficient was 0.97, showing a decrease of 3% per year in hospitalizations owing to ambulatory care sensitive conditions, a three-fold increase in FHS coverage and seven times more financial investment per capita in health services, from R$67.65 in 2001 to R$471.03 in 2011; FHS investments per capita in health and population coverage were negatively correlated to the rate of hospitalizations owing to ambulatory care sensitive conditions. financial investment and FHS expansion had led to major reductions in the rate of hospitalizations owing to ambulatory care sensitive conditions.

The Role of Sea Ice in 2 x CO2 Climate Model Sensitivity. Part 2; Hemispheric Dependencies

NASA Technical Reports Server (NTRS)

Rind, D.; Healy, R.; Parkinson, C.; Martinson, D.

1997-01-01

How sensitive are doubled CO2 simulations to GCM control-run sea ice thickness and extent? This issue is examined in a series of 10 control-run simulations with different sea ice and corresponding doubled CO2 simulations. Results show that with increased control-run sea ice coverage in the Southern Hemisphere, temperature sensitivity with climate change is enhanced, while there is little effect on temperature sensitivity of (reasonable) variations in control-run sea ice thickness. In the Northern Hemisphere the situation is reversed: sea ice thickness is the key parameter, while (reasonable) variations in control-run sea ice coverage are of less importance. In both cases, the quantity of sea ice that can be removed in the warmer climate is the determining factor. Overall, the Southern Hemisphere sea ice coverage change had a larger impact on global temperature, because Northern Hemisphere sea ice was sufficiently thick to limit its response to doubled CO2, and sea ice changes generally occurred at higher latitudes, reducing the sea ice-albedo feedback. In both these experiments and earlier ones in which sea ice was not allowed to change, the model displayed a sensitivity of -0.02 C global warming per percent change in Southern Hemisphere sea ice coverage.

High Resolution Separations and Improved Ion Production and Transmission in Metabolomics

PubMed Central

Metz, Thomas O.; Page, Jason S.; Baker, Erin S.; Tang, Keqi; Ding, Jie; Shen, Yufeng; Smith, Richard D.

2008-01-01

The goal of metabolomics analyses is the detection and quantitation of as many sample components as reasonably possible in order to identify compounds or “features” that can be used to characterize the samples under study. When utilizing electrospray ionization to produce ions for analysis by mass spectrometry (MS), it is important that metabolome sample constituents be efficiently separated prior to ion production, in order to minimize ionization suppression and thereby extend the dynamic range of the measurement, as well as the coverage of the metabolome. Similarly, optimization of the MS inlet and interface can lead to increased measurement sensitivity. This perspective review will focus on the role of high resolution liquid chromatography (LC) separations in conjunction with improved ion production and transmission for LC-MS-based metabolomics. Additional emphasis will be placed on the compromise between metabolome coverage and sample analysis throughput. PMID:19255623

A Max-Flow Based Algorithm for Connected Target Coverage with Probabilistic Sensors

PubMed Central

Shan, Anxing; Xu, Xianghua; Cheng, Zongmao; Wang, Wensheng

2017-01-01

Coverage is a fundamental issue in the research field of wireless sensor networks (WSNs). Connected target coverage discusses the sensor placement to guarantee the needs of both coverage and connectivity. Existing works largely leverage on the Boolean disk model, which is only a coarse approximation to the practical sensing model. In this paper, we focus on the connected target coverage issue based on the probabilistic sensing model, which can characterize the quality of coverage more accurately. In the probabilistic sensing model, sensors are only be able to detect a target with certain probability. We study the collaborative detection probability of target under multiple sensors. Armed with the analysis of collaborative detection probability, we further formulate the minimum ϵ-connected target coverage problem, aiming to minimize the number of sensors satisfying the requirements of both coverage and connectivity. We map it into a flow graph and present an approximation algorithm called the minimum vertices maximum flow algorithm (MVMFA) with provable time complex and approximation ratios. To evaluate our design, we analyze the performance of MVMFA theoretically and also conduct extensive simulation studies to demonstrate the effectiveness of our proposed algorithm. PMID:28587084

A Max-Flow Based Algorithm for Connected Target Coverage with Probabilistic Sensors.

PubMed

Shan, Anxing; Xu, Xianghua; Cheng, Zongmao; Wang, Wensheng

2017-05-25

Coverage is a fundamental issue in the research field of wireless sensor networks (WSNs). Connected target coverage discusses the sensor placement to guarantee the needs of both coverage and connectivity. Existing works largely leverage on the Boolean disk model, which is only a coarse approximation to the practical sensing model. In this paper, we focus on the connected target coverage issue based on the probabilistic sensing model, which can characterize the quality of coverage more accurately. In the probabilistic sensing model, sensors are only be able to detect a target with certain probability. We study the collaborative detection probability of target under multiple sensors. Armed with the analysis of collaborative detection probability, we further formulate the minimum ϵ -connected target coverage problem, aiming to minimize the number of sensors satisfying the requirements of both coverage and connectivity. We map it into a flow graph and present an approximation algorithm called the minimum vertices maximum flow algorithm (MVMFA) with provable time complex and approximation ratios. To evaluate our design, we analyze the performance of MVMFA theoretically and also conduct extensive simulation studies to demonstrate the effectiveness of our proposed algorithm.

Pre-Scheduled and Self Organized Sleep-Scheduling Algorithms for Efficient K-Coverage in Wireless Sensor Networks

PubMed Central

Hwang, I-Shyan

2017-01-01

The K-coverage configuration that guarantees coverage of each location by at least K sensors is highly popular and is extensively used to monitor diversified applications in wireless sensor networks. Long network lifetime and high detection quality are the essentials of such K-covered sleep-scheduling algorithms. However, the existing sleep-scheduling algorithms either cause high cost or cannot preserve the detection quality effectively. In this paper, the Pre-Scheduling-based K-coverage Group Scheduling (PSKGS) and Self-Organized K-coverage Scheduling (SKS) algorithms are proposed to settle the problems in the existing sleep-scheduling algorithms. Simulation results show that our pre-scheduled-based KGS approach enhances the detection quality and network lifetime, whereas the self-organized-based SKS algorithm minimizes the computation and communication cost of the nodes and thereby is energy efficient. Besides, SKS outperforms PSKGS in terms of network lifetime and detection quality as it is self-organized. PMID:29257078

Molecular Tools for the Detection of Nitrogen Cycling Archaea

PubMed Central

Rusch, Antje

2013-01-01

Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes. Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ), nitrogenase reductase (NifH), and nitrate reductases NapA/NarG. Sensitivity towards their archaeal target gene, phylogenetic specificity, and gene specificity were evaluated in silico and in vitro. Owing to their moderate sensitivity/coverage, the novel nirB-targeted primers are suitable for pure culture studies only. The nirA-targeted primers showed sufficient sensitivity and phylogenetic specificity, but poor gene specificity. The primers designed for amplification of archaeal nosZ performed well in all 3 criteria; their discrimination against bacterial homologs appears to be weakened when Archaea are strongly outnumbered by bacteria in a mixed community. The novel nifH-targeted primers showed high sensitivity and gene specificity, but failed to discriminate against bacterial homologs. Despite limitations, 4 of the new primer pairs are suitable tools in several molecular methods applied in archaeal ecology. PMID:23365509

VizieR Online Data Catalog: Second ROSAT PSPC Catalog (ROSAT, 2000)

NASA Astrophysics Data System (ADS)

Rosat, Consortium

2000-07-01

This catalogue contains sources from PSPC-ROSAT (Position-Sensitive Proportional Counter aboard the Roentgen Satellite), as provided by Max-Planck Institut fuer extraterrestrische Physik (MPE). It supersedes the 1994 version (Cat. ) The current release of the catalog is comprised of results from 4093 sequences (sky coverage of 14.5%). The complete version contains entries for 95,331 detections whereas the short version has 43,156 detections. 2189 obvious sources were not detected by the automated Standard Analysis Software System (SASS), and are not yet contained in this catalogue. These data have been screened by ROSAT data centers in the US, Germany, and the UK as a step in the production of the ROSAT RESULTS ARCHIVE. The RRA contains extracted source and associated products with an indication of reliability for the primary parameters. (3 data files).

Pd nanoparticle-modified electrodes for nonenzymatic hydrogen peroxide detection

NASA Astrophysics Data System (ADS)

Wang, Jue; Chen, Xue-jiao; Liao, Kai-ming; Wang, Guang-hou; Han, Min

2015-08-01

A hydrogen peroxide (H2O2) sensor based on Pd nanoparticles (NPs) and glassy carbon electrodes (GCEs) is fabricated. Pd NPs are deposited on GCEs by using a gas phase cluster beam deposition technique. The NP-deposited electrodes show enhanced electrocatalytic activity in reduction of H2O2. The electrode with an optimized NP coverage of 85 % has a high selective and stable nonenzymatic sensing ability of H2O2 with a low detection limit (3.4 × 10-7 M), high sensitivity (50.9 μA mM-1), and a wide linear range (from 1.0 × 10-6 to 6.0 × 10-3 M). The reduction peak potential of the electrode is close to -0.12 V, which enables high selective amperometric detection of H2O2 at a low applied potential.

An Optimized Hidden Node Detection Paradigm for Improving the Coverage and Network Efficiency in Wireless Multimedia Sensor Networks

PubMed Central

Alanazi, Adwan; Elleithy, Khaled

2016-01-01

Successful transmission of online multimedia streams in wireless multimedia sensor networks (WMSNs) is a big challenge due to their limited bandwidth and power resources. The existing WSN protocols are not completely appropriate for multimedia communication. The effectiveness of WMSNs varies, and it depends on the correct location of its sensor nodes in the field. Thus, maximizing the multimedia coverage is the most important issue in the delivery of multimedia contents. The nodes in WMSNs are either static or mobile. Thus, the node connections change continuously due to the mobility in wireless multimedia communication that causes an additional energy consumption, and synchronization loss between neighboring nodes. In this paper, we introduce an Optimized Hidden Node Detection (OHND) paradigm. The OHND consists of three phases: hidden node detection, message exchange, and location detection. These three phases aim to maximize the multimedia node coverage, and improve energy efficiency, hidden node detection capacity, and packet delivery ratio. OHND helps multimedia sensor nodes to compute the directional coverage. Furthermore, an OHND is used to maintain a continuous node– continuous neighbor discovery process in order to handle the mobility of the nodes. We implement our proposed algorithms by using a network simulator (NS2). The simulation results demonstrate that nodes are capable of maintaining direct coverage and detecting hidden nodes in order to maximize coverage and multimedia node mobility. To evaluate the performance of our proposed algorithms, we compared our results with other known approaches. PMID:27618048

An Optimized Hidden Node Detection Paradigm for Improving the Coverage and Network Efficiency in Wireless Multimedia Sensor Networks.

PubMed

Alanazi, Adwan; Elleithy, Khaled

2016-09-07

Successful transmission of online multimedia streams in wireless multimedia sensor networks (WMSNs) is a big challenge due to their limited bandwidth and power resources. The existing WSN protocols are not completely appropriate for multimedia communication. The effectiveness of WMSNs varies, and it depends on the correct location of its sensor nodes in the field. Thus, maximizing the multimedia coverage is the most important issue in the delivery of multimedia contents. The nodes in WMSNs are either static or mobile. Thus, the node connections change continuously due to the mobility in wireless multimedia communication that causes an additional energy consumption, and synchronization loss between neighboring nodes. In this paper, we introduce an Optimized Hidden Node Detection (OHND) paradigm. The OHND consists of three phases: hidden node detection, message exchange, and location detection. These three phases aim to maximize the multimedia node coverage, and improve energy efficiency, hidden node detection capacity, and packet delivery ratio. OHND helps multimedia sensor nodes to compute the directional coverage. Furthermore, an OHND is used to maintain a continuous node- continuous neighbor discovery process in order to handle the mobility of the nodes. We implement our proposed algorithms by using a network simulator (NS2). The simulation results demonstrate that nodes are capable of maintaining direct coverage and detecting hidden nodes in order to maximize coverage and multimedia node mobility. To evaluate the performance of our proposed algorithms, we compared our results with other known approaches.

Massively parallel sequencing of forensic STRs and SNPs using the Illumina® ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx™ Forensic Genomics System.

PubMed

Guo, Fei; Yu, Jiao; Zhang, Lu; Li, Jun

2017-11-01

The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples). Results showed that quantitative polymerase chain reaction (qPCR)-based sample quantification and library normalization and the appropriate number of pooled libraries and concentration of diluted libraries provided a greater level of MPS performance and repeatability. Repeatable and concordant genotypes were obtained by the ForenSeq Kit. Full profiles were obtained from ≥100pg input DNA for STRs and ≥200pg for SNPs. A sample with ≥5% minor contributors was considered as a mixture by imbalanced allele coverage ratio distribution, and full profiles from minor contributors were easily detected between 9:1 and 1:9 mixtures with known reference profiles. The ForenSeq Kit tolerated considerable concentrations of inhibitors like ≤200μM hematin and ≤50μg/ml humic acid, and >56% STR profiles and >88% SNP profiles were obtained from ≥200-bp degraded samples. Also, it was adapted to case-type samples. As a whole, the ForenSeq Kit is a well-performed, robust, reliable, reproducible and highly informative assay, and it can fully meet requirements for human identification. Further, sensitive QC indicator and automated sample comparison function in the ForenSeq™ Universal Analysis Software are quite helpful, so that we can concentrate on questionable genotypes and avoid tedious and time-consuming labor to maximum the time spent in data analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells.

PubMed

Han, Lin; Wu, Hua-Jun; Zhu, Haiying; Kim, Kun-Yong; Marjani, Sadie L; Riester, Markus; Euskirchen, Ghia; Zi, Xiaoyuan; Yang, Jennifer; Han, Jasper; Snyder, Michael; Park, In-Hyun; Irizarry, Rafael; Weissman, Sherman M; Michor, Franziska; Fan, Rong; Pan, Xinghua

2017-06-02

Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Biosensing via light scattering from plasmonic core-shell nanospheres coated with DNA molecules

NASA Astrophysics Data System (ADS)

Xie, Huai-Yi; Chen, Minfeng; Chang, Yia-Chung; Moirangthem, Rakesh Singh

2017-05-01

We present both experimental and theoretical studies for investigating DNA molecules attached on metallic nanospheres. We have developed an efficient and accurate numerical method to investigate light scattering from plasmonic nanospheres on a substrate covered by a shell, based on the Green's function approach with suitable spherical harmonic basis. Next, we use this method to study optical scattering from DNA molecules attached to metallic nanoparticles placed on a substrate and compare with experimental results. We obtain fairly good agreement between theoretical predictions and the measured ellipsometric spectra. The metallic nanoparticles were used to detect the binding with DNA molecules in a microfluidic setup via spectroscopic ellipsometry (SE), and a detectable change in ellipsometric spectra was found when DNA molecules are captured on Au nanoparticles. Our theoretical simulation indicates that the coverage of Au nanosphere by a submonolayer of DNA molecules, which is modeled by a thin layer of dielectric material (which may absorb light), can lead to a small but detectable spectroscopic shift in both the Ψ and Δ spectra with more significant change in Δ spectra in agreement with experimental results. Our studies demonstrated the ultrasensitive capability of SE for sensing submonolayer coverage of DNA molecules on Au nanospheres. Hence the spectroscopic ellipsometric measurements coupled with theoretical analysis via an efficient computation method can be an effective tool for detecting DNA molecules attached on Au nanoparticles, thus achieving label-free, non-destructive, and high-sensitivity biosensing with nanoscale resolution.

Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery

PubMed Central

Karas, Vlad O; Sinnott-Armstrong, Nicholas A; Varghese, Vici; Shafer, Robert W; Greenleaf, William J; Sherlock, Gavin

2018-01-01

Abstract Much of the within species genetic variation is in the form of single nucleotide polymorphisms (SNPs), typically detected by whole genome sequencing (WGS) or microarray-based technologies. However, WGS produces mostly uninformative reads that perfectly match the reference, while microarrays require genome-specific reagents. We have developed Diff-seq, a sequencing-based mismatch detection assay for SNP discovery without the requirement for specialized nucleic-acid reagents. Diff-seq leverages the Surveyor endonuclease to cleave mismatched DNA molecules that are generated after cross-annealing of a complex pool of DNA fragments. Sequencing libraries enriched for Surveyor-cleaved molecules result in increased coverage at the variant sites. Diff-seq detected all mismatches present in an initial test substrate, with specific enrichment dependent on the identity and context of the variation. Application to viral sequences resulted in increased observation of variant alleles in a biologically relevant context. Diff-Seq has the potential to increase the sensitivity and efficiency of high-throughput sequencing in the detection of variation. PMID:29361139

CNV-seq, a new method to detect copy number variation using high-throughput sequencing.

PubMed

Xie, Chao; Tammi, Martti T

2009-03-06

DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. Simulation of various sequencing methods with coverage between 0.1x to 8x show overall specificity between 91.7 - 99.9%, and sensitivity between 72.2 - 96.5%. We also show the results for assessment of CNV between two individual human genomes.

Community-owned resource persons for malaria vector control: enabling factors and challenges in an operational programme in Dar es Salaam, United Republic of Tanzania

PubMed Central

2011-01-01

Background Community participation in vector control and health services in general is of great interest to public health practitioners in developing countries, but remains complex and poorly understood. The Urban Malaria Control Program (UMCP) in Dar es Salaam, United Republic of Tanzania, implements larval control of malaria vector mosquitoes. The UMCP delegates responsibility for routine mosquito control and surveillance to community-owned resource persons (CORPs), recruited from within local communities via the elected local government. Methods A mixed method, cross-sectional survey assessed the ability of CORPs to detect mosquito breeding sites and larvae, and investigated demographic characteristics of the CORPs, their reasons for participating in the UMCP, and their work performance. Detection coverage was estimated as the proportion of wet habitats found by the investigator which had been reported by CORP. Detection sensitivity was estimated as the proportion of wet habitats found by the CORPS which the investigator found to contain Anopheles larvae that were also reported to be occupied by the CORP. Results The CORPs themselves perceived their role as professional rather than voluntary, with participation being a de facto form of employment. Habitat detection coverage was lower among CORPs that were recruited through the program administrative staff, compared to CORPs recruited by local government officials or health committees (Odds Ratio = 0.660, 95% confidence interval = [0.438, 0.995], P = 0.047). Staff living within their areas of responsibility had > 70% higher detection sensitivity for both Anopheline (P = 0.016) and Culicine (P = 0.012): positive habitats compared to those living outside those same areas. Discussion and conclusions Improved employment conditions as well as involving the local health committees in recruiting individual program staff, communication and community engagement skills are required to optimize achieving effective community participation, particularly to improve access to fenced compounds. A simpler, more direct, less extensive community-based surveillance system in the hands of a few, less burdened, better paid and maintained program personnel may improve performance and data quality. PMID:21955856

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry

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

Burnum-Johnson, Kristin E.; Nie, Song; Casey, Cameron P.

Current proteomics approaches are comprised of both broad discovery measurements as well as more quantitative targeted measurements. These two different measurement types are used to initially identify potentially important proteins (e.g., candidate biomarkers) and then enable improved quantification for a limited number of selected proteins. However, both approaches suffer from limitations, particularly the lower sensitivity, accuracy, and quantitation precision for discovery approaches compared to targeted approaches, and the limited proteome coverage provided by targeted approaches. Herein, we describe a new proteomics approach that allows both discovery and targeted monitoring (DTM) in a single analysis using liquid chromatography, ion mobility spectrometrymore » and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled peptides for target ions are spiked into tryptic digests and both the labeled and unlabeled peptides are broadly detected using LC-IMS-MS instrumentation, allowing the benefits of discovery and targeted approaches. To understand the possible improvement of the DTM approach, it was compared to LC-MS broad measurements using an accurate mass and time tag database and selected reaction monitoring (SRM) targeted measurements. The DTM results yielded greater peptide/protein coverage and a significant improvement in the detection of lower abundance species compared to LC-MS discovery measurements. DTM was also observed to have similar detection limits as SRM for the targeted measurements indicating its potential for combining the discovery and targeted approaches.« less

Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms.

PubMed

Chen, DaYang; Zhen, HeFu; Qiu, Yong; Liu, Ping; Zeng, Peng; Xia, Jun; Shi, QianYu; Xie, Lin; Zhu, Zhu; Gao, Ya; Huang, GuoDong; Wang, Jian; Yang, HuanMing; Chen, Fang

2018-03-21

Research based on a strategy of single-cell low-coverage whole genome sequencing (SLWGS) has enabled better reproducibility and accuracy for detection of copy number variations (CNVs). The whole genome amplification (WGA) method and sequencing platform are critical factors for successful SLWGS (<0.1 × coverage). In this study, we compared single cell and multiple cells sequencing data produced by the HiSeq2000 and Ion Proton platforms using two WGA kits and then comprehensively evaluated the GC-bias, reproducibility, uniformity and CNV detection among different experimental combinations. Our analysis demonstrated that the PicoPLEX WGA Kit resulted in higher reproducibility, lower sequencing error frequency but more GC-bias than the GenomePlex Single Cell WGA Kit (WGA4 kit) independent of the cell number on the HiSeq2000 platform. While on the Ion Proton platform, the WGA4 kit (both single cell and multiple cells) had higher uniformity and less GC-bias but lower reproducibility than those of the PicoPLEX WGA Kit. Moreover, on these two sequencing platforms, depending on cell number, the performance of the two WGA kits was different for both sensitivity and specificity on CNV detection. The results can help researchers who plan to use SLWGS on single or multiple cells to select appropriate experimental conditions for their applications.

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry*

PubMed Central

Burnum-Johnson, Kristin E.; Nie, Song; Casey, Cameron P.; Monroe, Matthew E.; Orton, Daniel J.; Ibrahim, Yehia M.; Gritsenko, Marina A.; Clauss, Therese R. W.; Shukla, Anil K.; Moore, Ronald J.; Purvine, Samuel O.; Shi, Tujin; Qian, Weijun; Liu, Tao; Baker, Erin S.; Smith, Richard D.

2016-01-01

Current proteomic approaches include both broad discovery measurements and quantitative targeted analyses. In many cases, discovery measurements are initially used to identify potentially important proteins (e.g. candidate biomarkers) and then targeted studies are employed to quantify a limited number of selected proteins. Both approaches, however, suffer from limitations. Discovery measurements aim to sample the whole proteome but have lower sensitivity, accuracy, and quantitation precision than targeted approaches, whereas targeted measurements are significantly more sensitive but only sample a limited portion of the proteome. Herein, we describe a new approach that performs both discovery and targeted monitoring (DTM) in a single analysis by combining liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled target peptides are spiked into tryptic digests and both the labeled and unlabeled peptides are detected using LC-IMS-MS instrumentation. Compared with the broad LC-MS discovery measurements, DTM yields greater peptide/protein coverage and detects lower abundance species. DTM also achieved detection limits similar to selected reaction monitoring (SRM) indicating its potential for combined high quality discovery and targeted analyses, which is a significant step toward the convergence of discovery and targeted approaches. PMID:27670688

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.

PubMed

Sepúlveda, Nuno; Campino, Susana G; Assefa, Samuel A; Sutherland, Colin J; Pain, Arnab; Clark, Taane G

2013-02-26

The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data.

Locations of Sampling Stations for Water Quality Monitoring in Water Distribution Networks.

PubMed

Rathi, Shweta; Gupta, Rajesh

2014-04-01

Water quality is required to be monitored in the water distribution networks (WDNs) at salient locations to assure the safe quality of water supplied to the consumers. Such monitoring stations (MSs) provide warning against any accidental contaminations. Various objectives like demand coverage, time for detection, volume of water contaminated before detection, extent of contamination, expected population affected prior to detection, detection likelihood and others, have been independently or jointly considered in determining optimal number and location of MSs in WDNs. "Demand coverage" defined as the percentage of network demand monitored by a particular monitoring station is a simple measure to locate MSs. Several methods based on formulation of coverage matrix using pre-specified coverage criteria and optimization have been suggested. Coverage criteria is defined as some minimum percentage of total flow received at the monitoring stations that passed through any upstream node included then as covered node of the monitoring station. Number of monitoring stations increases with the increase in the value of coverage criteria. Thus, the design of monitoring station becomes subjective. A simple methodology is proposed herein which priority wise iteratively selects MSs to achieve targeted demand coverage. The proposed methodology provided the same number and location of MSs for illustrative network as an optimization method did. Further, the proposed method is simple and avoids subjectivity that could arise from the consideration of coverage criteria. The application of methodology is also shown on a WDN of Dharampeth zone (Nagpur city WDN in Maharashtra, India) having 285 nodes and 367 pipes.

Offer of primary care services and detection of tuberculosis incidence in Brazil

PubMed Central

Pelissari, Daniele Maria; Bartholomay, Patricia; Jacobs, Marina Gasino; Arakaki-Sanchez, Denise; dos Anjos, Davllyn Santos Oliveira; Costa, Mara Lucia dos Santos; Cavalcanti, Pauline Cristine da Silva; Diaz-Quijano, Fredi Alexander

2018-01-01

ABSTRACT OBJECTIVE To evaluate the association between the health services offered by primary care teams and the detection of new tuberculosis cases in Brazil. METHODS This was an ecological study covering all Brazilian municipalities that registered at least one new tuberculosis case (diagnosed between 2012 to 2014 and notified in the Information System of Notifiable Diseases) and with at least one primary care team evaluated by the second cycle of the National Program for Improving Access and Quality of Primary Care (PMAQ-AB). The variables of the PMAQ-AB were classified as proximal or distal, according to their relation with the tuberculosis diagnosis. Then, they were tested hierarchically in multiple models (adjusted by States) using negative binomial regression. RESULTS An increase of 10% in the primary health care coverage was associated with a decrease of 2.24% in the tuberculosis detection rate (95%CI -3.35– -1.11). Regarding the proximal variables in relation to diagnosis, in the multiple model, the detection of tuberculosis was associated with the proportion of teams that conduct contact investigation (increase in Incidence Rate Ratio [IRR] = 2.97%, 95%CI 2.41–3.53), carry out tuberculosis active case finding (increase in IRR = 2.17%, 95%CI 1.48–2.87), and request culture for mycobacteria (increase in IRR = 1.87%, 95%CI 0.98–2.76). CONCLUSIONS The variables related to the search actions were positively associated with the detection of new tuberculosis cases, which suggests a significant contribution to the strengthening of the sensitivity of the surveillance system. On the other hand, primary care coverage was inversely associated with the tuberculosis detection rate, which could represent the overall effect of the primary care on transmission control, probably from the identification and early treatment of cases. PMID:29791528

Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry

PubMed Central

Sampath, Rangarajan; Mulholland, Niveen; Blyn, Lawrence B.; Massire, Christian; Whitehouse, Chris A.; Waybright, Nicole; Harter, Courtney; Bogan, Joseph; Miranda, Mary Sue; Smith, David; Baldwin, Carson; Wolcott, Mark; Norwood, David; Kreft, Rachael; Frinder, Mark; Lovari, Robert; Yasuda, Irene; Matthews, Heather; Toleno, Donna; Housley, Roberta; Duncan, David; Li, Feng; Warren, Robin; Eshoo, Mark W.; Hall, Thomas A.; Hofstadler, Steven A.; Ecker, David J.

2012-01-01

Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. PMID:22768032

Non-invasive prenatal testing for fetal chromosomal abnormalities by low-coverage whole-genome sequencing of maternal plasma DNA: review of 1982 consecutive cases in a single center.

PubMed

Lau, T K; Cheung, S W; Lo, P S S; Pursley, A N; Chan, M K; Jiang, F; Zhang, H; Wang, W; Jong, L F J; Yuen, O K C; Chan, H Y C; Chan, W S K; Choy, K W

2014-03-01

To review the performance of non-invasive prenatal testing (NIPT) by low-coverage whole-genome sequencing of maternal plasma DNA at a single center. The NIPT result and pregnancy outcome of 1982 consecutive cases were reviewed. NIPT was based on low coverage (0.1×) whole-genome sequencing of maternal plasma DNA. All subjects were contacted for pregnancy and fetal outcome. Of the 1982 NIPT tests, a repeat blood sample was required in 23 (1.16%). In one case, a conclusive report could not be issued, probably because of an abnormal vanished twin fetus. NIPT was positive for common trisomies in 29 cases (23 were trisomy 21, four were trisomy 18 and two were trisomy 13); all were confirmed by prenatal karyotyping (specificity=100%). In addition, 11 cases were positive for sex-chromosomal abnormalities (SCA), and nine cases were positive for other aneuploidies or deletion/duplication. Fourteen of these 20 subjects agreed to undergo further investigations, and the abnormality was found to be of fetal origin in seven, confined placental mosaicism (CPM) in four, of maternal origin in two and not confirmed in one. Overall, 85.7% of the NIPT-suspected SCA were of fetal origin, and 66.7% of the other abnormalities were caused by CPM. Two of the six cases suspected or confirmed to have CPM were complicated by early-onset growth restriction requiring delivery before 34 weeks. Fetal outcome of the NIPT-negative cases was ascertained in 1645 (85.15%). Three chromosomal abnormalities were not detected by NIPT, including one case each of a balanced translocation, unbalanced translocation and triploidy. There were no known false negatives involving the common trisomies (sensitivity=100%). Low-coverage whole-genome sequencing of maternal plasma DNA was highly accurate in detecting common trisomies. It also enabled the detection of other aneuploidies and structural chromosomal abnormalities with high positive predictive value. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd.

The Swift-BAT Hard X-Ray Transient Monitor

NASA Technical Reports Server (NTRS)

Krimm, H. A.; Holland, S. T.; Corbet, R. H. D.; Pearlman, A. B.; Romano, P.; Kennea, J. A.; Bloom, J. S.; Barthelmy, S. D.; Baumgartner, W. H.; Cummings, J. R.;

THE SWIFT/BAT HARD X-RAY TRANSIENT MONITOR

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

Krimm, H. A.; Holland, S. T.; Corbet, R. H. D.

2013-11-01

The Swift/Burst Alert Telescope (BAT) hard X-ray transient monitor provides near real-time coverage of the X-ray sky in the energy range 15-50 keV. The BAT observes 88% of the sky each day with a detection sensitivity of 5.3 mCrab for a full-day observation and a time resolution as fine as 64 s. The three main purposes of the monitor are (1) the discovery of new transient X-ray sources, (2) the detection of outbursts or other changes in the flux of known X-ray sources, and (3) the generation of light curves of more than 900 sources spanning over eight years. Themore » primary interface for the BAT transient monitor is a public Web site. Between 2005 February 12 and 2013 April 30, 245 sources have been detected in the monitor, 146 of them persistent and 99 detected only in outburst. Among these sources, 17 were previously unknown and were discovered in the transient monitor. In this paper, we discuss the methodology and the data processing and filtering for the BAT transient monitor and review its sensitivity and exposure. We provide a summary of the source detections and classify them according to the variability of their light curves. Finally, we review all new BAT monitor discoveries. For the new sources that are previously unpublished, we present basic data analysis and interpretations.« less

ASTER cloud coverage reassessment using MODIS cloud mask products

NASA Astrophysics Data System (ADS)

Tonooka, Hideyuki; Omagari, Kunjuro; Yamamoto, Hirokazu; Tachikawa, Tetsushi; Fujita, Masaru; Paitaer, Zaoreguli

2010-10-01

In the Advanced Spaceborne Thermal Emission and Reflection radiometer (ASTER) Project, two kinds of algorithms are used for cloud assessment in Level-1 processing. The first algorithm based on the LANDSAT-5 TM Automatic Cloud Cover Assessment (ACCA) algorithm is used for a part of daytime scenes observed with only VNIR bands and all nighttime scenes, and the second algorithm based on the LANDSAT-7 ETM+ ACCA algorithm is used for most of daytime scenes observed with all spectral bands. However, the first algorithm does not work well for lack of some spectral bands sensitive to cloud detection, and the two algorithms have been less accurate over snow/ice covered areas since April 2008 when the SWIR subsystem developed troubles. In addition, they perform less well for some combinations of surface type and sun elevation angle. We, therefore, have developed the ASTER cloud coverage reassessment system using MODIS cloud mask (MOD35) products, and have reassessed cloud coverage for all ASTER archived scenes (>1.7 million scenes). All of the new cloud coverage data are included in Image Management System (IMS) databases of the ASTER Ground Data System (GDS) and NASA's Land Process Data Active Archive Center (LP DAAC) and used for ASTER product search by users, and cloud mask images are distributed to users through Internet. Daily upcoming scenes (about 400 scenes per day) are reassessed and inserted into the IMS databases in 5 to 7 days after each scene observation date. Some validation studies for the new cloud coverage data and some mission-related analyses using those data are also demonstrated in the present paper.

Coverage-based constraints for IMRT optimization

NASA Astrophysics Data System (ADS)

Mescher, H.; Ulrich, S.; Bangert, M.

2017-09-01

Radiation therapy treatment planning requires an incorporation of uncertainties in order to guarantee an adequate irradiation of the tumor volumes. In current clinical practice, uncertainties are accounted for implicitly with an expansion of the target volume according to generic margin recipes. Alternatively, it is possible to account for uncertainties by explicit minimization of objectives that describe worst-case treatment scenarios, the expectation value of the treatment or the coverage probability of the target volumes during treatment planning. In this note we show that approaches relying on objectives to induce a specific coverage of the clinical target volumes are inevitably sensitive to variation of the relative weighting of the objectives. To address this issue, we introduce coverage-based constraints for intensity-modulated radiation therapy (IMRT) treatment planning. Our implementation follows the concept of coverage-optimized planning that considers explicit error scenarios to calculate and optimize patient-specific probabilities q(\\hat{d}, \\hat{v}) of covering a specific target volume fraction \\hat{v} with a certain dose \\hat{d} . Using a constraint-based reformulation of coverage-based objectives we eliminate the trade-off between coverage and competing objectives during treatment planning. In-depth convergence tests including 324 treatment plan optimizations demonstrate the reliability of coverage-based constraints for varying levels of probability, dose and volume. General clinical applicability of coverage-based constraints is demonstrated for two cases. A sensitivity analysis regarding penalty variations within this planing study based on IMRT treatment planning using (1) coverage-based constraints, (2) coverage-based objectives, (3) probabilistic optimization, (4) robust optimization and (5) conventional margins illustrates the potential benefit of coverage-based constraints that do not require tedious adjustment of target volume objectives.

A Dual Point-of-Care Test Shows Good Performance in Simultaneously Detecting Nontreponemal and Treponemal Antibodies in Patients With Syphilis: A Multisite Evaluation Study in China

PubMed Central

Yin, Yue-Ping; Chen, Xiang-Sheng; Wei, Wan-Hui; Gong, Kuang-Long; Cao, Wen-Ling; Yong, Gang; Feng, Liang; Huang, Shu-Jie; Wang, Dong-Mei; Han, Yan; Chen, Shao-Chun; Mabey, David; Peeling, Rosanna W.

2013-01-01

Background. Rapid point-of-care (POC) syphilis tests based on simultaneous detection of treponemal and nontreponemal antibodies (dual POC tests) offer the opportunity to increase coverage of syphilis screening and treatment. This study aimed to conduct a multisite performance evaluation of a dual POC syphilis test in China. Methods. Participants were recruited from patients at sexually transmitted infection clinics and high-risk groups in outreach settings in 6 sites in China. Three kinds of specimens (whole blood [WB], fingerprick blood [FB], and blood plasma [BP]) were used for evaluating sensitivity and specificity of the Dual Path Platform (DPP) Syphilis Screen and Confirm test using its treponemal and nontreponemal lines to compare Treponema pallidum particle agglutination (TPPA) assay and toluidine red unheated serum test (TRUST) as reference standards. Results. A total of 3134 specimens (WB 1323, FB 488, and BP 1323) from 1323 individuals were collected. The sensitivities as compared with TPPA were 96.7% for WB, 96.4% for FB, and 94.6% for BP, and the specificities were 99.3%, 99.1%, and 99.6%, respectively. The sensitivities as compared with TRUST were 87.2% for WB, 85.8% for FB, and 88.4% for BP, and the specificities were 94.4%, 96.1%, and 95.0%, respectively. For specimens with a TRUST titer of 1:4 or higher, the sensitivities were 100.0% for WB, 97.8% for FB, and 99.6% for BP. Conclusions. DPP test shows good sensitivity and specificity in detecting treponemal and nontreponemal antibodies in 3 kinds of specimens. It is hoped that this assay can be considered as an alternative in the diagnosis of syphilis, particularly in resource-limited areas. PMID:23132172

The Publicly Available Prebiotic Interstellar Molecular Survey (primos): Expanding Spectroscopic Characterizations, Extending to New Sources, and Adding to the Known Molecular Inventory

NASA Astrophysics Data System (ADS)

McGuire, Brett A.; Carroll, P. Brandon; Corby, Joanna F.; Loomis, Ryan A.; Blake, Geoffrey A.; Hollis, Jan M.; Lovas, Frank J.; Jewell, Philip R.; Remijan, Anthony J.

2013-06-01

The publicly available Green Bank Telescope PRebiotic Interstellar MOlecular Survey (PRIMOS) conducted towards Sgr B2(N) provides high resolution, high-sensitivity observations with near-continuous frequency coverage from ˜300 MHz - 50 GHz. Of the eleven new molecular detections in the last year, five (45%) are a direct result of the PRIMOS observations. Further, these observations have recently been used to detect the predicted, but previously unobserved, J = 1-0 and J=2-1 transitions of the newly detected l-C_3H^+ ion. Here, we discuss the analysis of these transitions, as well as recent work to extend the PRIMOS observations to three new regions of interest: VY Canis Majoris, IRC+10216, and NGC 2023. Finally, we highlight the utility of cm-wave surveys in new molecular detections, as well as the value of publicly-available surveys in the approaching era of data-enabled, analysis-limited astrochemistry.

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

Dithiothreitol-Regulated Coverage of Oligonucleotide-Modified Gold Nanoparticles To Achieve Optimized Biosensor Performance.

PubMed

Liang, Pingping; Canoura, Juan; Yu, Haixiang; Alkhamis, Obtin; Xiao, Yi

2018-01-31

DNA-modified gold nanoparticles (AuNPs) are useful signal-reporters for detecting diverse molecules through various hybridization- and enzyme-based assays. However, their performance is heavily dependent on the probe DNA surface coverage, which can influence both target binding and enzymatic processing of the bound probes. Current methods used to adjust the surface coverage of DNA-modified AuNPs require the production of multiple batches of AuNPs under different conditions, which is costly and laborious. We here develop a single-step assay utilizing dithiothreitol (DTT) to fine-tune the surface coverage of DNA-modified AuNPs. DTT is superior to the commonly used surface diluent, mercaptohexanol, as it is less volatile, allowing for the rapid and reproducible controlling of surface coverage on AuNPs with only micromolar concentrations of DTT. Upon adsorption, DTT forms a dense monolayer on gold surfaces, which provides antifouling capabilities. Furthermore, surface-bound DTT adopts a cyclic conformation, which reorients DNA probes into an upright position and provides ample space to promote DNA hybridization, aptamer assembly, and nuclease digestion. We demonstrate the effects of surface coverage on AuNP-based sensors using DTT-regulated DNA-modified AuNPs. We then use these AuNPs to visually detect DNA and cocaine in colorimetric assays based on enzyme-mediated AuNP aggregation. We determine that DTT-regulated AuNPs with lower surface coverage achieve shorter reaction times and lower detection limits relative to those for assays using untreated AuNPs or DTT-regulated AuNPs with high surface coverage. Additionally, we demonstrate that our DTT-regulated AuNPs can perform cocaine detection in 50% urine without any significant matrix effects. We believe that DTT regulation of surface coverage can be broadly employed for optimizing DNA-modified AuNP performance for use in biosensors as well as drug delivery and therapeutic applications.

Multi-mode acquisition (MMA): An MS/MS acquisition strategy for maximizing selectivity, specificity and sensitivity of DIA product ion spectra.

PubMed

Williams, Brad J; Ciavarini, Steve J; Devlin, Curt; Cohn, Steven M; Xie, Rong; Vissers, Johannes P C; Martin, LeRoy B; Caswell, Allen; Langridge, James I; Geromanos, Scott J

2016-08-01

In proteomics studies, it is generally accepted that depth of coverage and dynamic range is limited in data-directed acquisitions. The serial nature of the method limits both sensitivity and the number of precursor ions that can be sampled. To that end, a number of data-independent acquisition (DIA) strategies have been introduced with these methods, for the most part, immune to the sampling issue; nevertheless, some do have other limitations with respect to sensitivity. The major limitation with DIA approaches is interference, i.e., MS/MS spectra are highly chimeric and often incapable of being identified using conventional database search engines. Utilizing each available dimension of separation prior to ion detection, we present a new multi-mode acquisition (MMA) strategy multiplexing both narrowband and wideband DIA acquisitions in a single analytical workflow. The iterative nature of the MMA workflow limits the adverse effects of interference with minimal loss in sensitivity. Qualitative identification can be performed by selected ion chromatograms or conventional database search strategies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatial assessment of intertidal seagrass meadows using optical imaging systems and a lightweight drone

NASA Astrophysics Data System (ADS)

Duffy, James P.; Pratt, Laura; Anderson, Karen; Land, Peter E.; Shutler, Jamie D.

2018-01-01

Seagrass ecosystems are highly sensitive to environmental change. They are also in global decline and under threat from a variety of anthropogenic factors. There is now an urgency to establish robust monitoring methodologies so that changes in seagrass abundance and distribution in these sensitive coastal environments can be understood. Typical monitoring approaches have included remote sensing from satellites and airborne platforms, ground based ecological surveys and snorkel/scuba surveys. These techniques can suffer from temporal and spatial inconsistency, or are very localised making it hard to assess seagrass meadows in a structured manner. Here we present a novel technique using a lightweight (sub 7 kg) drone and consumer grade cameras to produce very high spatial resolution (∼4 mm pixel-1) mosaics of two intertidal sites in Wales, UK. We present a full data collection methodology followed by a selection of classification techniques to produce coverage estimates at each site. We trialled three classification approaches of varying complexity to investigate and illustrate the differing performance and capabilities of each. Our results show that unsupervised classifications perform better than object-based methods in classifying seagrass cover. We also found that the more sparsely vegetated of the two meadows studied was more accurately classified - it had lower root mean squared deviation (RMSD) between observed and classified coverage (9-9.5%) compared to a more densely vegetated meadow (RMSD 16-22%). Furthermore, we examine the potential to detect other biotic features, finding that lugworm mounds can be detected visually at coarser resolutions such as 43 mm pixel-1, whereas smaller features such as cockle shells within seagrass require finer grained data (<17 mm pixel-1).

Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction.

PubMed

Arbabi, Aryan; Rampášek, Ladislav; Brudno, Michael

2016-06-01

Non-invasive detection of aneuploidies in a fetal genome through analysis of cell-free DNA circulating in the maternal plasma is becoming a routine clinical test. Such tests, which rely on analyzing the read coverage or the allelic ratios at single-nucleotide polymorphism (SNP) loci, are not sensitive enough for smaller sub-chromosomal abnormalities due to sequencing biases and paucity of SNPs in a genome. We have developed an alternative framework for identifying sub-chromosomal copy number variations in a fetal genome. This framework relies on the size distribution of fragments in a sample, as fetal-origin fragments tend to be smaller than those of maternal origin. By analyzing the local distribution of the cell-free DNA fragment sizes in each region, our method allows for the identification of sub-megabase CNVs, even in the absence of SNP positions. To evaluate the accuracy of our method, we used a plasma sample with the fetal fraction of 13%, down-sampled it to samples with coverage of 10X-40X and simulated samples with CNVs based on it. Our method had a perfect accuracy (both specificity and sensitivity) for detecting 5 Mb CNVs, and after reducing the fetal fraction (to 11%, 9% and 7%), it could correctly identify 98.82-100% of the 5 Mb CNVs and had a true-negative rate of 95.29-99.76%. Our source code is available on GitHub at https://github.com/compbio-UofT/FSDA CONTACT: : brudno@cs.toronto.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.

PubMed

Bazak, Lily; Haviv, Ami; Barak, Michal; Jacob-Hirsch, Jasmine; Deng, Patricia; Zhang, Rui; Isaacs, Farren J; Rechavi, Gideon; Li, Jin Billy; Eisenberg, Eli; Levanon, Erez Y

2014-03-01

RNA molecules transmit the information encoded in the genome and generally reflect its content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed that the scope of editing is much larger than anticipated. We found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels (<1%). Moreover, using high coverage sequencing, we observed editing of transcripts resulting from residual antisense expression, doubling the number of edited sites in the human genome. Based on bioinformatic analyses and deep targeted sequencing, we estimate that there are over 100 million human Alu RNA editing sites, located in the majority of human genes. These findings set the stage for exploring how this primate-specific massive diversification of the transcriptome is utilized.

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research

PubMed Central

Salis, R. K.; Bruder, A.; Piggott, J. J.; Summerfield, T. C.; Matthaei, C. D.

2017-01-01

Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity). Community composition was assessed using amplicon sequencing (16S rRNA gene, V3-V4 region). DCD was the most pervasive stressor, affecting evenness and most abundant taxa, followed by sediment and flow velocity. Stressor pervasiveness was similar across taxonomic levels and lower levels did not perform better in detecting stressor effects. Community coverage decreased from 96% of all sequences for abundant phyla to 28% for species. Order-level responses were generally representative of responses of corresponding genera and species, suggesting that this level may represent the best compromise between stressor sensitivity and coverage of bacterial communities. PMID:28327636

A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes

PubMed Central

Hansen, Maren F; Neckmann, Ulrike; Lavik, Liss A S; Vold, Trine; Gilde, Bodil; Toft, Ragnhild K; Sjursen, Wenche

2014-01-01

The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing. PMID:24689082

Design of surface modifications for nanoscale sensor applications.

PubMed

Reimhult, Erik; Höök, Fredrik

2015-01-14

Nanoscale biosensors provide the possibility to miniaturize optic, acoustic and electric sensors to the dimensions of biomolecules. This enables approaching single-molecule detection and new sensing modalities that probe molecular conformation. Nanoscale sensors are predominantly surface-based and label-free to exploit inherent advantages of physical phenomena allowing high sensitivity without distortive labeling. There are three main criteria to be optimized in the design of surface-based and label-free biosensors: (i) the biomolecules of interest must bind with high affinity and selectively to the sensitive area; (ii) the biomolecules must be efficiently transported from the bulk solution to the sensor; and (iii) the transducer concept must be sufficiently sensitive to detect low coverage of captured biomolecules within reasonable time scales. The majority of literature on nanoscale biosensors deals with the third criterion while implicitly assuming that solutions developed for macroscale biosensors to the first two, equally important, criteria are applicable also to nanoscale sensors. We focus on providing an introduction to and perspectives on the advanced concepts for surface functionalization of biosensors with nanosized sensor elements that have been developed over the past decades (criterion (iii)). We review in detail how patterning of molecular films designed to control interactions of biomolecules with nanoscale biosensor surfaces creates new possibilities as well as new challenges.

Design of Surface Modifications for Nanoscale Sensor Applications

PubMed Central

Reimhult, Erik; Höök, Fredrik

2015-01-01

Nanoscale biosensors provide the possibility to miniaturize optic, acoustic and electric sensors to the dimensions of biomolecules. This enables approaching single-molecule detection and new sensing modalities that probe molecular conformation. Nanoscale sensors are predominantly surface-based and label-free to exploit inherent advantages of physical phenomena allowing high sensitivity without distortive labeling. There are three main criteria to be optimized in the design of surface-based and label-free biosensors: (i) the biomolecules of interest must bind with high affinity and selectively to the sensitive area; (ii) the biomolecules must be efficiently transported from the bulk solution to the sensor; and (iii) the transducer concept must be sufficiently sensitive to detect low coverage of captured biomolecules within reasonable time scales. The majority of literature on nanoscale biosensors deals with the third criterion while implicitly assuming that solutions developed for macroscale biosensors to the first two, equally important, criteria are applicable also to nanoscale sensors. We focus on providing an introduction to and perspectives on the advanced concepts for surface functionalization of biosensors with nanosized sensor elements that have been developed over the past decades (criterion (iii)). We review in detail how patterning of molecular films designed to control interactions of biomolecules with nanoscale biosensor surfaces creates new possibilities as well as new challenges. PMID:25594599

Bacteria-Templated NiO Nanoparticles/Microstructure for an Enzymeless Glucose Sensor.

PubMed

Vaidyanathan, Settu; Cherng, Jong-Yuh; Sun, An-Cheng; Chen, Chien-Yen

2016-07-11

The bacterial-induced hollow cylinder NiO (HCNiO) nanomaterial was utilized for the enzymeless (without GOx) detection of glucose in basic conditions. The determination of glucose in 0.05 M NaOH solution with high sensitivity was performed using cyclic voltammetry (CV) and amperometry (i-t). The fundamental electrochemical parameters were analyzed and the obtained values of diffusion coefficient (D), heterogeneous rate constant (ks), electroactive surface coverage (Г), and transfer coefficient (alpha-α) are 1.75 × 10(-6) cm²/s, 57.65 M(-1)·s(-1), 1.45 × 10(-10) mol/cm², and 0.52 respectively. The peak current of the i-t method shows two dynamic linear ranges of calibration curves 0.2 to 3.5 µM and 0.5 to 250 µM for the glucose electro-oxidation. The Ni(2+)/Ni(3+) couple with the HCNiO electrode and the electrocatalytic properties were found to be sensitive to the glucose oxidation. The green chemistry of NiO preparation from bacteria and the high catalytic ability of the oxyhydroxide (NiOOH) is the good choice for the development of a glucose sensor. The best obtained sensitivity and limit of detection (LOD) for this sensor were 3978.9 µA mM(-1)·cm(-2) and 0.9 µM, respectively.

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

PubMed Central

2013-01-01

Background The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. Results Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. Conclusions In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data. PMID:23442253

Employee responses to health insurance premium increases.

PubMed

Goldman, Dana P; Leibowitz, Arleen A; Robalino, David A

2004-01-01

To determine the sensitivity of employees' health insurance decisions--including the decision to not choose health maintenance organization or fee-for-service coverage--during periods of rapidly escalating healthcare costs. A retrospective cohort study of employee plan choices at a single large firm with a "cafeteria-style" benefits plan wherein employees paid all the additional cost of purchasing more generous insurance. We modeled the probability that an employee would drop coverage or switch plans in response to employee premium increases using data from a single large US company with employees across 47 states during the 3-year period of 1989 through 1991, a time of large premium increases within and across plans. Premium increases induced substantial plan switching. Single employees were more likely to respond to premium increases by dropping coverage, whereas families tended to switch to another plan. Premium increases of 10% induced 7% of single employees to drop or severely cut back on coverage; 13% to switch to another plan; and 80% to remain in their existing plan. Similar figures for those with family coverage were 11%, 12%, and 77%, respectively. Simulation results that control for known covariates show similar increases. When faced with a dramatic increase in premiums--on the order of 20%--nearly one fifth of the single employees dropped coverage compared with 10% of those with family coverage. Employee coverage decisions are sensitive to rapidly increasing premiums, and single employees may be likely to drop coverage. This finding suggests that sustained premium increases could induce substantial increases in the number of uninsured individuals.

Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array.

PubMed

Nowak, Rebecca G; Ambulos, Nicholas P; Schumaker, Lisa M; Mathias, Trevor J; White, Ruth A; Troyer, Jennifer; Wells, David; Charurat, Manhattan E; Bentzen, Søren M; Cullen, Kevin J

2017-06-13

Our next generation sequencing (NGS)-based human papillomavirus (HPV) genotyping assay showed a high degree of concordance with the Roche Linear Array (LA) with as little as 1.25 ng formalin-fixed paraffin-embedded-derived genomic DNA in head and neck and cervical cancer samples. This sensitive genotyping assay uses barcoded HPV PCR broad-spectrum general primers 5+/6+ (BSGP)5+/6+ applicable to population studies, but it's diagnostic performance has not been tested in cases with multiple concurrent HPV infections. We conducted a cross-sectional study to compare the positive and negative predictive value (PPV and NPV), sensitivity and specificity of the NGS assay to detect HPV genotype infections as compared to the LA. DNA was previously extracted from ten anal swab samples from men who have sex with men in Nigeria enrolled on the TRUST/RV368 cohort study. Two-sample tests of proportions were used to examine differences in the diagnostic performance of the NGS assay to detect high vs. low-risk HPV type-specific infections. In total there were 94 type-specific infections detected in 10 samples with a median of 9.5, range (9 to 10) per sample. Using the LA as the gold standard, 84.4% (95% CI: 75.2-91.2) of the same anal type-specific infections detected on the NGS assay had been detected by LA. The PPV and sensitivity differed significantly for high risk (PPV: 90%, 95% CI: 79.5-96.2; sensitivity: 93.1%, 95% CI: 83.3-98.1) as compared to low risk HPV (PPV: 73%, 95% CI: 54.1-87.7; sensitivity: 61.1, 95% CI: 43.5-76.9) (all p < 0.05). The NPV for all types was 92.5% (95% CI: 88.4-95.4). The NPV and specificity were similar for high and low risk HPVs (all p > 0.05). The NGS assay detected 10 HPV genotypes that were not among the 37 genotypes found on LA (30, 32, 43, 44, 74, 86, 87, 90, 91, 114). The NGS assay accurately detects multiple HPV infections in individual clinical specimens with limited sample volume and has extended coverage compared to LA.

Validity of vaccination cards and parental recall to estimate vaccination coverage: a systematic review of the literature.

PubMed

Miles, Melody; Ryman, Tove K; Dietz, Vance; Zell, Elizabeth; Luman, Elizabeth T

2013-03-15

Immunization programs frequently rely on household vaccination cards, parental recall, or both to calculate vaccination coverage. This information is used at both the global and national level for planning and allocating performance-based funds. However, the validity of household-derived coverage sources has not yet been widely assessed or discussed. To advance knowledge on the validity of different sources of immunization coverage, we undertook a global review of literature. We assessed concordance, sensitivity, specificity, positive and negative predictive value, and coverage percentage point difference when subtracting household vaccination source from a medical provider source. Median coverage difference per paper ranged from -61 to +1 percentage points between card versus provider sources and -58 to +45 percentage points between recall versus provider source. When card and recall sources were combined, median coverage difference ranged from -40 to +56 percentage points. Overall, concordance, sensitivity, specificity, positive and negative predictive value showed poor agreement, providing evidence that household vaccination information may not be reliable, and should be interpreted with care. While only 5 papers (11%) included in this review were from low-middle income countries, low-middle income countries often rely more heavily on household vaccination information for decision making. Recommended actions include strengthening quality of child-level data and increasing investments to improve vaccination card availability and card marking. There is also an urgent need for additional validation studies of vaccine coverage in low and middle income countries. Copyright © 2013. Published by Elsevier Ltd.

Next-generation sequencing of circulating tumor DNA to predict recurrence in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy.

PubMed

Chen, Yu-Hsiang; Hancock, Bradley A; Solzak, Jeffrey P; Brinza, Dumitru; Scafe, Charles; Miller, Kathy D; Radovich, Milan

2017-01-01

Next-generation sequencing to detect circulating tumor DNA is a minimally invasive method for tumor genotyping and monitoring therapeutic response. The majority of studies have focused on detecting circulating tumor DNA from patients with metastatic disease. Herein, we tested whether circulating tumor DNA could be used as a biomarker to predict relapse in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy. In this study, we analyzed samples from 38 early-stage triple-negative breast cancer patients with matched tumor, blood, and plasma. Extracted DNA underwent library preparation and amplification using the Oncomine Research Panel consisting of 134 cancer genes, followed by high-coverage sequencing and bioinformatics. We detected high-quality somatic mutations from primary tumors in 33 of 38 patients. TP53 mutations were the most prevalent (82%) followed by PIK3CA (16%). Of the 33 patients who had a mutation identified in their primary tumor, we were able to detect circulating tumor DNA mutations in the plasma of four patients (three TP53 mutations, one AKT1 mutation, one CDKN2A mutation). All four patients had recurrence of their disease (100% specificity), but sensitivity was limited to detecting only 4 of 13 patients who clinically relapsed (31% sensitivity). Notably, all four patients had a rapid recurrence (0.3, 4.0, 5.3, and 8.9 months). Patients with detectable circulating tumor DNA had an inferior disease free survival ( p  < 0.0001; median disease-free survival: 4.6 mos. vs. not reached; hazard ratio = 12.6, 95% confidence interval: 3.06-52.2). Our study shows that next-generation circulating tumor DNA sequencing of triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy can predict recurrence with high specificity, but moderate sensitivity. For those patients where circulating tumor DNA is detected, recurrence is rapid.

Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird.

PubMed

Biedrzycka, Aleksandra; Sebastian, Alvaro; Migalska, Magdalena; Westerdahl, Helena; Radwan, Jacek

2017-07-01

Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon coverage (range: 500-20 000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches. A third replicate employed unique barcoding to assess the extent of tag jumping, that is swapping of individual tag identifiers, which may confound genotyping. The reliability of MHC genotyping increased with coverage and approached or exceeded 90% within-method repeatability of allele calling at coverages of >5000 reads per amplicon. We found generally high agreement between genotyping methods, especially at high coverages. High reliability of the tested genotyping approaches was further supported by our analysis of the simulated data set, although the genotyping approach relying primarily on replication of variants in independent amplicons proved sensitive to repeatable errors. According to the most repeatable genotyping method, the number of co-amplifying variants per individual ranged from 19 to 42. Tag jumping was detectable, but at such low frequencies that it did not affect the reliability of genotyping. We thus demonstrate that gene families with many co-amplifying genes can be reliably genotyped using HTS, provided that there is sufficient per amplicon coverage. © 2016 John Wiley & Sons Ltd.

Parallel Proximity Detection for Computer Simulation

NASA Technical Reports Server (NTRS)

Steinman, Jeffrey S. (Inventor); Wieland, Frederick P. (Inventor)

1997-01-01

The present invention discloses a system for performing proximity detection in computer simulations on parallel processing architectures utilizing a distribution list which includes movers and sensor coverages which check in and out of grids. Each mover maintains a list of sensors that detect the mover's motion as the mover and sensor coverages check in and out of the grids. Fuzzy grids are includes by fuzzy resolution parameters to allow movers and sensor coverages to check in and out of grids without computing exact grid crossings. The movers check in and out of grids while moving sensors periodically inform the grids of their coverage. In addition, a lookahead function is also included for providing a generalized capability without making any limiting assumptions about the particular application to which it is applied. The lookahead function is initiated so that risk-free synchronization strategies never roll back grid events. The lookahead function adds fixed delays as events are scheduled for objects on other nodes.

Parallel Proximity Detection for Computer Simulations

NASA Technical Reports Server (NTRS)

Steinman, Jeffrey S. (Inventor); Wieland, Frederick P. (Inventor)

1998-01-01

The present invention discloses a system for performing proximity detection in computer simulations on parallel processing architectures utilizing a distribution list which includes movers and sensor coverages which check in and out of grids. Each mover maintains a list of sensors that detect the mover's motion as the mover and sensor coverages check in and out of the grids. Fuzzy grids are included by fuzzy resolution parameters to allow movers and sensor coverages to check in and out of grids without computing exact grid crossings. The movers check in and out of grids while moving sensors periodically inform the grids of their coverage. In addition, a lookahead function is also included for providing a generalized capability without making any limiting assumptions about the particular application to which it is applied. The lookahead function is initiated so that risk-free synchronization strategies never roll back grid events. The lookahead function adds fixed delays as events are scheduled for objects on other nodes.

First GRB detections with the AGILE Minicalorimeter

NASA Astrophysics Data System (ADS)

Marisaldi, M.; Labanti, C.; Fuschino, F.; Galli, M.; Tavani, M.; Bulgarelli, A.; Gianotti, F.; Trifoglio, M.; Argan, A.

2008-05-01

The Minicalorimeter (MCAL) onboard the AGILE satellite is a 1400 cm2 scintillation detector sensitive in the energy range 0.3-200 MeV. MCAL works both as a slave of the AGILE Silicon Tracker and as an autonomous detector for transient events (BURST mode). A dedicated onboard Burst Search logic scans BURST mode data in search of count rate increase. Peculiar characteristics of the detector are the high energy spectral coverage and a timing resolution of about 2 microseconds. Even if a trigger is not issued, BURST mode data are used to build a broad band energy spectrum (scientific ratemeters) organized in 11 bands for each of the two MCAL detection planes, with a time resolution of 1 second. After the first engineering commissioning phase, following the AGILE launch on 23rd April 2007, between 22nd June and 5th November 2007 eighteen GRBs were detected offline in the scientific ratemeters data, with a detection rate of about one per week. In this paper the capabilities of the detector will be described and an overview of the first detected GRBs will be given.

Amplicon-based next-generation sequencing of plasma cell-free DNA for detection of driver and resistance mutations in advanced non-small cell lung cancer.

PubMed

Guibert, N; Hu, Y; Feeney, N; Kuang, Y; Plagnol, V; Jones, G; Howarth, K; Beeler, J F; Paweletz, C P; Oxnard, G R

2018-04-01

Genomic analysis of plasma cell-free DNA is transforming lung cancer care; however, available assays are limited by cost, turnaround time, and imperfect accuracy. Here, we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1, and other rare genotypes) were collected while on therapy and analyzed blinded to tumor genotype. Plasma NGS was carried out using enhanced tagged amplicon sequencing of hotspots and coding regions from 36 genes, as well as intronic coverage for detection of ALK/ROS1 fusions. Diagnostic accuracy was compared with plasma droplet digital PCR (ddPCR) and tumor genotype. A total of 168 specimens from 46 patients were studied. Matched plasma NGS and ddPCR across 120 variants from 80 samples revealed high concordance of allelic fraction (R2 = 0.95). Pretreatment, sensitivity of plasma NGS for the detection of EGFR driver mutations was 100% (30/30), compared with 87% for ddPCR (26/30). A full spectrum of rare driver oncogenic mutations could be detected including sensitive detection of ALK/ROS1 fusions (8/9 detected, 89%). Studying 25 patients positive for EGFR T790M that developed resistance to osimertinib, 15 resistance mechanisms could be detected including tertiary EGFR mutations (C797S, Q791P) and mutations or amplifications of non-EGFR genes, some of which could be detected pretreatment or months before progression. This blinded analysis demonstrates the ability of amplicon-based plasma NGS to detect a full range of targetable genotypes in NSCLC, including fusion genes, with high accuracy. The ability of plasma NGS to detect a range of preexisting and acquired resistance mechanisms highlights its potential value as an alternative to single mutation digital PCR-based plasma assays for personalizing treatment of TKI resistance in lung cancer.

Multichroic Bolometric Detector Architecture for Cosmic Microwave Background Polarimetry Experiments

NASA Astrophysics Data System (ADS)

Suzuki, Aritoki

Characterization of the Cosmic Microwave Background (CMB) B-mode polarization signal will test models of inflationary cosmology, as well as constrain the sum of the neutrino masses and other cosmological parameters. The low intensity of the B-mode signal combined with the need to remove polarized galactic foregrounds requires a sensitive millimeter receiver and effective methods of foreground removal. Current bolometric detector technology is reaching the sensitivity limit set by the CMB photon noise. Thus, we need to increase the optical throughput to increase an experiment's sensitivity. To increase the throughput without increasing the focal plane size, we can increase the frequency coverage of each pixel. Increased frequency coverage per pixel has additional advantage that we can split the signal into frequency bands to obtain spectral information. The detection of multiple frequency bands allows for removal of the polarized foreground emission from synchrotron radiation and thermal dust emission, by utilizing its spectral dependence. Traditionally, spectral information has been captured with a multi-chroic focal plane consisting of a heterogeneous mix of single-color pixels. To maximize the efficiency of the focal plane area, we developed a multi-chroic pixel. This increases the number of pixels per frequency with same focal plane area. We developed multi-chroic antenna-coupled transition edge sensor (TES) detector array for the CMB polarimetry. In each pixel, a silicon lens-coupled dual polarized sinuous antenna collects light over a two-octave frequency band. The antenna couples the broadband millimeter wave signal into microstrip transmission lines, and on-chip filter banks split the broadband signal into several frequency bands. Separate TES bolometers detect the power in each frequency band and linear polarization. We will describe the design and performance of these devices and present optical data taken with prototype pixels and detector arrays. Our measurements show beams with percent level ellipticity, percent level cross-polarization leakage, and partitioned bands using banks of two and three filters. We will also describe the development of broadband anti-reflection coatings for the high dielectric constant lens. The broadband anti-reflection coating has approximately 100% bandwidth and no detectable loss at cryogenic temperature. We will describe a next generation CMB polarimetry experiment, the POLARBEAR-2, in detail. The POLARBEAR-2 would have focal planes with kilo-pixel of these detectors to achieve high sensitivity. We'll also introduce proposed experiments that would use multi-chroic detector array we developed in this work. We'll conclude by listing out suggestions for future multichroic detector development.

Wireless Metal Detection and Surface Coverage Sensing for All-Surface Induction Heating

PubMed Central

Kilic, Veli Tayfun; Unal, Emre; Demir, Hilmi Volkan

2016-01-01

All-surface induction heating systems, typically comprising small-area coils, face a major challenge in detecting the presence of a metallic vessel and identifying its partial surface coverage over the coils to determine which of the coils to power up. The difficulty arises due to the fact that the user can heat vessels made of a wide variety of metals (and their alloys). To address this problem, we propose and demonstrate a new wireless detection methodology that allows for detecting the presence of metallic vessels together with uniquely sensing their surface coverages while also identifying their effective material type in all-surface induction heating systems. The proposed method is based on telemetrically measuring simultaneously inductance and resistance of the induction coil coupled with the vessel in the heating system. Here, variations in the inductance and resistance values for an all-surface heating coil loaded by vessels (made of stainless steel and aluminum) at different positions were systematically investigated at different frequencies. Results show that, independent of the metal material type, unique identification of the surface coverage is possible at all freqeuncies. Additionally, using the magnitude and phase information extracted from the coupled coil impedance, unique identification of the vessel effective material is also achievable, this time independent of its surface coverage. PMID:26978367

The Swift/BAT Hard X-Ray Survey

NASA Technical Reports Server (NTRS)

Tueller, Jack; Markwardt, C. B.; Mushotzky, R. F.; Barthelmy, S. D.; Gehrels, N.; Krimm, H. A.; Skinner, G. K.; Falcone, A.; Kennea, J. A.

2006-01-01

The BAT instrument on Swift is a wide field (70 deg. '100 deg.) coded aperture instrument with a CdZnTe detector array sensitive to energies of 14-200 keV. Each day, the BAT survey typically covers 60% of the sky to a detection limit of 30 millicrab. BAT makes hard X-ray light curves of similar sensitivity and coverage to the X-ray light curves from XTE/ASM, but in an energy range where sources show remarkably different behavior. Integrating the BAT data produces an all sky map with a source detection limit at 15 months of a few 10(exp -11) ergs per square centimeter per second, depending on the exposure. This is the first uniform all-sky survey at energies high enough to be unaffected by absorption since HEAO 1 in 1977-8. BAT has detected greater than 200 AGN and greater than 180 galactic sources. At high galactic latitudes, the BAT sources are usually easy to identify, but many are heavily absorbed and there are a few quite surprising identifications. The BAT selected galaxies can be used to calculate LogN/LogS and the luminosity function for AGN which are complete and free from common systematics. Several crucial parameters for understanding the cosmic hard x-ray background are now determined.

Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry.

PubMed

Burnum-Johnson, Kristin E; Nie, Song; Casey, Cameron P; Monroe, Matthew E; Orton, Daniel J; Ibrahim, Yehia M; Gritsenko, Marina A; Clauss, Therese R W; Shukla, Anil K; Moore, Ronald J; Purvine, Samuel O; Shi, Tujin; Qian, Weijun; Liu, Tao; Baker, Erin S; Smith, Richard D

2016-12-01

Current proteomic approaches include both broad discovery measurements and quantitative targeted analyses. In many cases, discovery measurements are initially used to identify potentially important proteins (e.g. candidate biomarkers) and then targeted studies are employed to quantify a limited number of selected proteins. Both approaches, however, suffer from limitations. Discovery measurements aim to sample the whole proteome but have lower sensitivity, accuracy, and quantitation precision than targeted approaches, whereas targeted measurements are significantly more sensitive but only sample a limited portion of the proteome. Herein, we describe a new approach that performs both discovery and targeted monitoring (DTM) in a single analysis by combining liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled target peptides are spiked into tryptic digests and both the labeled and unlabeled peptides are detected using LC-IMS-MS instrumentation. Compared with the broad LC-MS discovery measurements, DTM yields greater peptide/protein coverage and detects lower abundance species. DTM also achieved detection limits similar to selected reaction monitoring (SRM) indicating its potential for combined high quality discovery and targeted analyses, which is a significant step toward the convergence of discovery and targeted approaches. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care

PubMed Central

Rennert, Hanna; Eng, Kenneth; Zhang, Tuo; Tan, Adrian; Xiang, Jenny; Romanel, Alessandro; Kim, Robert; Tam, Wayne; Liu, Yen-Chun; Bhinder, Bhavneet; Cyrta, Joanna; Beltran, Himisha; Robinson, Brian; Mosquera, Juan Miguel; Fernandes, Helen; Demichelis, Francesca; Sboner, Andrea; Kluk, Michael; Rubin, Mark A; Elemento, Olivier

2016-01-01

We describe Exome Cancer Test v1.0 (EXaCT-1), the first New York State-Department of Health-approved whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target enrichment followed by next-generation sequencing (Illumina) of tumour and matched constitutional control DNA. We present a detailed clinical development and validation pipeline suitable for simultaneous detection of somatic point/indel mutations and copy-number alterations (CNAs). A computational framework for data analysis, reporting and sign-out is also presented. For the validation, we tested EXaCT-1 on 57 tumours covering five distinct clinically relevant mutations. Results demonstrated elevated and uniform coverage compatible with clinical testing as well as complete concordance in variant quality metrics between formalin-fixed paraffin embedded and fresh-frozen tumours. Extensive sensitivity studies identified limits of detection threshold for point/indel mutations and CNAs. Prospective analysis of 337 cancer cases revealed mutations in clinically relevant genes in 82% of tumours, demonstrating that EXaCT-1 is an accurate and sensitive method for identifying actionable mutations, with reasonable costs and time, greatly expanding its utility for advanced cancer care. PMID:28781886

Analysis of cloud top height and cloud coverage from satellites using the O2 A and B bands

NASA Technical Reports Server (NTRS)

Kuze, Akihiko; Chance, Kelly V.

1994-01-01

Cloud height and cloud coverage detection are important for total ozone retrieval using ultraviolet and visible scattered light. Use of the O2 A and B bands, around 761 and 687 nm, by a satellite-borne instrument of moderately high spectral resolution viewing in the nadir makes it possible to detect cloud top height and related parameters, including fractional coverage. The measured values of a satellite-borne spectrometer are convolutions of the instrument slit function and the atmospheric transmittance between cloud top and satellite. Studies here determine the optical depth between a satellite orbit and the Earth or cloud top height to high accuracy using FASCODE 3. Cloud top height and a cloud coverage parameter are determined by least squares fitting to calculated radiance ratios in the oxygen bands. A grid search method is used to search the parameter space of cloud top height and the coverage parameter to minimize an appropriate sum of squares of deviations. For this search, nonlinearity of the atmospheric transmittance (i.e., leverage based on varying amounts of saturation in the absorption spectrum) is important for distinguishing between cloud top height and fractional coverage. Using the above-mentioned method, an operational cloud detection algorithm which uses minimal computation time can be implemented.

2MASS - The 2 Micron All Sky Survey

NASA Technical Reports Server (NTRS)

Kleinmann, S. G.

1992-01-01

This paper describes a new sky survey to be carried out in three wavebands, J(1.25 m), H(1.65 m), and K(2.2 m). The limiting sensitivity of the survey, 10 sigma detection of point sources with K not greater than 14 mag, coupled with its all-sky coverage, were selected primarily to support studies of the large-scale structure of the Milky Way and the Local Universe. The survey requires construction of a pair of observing facilities, one each for the Northern and Southern Hemispheres. Operations are scheduled to begin in 1995. The data will begin becoming publicly available soon thereafter.

The Ultraviolet Total Ozone Unit (TOU) IN-ORBIT PERFORMANCE AND CALIBRATION

NASA Astrophysics Data System (ADS)

Wang, Yongmei; Fu, Liping; Zhang, Zhongmou

The Ultraviolet Total Ozone Unit (TOU) was launched on 27 May 2008 on FY-3 meteorological satellite. The main purpose of TOU is to measure the incident solar radiation and backscattered ultraviolet radiance for retrieving daily global map of atmospheric ozone. TOU is a fixed grating and slit-array Ebert-Fastie grating spectrograph system. It has the multi-wavelengths detecting and two-dimensional scanning which enables global daily ground coverage. This paper discusses the recent working status of the instrument, including the sensitivity, measuring precision of solar irradiance, diffuser degradation and wavelength drift, and then presents the in-flight calibration and performance results.

High degree gravitational sensitivity from Mars orbiters for the GMM-1 gravity model

NASA Technical Reports Server (NTRS)

Lerch, F. J.; Smith, D. E.; Chan, J. C.; Patel, G. B.; Chinn, D. S.

1994-01-01

Orbital sensitivity of the gravity field for high degree terms (greater than 30) is analyzed on satellites employed in a Goddard Mars Model GMM-1, complete in spherical harmonics through degree and order 50. The model is obtained from S-band Doppler data on Mariner 9 (M9), Viking Orbiter 1 (VO1), and Viking Orbiter 2 (VO2) spacecraft, which were tracked by the NASA Deep Space Network on seven different highly eccentric orbits. The main sensitivity of the high degree terms is obtained from the VO1 and VO2 low orbits (300 km periapsis altitude), where significant spectral sensitivity is seen for all degrees out through degree 50. The velocity perturbations show a dominant effect at periapsis and significant effects out beyond the semi-latus rectum covering over 180 degrees of the orbital groundtrack for the low altitude orbits. Because of the wideband of periapsis motion covering nearly 180 degrees in w and +39 degrees in latitude coverage, the VO1 300 km periapsis altitude orbit with inclination of 39 degrees gave the dominant sensitivity in the GMM-1 solution for the high degree terms. Although the VO2 low periapsis orbit has a smaller band of periapsis mapping coverage, it strongly complements the VO1 orbit sensitivity for the GMM-1 solution with Doppler tracking coverage over a different inclination of 80 degrees.

Impact of coverage on the reliability of a fault tolerant computer

NASA Technical Reports Server (NTRS)

Bavuso, S. J.

1975-01-01

A mathematical reliability model is established for a reconfigurable fault tolerant avionic computer system utilizing state-of-the-art computers. System reliability is studied in light of the coverage probabilities associated with the first and second independent hardware failures. Coverage models are presented as a function of detection, isolation, and recovery probabilities. Upper and lower bonds are established for the coverage probabilities and the method for computing values for the coverage probabilities is investigated. Further, an architectural variation is proposed which is shown to enhance coverage.

Deep Space Network and Lunar Network Communication Coverage of the Moon

NASA Technical Reports Server (NTRS)

Lee, Charles H.; Cheung, Kar-Ming

2006-01-01

In this article, we describe the communication coverage analysis for the lunar network and the Earth ground stations. The first part of this article focuses on the direct communication coverage of the Moon from the Earth's ground stations. In particular, we assess the coverage performance of the Moon based on the existing Deep Space Network (DSN) antennas and the complimentary coverage of other potential stations at Hartebeesthoek, South Africa and at Santiago, Chile. We also address the coverage sensitivity based on different DSN antenna scenarios and their capability to provide single and redundant coverage of the Moon. The second part of this article focuses on the framework of the constrained optimization scheme to seek a stable constellation six relay satellites in two planes that not only can provide continuous communication coverage to any users on the Moon surface, but can also deliver data throughput in a highly efficient manner.

Deep whole-genome sequencing of 100 southeast Asian Malays.

PubMed

Wong, Lai-Ping; Ong, Rick Twee-Hee; Poh, Wan-Ting; Liu, Xuanyao; Chen, Peng; Li, Ruoying; Lam, Kevin Koi-Yau; Pillai, Nisha Esakimuthu; Sim, Kar-Seng; Xu, Haiyan; Sim, Ngak-Leng; Teo, Shu-Mei; Foo, Jia-Nee; Tan, Linda Wei-Lin; Lim, Yenly; Koo, Seok-Hwee; Gan, Linda Seo-Hwee; Cheng, Ching-Yu; Wee, Sharon; Yap, Eric Peng-Huat; Ng, Pauline Crystal; Lim, Wei-Yen; Soong, Richie; Wenk, Markus Rene; Aung, Tin; Wong, Tien-Yin; Khor, Chiea-Chuen; Little, Peter; Chia, Kee-Seng; Teo, Yik-Ying

2013-01-10

Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Deep Whole-Genome Sequencing of 100 Southeast Asian Malays

PubMed Central

Wong, Lai-Ping; Ong, Rick Twee-Hee; Poh, Wan-Ting; Liu, Xuanyao; Chen, Peng; Li, Ruoying; Lam, Kevin Koi-Yau; Pillai, Nisha Esakimuthu; Sim, Kar-Seng; Xu, Haiyan; Sim, Ngak-Leng; Teo, Shu-Mei; Foo, Jia-Nee; Tan, Linda Wei-Lin; Lim, Yenly; Koo, Seok-Hwee; Gan, Linda Seo-Hwee; Cheng, Ching-Yu; Wee, Sharon; Yap, Eric Peng-Huat; Ng, Pauline Crystal; Lim, Wei-Yen; Soong, Richie; Wenk, Markus Rene; Aung, Tin; Wong, Tien-Yin; Khor, Chiea-Chuen; Little, Peter; Chia, Kee-Seng; Teo, Yik-Ying

2013-01-01

Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies. PMID:23290073

Seismic array processing and computational infrastructure for improved monitoring of Alaskan and Aleutian seismicity and volcanoes

NASA Astrophysics Data System (ADS)

Lindquist, Kent Gordon

We constructed a near-real-time system, called Iceworm, to automate seismic data collection, processing, storage, and distribution at the Alaska Earthquake Information Center (AEIC). Phase-picking, phase association, and interprocess communication components come from Earthworm (U.S. Geological Survey). A new generic, internal format for digital data supports unified handling of data from diverse sources. A new infrastructure for applying processing algorithms to near-real-time data streams supports automated information extraction from seismic wavefields. Integration of Datascope (U. of Colorado) provides relational database management of all automated measurements, parametric information for located hypocenters, and waveform data from Iceworm. Data from 1997 yield 329 earthquakes located by both Iceworm and the AEIC. Of these, 203 have location residuals under 22 km, sufficient for hazard response. Regionalized inversions for local magnitude in Alaska yield Msb{L} calibration curves (logAsb0) that differ from the Californian Richter magnitude. The new curve is 0.2\\ Msb{L} units more attenuative than the Californian curve at 400 km for earthquakes north of the Denali fault. South of the fault, and for a region north of Cook Inlet, the difference is 0.4\\ Msb{L}. A curve for deep events differs by 0.6\\ Msb{L} at 650 km. We expand geographic coverage of Alaskan regional seismic monitoring to the Aleutians, the Bering Sea, and the entire Arctic by initiating the processing of four short-period, Alaskan seismic arrays. To show the array stations' sensitivity, we detect and locate two microearthquakes that were missed by the AEIC. An empirical study of the location sensitivity of the arrays predicts improvements over the Alaskan regional network that are shown as map-view contour plots. We verify these predictions by detecting an Msb{L} 3.2 event near Unimak Island with one array. The detection and location of four representative earthquakes illustrates the expansion of geographic coverage from array processing. Measurements at the arrays of systematic azimuth residuals, between 5sp° and 50sp° from 203 Aleutian events, reveal significant effects of heterogeneous structure on wavefields. Finally, algorithms to automatically detect earthquakes in continuous array data are demonstrated with the detection of an Aleutian earthquake.

Scalable Background-Limited Polarization-Sensitive Detectors for mm-wave Applications

NASA Technical Reports Server (NTRS)

Rostem, Karwan; Ali, Aamir; Appel, John W.; Bennett, Charles L.; Chuss, David T.; Colazo, Felipe A.; Crowe, Erik; Denis, Kevin L.; Essinger-Hileman, Tom; Marriage, Tobias A.;

Nonlinear terahertz coherent excitation of vibrational modes of liquids.

PubMed

Allodi, Marco A; Finneran, Ian A; Blake, Geoffrey A

2015-12-21

We report the first coherent excitation of intramolecular vibrational modes via the nonlinear interaction of a TeraHertz (THz) light field with molecular liquids. A terahertz-terahertz-Raman pulse sequence prepares the coherences with a broadband, high-energy, (sub)picosecond terahertz pulse, that are then measured in a terahertz Kerr effect spectrometer via phase-sensitive, heterodyne detection with an optical pulse. The spectrometer reported here has broader terahertz frequency coverage, and an increased sensitivity relative to previously reported terahertz Kerr effect experiments. Vibrational coherences are observed in liquid diiodomethane at 3.66 THz (122 cm(-1)), and in carbon tetrachloride at 6.50 THz (217 cm(-1)), in exact agreement with literature values of those intramolecular modes. This work opens the door to 2D spectroscopies, nonlinear in terahertz field, that can study the dynamics of condensed-phase molecular systems, as well as coherent control at terahertz frequencies.

Implications from XMM and Chandra Source Catalogs for Future Studies with Lynx

NASA Astrophysics Data System (ADS)

Ptak, Andrew

2018-01-01

Lynx will perform extremely sensitive X-ray surveys by combining very high-resolution imaging over a large field of view with a high effective area. These will include deep planned surveys and serendipitous source surveys. Here we discuss implications that can be gleaned from current Chandra and XMM-Newton serendipitous source surveys. These current surveys have discovered novel sources such as tidal disruption events, binary AGN, and ULX pulsars. In addition these surveys have detected large samples of normal galaxies, low-luminosity AGN and quasars due to the wide-area coverage of the Chandra and XMM-Newton source catalogs, allowing the evolution of these phenonema to be explored. The wide area Lynx surveys will probe down further in flux and will be coupled with very sensitive wide-area surveys such as LSST and SKA, allowing for detailed modeling of their SEDs and the discovery of rare, exotic sources and transient events.

Biology Today: Teaching and the Media.

ERIC Educational Resources Information Center

Flannery, Maura C.

1983-01-01

Provides examples of media coverage on interferon, herpes, and starch blockers, suggesting that biology teachers can put such coverage into broader perspective by answering student questions, explaining details, and sensitizing them to the limitations of the media. Includes resources to help teachers with this task. (JN)

Self-sampling with HPV mRNA analyses from vagina and urine compared with cervical samples.

PubMed

Asciutto, Katrin Christine; Ernstson, Avalon; Forslund, Ola; Borgfeldt, Christer

2018-04-01

In order to increase coverage in the organized cervical screening program, self-sampling with HPV analyses has been suggested. The aim was to compare human papillomavirus (HPV) mRNA detection in vaginal and urine self-collected samples with clinician-taken cervical samples and the corresponding clinician-taken histological specimens. Self-collected vaginal, urine and clinician-taken cervical samples were analyzed from 209 women with the Aptima mRNA assay (Hologic Inc, MA, USA). Cervical cytology, colposcopy, biopsy and/or the loop electrosurgical excision procedure (LEEP) were performed in every examination. The sensitivity of the HPV mRNA test in detecting high-grade squamous intraepithelial lesions (HSIL)/adenocarcinoma in situ (AIS)/cancer cases was as follows: for the vaginal self-samples 85.5% (95% CI; 75.0-92.8), the urinary samples 44.8% (95% CI; 32.6-57.4), and for routine cytology 81.7% (95% CI; 70.7-89.9). For the clinician-taken cervical HPV samples the sensitivity of the HPV mRNA test in detecting HSIL/AIS/cancer was 100.0% (95% CI; 94.9-100.0). The specificity of the HPV mRNA was similar for the clinician-taken cervical HPV samples and the self-samples: 49.0% vs. 48.1%. The urinary HPV samples had a specificity of 61.9% and cytology had a specificity of 93.3%. The sensitivity of the Aptima HPV mRNA test in detecting HSIL/AIS/cancer from vaginal self-samples was similar to that of routine cytology. The Aptima HPV mRNA vaginal self-sampling analysis may serve as a complement in screening programs. Copyright © 2018 Elsevier B.V. All rights reserved.

Sensitive and Specific Fluorescent Probes for Functional Analysis of the Three Major Types of Mammalian ABC Transporters

PubMed Central

Lebedeva, Irina V.; Pande, Praveen; Patton, Wayne F.

2011-01-01

An underlying mechanism for multi drug resistance (MDR) is up-regulation of the transmembrane ATP-binding cassette (ABC) transporter proteins. ABC transporters also determine the general fate and effect of pharmaceutical agents in the body. The three major types of ABC transporters are MDR1 (P-gp, P-glycoprotein, ABCB1), MRP1/2 (ABCC1/2) and BCRP/MXR (ABCG2) proteins. Flow cytometry (FCM) allows determination of the functional expression levels of ABC transporters in live cells, but most dyes used as indicators (rhodamine 123, DiOC2(3), calcein-AM) have limited applicability as they do not detect all three major types of ABC transporters. Dyes with broad coverage (such as doxorubicin, daunorubicin and mitoxantrone) lack sensitivity due to overall dimness and thus may yield a significant percentage of false negative results. We describe two novel fluorescent probes that are substrates for all three common types of ABC transporters and can serve as indicators of MDR in flow cytometry assays using live cells. The probes exhibit fast internalization, favorable uptake/efflux kinetics and high sensitivity of MDR detection, as established by multidrug resistance activity factor (MAF) values and Kolmogorov-Smirnov statistical analysis. Used in combination with general or specific inhibitors of ABC transporters, both dyes readily identify functional efflux and are capable of detecting small levels of efflux as well as defining the type of multidrug resistance. The assay can be applied to the screening of putative modulators of ABC transporters, facilitating rapid, reproducible, specific and relatively simple functional detection of ABC transporter activity, and ready implementation on widely available instruments. PMID:21799851

Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

PubMed Central

2011-01-01

Background Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes. Results We report the integration of the whole genome sequence of a single Holstein Friesian bull with data from single nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) array technologies to determine a comprehensive spectrum of genomic variation. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent (IBD) or in copy number variation (CNV) with results from SNP array genotyping. Coding insertions and deletions (indels) were found to be enriched for size in multiples of 3 and were located near the N- and C-termini of proteins. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. Conclusions Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. CNV discovery was affected dramatically by platform resolution and coverage biases. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants. PMID:22082336

Applications of Logic Coverage Criteria and Logic Mutation to Software Testing

ERIC Educational Resources Information Center

Kaminski, Garrett K.

2011-01-01

Logic is an important component of software. Thus, software logic testing has enjoyed significant research over a period of decades, with renewed interest in the last several years. One approach to detecting logic faults is to create and execute tests that satisfy logic coverage criteria. Another approach to detecting faults is to perform mutation…

Effect of the Brazilian Conditional Cash Transfer and Primary Health Care Programs on the New Case Detection Rate of Leprosy

PubMed Central

Nery, Joilda Silva; Pereira, Susan Martins; Rasella, Davide; Penna, Maria Lúcia Fernandes; Aquino, Rosana; Rodrigues, Laura Cunha; Barreto, Mauricio Lima; Penna, Gerson Oliveira

2014-01-01

Background Social determinants can affect the transmission of leprosy and its progression to disease. Not much is known about the effectiveness of welfare and primary health care policies on the reduction of leprosy occurrence. The aim of this study is to evaluate the impact of the Brazilian cash transfer (Bolsa Família Program-BFP) and primary health care (Family Health Program-FHP) programs on new case detection rate of leprosy. Methodology/Principal Findings We conducted the study with a mixed ecological design, a combination of an ecological multiple-group and time-trend design in the period 2004–2011 with the Brazilian municipalities as unit of analysis. The main independent variables were the BFP and FHP coverage at the municipal level and the outcome was new case detection rate of leprosy. Leprosy new cases, BFP and FHP coverage, population and other relevant socio-demographic covariates were obtained from national databases. We used fixed-effects negative binomial models for panel data adjusted for relevant socio-demographic covariates. A total of 1,358 municipalities were included in the analysis. In the studied period, while the municipal coverage of BFP and FHP increased, the new case detection rate of leprosy decreased. Leprosy new case detection rate was significantly reduced in municipalities with consolidated BFP coverage (Risk Ratio 0.79; 95% CI  = 0.74–0.83) and significantly increased in municipalities with FHP coverage in the medium (72–95%) (Risk Ratio 1.05; 95% CI  = 1.02–1.09) and higher coverage tertiles (>95%) (Risk Ratio 1.12; 95% CI  = 1.08–1.17). Conclusions At the same time the Family Health Program had been effective in increasing the new case detection rate of leprosy in Brazil, the Bolsa Família Program was associated with a reduction of the new case detection rate of leprosy that we propose reflects a reduction in leprosy incidence. PMID:25412418

Continuous All-Sky Cloud Measurements: Cloud Fraction Analysis Based on a Newly Developed Instrument

NASA Astrophysics Data System (ADS)

Aebi, C.; Groebner, J.; Kaempfer, N.; Vuilleumier, L.

2017-12-01

Clouds play an important role in the climate system and are also a crucial parameter for the Earth's surface energy budget. Ground-based measurements of clouds provide data in a high temporal resolution in order to quantify its influence on radiation. The newly developed all-sky cloud camera at PMOD/WRC in Davos (Switzerland), the infrared cloud camera (IRCCAM), is a microbolometer sensitive in the 8 - 14 μm wavelength range. To get all-sky information the camera is located on top of a frame looking downward on a spherical gold-plated mirror. The IRCCAM has been measuring continuously (day and nighttime) with a time resolution of one minute in Davos since September 2015. To assess the performance of the IRCCAM, two different visible all-sky cameras (Mobotix Q24M and Schreder VIS-J1006), which can only operate during daytime, are installed in Davos. All three camera systems have different software for calculating fractional cloud coverage from images. Our study analyzes mainly the fractional cloud coverage of the IRCCAM and compares it with the fractional cloud coverage calculated from the two visible cameras. Preliminary results of the measurement accuracy of the IRCCAM compared to the visible camera indicate that 78 % of the data are within ± 1 octa and even 93 % within ± 2 octas. An uncertainty of 1-2 octas corresponds to the measurement uncertainty of human observers. Therefore, the IRCCAM shows similar performance in detection of cloud coverage as the visible cameras and the human observers, with the advantage that continuous measurements with high temporal resolution are possible.

Suboptimal MMR2 vaccine coverage in six counties in Norway detected through the national immunisation registry, April 2014 to April 2017

PubMed Central

Hagerup-Jenssen, Maria; Kongsrud, Sigrun; Riise, Øystein Rolandsen

2017-01-01

In 2014, Norway became aware of potential low vaccination coverage for the second dose of measles-mumps-rubella vaccine (MMR2) in six of 19 counties. This was detected by comparing the national coverage (NC) for 16-year-olds extracted from the national immunisation registry SYSVAK with the annual status update for elimination of measles and rubella (ASU) reported to the World Health Organization (WHO). The existing method for calculating NC in 2014 did not show MMR2 coverage. ASU reporting on MMR2 was significantly lower then the NC and below the WHO-recommended 95% coverage. SYSVAK is based on the Norwegian personal identification numbers, which allows monitoring of vaccinations at aggregateded as well as individual level. It is an important tool for active surveillance of the performance of the Norwegian Childhood Immunisation Programme (NCIP). The method for calculating NC was improved in 2015 to reflect MMR2 coverage for 16-year-olds. As a result, Norway has improved its real-time surveillance and monitoring of the actual MMR2 coverage also through SYSVAK (the annual publication of NC). Vaccinators receive feedback for follow-up if 15-year-olds are missing MMR2. In 2017, only three counties had an MMR2 coverage below 90%. PMID:28489000

MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples.

PubMed

Malekpour, Seyed Amir; Pezeshk, Hamid; Sadeghi, Mehdi

2018-03-05

Currently a few tools are capable of detecting genome-wide Copy Number Variations (CNVs) based on sequencing of multiple samples. Although aberrations in mate pair insertion sizes provide additional hints for the CNV detection based on multiple samples, the majority of the current tools rely only on the depth of coverage. Here, we propose a new algorithm (MSeq-CNV) which allows detecting common CNVs across multiple samples. MSeq-CNV applies a mixture density for modeling aberrations in depth of coverage and abnormalities in the mate pair insertion sizes. Each component in this mixture density applies a Binomial distribution for modeling the number of mate pairs with aberration in the insertion size and also a Poisson distribution for emitting the read counts, in each genomic position. MSeq-CNV is applied on simulated data and also on real data of six HapMap individuals with high-coverage sequencing, in 1000 Genomes Project. These individuals include a CEU trio of European ancestry and a YRI trio of Nigerian ethnicity. Ancestry of these individuals is studied by clustering the identified CNVs. MSeq-CNV is also applied for detecting CNVs in two samples with low-coverage sequencing in 1000 Genomes Project and six samples form the Simons Genome Diversity Project.

Development and validation of duplex, triplex, and pentaplex real-time PCR screening assays for the detection of genetically modified organisms in food and feed.

PubMed

Huber, Ingrid; Block, Annette; Sebah, Daniela; Debode, Frédéric; Morisset, Dany; Grohmann, Lutz; Berben, Gilbert; Stebih, Dejan; Milavec, Mojca; Zel, Jana; Busch, Ulrich

2013-10-30

Worldwide, qualitative methods based on PCR are most commonly used as screening tools for genetically modified material in food and feed. However, the increasing number and diversity of genetically modified organisms (GMO) require effective methods for simultaneously detecting several genetic elements marking the presence of transgenic events. Herein we describe the development and validation of a pentaplex, as well as complementary triplex and duplex real-time PCR assays, for the detection of the most common screening elements found in commercialized GMOs: P-35S, T-nos, ctp2-cp4-epsps, bar, and pat. The use of these screening assays allows the coverage of many GMO events globally approved for commercialization. Each multiplex real-time PCR assay shows high specificity and sensitivity with an absolute limit of detection below 20 copies for the targeted sequences. We demonstrate by intra- and interlaboratory tests that the assays are robust as well as cost- and time-effective for GMO screening if applied in routine GMO analysis.

Liquid Biopsy in Lung Cancer: A Perspective From Members of the Pulmonary Pathology Society.

PubMed

Sholl, Lynette M; Aisner, Dara L; Allen, Timothy Craig; Beasley, Mary Beth; Cagle, Philip T; Capelozzi, Vera L; Dacic, Sanja; Hariri, Lida P; Kerr, Keith M; Lantuejoul, Sylvie; Mino-Kenudson, Mari; Raparia, Kirtee; Rekhtman, Natasha; Roy-Chowdhuri, Sinchita; Thunnissen, Eric; Tsao, Ming; Vivero, Marina; Yatabe, Yasushi

2016-08-01

Liquid biopsy has received extensive media coverage and has been called the holy grail of cancer detection. Attempts at circulating tumor cell and genetic material capture have been progressing for several years, and recent financially and technically feasible improvements of cell capture devices, plasma isolation techniques, and highly sensitive polymerase chain reaction- and sequencing-based methods have advanced the possibility of liquid biopsy of solid tumors. Although practical use of circulating RNA-based testing has been hindered by the need to fractionate blood to enrich for RNAs, the detection of circulating tumor cells has profited from advances in cell capture technology. In fact, the US Food and Drug Administration has approved one circulating tumor cell selection platform, the CellSearch System. Although the use of liquid biopsy in a patient population with a genomically defined solid tumor may potentially be clinically useful, it currently does not supersede conventional pretreatment tissue diagnosis of lung cancer. Liquid biopsy has not been validated for lung cancer diagnosis, and its lower sensitivity could lead to significant diagnostic delay if liquid biopsy were to be used in lieu of tissue biopsy. Ultimately, notwithstanding the enthusiasm encompassing liquid biopsy, its clinical utility remains unproven.

Direct electron transfer of glucose oxidase and dual hydrogen peroxide and glucose detection based on water-dispersible carbon nanotubes derivative.

PubMed

Chen, Hsiao-Chien; Tu, Yi-Ming; Hou, Chung-Che; Lin, Yu-Chen; Chen, Ching-Hsiang; Yang, Kuang-Hsuan

2015-03-31

A water-dispersible multi-walled carbon nanotubes (MWCNTs) derivative, MWCNTs-1-one-dihydroxypyridine (MWCNTs-Py) was synthesis via Friedel-Crafts chemical acylation. Raman spectra demonstrated the conjugated level of MWCNTs-Py was retained after this chemical modification. MWCNTs-Py showed dual hydrogen peroxide (H2O2) and glucose detections without mutual interference by adjusting pH value. It was sensitive to H2O2 in acidic solution and displayed the high performances of sensitivity, linear range, response time and stability; meanwhile it did not respond to H2O2 in neutral solution. In addition, this positively charged MWCNTs-Py could adsorb glucose oxidase (GOD) by electrostatic attraction. MWCNTs-Py-GOD/GC electrode showed the direct electron transfer (DET) of GOD with a pair of well-defined redox peaks, attesting the bioactivity of GOD was retained due to the non-destroyed immobilization. The high surface coverage of active GOD (3.5×10(-9) mol cm(-2)) resulted in exhibiting a good electrocatalytic activity toward glucose. This glucose sensor showed high sensitivity (68.1 μA mM(-1) cm(-2)) in a linear range from 3 μM to 7 mM in neutral buffer solution. The proposed sensor could distinguish H2O2 and glucose, thus owning high selectivity and reliability. Copyright © 2015. Published by Elsevier B.V.

Bacteria-Templated NiO Nanoparticles/Microstructure for an Enzymeless Glucose Sensor

PubMed Central

Vaidyanathan, Settu; Cherng, Jong-Yuh; Sun, An-Cheng; Chen, Chien-Yen

2016-01-01

The bacterial-induced hollow cylinder NiO (HCNiO) nanomaterial was utilized for the enzymeless (without GOx) detection of glucose in basic conditions. The determination of glucose in 0.05 M NaOH solution with high sensitivity was performed using cyclic voltammetry (CV) and amperometry (i–t). The fundamental electrochemical parameters were analyzed and the obtained values of diffusion coefficient (D), heterogeneous rate constant (ks), electroactive surface coverage (Г), and transfer coefficient (alpha-α) are 1.75 × 10−6 cm2/s, 57.65 M−1·s−1, 1.45 × 10−10 mol/cm2, and 0.52 respectively. The peak current of the i–t method shows two dynamic linear ranges of calibration curves 0.2 to 3.5 µM and 0.5 to 250 µM for the glucose electro-oxidation. The Ni2+/Ni3+ couple with the HCNiO electrode and the electrocatalytic properties were found to be sensitive to the glucose oxidation. The green chemistry of NiO preparation from bacteria and the high catalytic ability of the oxyhydroxide (NiOOH) is the good choice for the development of a glucose sensor. The best obtained sensitivity and limit of detection (LOD) for this sensor were 3978.9 µA mM−1·cm−2 and 0.9 µM, respectively. PMID:27409615

Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

NASA Astrophysics Data System (ADS)

Gajos, Katarzyna; Angelopoulou, Michailia; Petrou, Panagiota; Awsiuk, Kamil; Kakabakos, Sotirios; Haasnoot, Willem; Bernasik, Andrzej; Rysz, Jakub; Marzec, Mateusz M.; Misiakos, Konstantinos; Raptis, Ioannis; Budkowski, Andrzej

2016-11-01

Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays with dramatically improved both intra-chip response repeatability and assay detection sensitivity.

Effect of photoanode surface coverage by a sensitizer on the photovoltaic performance of titania based CdS quantum dot sensitized solar cells.

PubMed

Prasad, Rajendra M B; Pathan, Habib M

2016-04-08

In spite of the promising design and architecture, quantum dot sensitized solar cells (QDSSCs) have a long way to go before they attain the actual projected photoconversion efficiencies. Such an inferior performance displayed by QDSSCs is primarily because of many unwanted recombination losses of charge carriers at various interfaces of the cell. Electron recombination due to back electron transfer at the photoanode/electrolyte interface is an important one that needs to be addressed, to improve the efficiency of these third generation nanostructured solar cells. The present work highlights the importance of conformal coverage of CdS quantum dots (QDs) on the surface of the nanocrystalline titania photoanode in arresting such recombinations, leading to improvement in the performance of the cells. Using the successive ionic layer adsorption and reaction (SILAR) process, photoanodes are subjected to different amounts of CdS QD sensitization by varying the number of cycles of deposition. The sensitized electrodes are characterized using UV-visible spectroscopy, cyclic voltammetry and transmission electron microscopy to evaluate the extent of surface coverage of titania electrodes by QDs. Sandwich solar cells are then fabricated using these electrodes and characterized employing electrochemical impedance spectroscopy and J-V characteristics. It is observed that maximum solar cell efficiency is obtained for photoanodes with conformal coating of QDs and any further deposition of sensitizer leads to QD aggregation and so reduces the performance of the solar cells.

Quick, sensitive and specific detection and evaluation of quantification of minor variants by high-throughput sequencing.

PubMed

Leung, Ross Ka-Kit; Dong, Zhi Qiang; Sa, Fei; Chong, Cheong Meng; Lei, Si Wan; Tsui, Stephen Kwok-Wing; Lee, Simon Ming-Yuen

2014-02-01

Minor variants have significant implications in quasispecies evolution, early cancer detection and non-invasive fetal genotyping but their accurate detection by next-generation sequencing (NGS) is hampered by sequencing errors. We generated sequencing data from mixtures at predetermined ratios in order to provide insight into sequencing errors and variations that can arise for which simulation cannot be performed. The information also enables better parameterization in depth of coverage, read quality and heterogeneity, library preparation techniques, technical repeatability for mathematical modeling, theory development and simulation experimental design. We devised minor variant authentication rules that achieved 100% accuracy in both testing and validation experiments. The rules are free from tedious inspection of alignment accuracy, sequencing read quality or errors introduced by homopolymers. The authentication processes only require minor variants to: (1) have minimum depth of coverage larger than 30; (2) be reported by (a) four or more variant callers, or (b) DiBayes or LoFreq, plus SNVer (or BWA when no results are returned by SNVer), and with the interassay coefficient of variation (CV) no larger than 0.1. Quantification accuracy undermined by sequencing errors could neither be overcome by ultra-deep sequencing, nor recruiting more variant callers to reach a consensus, such that consistent underestimation and overestimation (i.e. low CV) were observed. To accommodate stochastic error and adjust the observed ratio within a specified accuracy, we presented a proof of concept for the use of a double calibration curve for quantification, which provides an important reference towards potential industrial-scale fabrication of calibrants for NGS.

Lunar surface remanent magnetic fields detected by the electron reflection method

NASA Technical Reports Server (NTRS)

Lin, R. P.; Anderson, K. A.; Bush, R.; Mcguire, R. E.; Mccoy, J. E.

1976-01-01

We present maps of the lunar surface remanent magnetic fields detected by the electron reflection method. These maps provide substantial coverage of the latitude band from 30 N southward to 30 S with a resolution of about 40 km and a sensitivity of about 0.2 gamma at the lunar surface. Regions of remanent magnetization are observed ranging in size from the resolution limit of 1.25 deg to above approximately 60 deg. The largest contiguous region fills the Big Backside Basin where it is intersected by the spacecraft orbital tracks. Preliminary analyses of the maps show that the source regions of lunar limb compressions correspond to regions of strong surface magnetism, and that there does not appear to be sharply discontinuous magnetization at the edges of maria. We also analyze the electron reflection observations to obtain information on the direction and distribution of magnetization in the Van de Graaff anomaly region.

The study of 'microsurfaces' using thermal desorption spectroscopy

NASA Technical Reports Server (NTRS)

Thomas, M. E.; Poppa, H.; Pound, G. M.

1979-01-01

The use of a newly combined ultrahigh vacuum technique for studying continuous and particulate evaporated thin films using thermal desorption spectroscopy (TDS), transmission electron microscopy (TEM), and transmission electron diffraction (TED) is discussed. It is shown that (1) CO thermal desorption energies of epitaxially deposited (111) Ni and (111) Pd surfaces agree perfectly with previously published data on bulk (111) single crystal, (2) contamination and surface structural differences can be detected using TDS as a surface probe and TEM as a complementary technique, and (3) CO desorption signals from deposited metal coverages of one-thousandth of a monolayer should be detectable. These results indicate that the chemisorption properties of supported 'microsurfaces' of metals can now be investigated with very high sensitivity. The combined use of TDS and TEM-TED experimental methods is a very powerful technique for fundamental studies in basic thin film physics and in catalysis.

NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.

PubMed

Chuang, Trees-Juen; Wu, Chan-Shuo; Chen, Chia-Ying; Hung, Li-Yuan; Chiang, Tai-Wei; Yang, Min-Yu

2016-02-18

Analysis of RNA-seq data often detects numerous 'non-co-linear' (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts (trans-spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method ('NCLscan'), which utilized a stepwise alignment strategy to almost completely eliminate false calls (>98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans-spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans-spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Probing cosmic strings with satellite CMB measurements

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

Jeong, E.; Baccigalupi, Carlo; Smoot, G.F., E-mail: ehjeong@sissa.it, E-mail: bacci@sissa.it, E-mail: gfsmoot@lbl.gov

2010-09-01

We study the problem of searching for cosmic string signal patterns in the present high resolution and high sensitivity observations of the Cosmic Microwave Background (CMB). This article discusses a technique capable of recognizing Kaiser-Stebbins effect signatures in total intensity anisotropy maps from isolated strings. We derive the statistical distributions of null detections from purely Gaussian fluctuations and instrumental performances of the operating satellites, and show that the biggest factor that produces confusion is represented by the acoustic oscillation features of the scale comparable to the size of horizon at recombination. Simulations show that the distribution of null detections convergesmore » to a χ{sup 2} distribution, with detectability threshold at 99% confidence level corresponding to a string induced step signal with an amplitude of about 100 μK which corresponds to a limit of roughly Gμ ∼ 1.5 × 10{sup −6}. We implement simulations for deriving the statistics of spurious detections caused by extra-Galactic and Galactic foregrounds. For diffuse Galactic foregrounds, which represents the dominant source of contamination, we construct sky masks outlining the available region of the sky where the Galactic confusion is sub-dominant, specializing our analysis to the case represented by the frequency coverage and nominal sensitivity and resolution of the Planck experiment. As for other CMB measurements, the maximum available area, corresponding to 7%, is reached where the foreground emission is expected to be minimum, in the 70–100 GHz interval.« less

A Census of Southern Pulsars at 185 MHz

NASA Astrophysics Data System (ADS)

Xue, Mengyao; Bhat, N. D. R.; Tremblay, S. E.; Ord, S. M.; Sobey, C.; Swainston, N. A.; Kaplan, D. L.; Johnston, Simon; Meyers, B. W.; McSweeney, S. J.

2017-12-01

The Murchison Widefield Array, and its recently developed Voltage Capture System, facilitates extending the low-frequency range of pulsar observations at high-time and -frequency resolution in the Southern Hemisphere, providing further information about pulsars and the ISM. We present the results of an initial time-resolved census of known pulsars using the Murchison Widefield Array. To significantly reduce the processing load, we incoherently sum the detected powers from the 128 Murchison Widefield Array tiles, which yields 10% of the attainable sensitivity of the coherent sum. This preserves the large field-of-view ( 450 deg2 at 185 MHz), allowing multiple pulsars to be observed simultaneously. We developed a WIde-field Pulsar Pipeline that processes the data from each observation and automatically folds every known pulsar located within the beam. We have detected 50 pulsars to date, 6 of which are millisecond pulsars. This is consistent with our expectation, given the telescope sensitivity and the sky coverage of the processed data ( 17 000 deg2). For 10 pulsars, we present the lowest frequency detections published. For a subset of the pulsars, we present multi-frequency pulse profiles by combining our data with published profiles from other telescopes. Since the Murchison Widefield Array is a low-frequency precursor to the Square Kilometre Array, we use our census results to forecast that a survey using the low-frequency component of the Square Kilometre Array Phase 1 can potentially detect around 9 400 pulsars.

Light Scattering by Lunar Exospheric Dust: What could be Learned from LRO LAMP and LADEE UVS?

NASA Astrophysics Data System (ADS)

Glenar, D. A.; Stubbs, T. J.; Richard, D. T.; Stern, S. A.; Retherford, K. D.; Gladstone, R.; Feldman, P. D.; Colaprete, A.; Delory, G. T.

2011-12-01

Two complementary spectrometers, namely the Lunar Reconnaissance Orbiter, Lyman Alpha Mapping Project (LAMP) and the planned Lunar Atmosphere and Dust Environment Explorer (LADEE) Ultraviolet Explorer (UVS) will carry out sensitive searches for high altitude exospheric dust, via detection of scattered sunlight. The combined spectral coverage of these instruments extends from far-UV to near-IR wavelengths. Over this wavelength range, grain size parameter (X=2πr/λ, with r the grain radius and λ the wavelength) changes dramatically, which makes broad wavelength coverage a good diagnostic of grain size. Utilizing different pointing geometries, both LAMP and UVS are able to observe dust over a range of scattering angles, as well as measure the dust vertical profile via limb measurements at multiple tangent heights. We summarize several categories of information that can be inferred from the data sets, using broadband simulations of horizon glow as observed at the limb. Grain scattering properties used in these simulations were computed for multiple grain shapes using Discrete-Dipole theory. Some cautionary remarks are included regarding the use of Mie theory to interpret scattering measurements.

Determining the Orbit Locations of Turkish Airborne Early Warning and Control Aircraft Over the Turkish Air Space

DTIC Science & Technology

2009-03-01

and Control (AEW&C) Aircraft. AEW&C aircraft has become vital to detect low altitude threats that a ground RADAR cannot detect because of obstacles...HARM). The concern is to cover and detect the threats as far as possible from Turkey within a risk that the commander accepts. The goal is to help...decision makers decide how many AEW aircraft are needed to obtain full coverage. In order to provide optimum results, a Maximal Coverage Location

Geographic information system (GIS) maps and malaria control monitoring: intervention coverage and health outcome in distal villages of Khammouane province, Laos

PubMed Central

Shirayama, Yoshihisa; Phompida, Samlane; Shibuya, Kenji

2009-01-01

Background Insecticide-treated nets (ITNs) are a key intervention to control malaria. The intervention coverage varies as a consequence of geographical accessibility to remote villages and limitations of financial and human resources for the intervention. People's adherence to the intervention, i.e., proper use of ITNs, also affects malaria health outcome. The study objective is to explore the impact of the intervention coverage and people's adherence to the intervention on malaria health outcome among targeted villages in various geographic locations. Methods Geographic information system (GIS) maps were developed using the data collected in an active case detection survey in Khammouane province, Laos. The survey was conducted using rapid diagnostic tests (RDTs) and a structured questionnaire at 23 sites in the province from June to July, the rainy season, in 2005. A total of 1,711 villagers from 403 households participated in the survey. Results As indicated on the GIS maps, villages with malaria cases, lower intervention coverage, and lower adherence were identified. Although no malaria case was detected in most villages with the best access to the district center, several cases were detected in the distal villages, where the intervention coverage and adherence to the intervention remained relatively lower. Conclusion Based on the data and maps, it was demonstrated that malaria remained unevenly distributed within districts. Balancing the intervention coverage in the distal villages with the overall coverage and continued promotion of the proper use of ITNs are necessary for a further reduction of malaria cases in the province. PMID:19772628

Geographic information system (GIS) maps and malaria control monitoring: intervention coverage and health outcome in distal villages of Khammouane province, Laos.

PubMed

Shirayama, Yoshihisa; Phompida, Samlane; Shibuya, Kenji

2009-09-22

Insecticide-treated nets (ITNs) are a key intervention to control malaria. The intervention coverage varies as a consequence of geographical accessibility to remote villages and limitations of financial and human resources for the intervention. People's adherence to the intervention, i.e., proper use of ITNs, also affects malaria health outcome. The study objective is to explore the impact of the intervention coverage and people's adherence to the intervention on malaria health outcome among targeted villages in various geographic locations. Geographic information system (GIS) maps were developed using the data collected in an active case detection survey in Khammouane province, Laos. The survey was conducted using rapid diagnostic tests (RDTs) and a structured questionnaire at 23 sites in the province from June to July, the rainy season, in 2005. A total of 1,711 villagers from 403 households participated in the survey. As indicated on the GIS maps, villages with malaria cases, lower intervention coverage, and lower adherence were identified. Although no malaria case was detected in most villages with the best access to the district center, several cases were detected in the distal villages, where the intervention coverage and adherence to the intervention remained relatively lower. Based on the data and maps, it was demonstrated that malaria remained unevenly distributed within districts. Balancing the intervention coverage in the distal villages with the overall coverage and continued promotion of the proper use of ITNs are necessary for a further reduction of malaria cases in the province.

I-SCAD® standoff chemical agent detector overview

NASA Astrophysics Data System (ADS)

Popa, Mirela O.; Griffin, Matthew T.

2012-06-01

This paper presents a system-level description of the I-SCAD® Standoff Chemical Agent Detector, a passive Fourier Transform InfraRed (FTIR) based remote sensing system, for detecting chemical vapor threats. The passive infrared detection system automatically searches the 7 to 14 micron region of the surrounding atmosphere for agent vapor clouds. It is capable of operating while on the move to accomplish reconnaissance, surveillance, and contamination avoidance missions. Additionally, the system is designed to meet the needs for application on air and sea as well as ground mobile and fixed site platforms. The lightweight, passive, and fully automatic detection system scans the surrounding atmosphere for chemical warfare agent vapors. It provides on-the-move, 360-deg coverage from a variety of tactical and reconnaissance platforms at distances up to 5 km. The core of the system is a rugged Michelson interferometer with a flexure spring bearing mechanism and bi-directional data acquisition capability. The modular system design facilitates interfacing to many platforms. A Reduced Field of View (RFOV) variant includes novel modifications to the scanner subcomponent assembly optical design that gives extended performance in detection range and detection probability without sacrificing existing radiometric sensitivity performance. This paper will deliver an overview of system.

A highly oriented hybrid microarray modified electrode fabricated by a template-free method for ultrasensitive electrochemical DNA recognition

NASA Astrophysics Data System (ADS)

Shi, Lei; Chu, Zhenyu; Dong, Xueliang; Jin, Wanqin; Dempsey, Eithne

2013-10-01

Highly oriented growth of a hybrid microarray was realized by a facile template-free method on gold substrates for the first time. The proposed formation mechanism involves an interfacial structure-directing force arising from self-assembled monolayers (SAMs) between gold substrates and hybrid crystals. Different SAMs and variable surface coverage of the assembled molecules play a critical role in the interfacial directing forces and influence the morphologies of hybrid films. A highly oriented hybrid microarray was formed on the highly aligned and vertical SAMs of 1,4-benzenedithiol molecules with rigid backbones, which afforded an intense structure-directing power for the oriented growth of hybrid crystals. Additionally, the density of the microarray could be adjusted by controlling the surface coverage of assembled molecules. Based on the hybrid microarray modified electrode with a large specific area (ca. 10 times its geometrical area), a label-free electrochemical DNA biosensor was constructed for the detection of an oligonucleotide fragment of the avian flu virus H5N1. The DNA biosensor displayed a significantly low detection limit of 5 pM (S/N = 3), a wide linear response from 10 pM to 10 nM, as well as excellent selectivity, good regeneration and high stability. We expect that the proposed template-free method can provide a new reference for the fabrication of a highly oriented hybrid array and the as-prepared microarray modified electrode will be a promising paradigm in constructing highly sensitive and selective biosensors.Highly oriented growth of a hybrid microarray was realized by a facile template-free method on gold substrates for the first time. The proposed formation mechanism involves an interfacial structure-directing force arising from self-assembled monolayers (SAMs) between gold substrates and hybrid crystals. Different SAMs and variable surface coverage of the assembled molecules play a critical role in the interfacial directing forces and influence the morphologies of hybrid films. A highly oriented hybrid microarray was formed on the highly aligned and vertical SAMs of 1,4-benzenedithiol molecules with rigid backbones, which afforded an intense structure-directing power for the oriented growth of hybrid crystals. Additionally, the density of the microarray could be adjusted by controlling the surface coverage of assembled molecules. Based on the hybrid microarray modified electrode with a large specific area (ca. 10 times its geometrical area), a label-free electrochemical DNA biosensor was constructed for the detection of an oligonucleotide fragment of the avian flu virus H5N1. The DNA biosensor displayed a significantly low detection limit of 5 pM (S/N = 3), a wide linear response from 10 pM to 10 nM, as well as excellent selectivity, good regeneration and high stability. We expect that the proposed template-free method can provide a new reference for the fabrication of a highly oriented hybrid array and the as-prepared microarray modified electrode will be a promising paradigm in constructing highly sensitive and selective biosensors. Electronic supplementary information (ESI) available: Four-probe method for determining the conductivity of the hybrid crystal (Fig. S1); stability comparisons of the hybrid films (Fig. S2); FESEM images of the hybrid microarray (Fig. S3); electrochemical characterizations of the hybrid films (Fig. S4); DFT simulations (Fig. S5); cross-sectional FESEM image of the hybrid microarray (Fig. S6); regeneration and stability tests of the DNA biosensor (Fig. S7). See DOI: 10.1039/c3nr03097k

Comparative evaluation of non-structural protein-antibody detecting ELISAs for foot-and-mouth disease sero-surveillance under intensive vaccination.

PubMed

Sharma, Gaurav Kumar; Mohapatra, Jajati Keshari; Mahajan, Sonalika; Matura, Rakesh; Subramaniam, Saravanan; Pattnaik, Bramhadev

2014-10-01

Foot-and-mouth disease is a highly infectious and contagious disease of livestock animals with transboundary and economical importance. Animals in the endemic settings are regularly vaccinated in addition to intensive surveillance for control of the disease. Under intensive vaccination, detection of infected animals among the vaccinated population is essential to monitor the infection and to track down the virus movement. Sero-surveillance and retrospective disease diagnosis is performed primarily by detecting antibodies against non-structural proteins (NSPs) of FMD virus which are usually absent in the inactivated vaccine formulations. The study was conducted with an objective to compare simultaneously performance of six NSP ELISAs in detecting infected animals in the areas covered under intensive vaccination, and to assess their fit-for-purpose attribute for sero-surveillance of FMD in India. A panel of bovine serum samples consisting of samples collected from infected with FMDV, vaccinated and naive animals were constituted. In addition, samples collected at random from areas having varied FMD situation and vaccination coverage were tested simultaneously by the six NSP ELISAs to compare their performances. The four indigenous assays showed varying degrees of correlation with the two commercial kits. The study validated that, in all the groups of samples, the indigenous assays were equally sensitive and specific as the two commercial kits. Among all the six assays, PrioCheck and in-house 3ABC I-ELISAs showed maximum sensitivity for detection of infected animals, whereas 3AB3 I-ELISA and 3ABC C-ELISA showed maximum specificity. The study concluded that the in-house available assays are equally capable as the commercially available kits for differentiation of infected animals under intensive vaccination and identifies the 3AB3 I-ELISA with optimum sensitivity and specificity for the purpose of sero-surveillance in India. Copyright © 2014 Elsevier B.V. All rights reserved.

Carbon Nanospikes Grown on Metal Wires as Microelectrode Sensors for Dopamine

PubMed Central

Zestos, Alexander G.; Yang, Cheng; Jacobs, Christopher B.; Hensley, Dale; Venton, B. Jill

2015-01-01

Carbon nanomaterials are advantageous as electrodes for neurotransmitter detection, but the difficulty of nanomaterials deposition on electrode substrates limits the reproducibility and future applications. In this study, we used plasma enhanced chemical vapor deposition (PECVD) to directly grow a thin layer of carbon nanospikes (CNS) on cylindrical metal substrates. No catalyst is required and the CNS surface coverage is uniform over the cylindrical metal substrate. The CNS growth was characterized on several metallic substrates including tantalum, niobium, palladium, and nickel wires. Using fast-scan cyclic voltammetry (FSCV), bare metal wires could not detect 1 μM dopamine while carbon nanospike coated wires could. The highest sensitivity and optimized S/N ratio was recorded from carbon nanospike-tantalum (CNS-Ta) microwires grown for 7.5 minutes, which had a LOD of 8 ± 2 nM for dopamine with FSCV. CNS-Ta microelectrodes were more reversible and had a smaller ΔEp for dopamine than carbon-fiber microelectrodes, suggesting faster electron transfer kinetics. The kinetics of dopamine redox were adsorption controlled at CNS-Ta microelectrodes and repeated electrochemical measurements displayed stability for up to ten hours in vitro and over a ten day period as well. The oxidation potential was significantly different for ascorbic acid and uric acid compared to dopamine. Growing carbon nanospikes on metal wires is a promising method to produce uniformly-coated, carbon nanostructured cylindrical microelectrodes for sensitive dopamine detection. PMID:26389138

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

Zestos, Alexander G.; Yang, Cheng; Jacobs, Christopher B.

Carbon nanomaterials are advantageous as electrodes for neurotransmitter detection, but the difficulty of nanomaterials deposition on electrode substrates limits the reproducibility and future applications. In our study, we used plasma enhanced chemical vapor deposition (PECVD) to directly grow a thin layer of carbon nanospikes (CNS) on cylindrical metal substrates. No catalyst is required and the CNS surface coverage is uniform over the cylindrical metal substrate. We characterized the CNS growth on several metallic substrates including tantalum, niobium, palladium, and nickel wires. Using fast-scan cyclic voltammetry (FSCV), bare metal wires could not detect 1 mu M dopamine while carbon nanospike coatedmore » wires could. Moreover, the highest sensitivity and optimized S/N ratio was recorded from carbon nanospike-tantalum (CNS-Ta) microwires grown for 7.5 minutes, which had a LOD of 8 +/- 2 nM for dopamine with FSCV. CNS-Ta microelectrodes were more reversible and had a smaller Delta E-p for dopamine than carbon-fiber microelectrodes, suggesting faster electron transfer kinetics. The kinetics of dopamine redox were adsorption controlled at CNS-Ta microelectrodes and repeated electrochemical measurements displayed stability for up to ten hours in vitro and over a ten day period as well. The oxidation potential was significantly different for ascorbic acid and uric acid compared to dopamine. Finally, growing carbon nanospikes on metal wires is a promising method to produce uniformly-coated, carbon nanostructured cylindrical microelectrodes for sensitive dopamine detection.« less

Article Spurs Community to Support Athlete, Team.

ERIC Educational Resources Information Center

Bates, Janelle

1999-01-01

Describes the coverage of an athlete's spinal cord injury by the "Wildcat News" (Woodrow Wilson High School, Dallas, Texas). Notes a fellow teammate (the sports editor) covered the accident. Discusses the efforts made to be sensitive to the situation and the needs of others. Appends an exercise concerning coverage of athletic injuries.…

The MIRAX Hard X-Ray Transient Mission

NASA Astrophysics Data System (ADS)

Rodrigues, Barbara; Braga, J.; Grindlay, J. E.; Allen, B.; Hong, J.; Barthelmy, S. D.; Rothschild, R. E.; Wilms, J.

2013-01-01

The MIRAX (Monitor e Imageador de Raios X) mission is designed to perform a hard X-ray (5-200 keV) survey of more than half of the sky with high localization power 1') and high sensitivity (26 mCrab for one orbit and 0.3 mCrab for one year). This will be achieved by a set of 4 coded-mask imagers that will operate in scanning mode in a near-Equatorial circular LEO with a lifetime of 4+ years. The pointing directions will maximize the coverage of the Central Galactic Plane. The main objective of MIRAX is to study with unprecedented depth and time coverage (milliseconds to years) a large sample of transient and variable phenomena on accreting neutron stars and black holes. The high cadence of the MIRAX detections will be well suited for simultaneous and follow-up observations in other wavelengths. The satellite bus and launch will be provided by Brazil, whereas the instrument development is a cooperative effort led by CfA and including INPE (Brazil), UCSD, MIT, NASA's GSFC, Caltech and the University of Erlangen-Nuremberg in Germany. The MIRAX detectors, developed at CfA, are position-sensitive 5mm-thick CdZnTe with 0.6mm pitch with 756 cm2 effective area at 10 keV (total for the 4 units). The energy resolution is ~2 keV at 60 keV. For exposures near the center of the field of view the sensitivity of MIRAX will approach that of Swift/BAT in the 15-150 keV range, whereas the low threshold will enable ~70 mCrab sensitivity on time scales of 100s at energies inaccessible to Swift/BAT and INTEGRAL. The first unit of one MIRAX telescope has been developed and flown in the protoEXIST-2 (P2) balloon experiment in Fort Sumner, NM, in early October 2012. In this work we describe the MIRAX instruments and discuss results of detector calibration and preliminary results of the P2 balloon flight.

Suboptimal MMR2 vaccine coverage in six counties in Norway detected through the national immunisation registry, April 2014 to April 2017.

PubMed

Hagerup-Jenssen, Maria; Kongsrud, Sigrun; Riise, Øystein Rolandsen

2017-04-27

In 2014, Norway became aware of potential low vaccination coverage for the second dose of measles-mumps-rubella vaccine (MMR2) in six of 19 counties. This was detected by comparing the national coverage (NC) for 16-year-olds extracted from the national immunisation registry SYSVAK with the annual status update for elimination of measles and rubella (ASU) reported to the World Health Organization (WHO). The existing method for calculating NC in 2014 did not show MMR2 coverage. ASU reporting on MMR2 was significantly lower then the NC and below the WHO-recommended 95% coverage. SYSVAK is based on the Norwegian personal identification numbers, which allows monitoring of vaccinations at aggregateded as well as individual level. It is an important tool for active surveillance of the performance of the Norwegian Childhood Immunisation Programme (NCIP). The method for calculating NC was improved in 2015 to reflect MMR2 coverage for 16-year-olds. As a result, Norway has improved its real-time surveillance and monitoring of the actual MMR2 coverage also through SYSVAK (the annual publication of NC). Vaccinators receive feedback for follow-up if 15-year-olds are missing MMR2. In 2017, only three counties had an MMR2 coverage below 90%. This article is copyright of The Authors, 2017.

A computational method for detecting copy number variations using scale-space filtering

PubMed Central

2013-01-01

Background As next-generation sequencing technology made rapid and cost-effective sequencing available, the importance of computational approaches in finding and analyzing copy number variations (CNVs) has been amplified. Furthermore, most genome projects need to accurately analyze sequences with fairly low-coverage read data. It is urgently needed to develop a method to detect the exact types and locations of CNVs from low coverage read data. Results Here, we propose a new CNV detection method, CNV_SS, which uses scale-space filtering. The scale-space filtering is evaluated by applying to the read coverage data the Gaussian convolution for various scales according to a given scaling parameter. Next, by differentiating twice and finding zero-crossing points, inflection points of scale-space filtered read coverage data are calculated per scale. Then, the types and the exact locations of CNVs are obtained by analyzing the finger print map, the contours of zero-crossing points for various scales. Conclusions The performance of CNV_SS showed that FNR and FPR stay in the range of 1.27% to 2.43% and 1.14% to 2.44%, respectively, even at a relatively low coverage (0.5x ≤C ≤2x). CNV_SS gave also much more effective results than the conventional methods in the evaluation of FNR, at 3.82% at least and 76.97% at most even when the coverage level of read data is low. CNV_SS source code is freely available from http://dblab.hallym.ac.kr/CNV SS/. PMID:23418726

The "collimator monitoring fill factor" of a two-dimensional detector array, a measure of its ability to detect collimation errors.

PubMed

Stelljes, Tenzin Sonam; Looe, Hui Khee; Harder, Dietrich; Poppe, Björn

2017-03-01

Two-dimensional detector arrays are routinely used for constancy checks and treatment plan verification in photon-beam radiotherapy. In addition to the spatial resolution of the dose profiles, the "coverage" of the radiation field with respect to the detection of any beam collimation deficiency appears as the second characteristic feature of a detector array. The here proposed "collimator monitoring fill factor" (CM fill factor) has been conceived to serve as a quantitative characteristic of this "coverage". The CM fill factor is defined as the probability of a 2D array to detect any collimator position error. Therefore, it is represented by the ratio of the "sensitive area" of a single detector, in which collimator position errors are detectable, and the geometrical "cell area" associated with this detector within the array. Numerical values of the CM fill factor have been Monte Carlo simulated for 2D detector arrays equipped with air-vented ionization chambers, liquid-filled ionization chambers and diode detectors and were compared with the "FWHM fill factor" defined by Gago-Arias et al. (2012). For arrays with vented ionization chambers, the differences between the CM fill factor and the FWHM fill factor are moderate, but occasionally the latter exceeds unity. For narrower detectors such as liquid-filled ionization chambers and Si diodes and for small sampling distances, large differences between the FWHM fill factor and the CM fill factor have been observed. These differences can be explained by the shapes of the fluence response functions of these narrow detectors. A new parameter "collimator monitoring fill factor" (CM fill factor), applicable to quantitate the collimator position error detection probability of a 2D detector array, has been proposed. It is designed as a help in classifying the clinical performance of two-dimensional detector arrays in photon-beam radiotherapy. © 2017 American Association of Physicists in Medicine.

HPV self-sampling in CIN2+ detection: sensitivity and specificity of different RLU cut-off of HC2 in specimens from 786 women.

PubMed

Bottari, F; Igidbashian, S; Boveri, S; Tricca, A; Gulmini, C; Sesia, M; Spolti, N; Sideri, M; Landoni, F; Sandri, M T

2017-04-01

Mortality for cervical cancer varies between the different regions of the world, with high rates in low-income countries where screening programmes are not present and organised. However, increasing screening coverage is still a priority in all countries: one way to do that is to base screening on self-sampled screening. The success of a self-sampling screening strategy depends on capacity to recruit unscreened women, on the performance and acceptability of the device and on the clinical performance of the high-risk human papillomavirus (HPV) test. This study based on 786 enrolled women investigates the best cut-off value of Hybrid Capture 2 HPV test (HC2) for self-sampled specimens in terms of sensitivity and specificity. In this population, we found that the sensitivity and the specificity for cervical intraepithelial neoplasia grade 2 or more detection of HC2 performed on self-sampled specimens were 82.5% and 82.8%, respectively considering the relative light units (RLU) cut-off value of 1. Increasing the cut-off value the sensitivity decreases and the specificity raises and the best area under the curve for the RLU cut-off value is 1. Our results confirm that the cut-off value of 1 suggested by Qiagen for PreservCyt specimen is the best cut-off value also for self-sampled specimens. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Two complementary reversed-phase separations for comprehensive coverage of the semipolar and nonpolar metabolome.

PubMed

Naser, Fuad J; Mahieu, Nathaniel G; Wang, Lingjue; Spalding, Jonathan L; Johnson, Stephen L; Patti, Gary J

2018-02-01

Although it is common in untargeted metabolomics to apply reversed-phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC) methods that have been systematically optimized for lipids and central carbon metabolites, here we show that these established protocols provide poor coverage of semipolar metabolites because of inadequate retention. Our objective was to develop an RPLC approach that improved detection of these metabolites without sacrificing lipid coverage. We initially evaluated columns recently released by Waters under the CORTECS line by analyzing 47 small-molecule standards that evenly span the nonpolar and semipolar ranges. An RPLC method commonly used in untargeted metabolomics was considered a benchmarking reference. We found that highly nonpolar and semipolar metabolites cannot be reliably profiled with any single method because of retention and solubility limitations of the injection solvent. Instead, we optimized a multiplexed approach using the CORTECS T3 column to analyze semipolar compounds and the CORTECS C 8 column to analyze lipids. Strikingly, we determined that combining these methods allowed detection of 41 of the total 47 standards, whereas our reference RPLC method detected only 10 of the 47 standards. We then applied credentialing to compare method performance at the comprehensive scale. The tandem method showed more than a fivefold increase in credentialing coverage relative to our RPLC benchmark. Our results demonstrate that comprehensive coverage of metabolites amenable to reversed-phase separation necessitates two reconstitution solvents and chromatographic methods. Thus, we suggest complementing HILIC methods with a dual T3 and C 8 RPLC approach to increase coverage of semipolar metabolites and lipids for untargeted metabolomics. Graphical abstract Analysis of semipolar and nonpolar metabolites necessitates two reversed-phase chromatography (RPLC) methods, which extend metabolome coverage more than fivefold for untargeted profiling. HILIC hydrophilic interaction liquid chromatography.

Detection limit of intragenic deletions with targeted array comparative genomic hybridization

PubMed Central

2013-01-01

Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. PMID:24304607

Event Coverage Detection and Event Source Determination in Underwater Wireless Sensor Networks.

PubMed

Zhou, Zhangbing; Xing, Riliang; Duan, Yucong; Zhu, Yueqin; Xiang, Jianming

2015-12-15

With the advent of the Internet of Underwater Things, smart things are deployed in the ocean space and establish underwater wireless sensor networks for the monitoring of vast and dynamic underwater environments. When events are found to have possibly occurred, accurate event coverage should be detected, and potential event sources should be determined for the enactment of prompt and proper responses. To address this challenge, a technique that detects event coverage and determines event sources is developed in this article. Specifically, the occurrence of possible events corresponds to a set of neighboring sensor nodes whose sensory data may deviate from a normal sensing range in a collective fashion. An appropriate sensor node is selected as the relay node for gathering and routing sensory data to sink node(s). When sensory data are collected at sink node(s), the event coverage is detected and represented as a weighted graph, where the vertices in this graph correspond to sensor nodes and the weight specified upon the edges reflects the extent of sensory data deviating from a normal sensing range. Event sources are determined, which correspond to the barycenters in this graph. The results of the experiments show that our technique is more energy efficient, especially when the network topology is relatively steady.

Event Coverage Detection and Event Source Determination in Underwater Wireless Sensor Networks

PubMed Central

Zhou, Zhangbing; Xing, Riliang; Duan, Yucong; Zhu, Yueqin; Xiang, Jianming

2015-01-01

With the advent of the Internet of Underwater Things, smart things are deployed in the ocean space and establish underwater wireless sensor networks for the monitoring of vast and dynamic underwater environments. When events are found to have possibly occurred, accurate event coverage should be detected, and potential event sources should be determined for the enactment of prompt and proper responses. To address this challenge, a technique that detects event coverage and determines event sources is developed in this article. Specifically, the occurrence of possible events corresponds to a set of neighboring sensor nodes whose sensory data may deviate from a normal sensing range in a collective fashion. An appropriate sensor node is selected as the relay node for gathering and routing sensory data to sink node(s). When sensory data are collected at sink node(s), the event coverage is detected and represented as a weighted graph, where the vertices in this graph correspond to sensor nodes and the weight specified upon the edges reflects the extent of sensory data deviating from a normal sensing range. Event sources are determined, which correspond to the barycenters in this graph. The results of the experiments show that our technique is more energy efficient, especially when the network topology is relatively steady. PMID:26694394

Automated measurement of stent strut coverage in intravascular optical coherence tomography

NASA Astrophysics Data System (ADS)

Ahn, Chi Young; Kim, Byeong-Keuk; Hong, Myeong-Ki; Jang, Yangsoo; Heo, Jung; Joo, Chulmin; Seo, Jin Keun

2015-02-01

Optical coherence tomography (OCT) is a non-invasive, cross-sectional imaging modality that has become a prominent imaging method in percutaneous intracoronary intervention. We present an automated detection algorithm for stent strut coordinates and coverage in OCT images. The algorithm for stent strut detection is composed of a coordinate transformation from the polar to the Cartesian domains and application of second derivative operators in the radial and the circumferential directions. Local region-based active contouring was employed to detect lumen boundaries. We applied the method to the OCT pullback images acquired from human patients in vivo to quantitatively measure stent strut coverage. The validation studies against manual expert assessments demonstrated high Pearson's coefficients ( R = 0.99) in terms of the stent strut coordinates, with no significant bias. An averaged Hausdorff distance of < 120 μm was obtained for vessel border detection. Quantitative comparison in stent strut to vessel wall distance found a bias of < 12.3 μm and a 95% confidence of < 110 μm.

Optical And Near-infrared Variability Among Distant Galactic Nuclei Of The CANDELS EGS Field

NASA Astrophysics Data System (ADS)

Grogin, Norman A.; Dahlen, T.; Donley, J.; Koekemoer, A. M.; Salvato, M.; CANDELS Collaboration

2014-01-01

The CANDELS HST Multi-cycle Treasury Program completed its observations of the EGS field in May 2013. The coverage comprises WFC3/IR exposures in J-band and H-band across a contiguous 200 square arcminutes, and coordinated parallel ACS/WFC exposures in V-band and I-band across a contiguous 270 square arcminutes that largely overlaps the WFC3/IR coverage. These observations were split between two epochs with 52-day spacing for the primary purpose of high-redshift supernovae (SNe) detection and follow-up. However, this combination of sensitivity, high resolution, and time spacing is also well-suited to detect optical and near-infrared variability ("ONIV") among moderate- to high-redshift galaxy nuclei (H<25AB mag; I<26AB mag). These data are sensitive to rest-frame variability time-scales of up to several weeks, and in combination with the original EGS ACS imaging from 2004, to time-scales of up to several years in the V- and I-bands. The overwhelming majority of these variable galaxy nuclei will be AGN; the small fraction arising from SNe have already been meticulously culled by the CANDELS high-redshift SNe search effort. These ONIV galaxy nuclei potentially represent a significant addition to the census of distant lower-luminosity AGN subject to multi-wavelength scrutiny with CANDELS. We present the preliminary results of our EGS variability analysis, including a comparison of the HST ONIVs with the known AGN candidates in the field from deep Spitzer and Chandra imaging, and from extensive ground-based optical spectroscopy as well as HST IR-grism spectroscopy. We also assess the redshift distribution of the ONIVs from both spectroscopy and from robust SED-fitting incorporating ancillary deep ground-based imaging along with the CANDELS VIJH photometry. We compare these results with our prior variability analysis of the similarly-observed CANDELS UDS field from 2011 and CANDELS COSMOS field from 2012.

4482 Element Multispectral Hybrid PV/PC HgCdTe IRFPA for High Resolution Coverage of 3.7 - 15.4 Micrometers for the AIRS Instrument

NASA Technical Reports Server (NTRS)

Rutter, James; Libonate, Scott; Denley, Brian; Gurnee, Mark N.; Robillard, Gene

1996-01-01

The Atmospheric Infrared Sounder (AIRS) is a key facility instrument in the NASA Earth Observing System (EOS) program, being implemented to obtain comprehensive long-term measurements of earth processes affecting global change. The instrument performs passive IR remote sensing using a high resolution grating spectrometer with a wide spectral coverage (3.7 - 15.4 m) directing radiation onto a hybrid HgCdTe IRFPA operating at 58K in a vacuum package cooled to 155K. The hybrid HgCdTe FPA consists of twelve modules, 10 with multiplexed photovoltaic detectors and two with individually leaded out photoconductive detectors. The complex FPA has a large optical footprint, 53 mm x 66 mm, and receives energy dispersed from the grating through a precision filter assembly containing 17 narrow band filters. The backside illuminated PV detector arrays are fabricated from P-on-n double layer LPE grown heterojunction detectors in a bilinear format of 50 m x 100 m detectors, with from 232 to 420 detectors per module. For the MWIR bands four PV modules cover the 3.7 m to 8.22 m region. Low detector capacitance and low noise preamplifiers in the ROIC are key to achieving high sensitivities in these bands. Uniform quantum efficiencies and detectivities exceeding 3E13 cm-rtHz/W have been achieved. The LWIR region is covered by six PV modules spanning 8.8 m to 13.75 m. High detector resistance and very low ROIC preamplifier input noise are key to achieving high sensitivity. A detectivity exceeding 2E11 cm-rtHz/W has been achieved at the longest wavelength. Two additional PC modules cover the longest spectral bands out to 15.4 m. This high performance multispectral focal plane has been built and integrated with the dewar assembly, and is currently being integrated with the complete AIRS sensor.

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

PubMed Central

Klambauer, Günter; Schwarzbauer, Karin; Mayr, Andreas; Clevert, Djork-Arné; Mitterecker, Andreas; Bodenhofer, Ulrich; Hochreiter, Sepp

2012-01-01

Quantitative analyses of next-generation sequencing (NGS) data, such as the detection of copy number variations (CNVs), remain challenging. Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate (FDR), even upon correction for GC content. In the context of association studies between CNVs and disease, a high FDR means many false CNVs, thereby decreasing the discovery power of the study after correction for multiple testing. We propose ‘Copy Number estimation by a Mixture Of PoissonS’ (cn.MOPS), a data processing pipeline for CNV detection in NGS data. In contrast to previous approaches, cn.MOPS incorporates modeling of depths of coverage across samples at each genomic position. Therefore, cn.MOPS is not affected by read count variations along chromosomes. Using a Bayesian approach, cn.MOPS decomposes variations in the depth of coverage across samples into integer copy numbers and noise by means of its mixture components and Poisson distributions, respectively. The noise estimate allows for reducing the FDR by filtering out detections having high noise that are likely to be false detections. We compared cn.MOPS with the five most popular methods for CNV detection in NGS data using four benchmark datasets: (i) simulated data, (ii) NGS data from a male HapMap individual with implanted CNVs from the X chromosome, (iii) data from HapMap individuals with known CNVs, (iv) high coverage data from the 1000 Genomes Project. cn.MOPS outperformed its five competitors in terms of precision (1–FDR) and recall for both gains and losses in all benchmark data sets. The software cn.MOPS is publicly available as an R package at http://www.bioinf.jku.at/software/cnmops/ and at Bioconductor. PMID:22302147

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate.

PubMed

Klambauer, Günter; Schwarzbauer, Karin; Mayr, Andreas; Clevert, Djork-Arné; Mitterecker, Andreas; Bodenhofer, Ulrich; Hochreiter, Sepp

2012-05-01

Quantitative analyses of next-generation sequencing (NGS) data, such as the detection of copy number variations (CNVs), remain challenging. Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate (FDR), even upon correction for GC content. In the context of association studies between CNVs and disease, a high FDR means many false CNVs, thereby decreasing the discovery power of the study after correction for multiple testing. We propose 'Copy Number estimation by a Mixture Of PoissonS' (cn.MOPS), a data processing pipeline for CNV detection in NGS data. In contrast to previous approaches, cn.MOPS incorporates modeling of depths of coverage across samples at each genomic position. Therefore, cn.MOPS is not affected by read count variations along chromosomes. Using a Bayesian approach, cn.MOPS decomposes variations in the depth of coverage across samples into integer copy numbers and noise by means of its mixture components and Poisson distributions, respectively. The noise estimate allows for reducing the FDR by filtering out detections having high noise that are likely to be false detections. We compared cn.MOPS with the five most popular methods for CNV detection in NGS data using four benchmark datasets: (i) simulated data, (ii) NGS data from a male HapMap individual with implanted CNVs from the X chromosome, (iii) data from HapMap individuals with known CNVs, (iv) high coverage data from the 1000 Genomes Project. cn.MOPS outperformed its five competitors in terms of precision (1-FDR) and recall for both gains and losses in all benchmark data sets. The software cn.MOPS is publicly available as an R package at http://www.bioinf.jku.at/software/cnmops/ and at Bioconductor.

Measuring Coverage in MNCH: Accuracy of Measuring Diagnosis and Treatment of Childhood Malaria from Household Surveys in Zambia

PubMed Central

Eisele, Thomas P.; Silumbe, Kafula; Yukich, Josh; Hamainza, Busiku; Keating, Joseph; Bennett, Adam; Miller, John M.

2013-01-01

Background To assess progress in the scale-up of rapid diagnostic tests and artemisinin-based combination therapies (ACTs) across Africa, malaria control programs have increasingly relied on standardized national household surveys to determine the proportion of children with a fever in the past 2 wk who received an effective antimalarial within 1–2 d of the onset of fever. Here, the validity of caregiver recall for measuring the primary coverage indicators for malaria diagnosis and treatment of children <5 y old is assessed. Methods and Findings A cross-sectional study was conducted in five public clinics in Kaoma District, Western Provence, Zambia, to estimate the sensitivity, specificity, and accuracy of caregivers' recall of malaria testing, diagnosis, and treatment, compared to a gold standard of direct observation at the health clinics. Compared to the gold standard of clinic observation, for recall for children with fever in the past 2 wk, the sensitivity for recalling that a finger/heel stick was done was 61.9%, with a specificity of 90.0%. The sensitivity and specificity of caregivers' recalling a positive malaria test result were 62.4% and 90.7%, respectively. The sensitivity and specificity of recalling that the child was given a malaria diagnosis, irrespective of whether a laboratory test was actually done, were 76.8% and 75.9%, respectively. The sensitivity and specificity for recalling that an ACT was given were 81.0% and 91.5%, respectively. Conclusions Based on these findings, results from household surveys should continue to be used for ascertaining the coverage of children with a fever in the past 2 wk that received an ACT. However, as recall of a malaria diagnosis remains suboptimal, its use in defining malaria treatment coverage is not recommended. Please see later in the article for the Editors' Summary PMID:23667337

Human papillomavirus vaccination coverage among females and males, National Health and Nutrition Examination Survey, United States, 2007-2016.

PubMed

Lewis, Rayleen M; Markowitz, Lauri E

2018-05-03

Human papillomavirus (HPV) vaccination has been routinely recommended at age 11-12 years in the United States for females since 2006 and males since 2011. Coverage can be estimated using self/parent-reported HPV vaccination collected in the National Health and Nutrition Examination Survey (NHANES) for a wider age range than other national surveys. We assessed vaccination coverage in 2015-2016, temporal trends by age, and the validity of self/parent-reported vaccination status. Participants aged 9-59 years completed an interview collecting demographic and vaccination information. Weighted coverage was estimated for two-year NHANES cycles by age group for 2007-2008 to 2015-2016 for females (N = 14318) and 2011-2012 to 2015-2016 for males (N = 7847). Temporal trends in coverage were assessed from 2007-2008 to 2011-2012 for females and from 2011-2012 to 2015-2016 for both sexes. Sensitivity and specificity of self/parent-reported vaccination were assessed using provider-verified vaccination records from a pilot study in 14-29 year-olds. In 2015-2016, ≥1 dose coverage among females was highest in 14-19 (54.7%) and 20-24 (56.0%) year-olds and lower in successively older age groups. Among males, ≥1 dose coverage was highest in 14-19 year-olds (39.5%) and lower at older ages. Coverage was similar in 9-13 year-old females and males. Between 2007-2008 and 2011-2012, there were increases among females younger than 30 years. Between 2011-2012 and 2015-2016, there were increases among female age groups including 20-39 year-olds; male coverage increased among ages 9-13, 14-19, and 20-24 years. Self/parent-reported receipt of ≥1 dose had a sensitivity and specificity of 87.0% and 83.3%. Performance was lower for 3 doses. While overall HPV vaccination coverage remains low, it is higher in females than males, except in 9-13 year-olds. There have been increases in coverage among many age groups, but coverage has stalled in younger females. Adequate validity was demonstrated for self/parent-reported vaccination of ≥1 dose, but not 3 doses, in a pilot study. Copyright © 2018 Elsevier Ltd. All rights reserved.

Estimation of the cost-effectiveness of HIV prevention portfolios for people who inject drugs in the United States: A model-based analysis

PubMed Central

Owens, Douglas K.; Goldhaber-Fiebert, Jeremy D.; Brandeau, Margaret L.

2017-01-01

Background The risks of HIV transmission associated with the opioid epidemic make cost-effective programs for people who inject drugs (PWID) a public health priority. Some of these programs have benefits beyond prevention of HIV—a critical consideration given that injection drug use is increasing across most United States demographic groups. To identify high-value HIV prevention program portfolios for US PWID, we consider combinations of four interventions with demonstrated efficacy: opioid agonist therapy (OAT), needle and syringe programs (NSPs), HIV testing and treatment (Test & Treat), and oral HIV pre-exposure prophylaxis (PrEP). Methods and findings We adapted an empirically calibrated dynamic compartmental model and used it to assess the discounted costs (in 2015 US dollars), health outcomes (HIV infections averted, change in HIV prevalence, and discounted quality-adjusted life years [QALYs]), and incremental cost-effectiveness ratios (ICERs) of the four prevention programs, considered singly and in combination over a 20-y time horizon. We obtained epidemiologic, economic, and health utility parameter estimates from the literature, previously published models, and expert opinion. We estimate that expansions of OAT, NSPs, and Test & Treat implemented singly up to 50% coverage levels can be cost-effective relative to the next highest coverage level (low, medium, and high at 40%, 45%, and 50%, respectively) and that OAT, which we assume to have immediate and direct health benefits for the individual, has the potential to be the highest value investment, even under scenarios where it prevents fewer infections than other programs. Although a model-based analysis can provide only estimates of health outcomes, we project that, over 20 y, 50% coverage with OAT could avert up to 22,000 (95% CI: 5,200, 46,000) infections and cost US$18,000 (95% CI: US$14,000, US$24,000) per QALY gained, 50% NSP coverage could avert up to 35,000 (95% CI: 8,900, 43,000) infections and cost US$25,000 (95% CI: US$7,000, US$76,000) per QALY gained, 50% Test & Treat coverage could avert up to 6,700 (95% CI: 1,200, 16,000) infections and cost US$27,000 (95% CI: US$15,000, US$48,000) per QALY gained, and 50% PrEP coverage could avert up to 37,000 (22,000, 58,000) infections and cost US$300,000 (95% CI: US$162,000, US$667,000) per QALY gained. When coverage expansions are allowed to include combined investment with other programs and are compared to the next best intervention, the model projects that scaling OAT coverage up to 50%, then scaling NSP coverage to 50%, then scaling Test & Treat coverage to 50% can be cost-effective, with each coverage expansion having the potential to cost less than US$50,000 per QALY gained relative to the next best portfolio. In probabilistic sensitivity analyses, 59% of portfolios prioritized the addition of OAT and 41% prioritized the addition of NSPs, while PrEP was not likely to be a priority nor a cost-effective addition. Our findings are intended to be illustrative, as data on achievable coverage are limited and, in practice, the expansion scenarios considered may exceed feasible levels. We assumed independence of interventions and constant returns to scale. Extensive sensitivity analyses allowed us to assess parameter sensitivity, but the use of a dynamic compartmental model limited the exploration of structural sensitivities. Conclusions We estimate that OAT, NSPs, and Test & Treat, implemented singly or in combination, have the potential to effectively and cost-effectively prevent HIV in US PWID. PrEP is not likely to be cost-effective in this population, based on the scenarios we evaluated. While local budgets or policy may constrain feasible coverage levels for the various interventions, our findings suggest that investments in combined prevention programs can substantially reduce HIV transmission and improve health outcomes among PWID. PMID:28542184

Estimation of the cost-effectiveness of HIV prevention portfolios for people who inject drugs in the United States: A model-based analysis.

PubMed

Bernard, Cora L; Owens, Douglas K; Goldhaber-Fiebert, Jeremy D; Brandeau, Margaret L

2017-05-01

The risks of HIV transmission associated with the opioid epidemic make cost-effective programs for people who inject drugs (PWID) a public health priority. Some of these programs have benefits beyond prevention of HIV-a critical consideration given that injection drug use is increasing across most United States demographic groups. To identify high-value HIV prevention program portfolios for US PWID, we consider combinations of four interventions with demonstrated efficacy: opioid agonist therapy (OAT), needle and syringe programs (NSPs), HIV testing and treatment (Test & Treat), and oral HIV pre-exposure prophylaxis (PrEP). We adapted an empirically calibrated dynamic compartmental model and used it to assess the discounted costs (in 2015 US dollars), health outcomes (HIV infections averted, change in HIV prevalence, and discounted quality-adjusted life years [QALYs]), and incremental cost-effectiveness ratios (ICERs) of the four prevention programs, considered singly and in combination over a 20-y time horizon. We obtained epidemiologic, economic, and health utility parameter estimates from the literature, previously published models, and expert opinion. We estimate that expansions of OAT, NSPs, and Test & Treat implemented singly up to 50% coverage levels can be cost-effective relative to the next highest coverage level (low, medium, and high at 40%, 45%, and 50%, respectively) and that OAT, which we assume to have immediate and direct health benefits for the individual, has the potential to be the highest value investment, even under scenarios where it prevents fewer infections than other programs. Although a model-based analysis can provide only estimates of health outcomes, we project that, over 20 y, 50% coverage with OAT could avert up to 22,000 (95% CI: 5,200, 46,000) infections and cost US$18,000 (95% CI: US$14,000, US$24,000) per QALY gained, 50% NSP coverage could avert up to 35,000 (95% CI: 8,900, 43,000) infections and cost US$25,000 (95% CI: US$7,000, US$76,000) per QALY gained, 50% Test & Treat coverage could avert up to 6,700 (95% CI: 1,200, 16,000) infections and cost US$27,000 (95% CI: US$15,000, US$48,000) per QALY gained, and 50% PrEP coverage could avert up to 37,000 (22,000, 58,000) infections and cost US$300,000 (95% CI: US$162,000, US$667,000) per QALY gained. When coverage expansions are allowed to include combined investment with other programs and are compared to the next best intervention, the model projects that scaling OAT coverage up to 50%, then scaling NSP coverage to 50%, then scaling Test & Treat coverage to 50% can be cost-effective, with each coverage expansion having the potential to cost less than US$50,000 per QALY gained relative to the next best portfolio. In probabilistic sensitivity analyses, 59% of portfolios prioritized the addition of OAT and 41% prioritized the addition of NSPs, while PrEP was not likely to be a priority nor a cost-effective addition. Our findings are intended to be illustrative, as data on achievable coverage are limited and, in practice, the expansion scenarios considered may exceed feasible levels. We assumed independence of interventions and constant returns to scale. Extensive sensitivity analyses allowed us to assess parameter sensitivity, but the use of a dynamic compartmental model limited the exploration of structural sensitivities. We estimate that OAT, NSPs, and Test & Treat, implemented singly or in combination, have the potential to effectively and cost-effectively prevent HIV in US PWID. PrEP is not likely to be cost-effective in this population, based on the scenarios we evaluated. While local budgets or policy may constrain feasible coverage levels for the various interventions, our findings suggest that investments in combined prevention programs can substantially reduce HIV transmission and improve health outcomes among PWID.

Polysialylated N-Glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations and Electrospray ionization-mass spectrometry

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

Kronewitter, Scott R.; Marginean, Ioan; Cox, Jonathan T.

The N-glycan diversity of human serum glycoproteins, i.e. the human blood serum N-glycome, is complex due to the range of glycan structures potentially synthesizable by human glycosylation enzymes. The reported glycome, however, is limited by methods of sample preparation, available analytical platforms, e.g., based upon electrospray ionization-mass spectrometry (ESI-MS), and software tools for data analysis. In this report, several improvements have been implemented in sample preparation and analysis to extend ESI-MS glycan characterization and to provide an improved view of glycan diversity. Sample preparation improvements include acidified, microwave-accelerated, PNGase F N-glycan release, and sodium borohydride reduction were optimized to improvemore » quantitative yields and conserve the number of glycoforms detected. Two-stage desalting (during solid phase extraction and on the analytical column) increased the sensitivity by reducing analyte signal division between multiple reducing-end-forms or cation adducts. On-line separations were improved by using extended length graphitized carbon columns and adding TFA as an acid modifier to a formic acid/reversed phase gradient which provides additional resolving power and significantly improved desorption of both large and heavily sialylated glycans. To improve MS sensitivity and provide gentler ionization conditions at the source-MS interface, subambient pressure ionization with nanoelectrospray (SPIN) has been utilized. When method improvements are combined together with the Glycomics Quintavariate Informed Quantification (GlyQ-IQ) recently described1 these technologies demonstrate the ability to significantly extend glycan detection sensitivity and provide expanded glycan coverage. We demonstrate application of these advances in the context of the human serum glycome, and for which our initial observations include detection of a new class of heavily sialylated N-glycans, including polysialylated N-glycans.« less

RoboTAP: Target priorities for robotic microlensing observations

NASA Astrophysics Data System (ADS)

Hundertmark, M.; Street, R. A.; Tsapras, Y.; Bachelet, E.; Dominik, M.; Horne, K.; Bozza, V.; Bramich, D. M.; Cassan, A.; D'Ago, G.; Figuera Jaimes, R.; Kains, N.; Ranc, C.; Schmidt, R. W.; Snodgrass, C.; Wambsganss, J.; Steele, I. A.; Mao, S.; Ment, K.; Menzies, J.; Li, Z.; Cross, S.; Maoz, D.; Shvartzvald, Y.

2018-01-01

Context. The ability to automatically select scientifically-important transient events from an alert stream of many such events, and to conduct follow-up observations in response, will become increasingly important in astronomy. With wide-angle time domain surveys pushing to fainter limiting magnitudes, the capability to follow-up on transient alerts far exceeds our follow-up telescope resources, and effective target prioritization becomes essential. The RoboNet-II microlensing program is a pathfinder project, which has developed an automated target selection process (RoboTAP) for gravitational microlensing events, which are observed in real time using the Las Cumbres Observatory telescope network. Aims: Follow-up telescopes typically have a much smaller field of view compared to surveys, therefore the most promising microlensing events must be automatically selected at any given time from an annual sample exceeding 2000 events. The main challenge is to select between events with a high planet detection sensitivity, with the aim of detecting many planets and characterizing planetary anomalies. Methods: Our target selection algorithm is a hybrid system based on estimates of the planet detection zones around a microlens. It follows automatic anomaly alerts and respects the expected survey coverage of specific events. Results: We introduce the RoboTAP algorithm, whose purpose is to select and prioritize microlensing events with high sensitivity to planetary companions. In this work, we determine the planet sensitivity of the RoboNet follow-up program and provide a working example of how a broker can be designed for a real-life transient science program conducting follow-up observations in response to alerts; we explore the issues that will confront similar programs being developed for the Large Synoptic Survey Telescope (LSST) and other time domain surveys.

Cavity-Enhanced Spectroscopy of Molecular Ions in the Mid-Infrared with Up-Conversion Detection and Brewster-Plate Spoilers

NASA Astrophysics Data System (ADS)

Markus, Charles R.; McCollum, Jefferson E.; Hodges, James Neil; Perry, Adam J.; McCall, Benjamin J.

2017-06-01

Molecular ions are challenging to study with conventional spectroscopic methods. Laboratory discharges produce ions in trace quantities which can be obscured by the abundant neutral molecules present. The technique Noise Immune Cavity Enhanced Optical Heterodyne Velocity Modulation Spectroscopy (NICE-OHVMS) overcomes these challenges by combining the ion-neutral discrimination of velocity modulation spectroscopy with the sensitivity of Noise-Immune Cavity-Enhanced Optical Heterodyne Molecular Spectroscopy (NICE-OHMS), and has been able to determine transition frequencies of molecular ions in the mid-infrared (mid-IR) with sub-MHz uncertainties when calibrated with an optical frequency comb. However, the extent of these studies was limited by the presence of fringes due to parasitic etalons and the speed and noise characteristics of mid-IR detectors. Recently, we have overcome these limitations by implementing up-conversion detection and dithered optics. We performed up-conversion using periodically poled lithium niobate to convert light from the mid-IR to the visible to be within the coverage of sensitive and fast silicon detectors while maintaining our heterodyne and velocity modulation signals. The parasitic etalons were removed by rapidly rotating CaF_2 windows with galvanometers, which is known as a Brewster-plate spoiler, which averaged out the fringes in detection. Together, these improved the sensitivity by more than an order of magnitude and have enabled extended spectroscopic surveys of molecular ions in the mid-IR. J. N. Hodges, A. J. Perry, P. A. Jenkins II, B. M. Siller, and B. J. McCall, J. Chem. Phys. (2013), 139, 164201. C. R. Webster, J. Opt. Soc. Am. B (1985), 2, 1464. C. R. Markus, A. J. Perry, J. N. Hodges, and B. J. McCall, Opt. Express (2017), 25, 3709-3721.

Computational imaging of defects in commercial substrates for electronic and photonic devices

NASA Astrophysics Data System (ADS)

Fukuzawa, Masayuki; Kashiwagi, Ryo; Yamada, Masayoshi

2012-03-01

Computational defect imaging has been performed in commercial substrates for electronic and photonic devices by combining the transmission profile acquired with an imaging type of linear polariscope and the computational algorithm to extract a small amount of birefringence. The computational images of phase retardation δ exhibited spatial inhomogeneity of defect-induced birefringence in GaP, LiNbO3, and SiC substrates, which were not detected by conventional 'visual inspection' based on simple optical refraction or transmission because of poor sensitivity. The typical imaging time was less than 30 seconds for 3-inch diameter substrate with the spatial resolution of 200 μm, while that by scanning polariscope was 2 hours to get the same spatial resolution. Since our proposed technique have been achieved high sensitivity, short imaging time, and wide coverage of substrate materials, which are practical advantages over the laboratory-scale apparatus such as X-ray topography and electron microscope, it is useful for nondestructive inspection of various commercial substrates in production of electronic and photonic devices.

How Can We Identify the Elimination of Infectious Diseases? Experience From an Active Measles Laboratory Surveillance System in the Republic of Korea.

PubMed

Yang, Tae Un; Kang, Hae Ji; Eom, Hye Eun; Park, Young-Joon; Park, Ok; Kim, Su Jin; Nam, Jeong-Gu; Kim, Sung Soon; Jeong, Eun Kyeong

2015-11-01

Global efforts have markedly decreased the disease burden of vaccine-preventable diseases. Many countries have made considerable progress toward the elimination of measles. As elimination is approached, the very low incidence achieved by high vaccination coverage has underscored the need for a sensitive and timely surveillance system. In the Republic of Korea, an active laboratory surveillance system (ALSS) was implemented to supplement the existing passive surveillance system in 2006. The ALSS connects 5 major commercial laboratories and the national measles reference laboratory, where referred samples with positive or equivocal results are retested. Annually, from 2009 to 2013, 3714 suspected cases were detected through the ALSS, an expansion of 8- to 57-fold, compared with only the passive surveillance system. The ALSS, with its sensitivity and timeliness, is a reasonable strategy to supplement the existing measles surveillance system and to help identify the elimination of measles. © 2015 APJPH.

Development of a tick-borne pathogen QPCR panel for detection of Anaplasma, Ehrlichia, Rickettsia, and Lyme disease Borrelia in animals.

PubMed

Shen, Zhenyu; Zhang, Michael Z; Stich, Roger W; Mitchell, William J; Zhang, Shuping

2018-05-23

Anaplasma spp., Ehrlichia spp., Rickettsia spp., and Lyme disease associated Borrelia spp. are the most common tick-borne pathogens reported to infect human beings worldwide and other animals, such as dogs and horses. In the present study, we developed a broad-coverage SYBR Green QPCR panel consisting of four individual assays for the detection and partial differentiation of the aforementioned pathogens. All assays were optimized to the same thermocycling condition and had a detection limit of 10 copies per reaction. The assays remained sensitive when used to test canine and equine blood DNA samples spiked with known amounts of synthetic DNA (gBlock) control template. The assays were specific, as evidenced by lack of cross reaction to non-target gBlock or other pathogens commonly tested in veterinary diagnostic labs. With appropriate Ct cutoff values for positive samples and negative controls and the melting temperature (TM) ranges established in the present study, the QPCR panel is suitable for accurate, convenient and rapid screening and confirmation of tick-borne pathogens in animals. Copyright © 2017. Published by Elsevier B.V.

Combining Surveillance Systems: Effective Merging of U.S. Veteran and Military Health Data

PubMed Central

Pavlin, Julie A.; Burkom, Howard S.; Elbert, Yevgeniy; Lucero-Obusan, Cynthia; Winston, Carla A.; Cox, Kenneth L.; Oda, Gina; Lombardo, Joseph S.; Holodniy, Mark

2013-01-01

Background The U.S. Department of Veterans Affairs (VA) and Department of Defense (DoD) had more than 18 million healthcare beneficiaries in 2011. Both Departments conduct individual surveillance for disease events and health threats. Methods We performed joint and separate analyses of VA and DoD outpatient visit data from October 2006 through September 2010 to demonstrate geographic and demographic coverage, timeliness of influenza epidemic awareness, and impact on spatial cluster detection achieved from a joint VA and DoD biosurveillance platform. Results Although VA coverage is greater, DoD visit volume is comparable or greater. Detection of outbreaks was better in DoD data for 58% and 75% of geographic areas surveyed for seasonal and pandemic influenza, respectively, and better in VA data for 34% and 15%. The VA system tended to alert earlier with a typical H3N2 seasonal influenza affecting older patients, and the DoD performed better during the H1N1 pandemic which affected younger patients more than normal influenza seasons. Retrospective analysis of known outbreaks demonstrated clustering evidence found in separate DoD and VA runs, which persisted with combined data sets. Conclusion The analyses demonstrate two complementary surveillance systems with evident benefits for the national health picture. Relative timeliness of reporting could be improved in 92% of geographic areas with access to both systems, and more information provided in areas where only one type of facility exists. Combining DoD and VA data enhances geographic cluster detection capability without loss of sensitivity to events isolated in either population and has a manageable effect on customary alert rates. PMID:24386335

In vitro comparative study of vibro-acoustography versus pulse-echo ultrasound in imaging permanent prostate brachytherapy seeds

PubMed Central

Mitri, F.G.; Davis, B.J.; Greenleaf, J.F.; Fatemi, M.

2010-01-01

Background Permanent prostate brachytherapy (PPB) is a common treatment for early stage prostate cancer. While the modern approach using trans-rectal ultrasound guidance has demonstrated excellent outcome, the efficacy of PPB depends on achieving complete radiation dose coverage of the prostate by obtaining a proper radiation source (seed) distribution. Currently, brachytherapy seed placement is guided by trans-rectal ultrasound imaging and fluoroscopy. A significant percentage of seeds are not detected by trans-rectal ultrasound because certain seed orientations are invisible making accurate intra-operative feedback of radiation dosimetry very difficult, if not impossible. Therefore, intra-operative correction of suboptimal seed distributions cannot easily be done with current methods. Vibro-acoustography (VA) is an imaging modality that is capable of imaging solids at any orientation, and the resulting images are speckle free. Objective and methods The purpose of this study is to compare the capabilities of VA and pulse-echo ultrasound in imaging PPB seeds at various angles and show the sensitivity of detection to seed orientation. In the VA experiment, two intersecting ultrasound beams driven at f1 = 3.00 MHz and f2 = 3.020 MHz respectively were focused on the seeds attached to a latex membrane while the amplitude of the acoustic emission produced at the difference frequency 20 kHz was detected by a low frequency hydrophone. Results Finite element simulations and results of experiments conducted under well-controlled conditions in a water tank on a series of seeds indicate that the seeds can be detected at any orientation with VA, whereas pulse-echo ultrasound is very sensitive to the seed orientation. Conclusion It is concluded that vibro-acoustography is superior to pulse-echo ultrasound for detection of PPB seeds. PMID:18538365

1SXPS: A Deep Swift X-Ray Telescope Point Source Catalog with Light Curves and Spectra

NASA Technical Reports Server (NTRS)

Evans, P. A.; Osborne, J. P.; Beardmore, A. P.; Page, K. L.; Willingale, R.; Mountford, C. J.; Pagani, C.; Burrows, D. N.; Kennea, J. A.; Perri, M.;

Diagnostic accuracy of a loop-mediated isothermal PCR assay for detection of Orientia tsutsugamushi during acute Scrub Typhus infection.

PubMed

Paris, Daniel H; Blacksell, Stuart D; Nawtaisong, Pruksa; Jenjaroen, Kemajittra; Teeraratkul, Achara; Chierakul, Wirongrong; Wuthiekanun, Vanaporn; Kantipong, Pacharee; Day, Nicholas P J

2011-09-01

There is an urgent need to develop rapid and accurate point-of-care (POC) technologies for acute scrub typhus diagnosis in low-resource, primary health care settings to guide clinical therapy. In this study we present the clinical evaluation of loop-mediated isothermal PCR assay (LAMP) in the context of a prospective fever study, including 161 patients from scrub typhus-endemic Chiang Rai, northern Thailand. A robust reference comparator set comprising following 'scrub typhus infection criteria' (STIC) was used: a) positive cell culture isolate and/or b) an admission IgM titer ≥1∶12,800 using the 'gold standard' indirect immunofluorescence assay (IFA) and/or c) a 4-fold rising IFA IgM titer and/or d) a positive result in at least two out of three PCR assays. Compared to the STIC criteria, all PCR assays (including LAMP) demonstrated high specificity ranging from 96-99%, with sensitivities varying from 40% to 56%, similar to the antibody based rapid test, which had a sensitivity of 47% and a specificity of 95%. The diagnostic accuracy of the LAMP assay was similar to realtime and nested conventional PCR assays, but superior to the antibody-based rapid test in the early disease course. The combination of DNA- and antibody-based detection methods increased sensitivity with minimal reduction of specificity, and expanded the timeframe of adequate diagnostic coverage throughout the acute phase of scrub typhus.

Non-enzymatic detection of glucose in fruits using TiO2-Mn3O4 hybrid nano interface

NASA Astrophysics Data System (ADS)

Jayanth Babu, K.; Sasya, Madhurantakam; Nesakumar, Noel; Shankar, Prabakaran; Gumpu, Manju Bhargavi; Ramachandra, Bhat Lakshmishri; Kulandaisamy, Arockia Jayalatha; Rayappan, John Bosco Balaguru

2017-08-01

Consumption of fruits leads to increase in glucose level in blood for diabetic patients, which in turn leads to peripheral, vascular, ocular complications and cardiac diseases. In this context, a non-enzymatic hybrid glucose biosensor was fabricated for the first time to detect glucose by immobilizing titanium oxide-manganese oxide (TiO2-Mn3O4) nanocomposite and chitosan membrane on to the surface of Pt working electrode (Pt/TiO2-Mn3O4/chitosan). TiO2-Mn3O4 nanocomposite catalyzed the oxidation of glucose to gluconolactone in the absence of glucose oxidase enzyme with high electron transfer rate, good biocompatibility and large surface coverage. Electrochemical measurements revealed the excellent sensing response of the developed biosensor towards glucose with a high sensitivity of 7.073 µA mM-1, linearity of 0.01-0.1 mM, low detection limit of 0.01 µM, reproducibility of 1.5% and stability of 98.8%. The electrochemical parameters estimated from the anodic process were subjected to linear regression models for the detection of unknown concentration of glucose in different fruit samples.

Integrated Computational Solution for Predicting Skin Sensitization Potential of Molecules

PubMed Central

Desai, Aarti; Singh, Vivek K.; Jere, Abhay

2016-01-01

Introduction Skin sensitization forms a major toxicological endpoint for dermatology and cosmetic products. Recent ban on animal testing for cosmetics demands for alternative methods. We developed an integrated computational solution (SkinSense) that offers a robust solution and addresses the limitations of existing computational tools i.e. high false positive rate and/or limited coverage. Results The key components of our solution include: QSAR models selected from a combinatorial set, similarity information and literature-derived sub-structure patterns of known skin protein reactive groups. Its prediction performance on a challenge set of molecules showed accuracy = 75.32%, CCR = 74.36%, sensitivity = 70.00% and specificity = 78.72%, which is better than several existing tools including VEGA (accuracy = 45.00% and CCR = 54.17% with ‘High’ reliability scoring), DEREK (accuracy = 72.73% and CCR = 71.44%) and TOPKAT (accuracy = 60.00% and CCR = 61.67%). Although, TIMES-SS showed higher predictive power (accuracy = 90.00% and CCR = 92.86%), the coverage was very low (only 10 out of 77 molecules were predicted reliably). Conclusions Owing to improved prediction performance and coverage, our solution can serve as a useful expert system towards Integrated Approaches to Testing and Assessment for skin sensitization. It would be invaluable to cosmetic/ dermatology industry for pre-screening their molecules, and reducing time, cost and animal testing. PMID:27271321

Implementation of Whole Genome Sequencing (WGS) for Identification and Characterization of Shiga Toxin-Producing Escherichia coli (STEC) in the United States

PubMed Central

Lindsey, Rebecca L.; Pouseele, Hannes; Chen, Jessica C.; Strockbine, Nancy A.; Carleton, Heather A.

2016-01-01

Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen capable of causing severe disease in humans. Rapid and accurate identification and characterization techniques are essential during outbreak investigations. Current methods for characterization of STEC are expensive and time-consuming. With the advent of rapid and cheap whole genome sequencing (WGS) benchtop sequencers, the potential exists to replace traditional workflows with WGS. The aim of this study was to validate tools to do reference identification and characterization from WGS for STEC in a single workflow within an easy to use commercially available software platform. Publically available serotype, virulence, and antimicrobial resistance databases were downloaded from the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org) and integrated into a genotyping plug-in with in silico PCR tools to confirm some of the virulence genes detected from WGS data. Additionally, down sampling experiments on the WGS sequence data were performed to determine a threshold for sequence coverage needed to accurately predict serotype and virulence genes using the established workflow. The serotype database was tested on a total of 228 genomes and correctly predicted from WGS for 96.1% of O serogroups and 96.5% of H serogroups identified by conventional testing techniques. A total of 59 genomes were evaluated to determine the threshold of coverage to detect the different WGS targets, 40 were evaluated for serotype and virulence gene detection and 19 for the stx gene subtypes. For serotype, 95% of the O and 100% of the H serogroups were detected at > 40x and ≥ 30x coverage, respectively. For virulence targets and stx gene subtypes, nearly all genes were detected at > 40x, though some targets were 100% detectable from genomes with coverage ≥20x. The resistance detection tool was 97% concordant with phenotypic testing results. With isolates sequenced to > 40x coverage, the different databases accurately predicted serotype, virulence, and resistance from WGS data, providing a fast and cheaper alternative to conventional typing techniques. PMID:27242777

Implementation of Whole Genome Sequencing (WGS) for Identification and Characterization of Shiga Toxin-Producing Escherichia coli (STEC) in the United States.

PubMed

Lindsey, Rebecca L; Pouseele, Hannes; Chen, Jessica C; Strockbine, Nancy A; Carleton, Heather A

2016-01-01

Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen capable of causing severe disease in humans. Rapid and accurate identification and characterization techniques are essential during outbreak investigations. Current methods for characterization of STEC are expensive and time-consuming. With the advent of rapid and cheap whole genome sequencing (WGS) benchtop sequencers, the potential exists to replace traditional workflows with WGS. The aim of this study was to validate tools to do reference identification and characterization from WGS for STEC in a single workflow within an easy to use commercially available software platform. Publically available serotype, virulence, and antimicrobial resistance databases were downloaded from the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org) and integrated into a genotyping plug-in with in silico PCR tools to confirm some of the virulence genes detected from WGS data. Additionally, down sampling experiments on the WGS sequence data were performed to determine a threshold for sequence coverage needed to accurately predict serotype and virulence genes using the established workflow. The serotype database was tested on a total of 228 genomes and correctly predicted from WGS for 96.1% of O serogroups and 96.5% of H serogroups identified by conventional testing techniques. A total of 59 genomes were evaluated to determine the threshold of coverage to detect the different WGS targets, 40 were evaluated for serotype and virulence gene detection and 19 for the stx gene subtypes. For serotype, 95% of the O and 100% of the H serogroups were detected at > 40x and ≥ 30x coverage, respectively. For virulence targets and stx gene subtypes, nearly all genes were detected at > 40x, though some targets were 100% detectable from genomes with coverage ≥20x. The resistance detection tool was 97% concordant with phenotypic testing results. With isolates sequenced to > 40x coverage, the different databases accurately predicted serotype, virulence, and resistance from WGS data, providing a fast and cheaper alternative to conventional typing techniques.

Barrier Coverage for 3D Camera Sensor Networks

PubMed Central

Wu, Chengdong; Zhang, Yunzhou; Jia, Zixi; Ji, Peng; Chu, Hao

2017-01-01

Barrier coverage, an important research area with respect to camera sensor networks, consists of a number of camera sensors to detect intruders that pass through the barrier area. Existing works on barrier coverage such as local face-view barrier coverage and full-view barrier coverage typically assume that each intruder is considered as a point. However, the crucial feature (e.g., size) of the intruder should be taken into account in the real-world applications. In this paper, we propose a realistic resolution criterion based on a three-dimensional (3D) sensing model of a camera sensor for capturing the intruder’s face. Based on the new resolution criterion, we study the barrier coverage of a feasible deployment strategy in camera sensor networks. Performance results demonstrate that our barrier coverage with more practical considerations is capable of providing a desirable surveillance level. Moreover, compared with local face-view barrier coverage and full-view barrier coverage, our barrier coverage is more reasonable and closer to reality. To the best of our knowledge, our work is the first to propose barrier coverage for 3D camera sensor networks. PMID:28771167

Barrier Coverage for 3D Camera Sensor Networks.

PubMed

Si, Pengju; Wu, Chengdong; Zhang, Yunzhou; Jia, Zixi; Ji, Peng; Chu, Hao

2017-08-03

Barrier coverage, an important research area with respect to camera sensor networks, consists of a number of camera sensors to detect intruders that pass through the barrier area. Existing works on barrier coverage such as local face-view barrier coverage and full-view barrier coverage typically assume that each intruder is considered as a point. However, the crucial feature (e.g., size) of the intruder should be taken into account in the real-world applications. In this paper, we propose a realistic resolution criterion based on a three-dimensional (3D) sensing model of a camera sensor for capturing the intruder's face. Based on the new resolution criterion, we study the barrier coverage of a feasible deployment strategy in camera sensor networks. Performance results demonstrate that our barrier coverage with more practical considerations is capable of providing a desirable surveillance level. Moreover, compared with local face-view barrier coverage and full-view barrier coverage, our barrier coverage is more reasonable and closer to reality. To the best of our knowledge, our work is the first to propose barrier coverage for 3D camera sensor networks.

Diversity arrays technology (DArT) markers in apple for genetic linkage maps.

PubMed

Schouten, Henk J; van de Weg, W Eric; Carling, Jason; Khan, Sabaz Ali; McKay, Steven J; van Kaauwen, Martijn P W; Wittenberg, Alexander H J; Koehorst-van Putten, Herma J J; Noordijk, Yolanda; Gao, Zhongshan; Rees, D Jasper G; Van Dyk, Maria M; Jaccoud, Damian; Considine, Michael J; Kilian, Andrzej

2012-03-01

Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

Contrast-enhanced magnetic resonance imaging of pulmonary lesions: description of a technique aiming clinical practice.

PubMed

Koenigkam-Santos, Marcel; Optazaite, Elzbieta; Sommer, Gregor; Safi, Seyer; Heussel, Claus Peter; Kauczor, Hans-Ulrich; Puderbach, Michael

2015-01-01

To propose a technique for evaluation of pulmonary lesions using contrast-enhanced MRI; to assess morphological patterns of enhancement and correlate quantitative analysis with histopathology. Thirty-six patients were prospectively studied. Volumetric-interpolated T1W images were obtained during consecutive breath holds after bolus triggered contrast injection. Volume coverage of first three acquisitions was limited (higher temporal resolution) and last acquisition obtained at 4th min. Two radiologists individually evaluated the patterns of enhancement. Region-of-interest-based signal intensity (SI)-time curves were created to assess quantitative parameters. Readers agreed moderately to substantially concerning lesions' enhancement pattern. SI-time curves could be created for all lesions. In comparison to benign, malignant lesions showed higher values of maximum enhancement, early peak, slope and 4th min enhancement. Early peak >15% showed 100% sensitivity to detect malignancy, maximum enhancement >40% showed 100% specificity. The proposed technique is robust, simple to perform and can be applied in clinical scenario. It allows visual evaluation of enhancement pattern/progression together with creation of SI-time curves and assessment of derived quantitative parameters. Perfusion analysis was highly sensitive to detect malignancy, in accordance to what is recommended by most recent guidelines on imaging evaluation of pulmonary lesions. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Optimal redistribution of an urban air quality monitoring network using atmospheric dispersion model and genetic algorithm

NASA Astrophysics Data System (ADS)

Hao, Yufang; Xie, Shaodong

2018-03-01

Air quality monitoring networks play a significant role in identifying the spatiotemporal patterns of air pollution, and they need to be deployed efficiently, with a minimum number of sites. The revision and optimal adjustment of existing monitoring networks is crucial for cities that have undergone rapid urban expansion and experience temporal variations in pollution patterns. The approach based on the Weather Research and Forecasting-California PUFF (WRF-CALPUFF) model and genetic algorithm (GA) was developed to design an optimal monitoring network. The maximization of coverage with minimum overlap and the ability to detect violations of standards were developed as the design objectives for redistributed networks. The non-dominated sorting genetic algorithm was applied to optimize the network size and site locations simultaneously for Shijiazhuang city, one of the most polluted cities in China. The assessment on the current network identified the insufficient spatial coverage of SO2 and NO2 monitoring for the expanding city. The optimization results showed that significant improvements were achieved in multiple objectives by redistributing the original network. Efficient coverage of the resulting designs improved to 60.99% and 76.06% of the urban area for SO2 and NO2, respectively. The redistributing design for multi-pollutant including 8 sites was also proposed, with the spatial representation covered 52.30% of the urban area and the overlapped areas decreased by 85.87% compared with the original network. The abilities to detect violations of standards were not improved as much as the other two objectives due to the conflicting nature between the multiple objectives. Additionally, the results demonstrated that the algorithm was slightly sensitive to the parameter settings, with the number of generations presented the most significant effect. Overall, our study presents an effective and feasible procedure for air quality network optimization at a city scale.

Redundancy management of inertial systems.

NASA Technical Reports Server (NTRS)

Mckern, R. A.; Musoff, H.

1973-01-01

The paper reviews developments in failure detection and isolation techniques applicable to gimballed and strapdown systems. It examines basic redundancy management goals of improved reliability, performance and logistic costs, and explores mechanizations available for both input and output data handling. The meaning of redundant system reliability in terms of available coverage, system MTBF, and mission time is presented and the practical hardware performance limitations of failure detection and isolation techniques are explored. Simulation results are presented illustrating implementation coverages attainable considering IMU performance models and mission detection threshold requirements. The implications of a complete GN&C redundancy management method on inertial techniques are also explored.

Validation and comparison of 15-D and EQ-5D-5L instruments in a Spanish Parkinson's disease population sample.

PubMed

García-Gordillo, Miguel Ángel; del Pozo-Cruz, Borja; Adsuar, José Carmelo; Sánchez-Martínez, Fernando Ignacio; Abellán-Perpiñán, José María

2014-05-01

To contribute to the ongoing discussion on the choice of a preference-based health-related quality of life (HRQoL) instrument to be used in cost-effectiveness analysis by studying and comparing the validity, sensitivity and relative efficiency of 15-D and EuroQol 5D 5L (EQ-5D-5L) in a Spanish Parkinson's disease (PD) population sample. One hundred and thirty-three volunteers were asked to complete an interview using 15-D and EQ-5D-5L. Spearman's rank correlation coefficient (r) was used to test the convergent validity of these instruments with specific PD measures. Sensitivity and efficiency were compared using receiver operating characteristic (ROC) curves and relative efficiency statistic, respectively. A strong correlation (r > 0.65; p < 0.001) was found between both 15-D and EQ-5D-5L utilities with the summary score of the PDQ-8, and a strong correlation (r > 0.50; p < 0.001) was found between 15-D and EQ-5D-5L utilities with the EQ-VAS. The areas under the ROC of both instruments all exceeded 0.5 (p < 0.001). The 15-D instrument was 4.1-29.8 % less efficient at detecting differences between patients with optimal HRQoL, while this instrument was 11 % more efficient at detecting differences between patients at mild and moderate to strong severity of the PD symptoms. 15-D and EQ-5D-5L are showed to be valid and sensitivity generic HRQoL measures in Spanish PD patients with both instruments showing similar HRQoL dimension coverage and ceiling/floor effects. The 15-D has better efficiency and greater sensitivity to detect clinical changes in PD severity of the symptoms meanwhile the EQ-5D-5L is better to detect clinical HRQoL changes. Additionally, the EQ-5D-5L questionnaire requires less time than 15-D to be administered, and it might be more appropriate for studies conducted in Spain, since a country-specific "value set" is available for this instrument and not for the 15-D.

Variation of Vegetation Ecological Water Consumption and Its Response to Vegetation Coverage Changes in the Rocky Desertification Areas in South China

PubMed Central

Zhou, Jinxing; Guo, Hongyan; Cui, Ming; Liu, Yuguo; Ning, Like; Tang, Fukai

2016-01-01

Over the past several decades, rocky desertification has led to severe ecological problems in karst areas in South China. After a rocky desertification treatment project was completed, the vegetation coverage changed greatly and, consequently, increased the ecology water consumption (approximately equal to the actual evapotranspiration) of the regional vegetation. Thus, it intensified the regional water stresses. This study explored the changes in the actual evapotranspiration (ETa) response to the vegetation coverage changes in the rocky desertification areas in South China based on the precipitation (P), potential evapotranspiration (ETp) and NDVI (the normalized difference vegetation index) datasets. The revised Bagrov model was used to simulate the actual evapotranspiration changes with the supposed increasing NDVI. The results indicated that the average NDVI value was lower when the rocky desertification was more severe. The ETa, evapotranspiration efficiency (ETa/ETp) and potential humidity (P/ETp) generally increased with the increasing NDVI. The sensitivity of the ETa response to vegetation coverage changes varied due to different precipitation conditions and different rocky desertification severities. The ETa was more sensitive under drought conditions. When a drought occurred, the ETa exhibited an average increase of 40~60 mm with the NDVI increasing of 0.1 in the rocky desertification areas. Among the 5 different severity categories of rocky desertification, the ETa values’ responses to NDVI changes were less sensitive in the severe rocky desertification areas but more sensitive in the extremely and potential rocky desertification areas. For example, with the NDVI increasing of 0.025, 0.05, 0.075, and 0.1, the corresponding ETa changes increased by an average of 2.64 mm, 10.62 mm, 19.19 mm, and 27.58 mm, respectively, in severe rocky desertification areas but by 4.94 mm, 14.99 mm, 26.80, and 37.13 mm, respectively, in extremely severe rocky desertification areas. Understanding the vegetation ecological water consumption response to the vegetation coverage changes is essential for the vegetation restoration and water stresses mitigation in rocky desertification areas. PMID:27798642

Variation of Vegetation Ecological Water Consumption and Its Response to Vegetation Coverage Changes in the Rocky Desertification Areas in South China.

PubMed

Wan, Long; Tong, Jing; Zhou, Jinxing; Guo, Hongyan; Cui, Ming; Liu, Yuguo; Ning, Like; Tang, Fukai

2016-01-01

Over the past several decades, rocky desertification has led to severe ecological problems in karst areas in South China. After a rocky desertification treatment project was completed, the vegetation coverage changed greatly and, consequently, increased the ecology water consumption (approximately equal to the actual evapotranspiration) of the regional vegetation. Thus, it intensified the regional water stresses. This study explored the changes in the actual evapotranspiration (ETa) response to the vegetation coverage changes in the rocky desertification areas in South China based on the precipitation (P), potential evapotranspiration (ETp) and NDVI (the normalized difference vegetation index) datasets. The revised Bagrov model was used to simulate the actual evapotranspiration changes with the supposed increasing NDVI. The results indicated that the average NDVI value was lower when the rocky desertification was more severe. The ETa, evapotranspiration efficiency (ETa/ETp) and potential humidity (P/ETp) generally increased with the increasing NDVI. The sensitivity of the ETa response to vegetation coverage changes varied due to different precipitation conditions and different rocky desertification severities. The ETa was more sensitive under drought conditions. When a drought occurred, the ETa exhibited an average increase of 40~60 mm with the NDVI increasing of 0.1 in the rocky desertification areas. Among the 5 different severity categories of rocky desertification, the ETa values' responses to NDVI changes were less sensitive in the severe rocky desertification areas but more sensitive in the extremely and potential rocky desertification areas. For example, with the NDVI increasing of 0.025, 0.05, 0.075, and 0.1, the corresponding ETa changes increased by an average of 2.64 mm, 10.62 mm, 19.19 mm, and 27.58 mm, respectively, in severe rocky desertification areas but by 4.94 mm, 14.99 mm, 26.80, and 37.13 mm, respectively, in extremely severe rocky desertification areas. Understanding the vegetation ecological water consumption response to the vegetation coverage changes is essential for the vegetation restoration and water stresses mitigation in rocky desertification areas.

[A new class of exciplex-formed probe detect of specific sequence DNA].

PubMed

Li, Qing-Yong; Zu, Yuan-Gang; Lü, Hong-Yan; Wang, Li-Min

2009-07-01

The present research was to develop the exciplex-based fluorescence detection of DNA. A SNP-containing region of cytochrome P450 2C9 DNA systems was evaluated to define some of the structural and associated requirement of this new class of exciplex-formed probe, and a 24-base target was selected which contains single-nucleotide polymorphisms (SNP) in genes coding for cytochrome P450. The two probes were all 12-base to give coverage of a 24-base target region to ensure specificity within the human genome. Exciplex partners used in this study were prepared using analogous phosphoramide attachment to the 3'- or 5'-phosphate group of the appropriate oligonucleotide probes. The target effectively assembled its own detector by hybridization from components which were non-fluorescent at the detection wavelength, leading to the huge improvement in terms of decreased background. This research provides details of the effects of different partner, position of partners and different excitation wavelengths for the split-oligonucleotide probe system for exciplex-based fluorescence detection of DNA. This study demonstrates that the emission intensity of the excimer formed by new pyrene derivative is the highest in these excimer and exciplex, and the excimer is easy to be formed and not sensitive to the position of partners. However the exciplex formed by the new pyrene derivative and naphthalene emitted strongly at -505 nm with large Stokes shifts (120-130 nm), and the monomer emission at 390 and 410 nm is nearly zero. Excitation wavelength of 400 nm is the best for I(e505)/I(m410) (exciplex emission at 505 nm/monomer emission at 410 nm) of the exciplex. This method features lower background and high sensitivity. Moreover the exciplex is sensitive to the steric factor, different position of partners and microenvironment, so this exciplex system is promising and could be tried to identify the SNP genes.

Nighttime sensitivity of ionospheric VLF measurements to X-ray bursts from a remote cosmic source

NASA Astrophysics Data System (ADS)

Raulin, Jean-Pierre; Trottet, Gérard; Giménez de Castro, C. Guillermo; Correia, Emilia; Macotela, E. Liliana

2014-06-01

On 22 January 2009, a series of X-ray bursts were emitted by the soft gamma ray repeater SGR J1550-5418. Some of these bursts produced enhanced ionization in the nighttime lower ionosphere. These ionospheric disturbances were studied using X-ray measurements from the Anti-Coincidence Shield of the Spectrometer for Integral onboard the International Gamma-Ray Astrophysics Laboratory and simultaneous phase and amplitude records from two VLF propagation paths between the transmitter Naval Radio Station, Pearl Harbor (Hawaii) and the receivers Radio Observatorio do Itapetinga (Brazil) and Estação Antarctica Commandante Ferraz (Antarctic Peninsula). The VLF measurements have been obtained with an unprecedented high time resolution of 20 ms. We find that the illumination factor I (illuminated path length times the cosine of the zenith angle), which characterizes the propagation paths underlying the flaring object, is a key parameter which determines the sensitivity threshold of the VLF detection of X-ray bursts from nonsolar transients. For the present VLF measurements of bursts from SGR J1550-5418, it is found that for I ≥ 1.8 Mm, all X-ray bursts with fluence in the 25 keV to 2 MeV range larger than F25_min 1.0 × 10-6 erg/cm2 produce a measurable ionospheric disturbance. Such a lower limit of the X-ray fluence value indicates that moderate X-ray bursts, as opposed to giant X-ray bursts, do produce ionospheric disturbances larger than the sensitivity limit of the VLF technique. Therefore, the frequency of detection of such events could be improved, for example by increasing the coverage of existing VLF receiving networks. The VLF detection of high-energy astrophysical bursts then appears as an important observational diagnostic to complement their detection in space. This would be especially important when space observations suffer from adverse conditions, like saturation, occultation from the Earth, or the passage of the spacecraft through the South Atlantic anomaly.

An evaluation of copy number variation detection tools for cancer using whole exome sequencing data.

PubMed

Zare, Fatima; Dow, Michelle; Monteleone, Nicholas; Hosny, Abdelrahman; Nabavi, Sheida

2017-05-31

Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has become primary strategy for sequencing patient samples and study their genomics aberrations. However, compared to whole genome sequencing, WES introduces more biases and noise that make CNV detection very challenging. Additionally, tumors' complexity makes the detection of cancer specific CNVs even more difficult. Although many CNV detection tools have been developed since introducing NGS data, there are few tools for somatic CNV detection for WES data in cancer. In this study, we evaluated the performance of the most recent and commonly used CNV detection tools for WES data in cancer to address their limitations and provide guidelines for developing new ones. We focused on the tools that have been designed or have the ability to detect cancer somatic aberrations. We compared the performance of the tools in terms of sensitivity and false discovery rate (FDR) using real data and simulated data. Comparative analysis of the results of the tools showed that there is a low consensus among the tools in calling CNVs. Using real data, tools show moderate sensitivity (~50% - ~80%), fair specificity (~70% - ~94%) and poor FDRs (~27% - ~60%). Also, using simulated data we observed that increasing the coverage more than 10× in exonic regions does not improve the detection power of the tools significantly. The limited performance of the current CNV detection tools for WES data in cancer indicates the need for developing more efficient and precise CNV detection methods. Due to the complexity of tumors and high level of noise and biases in WES data, employing advanced novel segmentation, normalization and de-noising techniques that are designed specifically for cancer data is necessary. Also, CNV detection development suffers from the lack of a gold standard for performance evaluation. Finally, developing tools with user-friendly user interfaces and visualization features can enhance CNV studies for a broader range of users.

First results from HAWC: monitoring the TeV gamma-ray sky

NASA Astrophysics Data System (ADS)

Lauer, Robert J.

2015-03-01

The High Altitude Water Cherenkov (HAWC) Observatory is a wide-field gamma-ray detector sensitive to primary energies between 100 GeV and 100 TeV. The array is being built at an altitude of 4100 m a.s.l. on the Sierra Negra volcano near Puebla, Mexico. Data taking has already started while construction continues, with the completion projected for early 2015. The design is optimized to detect extended air showers induced by gamma rays that pass through the array and to reconstruct the directions and energies of the primary photons. With a duty cycle close to 100% and a daily coverage of ~8 sr of the sky, HAWC will perform a survey of TeV emissions from many different sources. The northern active galactic nuclei will be monitored for up to 6 hours each day, providing unprecedented light curve coverage at energies comparable to those of imaging air Cherenkov telescopes. HAWC has been in scientific operation with more than 100 detector modules since August 2013. Here we present a preliminary look at the first results and discuss the efforts to integrate HAWC in multi-wavelength studies of extragalactic jets.

The Atmospheric Monitoring Strategy for the Cherenkov Telescope Array

NASA Astrophysics Data System (ADS)

Daniel, M. K.; CTA Consortium

2015-04-01

The Imaging Atmospheric Cherenkov Technique (IACT) is unusual in astronomy as the atmosphere actually forms an intrinsic part of the detector system, with telescopes indirectly detecting very high energy particles by the generation and transport of Cherenkov photons deep within the atmosphere. This means that accurate measurement, characterisation and monitoring of the atmosphere is at the very heart of successfully operating an IACT system. The Cherenkov Telescope Array (CTA) will be the next generation IACT observatory with an ambitious aim to improve the sensitivity of an order of magnitude over current facilities, along with corresponding improvements in angular and energy resolution and extended energy coverage, through an array of Large (23 m), Medium (12 m) and Small (4 m) sized telescopes spread over an area of order ~km2. Whole sky coverage will be achieved by operating at two sites: one in the northern hemisphere and one in the southern hemisphere. This proceedings will cover the characterisation of the candidate sites and the atmospheric calibration strategy. CTA will utilise a suite of instrumentation and analysis techniques for atmospheric modelling and monitoring regarding pointing forecasts, intelligent pointing selection for the observatory operations and for offline data correction.

Vehicle Integrated Prognostic Reasoner (VIPR) Metric Report

NASA Technical Reports Server (NTRS)

Cornhill, Dennis; Bharadwaj, Raj; Mylaraswamy, Dinkar

2013-01-01

This document outlines a set of metrics for evaluating the diagnostic and prognostic schemes developed for the Vehicle Integrated Prognostic Reasoner (VIPR), a system-level reasoner that encompasses the multiple levels of large, complex systems such as those for aircraft and spacecraft. VIPR health managers are organized hierarchically and operate together to derive diagnostic and prognostic inferences from symptoms and conditions reported by a set of diagnostic and prognostic monitors. For layered reasoners such as VIPR, the overall performance cannot be evaluated by metrics solely directed toward timely detection and accuracy of estimation of the faults in individual components. Among other factors, overall vehicle reasoner performance is governed by the effectiveness of the communication schemes between monitors and reasoners in the architecture, and the ability to propagate and fuse relevant information to make accurate, consistent, and timely predictions at different levels of the reasoner hierarchy. We outline an extended set of diagnostic and prognostics metrics that can be broadly categorized as evaluation measures for diagnostic coverage, prognostic coverage, accuracy of inferences, latency in making inferences, computational cost, and sensitivity to different fault and degradation conditions. We report metrics from Monte Carlo experiments using two variations of an aircraft reference model that supported both flat and hierarchical reasoning.

Carbon nanospikes grown on metal wires as microelectrode sensors for dopamine

DOE PAGES

Zestos, Alexander G.; Yang, Cheng; Jacobs, Christopher B.; ...

2015-09-14

Carbon nanomaterials are advantageous as electrodes for neurotransmitter detection, but the difficulty of nanomaterials deposition on electrode substrates limits the reproducibility and future applications. In our study, we used plasma enhanced chemical vapor deposition (PECVD) to directly grow a thin layer of carbon nanospikes (CNS) on cylindrical metal substrates. No catalyst is required and the CNS surface coverage is uniform over the cylindrical metal substrate. We characterized the CNS growth on several metallic substrates including tantalum, niobium, palladium, and nickel wires. Using fast-scan cyclic voltammetry (FSCV), bare metal wires could not detect 1 mu M dopamine while carbon nanospike coatedmore » wires could. Moreover, the highest sensitivity and optimized S/N ratio was recorded from carbon nanospike-tantalum (CNS-Ta) microwires grown for 7.5 minutes, which had a LOD of 8 +/- 2 nM for dopamine with FSCV. CNS-Ta microelectrodes were more reversible and had a smaller Delta E-p for dopamine than carbon-fiber microelectrodes, suggesting faster electron transfer kinetics. The kinetics of dopamine redox were adsorption controlled at CNS-Ta microelectrodes and repeated electrochemical measurements displayed stability for up to ten hours in vitro and over a ten day period as well. The oxidation potential was significantly different for ascorbic acid and uric acid compared to dopamine. Finally, growing carbon nanospikes on metal wires is a promising method to produce uniformly-coated, carbon nanostructured cylindrical microelectrodes for sensitive dopamine detection.« less

Tunable Fabry-Perot etalon-based long-wavelength infrared imaging spectroradiometer.

PubMed

Marinelli, W J; Gittins, C M; Gelb, A H; Green, B D

1999-04-20

Imaging spectrometry enables passive, stand-off detection and analysis of the chemical composition of gas plumes and surfaces over wide geographic areas. We describe the use of a long-wavelength infrared imaging spectroradiometer, comprised of a low-order tunable Fabry-Perot etalon coupled to a HgCdTe detector array, to perform multispectral detection of chemical vapor plumes. The tunable Fabry-Perot etalon used in this research provides coverage of the 9.5-14-microm spectral region with a resolution of 7-9 cm(-1). The etalon-based imaging system provides the opportunity to image a scene at only those wavelengths needed for chemical species identification and quantification and thereby minimize the data volume necessary for selective species detection. We present initial results using a brassboard imaging system for stand-off detection and quantification of chemical vapor plumes against near-ambient-temperature backgrounds. These data show detection limits of 22 parts per million by volume times meter (ppmv x m) and 0.6 ppmv x m for dimethyl methyphosphonate and SF6, respectively, for a gas/background DeltaT of 6 K. The system noise-equivalent spectral radiance is approximately 2 microW cm(-2) sr(-1) microm(-1). Model calculations are presented comparing the measured sensitivity of the sensor to the anticipated signal levels for two chemical release scenarios.

The Swift/BAT Hard X-ray Transient Monitor: A Status Report

NASA Astrophysics Data System (ADS)

Krimm, Hans A.; Bloom, J. S.; Markwardt, C.; Miler-Jones, J.; Gehrels, N.; Kennea, J. A.; Holland, S.; Sivakoff, G. R.; Swift/BAT Team

2013-04-01

The Swift/Burst Alert Telescope (BAT) hard X-ray transient monitor provides near real-time coverage of the X-ray sky in the energy range 15-50 keV. This monitor was first announced at the 2006 HEAD meeting. Seven years later, it continues to operate and provides near real-time light curves of more than 900 astrophysical sources. The BAT observes ~75% of the sky each day with a 3-sigma detection sensitivity of 7 mCrab for a full-day observation and a time resolution as fine as 64 seconds. The three main purposes of the monitor are (1) the discovery of new transient X-ray sources, (2) the detection of outbursts or other changes in the flux of known X-ray sources, and (3) the generation of archival light curves spanning nearly seven years. The primary interface for the BAT transient monitor is a public web page. Since February 2005, 223 sources have been detected in the monitor, 142 of them persistent and 81 detected only in outburst. From 2006-2013, fourteen new sources have been discovered by the BAT transient monitor. We will describe the methodology of the transient monitor, present a summary of its statistics, and discuss the detection of known and newly discovered sources.

The Swift/BAT Hard X-ray Transient Monitor: A Status Report

NASA Astrophysics Data System (ADS)

Krimm, Hans A.; Swift/BAT Team

2011-09-01

The Swift/Burst Alert Telescope (BAT) hard X-ray transient monitor provides near real-time coverage of the X-ray sky in the energy range 15-50 keV. This monitor was first announced at the 2006 HEAD meeting. Five years later, it continues to operate and provides near real-time light curves of more than 900 astrophysical sources. The BAT observes 75% of the sky each day with a 3-sigma detection sensitivity of 7 mCrab for a full-day observation and a time resolution as fine as 64 seconds. The three main purposes of the monitor are (1) the discovery of new transient X-ray sources, (2) the detection of outbursts or other changes in the flux of known X-ray sources, and (3) the generation of archival light curves spanning nearly seven years. The primary interface for the BAT transient monitor is a public web page. Since February 2005, 172 sources have been detected in the monitor, 89 of them persistent and 83 detected only in outburst. From 2006-2011, nine new sources have been discovered by the BAT transient monitor. We will describe the methodology of the transient monitor, present a summary of its statistics, and discuss the detection of known and newly discovered sources.

Coverage of breast cancer in the Australian print media--does advertising and editorial coverage reflect correct social marketing messages?

PubMed

Jones, Sandra C

2004-01-01

Early detection of breast cancer by mammographic screening has the potential to dramatically reduce mortality rates, but many women do not comply with screening recommendations. The media are an important source of health information for many women--through both direct social marketing advertisements and indirect dissemination of information via editorial content. This study investigated the accuracy of breast cancer detection messages in the top-selling Australian women's magazines and three weekend newspapers in the six-month period from December 2000 to May 2001 that included any reference to breast cancer and found that current coverage of breast cancer in the Australian print media conveys messages that are unlikely to encourage appropriate screening.

Investigation of lunar maria structure from cross-analysis of GRAIL gravity and Kaguya radar data

NASA Astrophysics Data System (ADS)

Zuber, M. T.; Ermakov, A.; Smith, D. E.; Mastroguiseppe, M.; Raguso, M.

2016-12-01

The Lunar Radar Sounder (LRS) on JAXA's Kaguya spacecraft investigated the subsurface structure of the Moon to a depth of a few km. GRAIL gravity models are potentially sensitive to subsurface structure at such depths. GRAIL gravity and LRS radar data are complementary since both are sensitive to density/compositional heterogeneities. Cross-correlation of GRAIL and LRS data has the potential to produce new constraints on the structure and evolution of the lunar maria. Originally, subsurface reflections within the lunar maria were detected with Lunar Sounder Experiment aboard Apollo 17. Subsurface layering was attributed to multiple episodes of volcanism. Later, Kaguya's LRS produced similar measurements but with global-scale coverage. Laboratory measurements show that density variations among mare basalts can be up to 200 kg m-3 or 7%. The LRS measurements have detected subsurface reflection in the upper 1 km of the crust. Combining these two estimates and using the Bouguer slab approximation, we estimate that anomalies of order 1-10 mGal are expected due to potentially varying density of surface and/or subsurface horizons. This accuracy is achievable with the latest GRAIL gravity models. The LRS surface backscattering power is indicative of surface and near sub-surface dielectric properties, which are sensitive to target density and roughness. We investigate the northwestern part of the Procellarum basin because it is the region with the strongest signal-to-noise ratios in gravity models within maria. To examine shallow subsurface structure, we map the surface received power by tracking the first return of radar echoes and compare it with gravity gradients, which are particularly sensitive to small-scale structures.

Hydrogen Epoch of Reionization Array (HERA)

NASA Astrophysics Data System (ADS)

DeBoer, David R.; HERA

2015-01-01

The Hydrogen Epoch of Reionization Arrays (HERA - reionization.org) roadmap uses the unique properties of the neutral hydrogen (HI) 21cm line to probe our cosmic dawn: from the birth of the first stars and black holes, through the full reionization of the primordial intergalactic medium (IGM). HERA is a collaboration between the Precision Array Probing the Epoch of Reionization (PAPER - eor.berkeley.edu), the US-based Murchison Widefield Array (MWA - mwatelescope.org), and MIT Epoch of Reionization (MITEOR) teams along with the South African SKA-SA, University of KwaZulu Natal and the University of Cambridge Cavendish Laborabory. HERA has recently been awarded a National Science Foundation Mid-Scale Innovation Program grant to begin the next phase.HERA leverages the operation of the PAPER and MWA telescopes to explore techniques and designs required to detect the primordial HI signal in the presence of systematics and radio continuum foreground emission some four orders of magnitude brighter. With this understanding, we are now able to remove foregrounds to the limits of our sensitivity, culminating in the first physically meaningful upper limits. A redundant calibration algorithm from MITEOR improves the sensitivity of the approach.Building on this, the next stage of HERA incorporates a 14m diameter antenna element that is optimized both for sensitivity and for minimizing foreground systematics. Arranging these elements in a compact hexagonal grid yields an array that facilitates calibration, leverages proven foreground removal techniques, and is scalable to large collecting areas. HERA will be located in the radio quiet environment of the SKA site in the Karoo region of South Africa (where PAPER is currently located). It will have a sensitivity close to two orders of magnitude better than PAPER and the MWA to ensure a robust detection. With its sensitivity and broader frequency coverage, HERA can paint an uninterrupted picture through reionization, back to the end of the Dark Ages.This paper will present a summary of the current understanding of the signal characteristics and measurements and describe the funded and planned HERA telescope to be built to detect and characterize the EoR power spectrum.

Real-time method for establishing a detection map for a network of sensors

DOEpatents

Nguyen, Hung D; Koch, Mark W; Giron, Casey; Rondeau, Daniel M; Russell, John L

2012-09-11

A method for establishing a detection map of a dynamically configurable sensor network. This method determines an appropriate set of locations for a plurality of sensor units of a sensor network and establishes a detection map for the network of sensors while the network is being set up; the detection map includes the effects of the local terrain and individual sensor performance. Sensor performance is characterized during the placement of the sensor units, which enables dynamic adjustment or reconfiguration of the placement of individual elements of the sensor network during network set-up to accommodate variations in local terrain and individual sensor performance. The reconfiguration of the network during initial set-up to accommodate deviations from idealized individual sensor detection zones improves the effectiveness of the sensor network in detecting activities at a detection perimeter and can provide the desired sensor coverage of an area while minimizing unintentional gaps in coverage.

Terahertz quantum-cascade lasers as high-power and wideband, gapless sources for spectroscopy.

PubMed

Röben, Benjamin; Lü, Xiang; Hempel, Martin; Biermann, Klaus; Schrottke, Lutz; Grahn, Holger T

2017-07-10

Terahertz (THz) quantum-cascade lasers (QCLs) are powerful radiation sources for high-resolution and high-sensitivity spectroscopy with a discrete spectrum between 2 and 5 THz as well as a continuous coverage of several GHz. However, for many applications, a radiation source with a continuous coverage of a substantially larger frequency range is required. We employed a multi-mode THz QCL operated with a fast ramped injection current, which leads to a collective tuning of equally-spaced Fabry-Pérot laser modes exceeding their separation. A continuous coverage over 72 GHz at about 4.7 THz was achieved. We demonstrate that the QCL is superior to conventional sources used in Fourier transform infrared spectroscopy in terms of the signal-to-noise ratio as well as the dynamic range by one to two orders of magnitude. Our results pave the way for versatile THz spectroscopic systems with unprecedented resolution and sensitivity across a wide frequency range.

Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants

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

Borucki, Monica K.; Lao, Victoria; Hwang, Mona

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater thanmore » 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Lastly, many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding.« less

Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants

DOE PAGES

Borucki, Monica K.; Lao, Victoria; Hwang, Mona; ...

2016-01-20

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater thanmore » 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Lastly, many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding.« less

a Performance Comparison of Feature Detectors for Planetary Rover Mapping and Localization

NASA Astrophysics Data System (ADS)

Wan, W.; Peng, M.; Xing, Y.; Wang, Y.; Liu, Z.; Di, K.; Teng, B.; Mao, X.; Zhao, Q.; Xin, X.; Jia, M.

2017-07-01

Feature detection and matching are key techniques in computer vision and robotics, and have been successfully implemented in many fields. So far there is no performance comparison of feature detectors and matching methods for planetary mapping and rover localization using rover stereo images. In this research, we present a comprehensive evaluation and comparison of six feature detectors, including Moravec, Förstner, Harris, FAST, SIFT and SURF, aiming for optimal implementation of feature-based matching in planetary surface environment. To facilitate quantitative analysis, a series of evaluation criteria, including distribution evenness of matched points, coverage of detected points, and feature matching accuracy, are developed in the research. In order to perform exhaustive evaluation, stereo images, simulated under different baseline, pitch angle, and interval of adjacent rover locations, are taken as experimental data source. The comparison results show that SIFT offers the best overall performance, especially it is less sensitive to changes of image taken at adjacent locations.

Optical Detection of Lightning from Space

NASA Technical Reports Server (NTRS)

Boccippio, Dennis J.; Christian, Hugh J.

1998-01-01

Optical sensors have been developed to detect lightning from space during both day and night. These sensors have been fielded in two existing satellite missions and may be included on a third mission in 2002. Satellite-hosted, optically-based lightning detection offers three unique capabilities: (1) the ability to reliably detect lightning over large, often remote, spatial regions, (2) the ability to sample all (IC and CG) lightning, and (3) the ability to detect lightning with uniform (i.e., not range-dependent) sensitivity or detection efficiency. These represent significant departures from conventional RF-based detection techniques, which typically have strong range dependencies (biases) or range limitations in their detection capabilities. The atmospheric electricity team of the NASA Marshall Space Flight Center's Global Hydrology and Climate Center has implemented a three-step satellite lightning research program which includes three phases: proof-of-concept/climatology, science algorithm development, and operational application. The first instrument in the program, the Optical Transient Detector (OTD), is deployed on a low-earth orbit (LEO) satellite with near-polar inclination, yielding global coverage. The sensor has a 1300 x 1300 sq km field of view (FOV), moderate detection efficiency, moderate localization accuracy, and little data bias. The OTD is a proof-of-concept instrument and its mission is primarily a global lightning climatology. The limited spatial accuracy of this instrument makes it suboptimal for use in case studies, although significant science knowledge has been gained from the instrument as deployed.

Clarifying coverages on the basis of tapes SnO2, SiO2, Si3N4 for photodiodes of ultraviolet and visible range

NASA Astrophysics Data System (ADS)

Dobrovolsciy, Yu. George; Perevertaylo, Vladimir L.; Shabashcevich, Boris G.; Pidkamin, Leonid J.

2009-10-01

It is shown, what coverage of dioxide of tin is instrumental in the rise of sensitiveness of photodiodes sensible in the ultraviolet region of spectrum on the basis of selenid zinc and phosphide of gallium to 0,12 A/W and 0,2 A/W accordingly in the maximum of spectral description of sensitiveness. All so it is shown, that tape of nitrid silicon - dioxide of silicon a bit better clarifies silicon photodiode, especially on a wave-length 700 nm. Gluing composition, in general, worsens admission of tapes, and in a greater degree the admission of tape of nitrid silicon - dioxide of silicon.

Inequities and their determinants in coverage of maternal health services in Burkina Faso.

PubMed

Mwase, Takondwa; Brenner, Stephan; Mazalale, Jacob; Lohmann, Julia; Hamadou, Saidou; Somda, Serge M A; Ridde, Valery; De Allegri, Manuela

2018-05-11

Poor and marginalized segments of society often display the worst health status due to limited access to health enhancing interventions. It follows that in order to enhance the health status of entire populations, inequities in access to health care services need to be addressed as an inherent element of any effort targeting Universal Health Coverage. In line with this observation and the need to generate evidence on the equity status quo in sub-Saharan Africa, we assessed the magnitude of the inequities and their determinants in coverage of maternal health services in Burkina Faso. We assessed coverage for three basic maternal care services (at least four antenatal care visits, facility-based delivery, and at least one postnatal care visit) using data from a cross-sectional household survey including a total of 6655 mostly rural, poor women who had completed a pregnancy in the 24 months prior to the survey date. We assessed equity along the dimensions of household wealth, distance to the health facility, and literacy using both simple comparative measures and concentration indices. We also ran hierarchical random effects regression to confirm the presence or absence of inequities due to household wealth, distance, and literacy, while controlling for potential confounders. Coverage of facility based delivery was high (89%), but suboptimal for at least four antenatal care visits (44%) and one postnatal care visit (53%). We detected inequities along the dimensions of household wealth, literacy and distance. Service coverage was higher among the least poor, those who were literate, and those living closer to a health facility. We detected a significant positive association between household wealth and all outcome variables, and a positive association between literacy and facility-based delivery. We detected a negative association between living farther away from the catchment facility and all outcome variables. Existing inequities in maternal health services in Burkina Faso are likely going to jeopardize the achievement of Universal Health Coverage. It is important that policy makers continue to strengthen and monitor the implementation of strategies that promote proportionate universalism and forge multi-sectoral approach in dealing with social determinants of inequities in maternal health services coverage.

Standard Information Models for Representing Adverse Sensitivity Information in Clinical Documents.

PubMed

Topaz, M; Seger, D L; Goss, F; Lai, K; Slight, S P; Lau, J J; Nandigam, H; Zhou, L

2016-01-01

Adverse sensitivity (e.g., allergy and intolerance) information is a critical component of any electronic health record system. While several standards exist for structured entry of adverse sensitivity information, many clinicians record this data as free text. This study aimed to 1) identify and compare the existing common adverse sensitivity information models, and 2) to evaluate the coverage of the adverse sensitivity information models for representing allergy information on a subset of inpatient and outpatient adverse sensitivity clinical notes. We compared four common adverse sensitivity information models: Health Level 7 Allergy and Intolerance Domain Analysis Model, HL7-DAM; the Fast Healthcare Interoperability Resources, FHIR; the Consolidated Continuity of Care Document, C-CDA; and OpenEHR, and evaluated their coverage on a corpus of inpatient and outpatient notes (n = 120). We found that allergy specialists' notes had the highest frequency of adverse sensitivity attributes per note, whereas emergency department notes had the fewest attributes. Overall, the models had many similarities in the central attributes which covered between 75% and 95% of adverse sensitivity information contained within the notes. However, representations of some attributes (especially the value-sets) were not well aligned between the models, which is likely to present an obstacle for achieving data interoperability. Also, adverse sensitivity exceptions were not well represented among the information models. Although we found that common adverse sensitivity models cover a significant portion of relevant information in the clinical notes, our results highlight areas needed to be reconciled between the standards for data interoperability.

Geographic applications of ERTS-1 imagery to landscape change. [Mississippi River and Great Smoky Mountains of Tennessee and North Carolina

NASA Technical Reports Server (NTRS)

Rehder, J. B. (Principal Investigator)

1973-01-01

The author has identified the following significant results. ERTS-1 has proven to be an effective earth-orbiting monitor of landscape change. Its regional coverage for large areal monitoring has been effective for the detection and mapping of agricultural plowing regions, for general forest cover mapping, for flood mapping, for strip mine mapping, and for short-lived precipitation mapping patterns. Paramount to the entire study has been the temporal coverage provided by ERTS. Without the cyclic coverage on an 18 day basis, temporal coverage would have been inadequate for the detection and mapping of strip mining landscape change, the analysis of agricultural landscape change based on plowing patterns, the analysis of urban-suburban growth changes, and the mapping of the Mississippi River floods. Cost benefits from ERTS are unquestionably superior to aircraft systems in regard to large regional coverage and cyclic temporal parameters. For the analysis of landscape change in large regions such as statewide areas or even areas of 10,000 square miles, ERTS is of cost benefit consideration. Not only does the cost of imagery favor ERTS but the reduction of man-hours using ERTS has been in the magnitude of 1:10.

Genetically modified porcine split-thickness skin grafts as an alternative to allograft for provision of temporary wound coverage: preliminary characterization.

PubMed

Leto Barone, Angelo A; Mastroianni, Melissa; Farkash, Evan A; Mallard, Christopher; Albritton, Alexander; Torabi, Radbeh; Leonard, David A; Kurtz, Josef M; Sachs, David H; Cetrulo, Curtis L

2015-05-01

Temporary coverage of severely burned patients with cadaver allograft skin represents an important component of burn care, but is limited by availability and cost. Porcine skin shares many physical properties with human skin, but is susceptible to hyperacute rejection due to preformed antibodies to α-1,3-galactose (Gal), a carbohydrate on all porcine cells. Our preliminary studies have suggested that skin grafts from α-1,3-galactosyltransferase knock out (GalT-KO) miniature swine might provide temporary wound coverage comparable to allografts, since GalT-KO swine lack this carbohydrate. To further evaluate this possibility, eight non-human primates received primary autologous, allogeneic, GalT-KO, and GalT+xenogeneic skin grafts. Additionally, secondary grafts were placed to assess whether sensitization would affect the rejection time course of identical-type grafts. We demonstrate that both GalT-KO xenografts and allografts provide temporary coverage of partial- and full-thickness wounds for up to 11 days. In contrast, GalT+xenografts displayed hyperacute rejection, with no signs of vascularization and rapid avulsion from wounds. Furthermore, secondary GalT-KO transplants failed to vascularize, demonstrating that primary graft rejection sensitizes the recipient. We conclude that GalT-KO xenografts may provide temporary coverage of wounds for a duration equivalent to allografts, and thus, could serve as a readily available alternative treatment of severe burns. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

Development of nanosecond time-resolved infrared detection at the LEAF pulse radiolysis facility

DOE PAGES

Grills, David C.; Farrington, Jaime A.; Layne, Bobby H.; ...

2015-04-27

When coupled with transient absorption spectroscopy, pulse radiolysis, which utilizes high-energy electron pulses from an accelerator, is a powerful tool for investigating the kinetics and thermodynamics of a wide range of radiation-induced redox and electron transfer processes. The majority of these investigations detect transient species in the UV, visible, or near-IR spectral regions. Unfortunately, the often-broad and featureless absorption bands in these regions can make the definitive identification of intermediates difficult. Time-resolved vibrational spectroscopy would offer much improved structural characterization, but has received only limited application in pulse radiolysis. In this paper, we describe in detail the development of amore » unique nanosecond time-resolved infrared (TRIR) detection capability for condensed-phase pulse radiolysis on a new beam line at the LEAF facility of Brookhaven National Laboratory. The system makes use of a suite of high-power, continuous wave external-cavity quantum cascade lasers as the IR probe source, with coverage from 2330-1051 cm⁻¹. The response time of the TRIR detection setup is ~40 ns, with a typical sensitivity of ~100 µOD after 4-8 signal averages using a dual-beam probe/reference normalization detection scheme. As a result, this new detection method has enabled mechanistic investigations of a range of radiation-induced chemical processes, some of which are highlighted here.« less

Development of a general method for detection and quantification of the P35S promoter based on assessment of existing methods

PubMed Central

Wu, Yuhua; Wang, Yulei; Li, Jun; Li, Wei; Zhang, Li; Li, Yunjing; Li, Xiaofei; Li, Jun; Zhu, Li; Wu, Gang

2014-01-01

The Cauliflower mosaic virus (CaMV) 35S promoter (P35S) is a commonly used target for detection of genetically modified organisms (GMOs). There are currently 24 reported detection methods, targeting different regions of the P35S promoter. Initial assessment revealed that due to the absence of primer binding sites in the P35S sequence, 19 of the 24 reported methods failed to detect P35S in MON88913 cotton, and the other two methods could only be applied to certain GMOs. The rest three reported methods were not suitable for measurement of P35S in some testing events, because SNPs in binding sites of the primer/probe would result in abnormal amplification plots and poor linear regression parameters. In this study, we discovered a conserved region in the P35S sequence through sequencing of P35S promoters from multiple transgenic events, and developed new qualitative and quantitative detection systems targeting this conserved region. The qualitative PCR could detect the P35S promoter in 23 unique GMO events with high specificity and sensitivity. The quantitative method was suitable for measurement of P35S promoter, exhibiting good agreement between the amount of template and Ct values for each testing event. This study provides a general P35S screening method, with greater coverage than existing methods. PMID:25483893

Cost-Effectiveness of Opt-Out Chlamydia Testing for High-Risk Young Women in the U.S.

PubMed

Owusu-Edusei, Kwame; Hoover, Karen W; Gift, Thomas L

2016-08-01

In spite of chlamydia screening recommendations, U.S. testing coverage continues to be low. This study explored the cost-effectiveness of a patient-directed, universal, opportunistic Opt-Out Testing strategy (based on insurance coverage, healthcare utilization, and test acceptance probabilities) for all women aged 15-24 years compared with current Risk-Based Screening (30% coverage) from a societal perspective. Based on insurance coverage (80%); healthcare utilization (83%); and test acceptance (75%), the proposed Opt-Out Testing strategy would have an expected annual testing coverage of approximately 50% for sexually active women aged 15-24 years. A basic compartmental heterosexual transmission model was developed to account for population-level transmission dynamics. Two groups were assumed based on self-reported sexual activity. All model parameters were obtained from the literature. Costs and benefits were tracked over a 50-year period. The relative sensitivity of the estimated incremental cost-effectiveness ratios to the variables/parameters was determined. This study was conducted in 2014-2015. Based on the model, the Opt-Out Testing strategy decreased the overall chlamydia prevalence by >55% (2.7% to 1.2%). The Opt-Out Testing strategy was cost saving compared with the current Risk-Based Screening strategy. The estimated incremental cost-effectiveness ratio was most sensitive to the female pre-opt out prevalence, followed by the probability of female sequelae and discount rate. The proposed Opt-Out Testing strategy was cost saving, improving health outcomes at a lower net cost than current testing. However, testing gaps would remain because many women might not have health insurance coverage, or not utilize health care. Published by Elsevier Inc.

An A Priori Multiobjective Optimization Model of a Search and Rescue Network

DTIC Science & Technology

1992-03-01

sequences. Classical sensitivity analysis and tolerance analysis were used to analyze the frequency assignments generated by the different weight...function for excess coverage of a frequency. Sensitivity analysis is used to investigate the robustness of the frequency assignments produced by the...interest. The linear program solution is used to produce classical sensitivity analysis for the weight ranges. 17 III. Model Formulation This chapter

A Commercial Architecture for Satellite Imagery

DTIC Science & Technology

2006-09-01

incorporates image detection from the visible and near - infrared wavelengths, 3) 16 Ball Aerospace...present limited total area coverage since the field of regard is smallest. The opposite is true for resolution and total area coverage near apogee. The...27 B. SENSOR FIELD OF REGARD ...................................................................27 1. Spherical Analysis

Greedy Sparse Approaches for Homological Coverage in Location Unaware Sensor Networks

DTIC Science & Technology

2017-12-08

GlobalSIP); 2013 Dec; Austin , TX . p. 595– 598. 33. Farah C, Schwaner F, Abedi A, Worboys M. Distributed homology algorithm to detect topological events...ARL-TR-8235•DEC 2017 US Army Research Laboratory Greedy Sparse Approaches for Homological Coverage in Location-Unaware Sensor Net- works by Terrence...8235•DEC 2017 US Army Research Laboratory Greedy Sparse Approaches for Homological Coverage in Location-Unaware Sensor Net- works by Terrence J Moore

Switch from oral to inactivated poliovirus vaccine in Yogyakarta Province, Indonesia: summary of coverage, immunity, and environmental surveillance.

PubMed

Wahjuhono, Gendro; Revolusiana; Widhiastuti, Dyah; Sundoro, Julitasari; Mardani, Tri; Ratih, Woro Umi; Sutomo, Retno; Safitri, Ida; Sampurno, Ondri Dwi; Rana, Bardan; Roivainen, Merja; Kahn, Anna-Lea; Mach, Ondrej; Pallansch, Mark A; Sutter, Roland W

2014-11-01

Inactivated poliovirus vaccine (IPV) is rarely used in tropical developing countries. To generate additional scientific information, especially on the possible emergence of vaccine-derived polioviruses (VDPVs) in an IPV-only environment, we initiated an IPV introduction project in Yogyakarta, an Indonesian province. In this report, we present the coverage, immunity, and VDPV surveillance results. In Yogyakarta, we established environmental surveillance starting in 2004; and conducted routine immunization coverage and seroprevalence surveys before and after a September 2007 switch from oral poliovirus vaccine (OPV) to IPV, using standard coverage and serosurvey methods. Rates and types of polioviruses found in sewage samples were analyzed, and all poliovirus isolates after the switch were sequenced. Vaccination coverage (>95%) and immunity (approximately 100%) did not change substantially before and after the IPV switch. No VDPVs were detected. Before the switch, 58% of environmental samples contained Sabin poliovirus; starting 6 weeks after the switch, Sabin polioviruses were rarely isolated, and if they were, genetic sequencing suggested recent introductions. This project demonstrated that under almost ideal conditions (good hygiene, maintenance of universally high IPV coverage, and corresponding high immunity against polioviruses), no emergence and circulation of VDPV could be detected in a tropical developing country setting. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Effective case/infection ratio of poliomyelitis in vaccinated populations.

PubMed

Bencskó, G; Ferenci, T

2016-07-01

Recent polio outbreaks in Syria and Ukraine, and isolation of poliovirus from asymptomatic carriers in Israel have raised concerns that polio might endanger Europe. We devised a model to calculate the time needed to detect the first case should the disease be imported into Europe, taking the effect of vaccine coverage - both from inactivated and oral polio vaccines, also considering their differences - on the length of silent transmission into account by deriving an 'effective' case/infection ratio that is applicable for vaccinated populations. Using vaccine coverage data and the newly developed model, the relationship between this ratio and vaccine coverage is derived theoretically and is also numerically determined for European countries. This shows that unnoticed transmission is longer for countries with higher vaccine coverage and a higher proportion of IPV-vaccinated individuals among those vaccinated. Assuming borderline transmission (R = 1·1), the expected time to detect the first case is between 326 days and 512 days in different countries, with the number of infected individuals between 235 and 1439. Imperfect surveillance further increases these numbers, especially the number of infected until detection. While longer silent transmission does not increase the number of clinical diseases, it can make the application of traditional outbreak response methods more complicated, among others.

A testing-coverage software reliability model considering fault removal efficiency and error generation.

PubMed

Li, Qiuying; Pham, Hoang

2017-01-01

In this paper, we propose a software reliability model that considers not only error generation but also fault removal efficiency combined with testing coverage information based on a nonhomogeneous Poisson process (NHPP). During the past four decades, many software reliability growth models (SRGMs) based on NHPP have been proposed to estimate the software reliability measures, most of which have the same following agreements: 1) it is a common phenomenon that during the testing phase, the fault detection rate always changes; 2) as a result of imperfect debugging, fault removal has been related to a fault re-introduction rate. But there are few SRGMs in the literature that differentiate between fault detection and fault removal, i.e. they seldom consider the imperfect fault removal efficiency. But in practical software developing process, fault removal efficiency cannot always be perfect, i.e. the failures detected might not be removed completely and the original faults might still exist and new faults might be introduced meanwhile, which is referred to as imperfect debugging phenomenon. In this study, a model aiming to incorporate fault introduction rate, fault removal efficiency and testing coverage into software reliability evaluation is developed, using testing coverage to express the fault detection rate and using fault removal efficiency to consider the fault repair. We compare the performance of the proposed model with several existing NHPP SRGMs using three sets of real failure data based on five criteria. The results exhibit that the model can give a better fitting and predictive performance.

Automatic stent strut detection in intravascular OCT images using image processing and classification technique

NASA Astrophysics Data System (ADS)

Lu, Hong; Gargesha, Madhusudhana; Wang, Zhao; Chamie, Daniel; Attizani, Guilherme F.; Kanaya, Tomoaki; Ray, Soumya; Costa, Marco A.; Rollins, Andrew M.; Bezerra, Hiram G.; Wilson, David L.

2013-02-01

Intravascular OCT (iOCT) is an imaging modality with ideal resolution and contrast to provide accurate in vivo assessments of tissue healing following stent implantation. Our Cardiovascular Imaging Core Laboratory has served >20 international stent clinical trials with >2000 stents analyzed. Each stent requires 6-16hrs of manual analysis time and we are developing highly automated software to reduce this extreme effort. Using classification technique, physically meaningful image features, forward feature selection to limit overtraining, and leave-one-stent-out cross validation, we detected stent struts. To determine tissue coverage areas, we estimated stent "contours" by fitting detected struts and interpolation points from linearly interpolated tissue depths to a periodic cubic spline. Tissue coverage area was obtained by subtracting lumen area from the stent area. Detection was compared against manual analysis of 40 pullbacks. We obtained recall = 90+/-3% and precision = 89+/-6%. When taking struts deemed not bright enough for manual analysis into consideration, precision improved to 94+/-6%. This approached inter-observer variability (recall = 93%, precision = 96%). Differences in stent and tissue coverage areas are 0.12 +/- 0.41 mm2 and 0.09 +/- 0.42 mm2, respectively. We are developing software which will enable visualization, review, and editing of automated results, so as to provide a comprehensive stent analysis package. This should enable better and cheaper stent clinical trials, so that manufacturers can optimize the myriad of parameters (drug, coverage, bioresorbable versus metal, etc.) for stent design.

Urbanization reduces and homogenizes trait diversity in stream macroinvertebrate communities.

PubMed

Barnum, Thomas R; Weller, Donald E; Williams, Meghan

2017-12-01

More than one-half of the world's population lives in urban areas, so quantifying the effects of urbanization on ecological communities is important for understanding whether anthropogenic stressors homogenize communities across environmental and climatic gradients. We examined the relationship of impervious surface coverage (a marker of urbanization) and the structure of stream macroinvertebrate communities across the state of Maryland and within each of Maryland's three ecoregions: Coastal Plain, Piedmont, and Appalachian, which differ in stream geomorphology and community composition. We considered three levels of trait organization: individual traits, unique combinations of traits, and community metrics (functional richness, functional evenness, and functional divergence) and three levels of impervious surface coverage (low [<2.5%], medium [2.5% to 10%], and high [>10%]). The prevalence of an individual trait differed very little between low impervious surface and high impervious surface sites. The arrangement of trait combinations in community trait space for each ecoregion differed when impervious surface coverage was low, but the arrangement became more similar among ecoregions as impervious surface coverage increased. Furthermore, trait combinations that occurred only at low or medium impervious surface coverage were clustered in a subset of the community trait space, indicating that impervious surface affected the presence of only a subset of trait combinations. Functional richness declined with increasing impervious surface, providing evidence for environmental filtering. Community metrics that include abundance were also sensitive to increasing impervious surface coverage: functional divergence decreased while functional evenness increased. These changes demonstrate that increasing impervious surface coverage homogenizes the trait diversity of macroinvertebrate communities in streams, despite differences in initial community composition and stream geomorphology among ecoregions. Community metrics were also more sensitive to changes in the abundance rather than the gain or loss of trait combinations, showing the potential for trait-based approaches to serve as early warning indicators of environmental stress for monitoring and biological assessment programs. © 2017 by the Ecological Society of America.

Measles outbreak investigation in Guji zone of Oromia Region, Ethiopia.

PubMed

Belda, Ketema; Tegegne, Ayesheshem Ademe; Mersha, Amare Mengistu; Bayenessagne, Mekonnen Getahun; Hussein, Ibrahim; Bezabeh, Belay

2017-01-01

Despite the increase of immunization coverage (administrative) of measles in the country, there are widespread outbreaks of measles. In this respect, we investigated one of the outbreaks that occurred in hard to reach kebeles of Guji Zone, Oromia region, to identify the contributing factors that lead to the protracted outbreak of measles. We used a cross-sectional study design to investigate a measles outbreak in Guji zone, Oromia region. Data entry and analysis was performed using EPI-Info version 7.1.0.6 and MS-Microsoft Excel. In three months' time a total of 1059 suspected cases and two deaths were reported from 9 woredas affected by a measles outbreak in Guji zone. The cumulative attack rate of 81/100,000 population and case fatality ratio of 0.2% was recorded. Of these, 821 (77.5%) cases were < 15 years of age, and 742 (70%) were zero doses of measles vaccine. Although, all age groups were affected under five years old were more affected 495 (48%) than any other age groups. In response to the outbreak, an outbreak response immunization was organized at the 11th week of the epidemic, when the epidemic curve started to decline. 6 months to14 years old were targeted for outbreak response immunization and the overall coverage was 97 % (range: 90-103%). Case management with vitamin A supplementation, active case search, and health education was some of the activities carried out to curb the outbreak. We conclude that low routine immunization coverage in conjunction with low access to routine immunization in hard to reach areas, low community awareness in utilization of immunization service, inadequate cold chain management and delivery of a potent vaccine in hard to reach woredas/kebeles were likely contributed to the outbreak that's triggered a broad spread epidemic affecting mostly children without any vaccination. We also figured that the case-based surveillance lacks sensitivity and timely confirmation of the outbreak, which as a result outbreak response immunization were delayed. We recommend establishing reaching every child (REC) strategy in Guji zone with particular emphasis too hard reach areas to enhance the current immunization service, and furthermore to conduct data quality self-assessment or cluster coverage survey to verify the reported high vaccination coverage in some kebeles. We also recommend conducting the second opportunity as a form of supplemental immunization activities in 2-3 year interval or consider the national second dose introduction in the routine immunization system to improve population immunity. We further recommend that there is a need to boost the sensitivity of case-based surveillance system to be able to early detect, confirm and react to future epidemics.

First imaging results from Apertif, a phased-array feed for WSRT

NASA Astrophysics Data System (ADS)

Adams, Elizabeth A.; Adebahr, Björn; de Blok, Willem J. G.; Hess, Kelley M.; Hut, Boudewijn; Lucero, Danielle M.; Maccagni, Filippo; Morganti, Raffaella; Oosterloo, Tom; Staveley-Smith, Lister; van der Hulst, Thijs; Verheijen, Marc; Verstappen, Joris

2017-01-01

Apertif is a phased-array feed for the Westerbork Synthesis Radio Telescope (WSRT), increasing the field of view of the telescope by a factor of twenty-five. In 2017, three legacy surveys will commence: a shallow imaging survey, a medium-deep imaging survey, and a pulsars and fast transients survey. The medium-deep imaging survey will include coverage of the northern Herschel Atlas field, the CVn region, HetDex, and the Perseus-Pisces supercluster. The shallow imaging survey increases overlap with HetDex, has expanded coverage of the Perseus-Pisces supercluster, and includes part of the Zone of Avoidance. Both imaging surveys are coordinating with MaNGA and will have WEAVE follow-up. The imaging surveys will be done in full polarization over the frequency range 1130-1430 MHz, which corresponds to redshifts of z=0-0.256 for neutral hydrogen (HI). The spectral resolution is 12.2 kHz, or an HI velocity resolution of 2.6 km/s at z=0 and 3.2 km/s at z=0.256. The full resolution images will have a beam size of 15"x15"/sin(declination), and tapered data products (i.e., 30" resolution images) will also be available. The shallow survey will cover ~3500 square degrees with a four-sigma HI imaging sensitivity of 2.5x10^20 atoms cm^-2 (20 km/s linewidth) at the highest resolution and a continuum sensitivity of 15 uJy/beam (11 uJy/beam for polarization data). The current plan calls for the medium deep survey to cover 450 square degrees and provide an HI imaging sensitivity of 1.0x10^20 atoms cm^-2 at the highest resolution and a continuum sensitivity of 6 uJy/beam, close to the confusion limit (4 uJy/beam for polarization data, not confusion limited). Up-to-date information on Apertif and the planned surveys can be found at: http://www.apertif.nl.Commissioning of the Apertif instrument is currently underway. Here we present first results from the image commissioning, including the detection of HI absorption plus continuum and HI imaging. These results highlight the data quality that will be achieved for the surveys.

Development of a sensitive, generic and easy to use organophosphate skin disclosure kit.

PubMed

Worek, Franz; Wosar, Andreas; Baumann, Madlen; Thiermann, Horst; Wille, Timo

2017-10-05

Various organophosphorus compounds (OP), primarily the nerve agent VX and other V-agents, are highly toxic to humans after skin exposure. Percutaneous exposure by such OP results in a delayed onset of toxic signs which enables the initiation of specific countermeasures if contamination is detected rapidly. Presently available mobile detection systems can hardly detect skin exposure by low volatile OP. In order to fill this gap an OP skin disclosure kit was developed which should fulfill different requirements, i.e. a high sensitivity, coverage of human toxic OP, easy handling, rapid results, small dimension and weight. The kit includes a cotton swab to sample skin, human AChE as target and chemicals for a color reaction based on the Ellman assay which is recorded by visual inspection. OP is dissolved from the sampler in a test tube filled with phosphate buffer (0.1M, pH 7.4) and incubated with lyophilized human AChE for 1min. The reaction with acetylthiocholine and 5,5'-dithio-bis-2-nitrobenzoic acid (1min) results in a rich yellow color in the absence of OP and in contrast, in transparent or pale yellow buffer in the presence of OP. At the recommended conditions, the limit of detection is 100ng VX and Russian VX and 50ng Chinese VX on plain surface and 200ng VX on rat skin. With activated pesticides, paraoxon and malaoxon, a concentration of ∼10μg can be detected on plain surface. The ready-to-use kit has a weight of 16g and a size of 10×12×1cm. In the end, this kit has the potential to fill a major gap and to enable timely detection of OP skin exposure and initiation of life-saving countermeasures. Copyright © 2017 Elsevier B.V. All rights reserved.

3D plasmonic transducer based on gold nanoparticles produced by laser ablation on silica nanowires

NASA Astrophysics Data System (ADS)

Gontad, F.; Caricato, A. P.; Manera, M. G.; Colombelli, A.; Resta, V.; Taurino, A.; Cesaria, M.; Leo, C.; Convertino, A.; Klini, A.; Perrone, A.; Rella, R.; Martino, M.

2016-05-01

Silica two-dimensional substrates and nanowires (NWs) forests have been successfully decorated with Au nanoparticles (NPs) through laser ablation by using a pulsed ArF excimer laser, for sensor applications. A uniform coverage of both substrate surfaces with NPs has been achieved controlling the number of laser pulses. The annealing of the as-deposited particles resulted in a uniform well-defined distribution of spherical NPs with an increased average diameter up to 25 nm. The deposited samples on silica NWs forest present a very good plasmonic resonance which resulted to be very sensitive to the changes of the environment (ethanol/water solutions with increasing concentration of ethanol) allowing the detection of changes on the second decimal digit of the refractive index, demonstrating its potentiality for further biosensing functionalities.

Process analysis of recycled thermoplasts from consumer electronics by laser-induced plasma spectroscopy.

PubMed

Fink, Herbert; Panne, Ulrich; Niessner, Reinhard

2002-09-01

An experimental setup for direct elemental analysis of recycled thermoplasts from consumer electronics by laser-induced plasma spectroscopy (LIPS, or laser-induced breakdown spectroscopy, LIBS) was realized. The combination of a echelle spectrograph, featuring a high resolution with a broad spectral coverage, with multivariate methods, such as PLS, PCR, and variable subset selection via a genetic algorithm, resulted in considerable improvements in selectivity and sensitivity for this complex matrix. With a normalization to carbon as internal standard, the limits of detection were in the ppm range. A preliminary pattern recognition study points to the possibility of polymer recognition via the line-rich echelle spectra. Several experiments at an extruder within a recycling plant demonstrated successfully the capability of LIPS for different kinds of routine on-line process analysis.

Evidence for high-energy extraterrestrial neutrinos at the IceCube detector.

PubMed

Aartsen, M G; Abbasi, R; Abdou, Y; Ackermann, M; Adams, J; Aguilar, J A; Ahlers, M; Altmann, D; Auffenberg, J; Bai, X; Baker, M; Barwick, S W; Baum, V; Bay, R; Beatty, J J; Bechet, S; Becker Tjus, J; Becker, K-H; Benabderrahmane, M L; BenZvi, S; Berghaus, P; Berley, D; Bernardini, E; Bernhard, A; Bertrand, D; Besson, D Z; Binder, G; Bindig, D; Bissok, M; Blaufuss, E; Blumenthal, J; Boersma, D J; Bohaichuk, S; Bohm, C; Bose, D; Böser, S; Botner, O; Brayeur, L; Bretz, H-P; Brown, A M; Bruijn, R; Brunner, J; Carson, M; Casey, J; Casier, M; Chirkin, D; Christov, A; Christy, B; Clark, K; Clevermann, F; Coenders, S; Cohen, S; Cowen, D F; Cruz Silva, A H; Danninger, M; Daughhetee, J; Davis, J C; Day, M; De Clercq, C; De Ridder, S; Desiati, P; de Vries, K D; de With, M; DeYoung, T; Díaz-Vélez, J C; Dunkman, M; Eagan, R; Eberhardt, B; Eichmann, B; Eisch, J; Ellsworth, R W; Euler, S; Evenson, P A; Fadiran, O; Fazely, A R; Fedynitch, A; Feintzeig, J; Feusels, T; Filimonov, K; Finley, C; Fischer-Wasels, T; Flis, S; Franckowiak, A; Frantzen, K; Fuchs, T; Gaisser, T K; Gallagher, J; Gerhardt, L; Gladstone, L; Glüsenkamp, T; Goldschmidt, A; Golup, G; Gonzalez, J G; Goodman, J A; Góra, D; Grandmont, D T; Grant, D; Groß, A; Ha, C; Haj Ismail, A; Hallen, P; Hallgren, A; Halzen, F; Hanson, K; Heereman, D; Heinen, D; Helbing, K; Hellauer, R; Hickford, S; Hill, G C; Hoffman, K D; Hoffmann, R; Homeier, A; Hoshina, K; Huelsnitz, W; Hulth, P O; Hultqvist, K; Hussain, S; Ishihara, A; Jacobi, E; Jacobsen, J; Jagielski, K; Japaridze, G S; Jero, K; Jlelati, O; Kaminsky, B; Kappes, A; Karg, T; Karle, A; Kelley, J L; Kiryluk, J; Kläs, J; Klein, S R; Köhne, J-H; Kohnen, G; Kolanoski, H; Köpke, L; Kopper, C; Kopper, S; Koskinen, D J; Kowalski, M; Krasberg, M; Krings, K; Kroll, G; Kunnen, J; Kurahashi, N; Kuwabara, T; Labare, M; Landsman, H; Larson, M J; Lesiak-Bzdak, M; Leuermann, M; Leute, J; Lünemann, J; Madsen, J; Maggi, G; Maruyama, R; Mase, K; Matis, H S; McNally, F; Meagher, K; Merck, M; Meures, T; Miarecki, S; Middell, E; Milke, N; Miller, J; Mohrmann, L; Montaruli, T; Morse, R; Nahnhauer, R; Naumann, U; Niederhausen, H; Nowicki, S C; Nygren, D R; Obertacke, A; Odrowski, S; Olivas, A; O'Murchadha, A; Paul, L; Pepper, J A; Pérez de los Heros, C; Pfendner, C; Pieloth, D; Pinat, E; Posselt, J; Price, P B; Przybylski, G T; Rädel, L; Rameez, M; Rawlins, K; Redl, P; Reimann, R; Resconi, E; Rhode, W; Ribordy, M; Richman, M; Riedel, B; Rodrigues, J P; Rott, C; Ruhe, T; Ruzybayev, B; Ryckbosch, D; Saba, S M; Salameh, T; Sander, H-G; Santander, M; Sarkar, S; Schatto, K; Scheriau, F; Schmidt, T; Schmitz, M; Schoenen, S; Schöneberg, S; Schönwald, A; Schukraft, A; Schulte, L; Schulz, O; Seckel, D; Sestayo, Y; Seunarine, S; Shanidze, R; Sheremata, C; Smith, M W E; Soldin, D; Spiczak, G M; Spiering, C; Stamatikos, M; Stanev, T; Stasik, A; Stezelberger, T; Stokstad, R G; Stößl, A; Strahler, E A; Ström, R; Sullivan, G W; Taavola, H; Taboada, I; Tamburro, A; Tepe, A; Ter-Antonyan, S; Tešić, G; Tilav, S; Toale, P A; Toscano, S; Unger, E; Usner, M; van Eijndhoven, N; Van Overloop, A; van Santen, J; Vehring, M; Voge, M; Vraeghe, M; Walck, C; Waldenmaier, T; Wallraff, M; Weaver, Ch; Wellons, M; Wendt, C; Westerhoff, S; Whitehorn, N; Wiebe, K; Wiebusch, C H; Williams, D R; Wissing, H; Wolf, M; Wood, T R; Woschnagg, K; Xu, D L; Xu, X W; Yanez, J P; Yodh, G; Yoshida, S; Zarzhitsky, P; Ziemann, J; Zierke, S; Zoll, M

2013-11-22

We report on results of an all-sky search for high-energy neutrino events interacting within the IceCube neutrino detector conducted between May 2010 and May 2012. The search follows up on the previous detection of two PeV neutrino events, with improved sensitivity and extended energy coverage down to about 30 TeV. Twenty-six additional events were observed, substantially more than expected from atmospheric backgrounds. Combined, both searches reject a purely atmospheric origin for the 28 events at the 4σ level. These 28 events, which include the highest energy neutrinos ever observed, have flavors, directions, and energies inconsistent with those expected from the atmospheric muon and neutrino backgrounds. These properties are, however, consistent with generic predictions for an additional component of extraterrestrial origin.

Spiral CT scanning technique in the detection of aspiration of LEGO foreign bodies.

PubMed

Applegate, K E; Dardinger, J T; Lieber, M L; Herts, B R; Davros, W J; Obuchowski, N A; Maneker, A

2001-12-01

Radiolucent foreign bodies (FBs) such as plastic objects and toys remain difficult to identify on conventional radiographs of the neck and chest. Children may present with a variety of respiratory complaints, which may or may not be due to a FB. To determine whether radiolucent FBs such as plastic LEGOs and peanuts can be seen in the tracheobronchial tree or esophagus using low-dose spiral CT, and, if visible, to determine the optimal CT imaging technique. Multiple spiral sequences were performed while varying the CT parameters and the presence and location of FBs in either the trachea or the esophagus first on a neck phantom and then a cadaver. Sequences were rated by three radiologists blinded to the presence of a FB using a single scoring system. The LEGO was well visualized in the trachea by all three readers (both lung and soft-tissue windowing: combined sensitivity 89 %, combined specificity 89 %) and to a lesser extent in the esophagus (combined sensitivity 31 %, combined specificity 100 %). The peanut was not well visualized (combined sensitivity < 35 %). The optimal technique for visualizing the LEGO was 120 kV, 90 mA, 3-mm collimation, 0.75 s/revolution, and 2.0 pitch. This allowed for coverage of the cadaver tracheobronchial tree (approximately 11 cm) in about 18 s. Although statistical power was low for detecting significant differences, all three readers noted higher average confidence ratings with lung windowing among 18 LEGO-in-trachea scans. Rapid, low-dose spiral CT may be used to visualize LEGO FBs in the airway or esophagus. Peanuts were not well visualized.

First results of a novel Silicon Drift Detector array designed for low energy X-ray fluorescence spectroscopy

NASA Astrophysics Data System (ADS)

Rachevski, Alexandre; Ahangarianabhari, Mahdi; Bellutti, Pierluigi; Bertuccio, Giuseppe; Brigo, Elena; Bufon, Jernej; Carrato, Sergio; Castoldi, Andrea; Cautero, Giuseppe; Fabiani, Sergio; Giacomini, Gabriele; Gianoncelli, Alessandra; Giuressi, Dario; Guazzoni, Chiara; Kourousias, George; Liu, Chang; Menk, Ralf Hendrik; Montemurro, Giuseppe Vito; Picciotto, Antonino; Piemonte, Claudio; Rashevskaya, Irina; Shi, Yongbiao; Stolfa, Andrea; Vacchi, Andrea; Zampa, Gianluigi; Zampa, Nicola; Zorzi, Nicola

2016-07-01

We developed a trapezoidal shaped matrix with 8 cells of Silicon Drift Detectors (SDD) featuring a very low leakage current (below 180 pA/cm2 at 20 °C) and a shallow uniformly implanted p+ entrance window that enables sensitivity down to few hundreds of eV. The matrix consists of a completely depleted volume of silicon wafer subdivided into 4 square cells and 4 half-size triangular cells. The energy resolution of a single square cell, readout by the ultra-low noise SIRIO charge sensitive preamplifier, is 158 eV FWHM at 5.9 keV and 0 °C. The total sensitive area of the matrix is 231 mm2 and the wafer thickness is 450 μm. The detector was developed in the frame of the INFN R&D project ReDSoX in collaboration with FBK, Trento. Its trapezoidal shape was chosen in order to optimize the detection geometry for the experimental requirements of low energy X-ray fluorescence (LEXRF) spectroscopy, aiming at achieving a large detection angle. We plan to exploit the complete detector at the TwinMic spectromicroscopy beamline at the Elettra Synchrotron (Trieste, Italy). The complete system, composed of 4 matrices, increases the solid angle coverage of the isotropic photoemission hemisphere about 4 times over the present detector configuration. We report on the layout of the SDD matrix and of the experimental set-up, as well as the spectroscopic performance measured both in the laboratory and at the experimental beamline.

A global hydrographic array for early detection of floods and droughts

NASA Astrophysics Data System (ADS)

Brakenridge, G.; Nghiem, S.; Caquard, S.

An array of over 700 20 km-long river gaging reaches, distributed world-wide, is imaged by the SeaWinds radar scatterometer aboard QuikSCAT every 2.5 days. Strongly negative HH/VV polarity ratios indicate large amounts of surface water. We set individual reach thresholds so that the transition from bankfull to overbank river flow can be identified according to changes in this ratio. Similarly, the wide-swath MODIS optical sensors provide frequent repeat coverage of the reaches at much higher spatial resolution (250 m). In this case, several reach water surface area thresholds can be identified: low flow or drought conditions, normal in-channel flow, overbank flow, and extreme flood conditions. Sustained data collection for the reaches by both sensors allows the radar response to changing surface water to be defined, and allows evaluation of the sensitivity of the MODIS data to river discharge changes. New approaches, such as ``unmixing'' analysis of mixed water/land MODIS pixels can extend detection limits to smaller rivers and streams. It is now possible for wide-area, frequent revisit terrestrial remote sensing to provide human society with early warning of both floods and droughts and by direct observation of the runoff component of the Earth's hydrologic cycle. Examples of both radar and optical approaches towards this end are at the web sites below: http://www.dartmouth.edu/˜ floods/Modisrapidresponse.html http://www.dartmouth.edu/˜ floods/sensorweb/SensorWebindex.html http://www.dartmouth.edu/˜ floods/Quikscat/Regional2/CurrentTisza.jpg} In particular, early flood detection results are obtained over an extensive region in eastern Europe including the Tisza River basin, Romania, Hungary, and adjacent nations. Flood detection maps are updated weekly at the web site. The combination of QuikSCAT and MODIS takes advantage of the large-area coverage of these sensors together with the high temporal resolution of QuikSCAT and the high spatial resolution of MODIS. Such capabilities are also appropriate for early flood detection in Asian monsoon regions including India, Pakistan, Bangladesh, China, and southeast Asia.

High Throughput Transcriptomics @ USEPA (Toxicology ...

EPA Pesticide Factsheets

The ideal chemical testing approach will provide complete coverage of all relevant toxicological responses. It should be sensitive and specific It should identify the mechanism/mode-of-action (with dose-dependence). It should identify responses relevant to the species of interest. Responses should ideally be translated into tissue-, organ-, and organism-level effects. It must be economical and scalable. Using a High Throughput Transcriptomics platform within US EPA provides broader coverage of biological activity space and toxicological MOAs and helps fill the toxicological data gap. Slide presentation at the 2016 ToxForum on using High Throughput Transcriptomics at US EPA for broader coverage biological activity space and toxicological MOAs.

Public health surveillance and infectious disease detection.

PubMed

Morse, Stephen S

2012-03-01

Emerging infectious diseases, such as HIV/AIDS, SARS, and pandemic influenza, and the anthrax attacks of 2001, have demonstrated that we remain vulnerable to health threats caused by infectious diseases. The importance of strengthening global public health surveillance to provide early warning has been the primary recommendation of expert groups for at least the past 2 decades. However, despite improvements in the past decade, public health surveillance capabilities remain limited and fragmented, with uneven global coverage. Recent initiatives provide hope of addressing this issue, and new technological and conceptual advances could, for the first time, place capability for global surveillance within reach. Such advances include the revised International Health Regulations (IHR 2005) and the use of new data sources and methods to improve global coverage, sensitivity, and timeliness, which show promise for providing capabilities to extend and complement the existing infrastructure. One example is syndromic surveillance, using nontraditional and often automated data sources. Over the past 20 years, other initiatives, including ProMED-mail, GPHIN, and HealthMap, have demonstrated new mechanisms for acquiring surveillance data. In 2009 the U.S. Agency for International Development (USAID) began the Emerging Pandemic Threats (EPT) program, which includes the PREDICT project, to build global capacity for surveillance of novel infections that have pandemic potential (originating in wildlife and at the animal-human interface) and to develop a framework for risk assessment. Improved understanding of factors driving infectious disease emergence and new technological capabilities in modeling, diagnostics and pathogen identification, and communications, such as using the increasing global coverage of cellphones for public health surveillance, can further enhance global surveillance.

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data

PubMed Central

Li, Ben; Petit III, Robert A.; Qin, Zhaohui S.; Darrow, Lyndsey

2016-01-01

In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at >100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain >87% sensitivity and >94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S. aureus at genome coverage >0.025. In both projects, CC8 and CC30 were the most common S. aureus clonal complexes encountered. We found evidence that the subtype composition at different body sites of the same individual were more similar than random sampling and more limited evidence that certain body sites were enriched for particular subtypes. One surprising finding was the apparent high frequency of CC398, a lineage often associated with livestock, in samples from the tongue dorsum. Epidemiologic analysis of the HMP subject population suggested that high BMI (body mass index) and health insurance are possibly associated with S. aureus carriage but there was limited power to identify factors linked to carriage of even the most common subtype. In the NYC subway data, we found a small signal of geographic distance affecting subtype clustering but other unknown factors influence taxonomic distribution of the species around the city. PMID:27781166

Strategies for minimizing sample size for use in airborne LiDAR-based forest inventory

USGS Publications Warehouse

Junttila, Virpi; Finley, Andrew O.; Bradford, John B.; Kauranne, Tuomo

2013-01-01

Recently airborne Light Detection And Ranging (LiDAR) has emerged as a highly accurate remote sensing modality to be used in operational scale forest inventories. Inventories conducted with the help of LiDAR are most often model-based, i.e. they use variables derived from LiDAR point clouds as the predictive variables that are to be calibrated using field plots. The measurement of the necessary field plots is a time-consuming and statistically sensitive process. Because of this, current practice often presumes hundreds of plots to be collected. But since these plots are only used to calibrate regression models, it should be possible to minimize the number of plots needed by carefully selecting the plots to be measured. In the current study, we compare several systematic and random methods for calibration plot selection, with the specific aim that they be used in LiDAR based regression models for forest parameters, especially above-ground biomass. The primary criteria compared are based on both spatial representativity as well as on their coverage of the variability of the forest features measured. In the former case, it is important also to take into account spatial auto-correlation between the plots. The results indicate that choosing the plots in a way that ensures ample coverage of both spatial and feature space variability improves the performance of the corresponding models, and that adequate coverage of the variability in the feature space is the most important condition that should be met by the set of plots collected.

Whole-Body Single-Bed Time-of-Flight RPC-PET: Simulation of Axial and Planar Sensitivities With NEMA and Anthropomorphic Phantoms

NASA Astrophysics Data System (ADS)

Crespo, Paulo; Reis, João; Couceiro, Miguel; Blanco, Alberto; Ferreira, Nuno C.; Marques, Rui Ferreira; Martins, Paulo; Fonte, Paulo

2012-06-01

A single-bed, whole-body positron emission tomograph based on resistive plate chambers has been proposed (RPC-PET). An RPC-PET system with an axial field-of-view (AFOV) of 2.4 m has been shown in simulation to have higher system sensitivity using the NEMA NU2-1994 protocol than commercial PET scanners. However, that protocol does not correlate directly with lesion detectability. The latter is better correlated with the planar (slice) sensitivity, obtained with a NEMA NU2-2001 line-source phantom. After validation with published data for the GE Advance, Siemens TruePoint and TrueV, we study by simulation their axial sensitivity profiles, comparing results with RPC-PET. Planar sensitivities indicate that RPC-PET is expected to outperform 16-cm (22-cm) AFOV scanners by a factor 5.8 (3.0) for 70-cm-long scans. For 1.5-m scans (head to mid-legs), the sensitivity gain increases to 11.7 (6.7). Yet, PET systems with large AFOV provide larger coverage but also larger attenuation in the object. We studied these competing effects with both spherical- and line-sources immersed in a 27-cm-diameter water cylinder. For 1.5-m-long scans, the planar sensitivity drops one order of magnitude in all scanners, with RPC-PET outperforming 16-cm (22-cm) AFOV scanners by a factor 9.2 (5.3) without considering the TOF benefit. A gain in the effective sensitivity is expected with TOF iterative reconstruction. Finally, object scatter in an anthropomorphic phantom is similar for RPC-PET and modern, scintillator-based scanners, although RPC-PET benefits further if its TOF information is utilized to exclude scatter events occurring outside the anthropomorphic phantom.

Unblinding the dark matter blind spots

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

Han, Tao; Kling, Felix; Su, Shufang

The dark matter (DM) blind spots in the Minimal Supersymmetric Standard Model (MSSM) refer to the parameter regions where the couplings of the DM particles to the $Z$-boson or the Higgs boson are almost zero, leading to vanishingly small signals for the DM direct detections. In this paper, we carry out comprehensive analyses for the DM searches under the blind-spot scenarios in MSSM. Guided by the requirement of acceptable DM relic abundance, we explore the complementary coverage for the theory parameters at the LHC, the projection for the future underground DM direct searches, and the indirect searches from the relicmore » DM annihilation into photons and neutrinos. We find that (i) the spin-independent (SI) blind spots may be rescued by the spin-dependent (SD) direct detection in the future underground experiments, and possibly by the indirect DM detections from IceCube and SuperK neutrino experiments; (ii) the detection of gamma rays from Fermi-LAT may not reach the desirable sensitivity for searching for the DM blind-spot regions; (iii) the SUSY searches at the LHC will substantially extend the discovery region for the blind-spot parameters. As a result, the dark matter blind spots thus may be unblinded with the collective efforts in future DM searches.« less

Unblinding the dark matter blind spots

DOE PAGES

Han, Tao; Kling, Felix; Su, Shufang; ...

2017-02-10

The dark matter (DM) blind spots in the Minimal Supersymmetric Standard Model (MSSM) refer to the parameter regions where the couplings of the DM particles to the $Z$-boson or the Higgs boson are almost zero, leading to vanishingly small signals for the DM direct detections. In this paper, we carry out comprehensive analyses for the DM searches under the blind-spot scenarios in MSSM. Guided by the requirement of acceptable DM relic abundance, we explore the complementary coverage for the theory parameters at the LHC, the projection for the future underground DM direct searches, and the indirect searches from the relicmore » DM annihilation into photons and neutrinos. We find that (i) the spin-independent (SI) blind spots may be rescued by the spin-dependent (SD) direct detection in the future underground experiments, and possibly by the indirect DM detections from IceCube and SuperK neutrino experiments; (ii) the detection of gamma rays from Fermi-LAT may not reach the desirable sensitivity for searching for the DM blind-spot regions; (iii) the SUSY searches at the LHC will substantially extend the discovery region for the blind-spot parameters. As a result, the dark matter blind spots thus may be unblinded with the collective efforts in future DM searches.« less

MRI monitoring of focused ultrasound sonications near metallic hardware.

PubMed

Weber, Hans; Ghanouni, Pejman; Pascal-Tenorio, Aurea; Pauly, Kim Butts; Hargreaves, Brian A

2018-07-01

To explore the temperature-induced signal change in two-dimensional multi-spectral imaging (2DMSI) for fast thermometry near metallic hardware to enable MR-guided focused ultrasound surgery (MRgFUS) in patients with implanted metallic hardware. 2DMSI was optimized for temperature sensitivity and applied to monitor focus ultrasound surgery (FUS) sonications near metallic hardware in phantoms and ex vivo porcine muscle tissue. Further, we evaluated its temperature sensitivity for in vivo muscle in patients without metallic hardware. In addition, we performed a comparison of temperature sensitivity between 2DMSI and conventional proton-resonance-frequency-shift (PRFS) thermometry at different distances from metal devices and different signal-to-noise ratios (SNR). 2DMSI thermometry enabled visualization of short ultrasound sonications near metallic hardware. Calibration using in vivo muscle yielded a constant temperature sensitivity for temperatures below 43 °C. For an off-resonance coverage of ± 6 kHz, we achieved a temperature sensitivity of 1.45%/K, resulting in a minimum detectable temperature change of ∼2.5 K for an SNR of 100 with a temporal resolution of 6 s per frame. The proposed 2DMSI thermometry has the potential to allow MR-guided FUS treatments of patients with metallic hardware and therefore expand its reach to a larger patient population. Magn Reson Med 80:259-271, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Do Medicaid benefit expansions have teeth? The effect of Medicaid adult dental coverage on the use of dental services and oral health.

PubMed

Decker, Sandra L; Lipton, Brandy J

2015-12-01

This article examines the effect of Medicaid adult dental coverage on use of dental care and dental health outcomes using state-level variation in dental coverage during 2000-2012. Our findings imply that dental coverage is associated with an increase in the likelihood of a recent dental visit, with the size of the effect increasing with Medicaid payment rates to dentists, and a reduction in the likelihood of untreated dental caries. We are among the first to detect an effect of Medicaid coverage on a clinical health outcome other than mortality. These findings may have implications for states expanding Medicaid coverage to adults with incomes of up to 138% of the federal poverty threshold under the Affordable Care Act as most of these states offer an adult dental benefit. Copyright © 2015 Elsevier B.V. All rights reserved.

High Sensitivity Combined with Extended Structural Coverage of Labile Compounds via Nanoelectrospray Ionization at Subambient Pressures

DOE PAGES

Cox, Jonathan T.; Kronewitter, Scott R.; Shukla, Anil K.; ...

2014-09-15

Subambient pressure ionization with nanoelectrospray (SPIN) has proven to be effective in producing ions with high efficiency and transmitting them to low pressures for high sensitivity mass spectrometry (MS) analysis. Here we present evidence that not only does the SPIN source improve MS sensitivity but also allows for gentler ionization conditions. The gentleness of a conventional heated capillary electrospray ionization (ESI) source and the SPIN source was compared by the liquid chromatography mass spectrometry (LC-MS) analysis of colominic acid. Colominic acid is a mixture of sialic acid polymers of different lengths containing labile glycosidic linkages between monomer units necessitating amore » gentle ion source. By coupling the SPIN source with high resolution mass spectrometry and using advanced data processing tools, we demonstrate much extended coverage of sialic acid polymer chains as compared to using the conventional ESI source. Additionally we show that SPIN-LC-MS is effective in elucidating polymer features with high efficiency and high sensitivity previously unattainable by the conventional ESI-LC-MS methods.« less

Metabolite Analysis and Histology on the Exact Same Tissue: Comprehensive Metabolomic Profiling and Metabolic Classification of Prostate Cancer

NASA Astrophysics Data System (ADS)

Huan, Tao; Troyer, Dean A.; Li, Liang

2016-08-01

We report a method of metabolomic profiling of intact tissue based on molecular preservation by extraction and fixation (mPREF) and high-performance chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS). mPREF extracts metabolites by aqueous methanol from tissue biopsies without altering tissue architecture and thus conventional histology can be performed on the same tissue. In a proof-of-principle study, we applied dansylation LC-MS to profile the amine/phenol submetabolome of prostate needle biopsies from 25 patient samples derived from 16 subjects. 2900 metabolites were consistently detected in more than 50% of the samples. This unprecedented coverage allowed us to identify significant metabolites for differentiating tumor and normal tissues. The panel of significant metabolites was refined using 36 additional samples from 18 subjects. Receiver Operating Characteristic (ROC) analysis showed area-under-the-curve (AUC) of 0.896 with sensitivity of 84.6% and specificity of 83.3% using 7 metabolites. A blind study of 24 additional validation samples gave a specificity of 90.9% at the same sensitivity of 84.6%. The mPREF extraction can be readily implemented into the existing clinical workflow. Our method of combining mPREF with CIL LC-MS offers a powerful and convenient means of performing histopathology and discovering or detecting metabolite biomarkers in the same tissue biopsy.

N-mixture models for estimating population size from spatially replicated counts

USGS Publications Warehouse

Royle, J. Andrew

2004-01-01

Spatial replication is a common theme in count surveys of animals. Such surveys often generate sparse count data from which it is difficult to estimate population size while formally accounting for detection probability. In this article, i describe a class of models (n-mixture models) which allow for estimation of population size from such data. The key idea is to view site-specific population sizes, n, as independent random variables distributed according to some mixing distribution (e.g., Poisson). Prior parameters are estimated from the marginal likelihood of the data, having integrated over the prior distribution for n. Carroll and lombard (1985, journal of american statistical association 80, 423-426) proposed a class of estimators based on mixing over a prior distribution for detection probability. Their estimator can be applied in limited settings, but is sensitive to prior parameter values that are fixed a priori. Spatial replication provides additional information regarding the parameters of the prior distribution on n that is exploited by the n-mixture models and which leads to reasonable estimates of abundance from sparse data. A simulation study demonstrates superior operating characteristics (bias, confidence interval coverage) of the n-mixture estimator compared to the caroll and lombard estimator. Both estimators are applied to point count data on six species of birds illustrating the sensitivity to choice of prior on p and substantially different estimates of abundance as a consequence.

Photodecomposition of Mo(CO)[sub 6]/Si(111) 7[times]7: CO state-resolved evidence for excited state relaxation and quenching

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

Chu, P.M.; Buntin, S.A.; Richter, L.J.

1994-08-15

State-resolved detection techniques have been used to characterize the ultraviolet photodecomposition dynamics of Mo(CO)[sub 6] on Si(111) 7[times]7 at 100 K. Details of the excitation/fragmentation mechanism including adsorbate energy transfer were examined by measuring the cross sections and the internal and translational energies of the photoejected CO from submonolayer through multilayer coverage regimes. The CO energy distributions are found to be independent of Mo(CO)[sub 6] coverage, and can be characterized by two components with markedly different mean energies. In contrast to the coverage independence of the measured energy disposal, the cross section was found to decrease by a factor ofmore » 3 from multilayer coverages to submonolayer coverages.« less

Simulation of the spatial frequency-dependent sensitivities of Acoustic Emission sensors

NASA Astrophysics Data System (ADS)

Boulay, N.; Lhémery, A.; Zhang, F.

2018-05-01

Typical configurations of nondestructive testing by Acoustic Emission (NDT/AE) make use of multiple sensors positioned on the tested structure for detecting evolving flaws and possibly locating them by triangulation. Sensors positions must be optimized for ensuring global coverage sensitivity to AE events and minimizing their number. A simulator of NDT/AE is under development to provide help with designing testing configurations and with interpreting measurements. A global model performs sub-models simulating the various phenomena taking place at different spatial and temporal scales (crack growth, AE source and radiation, wave propagation in the structure, reception by sensors). In this context, accurate modelling of sensors behaviour must be developed. These sensors generally consist of a cylindrical piezoelectric element of radius approximately equal to its thickness, without damping and bonded to its case. Sensors themselves are bonded to the structure being tested. Here, a multiphysics finite element simulation tool is used to study the complex behaviour of AE sensor. The simulated behaviour is shown to accurately reproduce the high-amplitude measured contributions used in the AE practice.

Remote sensing of life: polarimetric signatures of photosynthetic pigments as sensitive biomarkers

NASA Astrophysics Data System (ADS)

Berdyugina, Svetlana V.; Kuhn, Jeff R.; Harrington, David M.; Šantl-Temkiv, Tina; Messersmith, E. John

2016-01-01

We develop a polarimetry-based remote-sensing method for detecting and identifying life forms in distant worlds and distinguishing them from non-biological species. To achieve this we have designed and built a bio-polarimetric laboratory experiment BioPol for measuring optical polarized spectra of various biological and non-biological samples. Here we focus on biological pigments, which are common in plants and bacteria that employ them either for photosynthesis or for protection against reactive oxygen species. Photosynthesis, which provides organisms with the ability to use light as a source of energy, emerged early in the evolution of life on Earth. The ability to harvest such a significant energy resource could likely also develop on habited exoplanets. Thus, we investigate the detectability of biomolecules that can capture photons of particular wavelengths and contribute to storing their energy in chemical bonds. We have carried out laboratory spectropolarimetric measurements of a representative sample of plants containing various amounts of pigments such as chlorophyll, carotenoids and others. We have also measured a variety of non-biological samples (sands, rocks). Using our lab measurements, we have modelled intensity and polarized spectra of Earth-like planets having different surface coverage by photosynthetic organisms, deserted land and ocean, as well as clouds. Our results demonstrate that linearly polarized spectra provide very sensitive and rather unambiguous detection of photosynthetic pigments of various kinds. Our work paves the path towards analogous measurements of microorganisms and remote sensing of microbial ecology on the Earth and of extraterrestrial life on other planets and moons.

Scattered Light Polarimetry of Exoplanets

NASA Astrophysics Data System (ADS)

Wiktorowicz, S.

2014-12-01

The last decade has witnessed an explosion in atmospheric characterization of spatially unresolved exoplanets using transmission spectra of transiting planets, but understanding has been hampered by degeneracies resolvable through blue optical observations. Here, scattered light is more important than the Wien tail of re-radiated thermal emission. Therefore, the next frontier in exoplanet characterization lies in the direct detection of scattered light. The polarization state of starlight scattered by a planetary atmosphere distinguishes it from the direct light from the host star, and the inherently differential nature of polarimetry reduces systematic effects to the point where ground-based detections are possible. Furthermore, polarimetry is uniquely sensitive to the size distribution, shape, and chemical composition of atmospheric cloud particles as well as to the scattering optical depth. I will review the current state of exoplanet polarimetry, which is dominated not by photon noise but by non-Gaussian systematic effects. Ground-based detection of order ten exoplanet photons relative to the host star's million requires dense orbital phase coverage and therefore long observing programs. However, variability inherent in the host star, interstellar medium, Earth's atmosphere, the telescope, and the instrument at all timescales must be measured and subtracted in order to definitively uncover scattered light from the exoplanet. While polarimetry is in principle sensitive to exoplanets regardless of orbital inclination, repeated observations of transiting exoplanet systems during secondary eclipse events are required to measure the polarimetric variability of the system that cannot be due to the planet. The emergence of scattered light polarimetry as a robust tool for the study of exoplanet atmospheres, and eventually surfaces, therefore requires diligent attention to the role of systematic effects.

Shifted Transversal Design smart-pooling for high coverage interactome mapping

PubMed Central

Xin, Xiaofeng; Rual, Jean-François; Hirozane-Kishikawa, Tomoko; Hill, David E.; Vidal, Marc; Boone, Charles; Thierry-Mieg, Nicolas

2009-01-01

“Smart-pooling,” in which test reagents are multiplexed in a highly redundant manner, is a promising strategy for achieving high efficiency, sensitivity, and specificity in systems-level projects. However, previous applications relied on low redundancy designs that do not leverage the full potential of smart-pooling, and more powerful theoretical constructions, such as the Shifted Transversal Design (STD), lack experimental validation. Here we evaluate STD smart-pooling in yeast two-hybrid (Y2H) interactome mapping. We employed two STD designs and two established methods to perform ORFeome-wide Y2H screens with 12 baits. We found that STD pooling achieves similar levels of sensitivity and specificity as one-on-one array-based Y2H, while the costs and workloads are divided by three. The screening-sequencing approach is the most cost- and labor-efficient, yet STD identifies about twofold more interactions. Screening-sequencing remains an appropriate method for quickly producing low-coverage interactomes, while STD pooling appears as the method of choice for obtaining maps with higher coverage. PMID:19447967

Structured product labeling improves detection of drug-intolerance issues.

PubMed

Schadow, Gunther

2009-01-01

This study sought to assess the value of the Health Level 7/U.S. Food and Drug Administration Structured Product Labeling (SPL) drug knowledge representation standard and its associated terminology sources for drug-intolerance (allergy) decision support in computerized provider order entry (CPOE) systems. The Regenstrief Institute CPOE drug-intolerance issue detection system and its knowledge base was compared with a method based on existing SPL label content enriched with knowledge sources used with SPL (NDF-RT/MeSH). Both methods were applied to a large set of drug-intolerance (allergy) records, drug orders, and medication dispensing records covering >50,000 patients over 30 years. The number of drug-intolerance issues detected by both methods was counted, as well as the number of patients with issues, number of distinct drugs, and number of distinct intolerances. The difference between drug-intolerance issues detected or missed by either method was qualitatively analyzed. Although <70% of terms were mapped to SPL, the new approach detected four times as many drug-intolerance issues on twice as many patients. The SPL-based approach is more sensitive and suggests that mapping local dictionaries to SPL, and enhancing the depth and breadth of coverage of SPL content are worth accelerating. The study also highlights specificity problems known to trouble drug-intolerance decision support and suggests how terminology and methods of recording drug intolerances could be improved.

Development of a reverse transcription quantitative polymerase chain reaction-based assay for broad coverage detection of African and Asian Zika virus lineages.

PubMed

Yang, Yang; Wong, Gary; Ye, Baoguo; Li, Shihua; Li, Shanqin; Zheng, Haixia; Wang, Qiang; Liang, Mifang; Gao, George F; Liu, Lei; Liu, Yingxia; Bi, Yuhai

2017-06-01

The Zika virus (ZIKV) is an arbovirus that has spread rapidly worldwide within recent times. There is accumulating evidence that associates ZIKV infections with Guillain-Barré Syndrome (GBS) and microcephaly in humans. The ZIKV is genetically diverse and can be separated into Asian and African lineages. A rapid, sensitive, and specific assay is needed for the detection of ZIKV across various pandemic regions. So far, the available primers and probes do not cover the genetic diversity and geographic distribution of all ZIKV strains. To this end, we have developed a one-step quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay based on conserved sequences in the ZIKV envelope (E) gene. The detection limit of the assay was determined to be five RNA transcript copies and 2.94 × 10 -3 50% tissue culture infectious doses (TCID 50 ) of live ZIKV per reaction. The assay was highly specific and able to detect five different ZIKV strains covering the Asian and African lineages without nonspecific amplification, when tested against other flaviviruses. The assay was also successful in testing for ZIKV in clinical samples. Our assay represents an improvement over the current methods available for the detection ZIKV and would be valuable as a diagnostic tool in various pandemic regions.

Structured Product Labeling Improves Detection of Drug-intolerance Issues

PubMed Central

Schadow, Gunther

2009-01-01

Objectives This study sought to assess the value of the Health Level 7/U.S. Food and Drug Administration Structured Product Labeling (SPL) drug knowledge representation standard and its associated terminology sources for drug-intolerance (allergy) decision support in computerized provider order entry (CPOE) systems. Design The Regenstrief Institute CPOE drug-intolerance issue detection system and its knowledge base was compared with a method based on existing SPL label content enriched with knowledge sources used with SPL (NDF-RT/MeSH). Both methods were applied to a large set of drug-intolerance (allergy) records, drug orders, and medication dispensing records covering >50,000 patients over 30 years. Measurements The number of drug-intolerance issues detected by both methods was counted, as well as the number of patients with issues, number of distinct drugs, and number of distinct intolerances. The difference between drug-intolerance issues detected or missed by either method was qualitatively analyzed. Results Although <70% of terms were mapped to SPL, the new approach detected four times as many drug-intolerance issues on twice as many patients. Conclusion The SPL-based approach is more sensitive and suggests that mapping local dictionaries to SPL, and enhancing the depth and breadth of coverage of SPL content are worth accelerating. The study also highlights specificity problems known to trouble drug-intolerance decision support and suggests how terminology and methods of recording drug intolerances could be improved. PMID:18952933

A large high-efficiency multi-layered Micromegas thermal neutron detector

NASA Astrophysics Data System (ADS)

Tsiledakis, G.; Delbart, A.; Desforge, D.; Giomataris, I.; Menelle, A.; Papaevangelou, T.

2017-09-01

Due to the so-called 3He shortage crisis, many detection techniques used nowadays for thermal neutrons are based on alternative converters. Thin films of 10B or 10B4C are used to convert neutrons into ionizing particles which are subsequently detected in gas proportional counters, but only for small or medium sensitive areas so far. The micro-pattern gaseous detector Micromegas has been developed for several years in Saclay and is used in a wide variety of neutron experiments combining high accuracy, high rate capability, excellent timing properties and robustness. We propose here a large high-efficiency Micromegas-based neutron detector with several 10B4C thin layers mounted inside the gas volume for thermal neutron detection. The principle and the fabrication of a single detector unit prototype with overall dimension of ~ 15 × 15 cm2 and a flexibility of modifying the number of layers of 10B4C neutron converters are described and simulated results are reported, demonstrating that typically five 10B4C layers of 1-2 μm thickness can lead to a detection efficiency of 20-40% for thermal neutrons and a spatial resolution of sub-mm. The design is well adapted to large sizes making possible the construction of a mosaic of several such detector units with a large area coverage and a high detection efficiency, showing the good potential of this novel technique.

Shape-based retrieval of CNV regions in read coverage data.

PubMed

Hong, Sangkyun; Yoon, Jeehee; Hong, Dongwan; Lee, Unjoo; Kim, Baeksop; Park, Sanghyun

2014-01-01

This study proposes a novel copy number variation (CNV) detection method, CNV_shape, based on variations in the shape of the read coverage data which are obtained from millions of short reads aligned to a reference sequence. The proposed method carries out two transforms, mean shift transform and mean slope transform, to extract the shape of a CNV more precisely from real human data, which are vulnerable to experimental and biological noises. The mean shift transform is a procedure for gaining a preliminary estimation of the CNVs by statistically evaluating moving averages of given read coverage data. The mean slope transform extracts candidate CNVs by filtering out non-stationary sub-regions from each of the primary CNVs pre-estimated in the mean shift procedure. Each of the candidate CNVs is merged with neighbours depending on the merging score to be finally identified as a putative CNV, where the merging score is estimated by the ratio of the positions with non-zero values of the mean shift transform to the total length of the region including two neighbouring candidate CNVs and the interval between them. The proposed CNV detection method was validated experimentally with simulated data and real human data. The simulated data with coverage in the range of 1x to 10x were generated for various sampling sizes and p-values. Five individual human genomes were used as real human data. The results show that relatively small CNVs (> 1 kbp) can be detected from low coverage (> 1.7x) data. The results also reveal that, in contrast to conventional methods, performance improvement from 8.18 to 87.90% was achieved in CNV_shape. The outcomes suggest that the proposed method is very effective in reducing noises inherent in real data as well as in detecting CNVs of various sizes and types.

Health and Economic Implications of National Treatment Coverage for Cardiovascular Disease in India: Cost-Effectiveness Analysis.

PubMed

Basu, Sanjay; Bendavid, Eran; Sood, Neeraj

2015-11-01

Whether to cover cardiovascular disease costs is an increasingly pressing question for low- and middle-income countries. We sought to identify the impact of expanding national insurance to cover primary prevention, secondary prevention, and tertiary treatment for cardiovascular disease in India. We incorporated data from coverage experiments into a validated microsimulation model of myocardial infarction and stroke in India to evaluate the cost-effectiveness of alternate coverage strategies. Coverage of primary prevention alone saved 3.6 million disability-adjusted life-years (DALY) per annum at an incremental cost-effectiveness ratio of $469 per DALY averted when compared with the status quo of no coverage. Coverage of primary and secondary preventions was dominated by a strategy of covering primary prevention and tertiary treatment, which prevented 6.6 million DALYs at an incremental cost-effectiveness ratio of $2241 per DALY averted, when compared with that of primary prevention alone. The combination of all 3 categories yielded the greatest impact at an incremental cost per DALY averted of $5588 when compared with coverage of primary prevention plus tertiary treatment. When compared with the status quo of no coverage, coverage of all 3 categories of prevention/treatment yielded an incremental cost-effectiveness ratio of $1331 per DALY averted. In sensitivity analyses, coverage of primary preventive treatments remained cost-effective even if adherence and access to therapy were low, but tertiary coverage would require avoiding unnecessary procedures to remain cost-effective. Coverage of all 3 major types of cardiovascular treatment would be expected to have high impact and reasonable cost-effectiveness in India across a broad spectrum of access and adherence levels. © 2015 American Heart Association, Inc.

78 FR 35262 - Detection and Avoidance of Counterfeit Electronic Parts

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-12

... DEPARTMENT OF DEFENSE Defense Acquisition Regulations System [DFARS Case 2012-D055] Detection and Avoidance of Counterfeit Electronic Parts AGENCY: Defense Acquisition Regulations System, Department of... detection and avoidance coverage proposed to be included in the Defense Federal Acquisition Regulation...

A testing-coverage software reliability model considering fault removal efficiency and error generation

PubMed Central

Li, Qiuying; Pham, Hoang

2017-01-01

In this paper, we propose a software reliability model that considers not only error generation but also fault removal efficiency combined with testing coverage information based on a nonhomogeneous Poisson process (NHPP). During the past four decades, many software reliability growth models (SRGMs) based on NHPP have been proposed to estimate the software reliability measures, most of which have the same following agreements: 1) it is a common phenomenon that during the testing phase, the fault detection rate always changes; 2) as a result of imperfect debugging, fault removal has been related to a fault re-introduction rate. But there are few SRGMs in the literature that differentiate between fault detection and fault removal, i.e. they seldom consider the imperfect fault removal efficiency. But in practical software developing process, fault removal efficiency cannot always be perfect, i.e. the failures detected might not be removed completely and the original faults might still exist and new faults might be introduced meanwhile, which is referred to as imperfect debugging phenomenon. In this study, a model aiming to incorporate fault introduction rate, fault removal efficiency and testing coverage into software reliability evaluation is developed, using testing coverage to express the fault detection rate and using fault removal efficiency to consider the fault repair. We compare the performance of the proposed model with several existing NHPP SRGMs using three sets of real failure data based on five criteria. The results exhibit that the model can give a better fitting and predictive performance. PMID:28750091

Nanostructuring of Biosensing Electrodes with Nanodiamonds for Antibody Immobilization

PubMed Central

2015-01-01

While chemical vapor deposition of diamond films is currently cost prohibitive for biosensor construction, in this paper, we show that sonication-assisted nanostructuring of biosensing electrodes with nanodiamonds (NDs) allows harnessing the hydrolytic stability of the diamond biofunctionalization chemistry for real-time continuous sensing, while improving the detector sensitivity and stability. We find that the higher surface coverages were important for improved bacterial capture and can be achieved through proper choice of solvent, ND concentration, and seeding time. A mixture of methanol and dimethyl sulfoxide provides the highest surface coverage (33.6 ± 3.4%) for the NDs with positive zeta-potential, compared to dilutions of dimethyl sulfoxide with acetone, ethanol, isopropyl alcohol, or water. Through impedance spectroscopy of ND-seeded interdigitated electrodes (IDEs), we found that the ND seeds serve as electrically conductive islands only a few nanometers apart. Also we show that the seeded NDs are amply hydrogenated to be decorated with antibodies using the UV-alkene chemistry, and higher bacterial captures can be obtained compared to our previously reported work with diamond films. When sensing bacteria from 106 cfu/mL E. coliO157:H7, the resistance to charge transfer at the IDEs decreased by ∼38.8%, which is nearly 1.5 times better than that reported previously using redox probes. Further in the case of 108 cfu/mL E. coliO157:H7, the charge transfer resistance changed by ∼46%, which is similar to the magnitude of improvement reported using magnetic nanoparticle-based sample enrichment prior to impedance detection. Thus ND seeding allows impedance biosensing in low conductivity solutions with competitive sensitivity. PMID:24397797

Determination of Interannual to Decadal Changes in Ice Sheet Mass Balance from Satellite Altimetry

NASA Technical Reports Server (NTRS)

Zwally, H. Jay; Busalacchi, Antonioa J. (Technical Monitor)

2001-01-01

A major uncertainty in predicting sea level rise is the sensitivity of ice sheet mass balance to climate change, as well as the uncertainty in present mass balance. Since the annual water exchange is about 8 mm of global sea level equivalent, the +/- 25% uncertainty in current mass balance corresponds to +/- 2 mm/yr in sea level change. Furthermore, estimates of the sensitivity of the mass balance to temperature change range from perhaps as much as - 10% to + 10% per K. Although the overall ice mass balance and seasonal and inter-annual variations can be derived from time-series of ice surface elevations from satellite altimetry, satellite radar altimeters have been limited in spatial coverage and elevation accuracy. Nevertheless, new data analysis shows mixed patterns of ice elevation increases and decreases that are significant in terms of regional-scale mass balances. In addition, observed seasonal and interannual variations in elevation demonstrate the potential for relating the variability in mass balance to changes in precipitation, temperature, and melting. From 2001, NASA's ICESat laser altimeter mission will provide significantly better elevation accuracy and spatial coverage to 86 deg latitude and to the margins of the ice sheets. During 3 to 5 years of ICESat-1 operation, an estimate of the overall ice sheet mass balance and sea level contribution will be obtained. The importance of continued ice monitoring after the first ICESat is illustrated by the variability in the area of Greenland surface melt observed over 17-years and its correlation with temperature. In addition, measurement of ice sheet changes, along with measurements of sea level change by a series of ocean altimeters, should enable direct detection of ice level and global sea level correlations.

Measles.

PubMed

Rota, Paul A; Moss, William J; Takeda, Makoto; de Swart, Rik L; Thompson, Kimberly M; Goodson, James L

2016-07-14

Measles is an infectious disease in humans caused by the measles virus (MeV). Before the introduction of an effective measles vaccine, virtually everyone experienced measles during childhood. Symptoms of measles include fever and maculopapular skin rash accompanied by cough, coryza and/or conjunctivitis. MeV causes immunosuppression, and severe sequelae of measles include pneumonia, gastroenteritis, blindness, measles inclusion body encephalitis and subacute sclerosing panencephalitis. Case confirmation depends on clinical presentation and results of laboratory tests, including the detection of anti-MeV IgM antibodies and/or viral RNA. All current measles vaccines contain a live attenuated strain of MeV, and great progress has been made to increase global vaccination coverage to drive down the incidence of measles. However, endemic transmission continues in many parts of the world. Measles remains a considerable cause of childhood mortality worldwide, with estimates that >100,000 fatal cases occur each year. Case fatality ratio estimates vary from <0.01% in industrialized countries to >5% in developing countries. All six WHO regions have set goals to eliminate endemic transmission of MeV by achieving and maintaining high levels of vaccination coverage accompanied by a sensitive surveillance system. Because of the availability of a highly effective and relatively inexpensive vaccine, the monotypic nature of the virus and the lack of an animal reservoir, measles is considered a candidate for eradication.

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH.

PubMed

Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Gospocic, Janko; Gupte, Rohit; Bonasio, Roberto; Kim, Junhyong; Murray, John; Raj, Arjun

2018-02-28

Although single-cell RNA sequencing can reliably detect large-scale transcriptional programs, it is unclear whether it accurately captures the behavior of individual genes, especially those that express only in rare cells. Here, we use single-molecule RNA fluorescence in situ hybridization as a gold standard to assess trade-offs in single-cell RNA-sequencing data for detecting rare cell expression variability. We quantified the gene expression distribution for 26 genes that range from ubiquitous to rarely expressed and found that the correspondence between estimates across platforms improved with both transcriptome coverage and increased number of cells analyzed. Further, by characterizing the trade-off between transcriptome coverage and number of cells analyzed, we show that when the number of genes required to answer a given biological question is small, then greater transcriptome coverage is more important than analyzing large numbers of cells. More generally, our report provides guidelines for selecting quality thresholds for single-cell RNA-sequencing experiments aimed at rare cell analyses. Copyright © 2018 Elsevier Inc. All rights reserved.

Study of the Vibrational Modes of Subsurface Oxygen on Al (111) Using Diode Laser Infrared Reflection-Absorption Spectroscopy.

DTIC Science & Technology

1987-10-15

apparent shift of this band to higher energy with increasing coverage, observed at lower resolution (but higher sensitivity) in electron energy loss...apparent shift of this band to higher energy with increasing coverage, observed at lower resolution (but higher sen- sitivity) in electron energy ...11 using high-resolution electron energy -loss spectroscopy (EELS), is especially intriguing. 02 dissociates on this surface to populate two types of

Vectorial capacity and vector control: reconsidering sensitivity to parameters for malaria elimination

PubMed Central

Brady, Oliver J.; Godfray, H. Charles J.; Tatem, Andrew J.; Gething, Peter W.; Cohen, Justin M.; McKenzie, F. Ellis; Perkins, T. Alex; Reiner, Robert C.; Tusting, Lucy S.; Sinka, Marianne E.; Moyes, Catherine L.; Eckhoff, Philip A.; Scott, Thomas W.; Lindsay, Steven W.; Hay, Simon I.; Smith, David L.

2016-01-01

Background Major gains have been made in reducing malaria transmission in many parts of the world, principally by scaling-up coverage with long-lasting insecticidal nets and indoor residual spraying. Historically, choice of vector control intervention has been largely guided by a parameter sensitivity analysis of George Macdonald's theory of vectorial capacity that suggested prioritizing methods that kill adult mosquitoes. While this advice has been highly successful for transmission suppression, there is a need to revisit these arguments as policymakers in certain areas consider which combinations of interventions are required to eliminate malaria. Methods and Results Using analytical solutions to updated equations for vectorial capacity we build on previous work to show that, while adult killing methods can be highly effective under many circumstances, other vector control methods are frequently required to fill effective coverage gaps. These can arise due to pre-existing or developing mosquito physiological and behavioral refractoriness but also due to additive changes in the relative importance of different vector species for transmission. Furthermore, the optimal combination of interventions will depend on the operational constraints and costs associated with reaching high coverage levels with each intervention. Conclusions Reaching specific policy goals, such as elimination, in defined contexts requires increasingly non-generic advice from modelling. Our results emphasize the importance of measuring baseline epidemiology, intervention coverage, vector ecology and program operational constraints in predicting expected outcomes with different combinations of interventions. PMID:26822603

Photometric transit search for planets around cool stars from the western Italian Alps: a pilot study

NASA Astrophysics Data System (ADS)

Giacobbe, P.; Damasso, M.; Sozzetti, A.; Toso, G.; Perdoncin, M.; Calcidese, P.; Bernagozzi, A.; Bertolini, E.; Lattanzi, M. G.; Smart, R. L.

2012-08-01

We present the results of a year-long photometric monitoring campaign of a sample of 23 nearby (d < 60 pc), bright (J < 12) dM stars carried out at the Astronomical Observatory of the Autonomous Region of the Aosta Valley, in the western Italian Alps. This programme represents a 'pilot study' for a long-term photometric transit search for planets around a large sample of nearby M dwarfs, due to start with an array of identical 40-cm class telescopes by the Spring of 2012. In this study, we set out to (i) demonstrate the sensitivity to <4 R⊕ transiting planets with periods of a few days around our programme stars, through a two-fold approach that combines a characterization of the statistical noise properties of our photometry with the determination of transit detection probabilities via simulations; and (ii) where possible, improve our knowledge of some astrophysical properties (e.g. activity, rotation) of our targets by combining spectroscopic information and our differential photometric measurements. We achieve a typical nightly root mean square (RMS) photometric precision of ˜5 mmag, with little or no dependence on the instrumentation used or on the details of the adopted methods for differential photometry. The presence of correlated (red) noise in our data degrades the precision by a factor of ˜1.3 with respect to a pure white noise regime. Based on a detailed stellar variability analysis (i) we detected no transit-like events (an expected result, given the sample size); (ii) we determined photometric rotation periods of ˜0.47 and ˜0.22 d for LHS 3445 and GJ 1167A, respectively; (iii) these values agree with the large projected rotational velocities (˜25 and ˜33 km s-1, respectively) inferred for both stars based on the analysis of archival spectra; (iv) the estimated inclinations of the stellar rotation axes for LHS 3445 and GJ 1167A are consistent with those derived using a simple spot model; and (v) short-term, low-amplitude flaring events were recorded for LHS 3445 and LHS 2686. Finally, based on simulations of transit signals of given period and amplitude injected in the actual (nightly reduced) photometric data for our sample, we derive a relationship between transit detection probability and phase coverage. We find that, using the Box-fitting Least Squares search algorithm, even when the phase coverage approaches 100 per cent, there is a limit to the detection probability of ≈90 per cent. Around programme stars with phase coverage > 50 per cent, we would have had >80 per cent chances of detecting planets with P < 1 d inducing fractional transit depths > 0.5 per cent, corresponding to minimum detectable radii in the range ˜1.0-2.2 R⊕. These findings are illustrative of our high readiness level ahead of the main survey start.

Workers on the margin: who drops health coverage when prices rise?

PubMed

Okeke, Edward N; Hirth, Richard A; Grazier, Kyle

2010-01-01

We revisit the question of price elasticity of employer-sponsored insurance (ESI) take-up by directly examining changes in the take-up of ESI at a large firm in response to exogenous changes in employee premium contributions. We find that, on average, a 10% increase in the employee's out-of-pocket premium increases the probability of dropping coverage by approximately 1%. More importantly, we find heterogeneous impacts: married workers are much more price-sensitive than single employees, and lower-paid workers are disproportionately more likely to drop coverage than higher-paid workers. Elasticity estimates for employees below the 25th percentile of salary distribution in our sample are nearly twice the average.

Cost-effectiveness of 64-slice CT angiography compared to conventional coronary angiography based on a coverage with evidence development study in Ontario.

PubMed

Goeree, Ron; Blackhouse, Gord; Bowen, James M; O'Reilly, Daria; Sutherland, Simone; Hopkins, Robert; Chow, Benjamin; Freeman, Michael; Provost, Yves; Dennie, Carole; Cohen, Eric; Marcuzzi, Dan; Iwanochko, Robert; Moody, Alan; Paul, Narinder; Parker, John D

2013-10-01

Conventional coronary angiography (CCA) is the standard diagnostic for coronary artery disease (CAD), but multi-detector computed tomography coronary angiography (CTCA) is a non-invasive alternative. A multi-center coverage with evidence development study was undertaken and combined with an economic model to estimate the cost-effectiveness of CTCA followed by CCA vs CCA alone. Alternative assumptions were tested in patient scenario and sensitivity analyses. CCA was found to dominate CTCA, however, CTCA was relatively more cost-effective in females, in advancing age, in patients with lower pre-test probabilities of CAD, the higher the sensitivity of CTCA and the lower the probability of undergoing a confirmatory CCA following a positive CTCA. RESULTS were very sensitive to alternative patient populations and modeling assumptions. Careful consideration of patient characteristics, procedures to improve the diagnostic yield of CTCA and selective use of CCA following CTCA will impact whether CTCA is cost-effective or dominates CCA.

CNV-RF Is a Random Forest-Based Copy Number Variation Detection Method Using Next-Generation Sequencing.

PubMed

Onsongo, Getiria; Baughn, Linda B; Bower, Matthew; Henzler, Christine; Schomaker, Matthew; Silverstein, Kevin A T; Thyagarajan, Bharat

2016-11-01

Simultaneous detection of small copy number variations (CNVs) (<0.5 kb) and single-nucleotide variants in clinically significant genes is of great interest for clinical laboratories. The analytical variability in next-generation sequencing (NGS) and artifacts in coverage data because of issues with mappability along with lack of robust bioinformatics tools for CNV detection have limited the utility of targeted NGS data to identify CNVs. We describe the development and implementation of a bioinformatics algorithm, copy number variation-random forest (CNV-RF), that incorporates a machine learning component to identify CNVs from targeted NGS data. Using CNV-RF, we identified 12 of 13 deletions in samples with known CNVs, two cases with duplications, and identified novel deletions in 22 additional cases. Furthermore, no CNVs were identified among 60 genes in 14 cases with normal copy number and no CNVs were identified in another 104 patients with clinical suspicion of CNVs. All positive deletions and duplications were confirmed using a quantitative PCR method. CNV-RF also detected heterozygous deletions and duplications with a specificity of 50% across 4813 genes. The ability of CNV-RF to detect clinically relevant CNVs with a high degree of sensitivity along with confirmation using a low-cost quantitative PCR method provides a framework for providing comprehensive NGS-based CNV/single-nucleotide variant detection in a clinical molecular diagnostics laboratory. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Design and scheduling for periodic concurrent error detection and recovery in processor arrays

NASA Technical Reports Server (NTRS)

Wang, Yi-Min; Chung, Pi-Yu; Fuchs, W. Kent

1992-01-01

Periodic application of time-redundant error checking provides the trade-off between error detection latency and performance degradation. The goal is to achieve high error coverage while satisfying performance requirements. We derive the optimal scheduling of checking patterns in order to uniformly distribute the available checking capability and maximize the error coverage. Synchronous buffering designs using data forwarding and dynamic reconfiguration are described. Efficient single-cycle diagnosis is implemented by error pattern analysis and direct-mapped recovery cache. A rollback recovery scheme using start-up control for local recovery is also presented.

Genome-wide copy number variation in the bovine genome detected using low coverage sequence of popular beef breeds

USDA-ARS?s Scientific Manuscript database

Copy number variations (CNVs) are large insertions, deletions or duplications in the genome that vary between members of a species and are known to affect a wide variety of phenotypic traits. In this study, we identified CNVs in a population of bulls using low coverage next-generation sequence data....

Integration of lidar and Landsat ETM+ data for estimating and mapping forest canopy height.

Treesearch

Andrew T. Hudak; Michael A. Lefsky; Warren B. Cohen; Mercedes Berterretche

2002-01-01

Light detection and ranging (LIDAR) data provide accurate measurements of forest canopy structure in the vertical plane; however, current LIDAR sensors have limited coverage in the horizontal plane. Landsat data provide extensive coverage of generalized forest structural classes in the horizontal plane but are relatively insensitive to variation in forest canopy height...

Explanatory Supplement to the AllWISE Data Release Products

NASA Astrophysics Data System (ADS)

Cutri, R. M.; Wright, E. L.; Conrow, T.; Fowler, J. W.; Eisenhardt, P. R. M.; Grillmair, C.; Kirkpatrick, J. D.; Masci, F.; McCallon, H. L.; Wheelock, S. L.; Fajardo-Acosta, S.; Yan, L.; Benford, D.; Harbut, M.; Jarrett, T.; Lake, S.; Leisawitz, D.; Ressler, M. E.; Stanford, S. A.; Tsai, C. W.; Liu, F.; Helou, G.; Mainzer, A.; Gettings, D.; Gonzalez, A.; Hoffman, D.; Marsh, K. A.; Padgett, D.; Skrutskie, M. F.; Beck, R. P.; Papin, M.; Wittman, M.

2013-11-01

The AllWISE program builds upon the successful Wide-field Infrared Survey Explorer (WISE; Wright et al. 2010) mission by combining data from all WISE and NEOWISE (Mainzer et al. 2011) survey phases to form the most comprehensive view of the mid-infrared sky currently available. By combining the data from two complete sky coverage epochs in an advanced data processing system, AllWISE has generated new products that have enhanced photometric sensitivity and accuracy, and improved astrometric precision compared with the earlier WISE All-Sky Data Release. Exploiting the 6 month baseline between the WISE sky coverage epochs enables AllWISE to measure source motions for the first time, and to compute improved flux variability statistics. AllWISE data release products include: a Source Catalog that contains 4-band fluxes, positions, apparent motion measurements, and flux variability statistics for over 747 million objects detected at SNR>5 in the combined exposures; a Multiepoch Photometry Database containing over 42 billion time-tagged, single-exposure fluxes for each object detected on the combined exposures; and an Image Atlas of 18,240 4-band calibrated FITS images, depth-of-coverage and noise maps that cover the sky produced by coadding nearly 7.9 million single-exposure images from the cryogenic and post-cryogenic survey phases. The Explanatory Supplement to the AllWISE Data Release Products is a general guide for users of the AllWISE data. The Supplement contains detailed descriptions of the format and characteristics of the AllWISE data products, as well as a summary of cautionary notes that describe known limitations. The Supplement is an on-line document that is updated frequently to provide the most current information for users of the AllWISE data products. The Explanatory Supplement is maintained at: http://wise2.ipac.caltech.edu/docs/release/allwise/expsup/index.html AllWISE makes use of data from WISE, which is a joint project of the University of California, Los Angeles, and the Jet Propulsion Laboratory/California Institute of Technology, and NEOWISE, which is a project of the Jet Propulsion Laboratory/California Institute of Technology. WISE and NEOWISE are funded by the National Aeronautics and Space Administration.

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB.

PubMed

Liu, Guohong; Weston, Christopher Q; Pham, Long K; Waltz, Shannon; Barnes, Helen; King, Paula; Sphar, Dan; Yamamoto, Robert T; Forsyth, R Allyn

2016-01-01

We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.

TANDIR: projectile warning system using uncooled bolometric technology

NASA Astrophysics Data System (ADS)

Horovitz-Limor, Z.; Zahler, M.

2007-04-01

Following the demand for affordable, various range and light-weight protection against ATGM's, Elisra develops a cost-effective passive IR system for ground vehicles. The system is based on wide FOV uncooled bolometric sensors with full azimuth coverage and a lightweight processing & control unit. The system design is based on the harsh environmental conditions. The basic algorithm discriminates the target from its clutter and predicts the time to impact (TTI) and the target aiming direction with relation to vehicle. The current detector format is 320*240 pixels and frame rate is 60 Hz, Spectral response is on Far Infrared (8-14μ). The digital video output has 14bit resolution & wide dynamic range. Future goal is to enhance detection performance by using large format uncooled detector (640X480) with improved sensitivity and higher frame rates (up to 120HZ).

Optimize the Coverage Probability of Prediction Interval for Anomaly Detection of Sensor-Based Monitoring Series

PubMed Central

Liu, Datong; Peng, Yu; Peng, Xiyuan

2018-01-01

Effective anomaly detection of sensing data is essential for identifying potential system failures. Because they require no prior knowledge or accumulated labels, and provide uncertainty presentation, the probability prediction methods (e.g., Gaussian process regression (GPR) and relevance vector machine (RVM)) are especially adaptable to perform anomaly detection for sensing series. Generally, one key parameter of prediction models is coverage probability (CP), which controls the judging threshold of the testing sample and is generally set to a default value (e.g., 90% or 95%). There are few criteria to determine the optimal CP for anomaly detection. Therefore, this paper designs a graphic indicator of the receiver operating characteristic curve of prediction interval (ROC-PI) based on the definition of the ROC curve which can depict the trade-off between the PI width and PI coverage probability across a series of cut-off points. Furthermore, the Youden index is modified to assess the performance of different CPs, by the minimization of which the optimal CP is derived by the simulated annealing (SA) algorithm. Experiments conducted on two simulation datasets demonstrate the validity of the proposed method. Especially, an actual case study on sensing series from an on-orbit satellite illustrates its significant performance in practical application. PMID:29587372

Real-time incident detection using social media data.

DOT National Transportation Integrated Search

2016-05-09

The effectiveness of traditional incident detection is often limited by sparse sensor coverage, and reporting incidents to emergency response systems : is labor-intensive. This research project mines tweet texts to extract incident information on bot...

On-chip multiplexed solid-phase nucleic acid hybridization assay using spatial profiles of immobilized quantum dots and fluorescence resonance energy transfer.

PubMed

Noor, M Omair; Tavares, Anthony J; Krull, Ulrich J

2013-07-25

A microfluidic based solid-phase assay for the multiplexed detection of nucleic acid hybridization using quantum dot (QD) mediated fluorescence resonance energy transfer (FRET) is described herein. The glass surface of hybrid glass-polydimethylsiloxane (PDMS) microfluidic channels was chemically modified to assemble the biorecognition interface. Multiplexing was demonstrated using a detection system that was comprised of two colors of immobilized semi-conductor QDs and two different oligonucleotide probe sequences. Green-emitting and red-emitting QDs were paired with Cy3 and Alexa Fluor 647 (A647) labeled oligonucleotides, respectively. The QDs served as energy donors for the transduction of dye labeled oligonucleotide targets. The in-channel assembly of the biorecognition interface and the subsequent introduction of oligonucleotide targets was accomplished within minutes using a combination of electroosmotic flow and electrophoretic force. The concurrent quantification of femtomole quantities of two target sequences was possible by measuring the spatial coverage of FRET sensitized emission along the length of the channel. In previous reports, multiplexed QD-FRET hybridization assays that employed a ratiometric method for quantification had challenges associated with lower analytical sensitivity arising from both donor and acceptor dilution that resulted in reduced energy transfer pathways as compared to single-color hybridization assays. Herein, a spatial method for quantification that is based on in-channel QD-FRET profiles provided higher analytical sensitivity in the multiplexed assay format as compared to single-color hybridization assays. The selectivity of the multiplexed hybridization assays was demonstrated by discrimination between a fully-complementary sequence and a 3 base pair sequence at a contrast ratio of 8 to 1. Copyright © 2013 Elsevier B.V. All rights reserved.

Assessing the Relationship of Ancient and Modern Populations

PubMed Central

Schraiber, Joshua G.

2018-01-01

Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach, such as selecting a read at random for each site, to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population, while accounting for sequencing error and postmortem damage by analyzing raw reads from multiple ancient individuals simultaneously. We show that, when analyzing SNP data, it is better to sequence more ancient samples to low coverage: two samples sequenced to 0.5× coverage provide better resolution than a single sample sequenced to 2× coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that, with even a few high coverage individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth. PMID:29167200

Total-Body PET: Maximizing Sensitivity to Create New Opportunities for Clinical Research and Patient Care.

PubMed

Cherry, Simon R; Jones, Terry; Karp, Joel S; Qi, Jinyi; Moses, William W; Badawi, Ramsey D

2018-01-01

PET is widely considered the most sensitive technique available for noninvasively studying physiology, metabolism, and molecular pathways in the living human being. However, the utility of PET, being a photon-deficient modality, remains constrained by factors including low signal-to-noise ratio, long imaging times, and concerns about radiation dose. Two developments offer the potential to dramatically increase the effective sensitivity of PET. First by increasing the geometric coverage to encompass the entire body, sensitivity can be increased by a factor of about 40 for total-body imaging or a factor of about 4-5 for imaging a single organ such as the brain or heart. The world's first total-body PET/CT scanner is currently under construction to demonstrate how this step change in sensitivity affects the way PET is used both in clinical research and in patient care. Second, there is the future prospect of significant improvements in timing resolution that could lead to further effective sensitivity gains. When combined with total-body PET, this could produce overall sensitivity gains of more than 2 orders of magnitude compared with existing state-of-the-art systems. In this article, we discuss the benefits of increasing body coverage, describe our efforts to develop a first-generation total-body PET/CT scanner, discuss selected application areas for total-body PET, and project the impact of further improvements in time-of-flight PET. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.

Myocardial perfusion magnetic resonance imaging using sliding-window conjugate-gradient highly constrained back-projection reconstruction for detection of coronary artery disease.

PubMed

Ma, Heng; Yang, Jun; Liu, Jing; Ge, Lan; An, Jing; Tang, Qing; Li, Han; Zhang, Yu; Chen, David; Wang, Yong; Liu, Jiabin; Liang, Zhigang; Lin, Kai; Jin, Lixin; Bi, Xiaoming; Li, Kuncheng; Li, Debiao

2012-04-15

Myocardial perfusion magnetic resonance imaging (MRI) with sliding-window conjugate-gradient highly constrained back-projection reconstruction (SW-CG-HYPR) allows whole left ventricular coverage, improved temporal and spatial resolution and signal/noise ratio, and reduced cardiac motion-related image artifacts. The accuracy of this technique for detecting coronary artery disease (CAD) has not been determined in a large number of patients. We prospectively evaluated the diagnostic performance of myocardial perfusion MRI with SW-CG-HYPR in patients with suspected CAD. A total of 50 consecutive patients who were scheduled for coronary angiography with suspected CAD underwent myocardial perfusion MRI with SW-CG-HYPR at 3.0 T. The perfusion defects were interpreted qualitatively by 2 blinded observers and were correlated with x-ray angiographic stenoses ≥50%. The prevalence of CAD was 56%. In the per-patient analysis, the sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of SW-CG-HYPR was 96% (95% confidence interval 82% to 100%), 82% (95% confidence interval 60% to 95%), 87% (95% confidence interval 70% to 96%), 95% (95% confidence interval 74% to100%), and 90% (95% confidence interval 82% to 98%), respectively. In the per-vessel analysis, the corresponding values were 98% (95% confidence interval 91% to 100%), 89% (95% confidence interval 80% to 94%), 86% (95% confidence interval 76% to 93%), 99% (95% confidence interval 93% to 100%), and 93% (95% confidence interval 89% to 97%), respectively. In conclusion, myocardial perfusion MRI using SW-CG-HYPR allows whole left ventricular coverage and high resolution and has high diagnostic accuracy in patients with suspected CAD. Copyright © 2012 Elsevier Inc. All rights reserved.

Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends

PubMed Central

Chan, K. C. Allen; Jiang, Peiyong; Sun, Kun; Cheng, Yvonne K. Y.; Tong, Yu K.; Cheng, Suk Hang; Wong, Ada I. C.; Hudecova, Irena; Leung, Tak Y.; Chiu, Rossa W. K.; Lo, Yuk Ming Dennis

2016-01-01

Plasma DNA obtained from a pregnant woman was sequenced to a depth of 270× haploid genome coverage. Comparing the maternal plasma DNA sequencing data with the parental genomic DNA data and using a series of bioinformatics filters, fetal de novo mutations were detected at a sensitivity of 85% and a positive predictive value of 74%. These results represent a 169-fold improvement in the positive predictive value over previous attempts. Improvements in the interpretation of the sequence information of every base position in the genome allowed us to interrogate the maternal inheritance of the fetus for 618,271 of 656,676 (94.2%) heterozygous SNPs within the maternal genome. The fetal genotype at each of these sites was deduced individually, unlike previously, where the inheritance was determined for a collection of sites within a haplotype. These results represent a 90-fold enhancement in the resolution in determining the fetus’s maternal inheritance. Selected genomic locations were more likely to be found at the ends of plasma DNA molecules. We found that a subset of such preferred ends exhibited selectivity for fetal- or maternal-derived DNA in maternal plasma. The ratio of the number of maternal plasma DNA molecules with fetal preferred ends to those with maternal preferred ends showed a correlation with the fetal DNA fraction. Finally, this second generation approach for noninvasive fetal whole-genome analysis was validated in a pregnancy diagnosed with cardiofaciocutaneous syndrome with maternal plasma DNA sequenced to 195× coverage. The causative de novo BRAF mutation was successfully detected through the maternal plasma DNA analysis. PMID:27799561

Low-level APC mutational mosaicism is the underlying cause in a substantial fraction of unexplained colorectal adenomatous polyposis cases.

PubMed

Spier, Isabel; Drichel, Dmitriy; Kerick, Martin; Kirfel, Jutta; Horpaopan, Sukanya; Laner, Andreas; Holzapfel, Stefanie; Peters, Sophia; Adam, Ronja; Zhao, Bixiao; Becker, Tim; Lifton, Richard P; Perner, Sven; Hoffmann, Per; Kristiansen, Glen; Timmermann, Bernd; Nöthen, Markus M; Holinski-Feder, Elke; Schweiger, Michal R; Aretz, Stefan

2016-03-01

In 30-50% of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, or POLE or POLD1, causing polymerase-proofreading-associated polyposis can be identified, although a hereditary aetiology is likely. This study aimed to explore the impact of APC mutational mosaicism in unexplained polyposis. To comprehensively screen for somatic low-level APC mosaicism, high-coverage next-generation sequencing of the APC gene was performed using DNA from leucocytes and a total of 53 colorectal tumours from 20 unrelated patients with unexplained sporadic adenomatous polyposis. APC mosaicism was assumed if the same loss-of-function APC mutation was present in ≥ 2 anatomically separated colorectal adenomas/carcinomas per patient. All mutations were validated using diverse methods. In 25% (5/20) of patients, somatic mosaicism of a pathogenic APC mutation was identified as underlying cause of the disease. In 2/5 cases, the mosaic level in leucocyte DNA was slightly below the sensitivity threshold of Sanger sequencing; while in 3/5 cases, the allelic fraction was either very low (0.1-1%) or no mutations were detectable. The majority of mosaic mutations were located outside the somatic mutation cluster region of the gene. The present data indicate a high prevalence of pathogenic mosaic APC mutations below the detection thresholds of routine diagnostics in adenomatous polyposis, even if high-coverage sequencing of leucocyte DNA alone is taken into account. This has important implications for both routine work-up and strategies to identify new causative genes in this patient group. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry and PCR-based rapid diagnosis of Staphylococcus aureus bacteraemia.

PubMed

Clerc, O; Prod'hom, G; Senn, L; Jaton, K; Zanetti, G; Calandra, T; Greub, G

2014-04-01

Effective empirical treatment is of paramount importance to improve the outcome of patients with Staphylococcus aureus bacteraemia. We aimed to evaluate a PCR-based rapid diagnosis of methicillin resistance (GeneXpert MRSA) after early detection of S. aureus bacteraemia using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Patients with a first episode of S. aureus bacteraemia identified using MALDI-TOF MS were randomized in a prospective interventional open study between October 2010 and August 2012. In the control group, antibiotic susceptibility testing was performed after MALDI-TOF MS identification on blood culture pellets. In the intervention group, a GeneXpert MRSA was performed after S. aureus identification. The primary outcome was the performance of GeneXpert MRSA directly on blood cultures. We then assessed the impact of early diagnosis of methicillin resistance on the empirical treatment. In all, 197 episodes of S. aureus bacteraemia were included in the study, of which 106 were included in the intervention group. Median time from MALDI-TOF MS identification to GeneXpert MRSA result was 97 min (range 25-250). Detection of methicillin resistance using GeneXpert MRSA had a sensitivity of 99% and a specificity of 100%. There was less unnecessary coverage of MRSA in the intervention group (17.1% versus 29.2%, p 0.09). GeneXpert MRSA was highly reliable in diagnosing methicillin resistance when performed directly on positive blood cultures. This could help to avoid unnecessary prescriptions of anti-MRSA agents and promote the introduction of earlier adequate coverage in unsuspected cases. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Using Pennsylvania's Three Mile Island Accident as a Case Study to Analyze Newspaper Coverage: A Diary of Events and Suggestions for Teaching Strategies.

ERIC Educational Resources Information Center

Susskind, Jacob L.

1983-01-01

Methods for studying the coverage of the same current news story in several newspapers are outlined. Secondary school students critically examine news reporting, detect false or propagandistic reports, and learn to weigh and judge evidence. An example using the Three Mile Island nuclear accident is provided. (KC)

The accuracy of mother's reports about their children's vaccination status.

PubMed

Gareaballah, E T; Loevinsohn, B P

1989-01-01

Estimates of measles vaccination coverage in the Sudan vary on average by 23 percentage points, depending on whether or not information supplied by mothers who have lost their children's vaccination cards is included. To determine the accuracy of mother's reports, we collected data during four large coverage surveys in which illiterate mothers with vaccination cards were asked about their children's vaccination status and their answers were compared with the information given on the cards. Mothers' replies were very accurate. For example, for measles vaccination, the data supplied were both sensitive (87%) and specific (79%) compared with those on the vaccination cards. For both DPT and measles vaccination, accurate estimates of the true coverage rates could therefore be obtained by relying solely on mothers' reports. Within +/- 1 month, 78% of the women knew the age at which their children had received their first dose of poliovaccine. Ignoring mothers' reports of their children's vaccination status could therefore result in serious underestimates of the true vaccination coverage. A simple method of dealing with the problem posed by lost vaccination cards during coverage surveys is also suggested.

Coverage dependent molecular assembly of anthraquinone on Au(111)

NASA Astrophysics Data System (ADS)

DeLoach, Andrew S.; Conrad, Brad R.; Einstein, T. L.; Dougherty, Daniel B.

2017-11-01

A scanning tunneling microscopy study of anthraquinone (AQ) on the Au(111) surface shows that the molecules self-assemble into several structures depending on the local surface coverage. At high coverages, a close-packed saturated monolayer is observed, while at low coverages, mobile surface molecules coexist with stable chiral hexamer clusters. At intermediate coverages, a disordered 2D porous network interlinking close-packed islands is observed in contrast to the giant honeycomb networks observed for the same molecule on Cu(111). This difference verifies the predicted extreme sensitivity [J. Wyrick et al., Nano Lett. 11, 2944 (2011)] of the pore network to small changes in the surface electronic structure. Quantitative analysis of the 2D pore network reveals that the areas of the vacancy islands are distributed log-normally. Log-normal distributions are typically associated with the product of random variables (multiplicative noise), and we propose that the distribution of pore sizes for AQ on Au(111) originates from random linear rate constants for molecules to either desorb from the surface or detach from the region of a nucleated pore.

Coverage dependent molecular assembly of anthraquinone on Au(111).

PubMed

DeLoach, Andrew S; Conrad, Brad R; Einstein, T L; Dougherty, Daniel B

2017-11-14

A scanning tunneling microscopy study of anthraquinone (AQ) on the Au(111) surface shows that the molecules self-assemble into several structures depending on the local surface coverage. At high coverages, a close-packed saturated monolayer is observed, while at low coverages, mobile surface molecules coexist with stable chiral hexamer clusters. At intermediate coverages, a disordered 2D porous network interlinking close-packed islands is observed in contrast to the giant honeycomb networks observed for the same molecule on Cu(111). This difference verifies the predicted extreme sensitivity [J. Wyrick et al., Nano Lett. 11, 2944 (2011)] of the pore network to small changes in the surface electronic structure. Quantitative analysis of the 2D pore network reveals that the areas of the vacancy islands are distributed log-normally. Log-normal distributions are typically associated with the product of random variables (multiplicative noise), and we propose that the distribution of pore sizes for AQ on Au(111) originates from random linear rate constants for molecules to either desorb from the surface or detach from the region of a nucleated pore.

Achieving Crossed Strong Barrier Coverage in Wireless Sensor Network.

PubMed

Han, Ruisong; Yang, Wei; Zhang, Li

2018-02-10

Barrier coverage has been widely used to detect intrusions in wireless sensor networks (WSNs). It can fulfill the monitoring task while extending the lifetime of the network. Though barrier coverage in WSNs has been intensively studied in recent years, previous research failed to consider the problem of intrusion in transversal directions. If an intruder knows the deployment configuration of sensor nodes, then there is a high probability that it may traverse the whole target region from particular directions, without being detected. In this paper, we introduce the concept of crossed barrier coverage that can overcome this defect. We prove that the problem of finding the maximum number of crossed barriers is NP-hard and integer linear programming (ILP) is used to formulate the optimization problem. The branch-and-bound algorithm is adopted to determine the maximum number of crossed barriers. In addition, we also propose a multi-round shortest path algorithm (MSPA) to solve the optimization problem, which works heuristically to guarantee efficiency while maintaining near-optimal solutions. Several conventional algorithms for finding the maximum number of disjoint strong barriers are also modified to solve the crossed barrier problem and for the purpose of comparison. Extensive simulation studies demonstrate the effectiveness of MSPA.

Effectiveness of VIA, Pap, and HPV DNA Testing in a Cervical Cancer Screening Program in a Peri-Urban Community in Andhra Pradesh, India

PubMed Central

Gravitt, Patti E.; Paul, Proma; Katki, Hormuzd A.; Vendantham, Haripriya; Ramakrishna, Gayatri; Sudula, Mrudula; Kalpana, Basany; Ronnett, Brigitte M.; Vijayaraghavan, K.; Shah, Keerti V.

2010-01-01

Background While many studies have compared the efficacy of Pap cytology, visual inspection with acetic acid (VIA) and human papillomavirus (HPV) DNA assays for the detection cervical intraepithelial neoplasia and cancer, few have evaluated the program effectiveness. Methods and Findings A population-based sample of 5603 women from Medchal Mandal in Andhra Pradesh, India were invited to participate in a study comparing Pap cytology, VIA, and HPV DNA screening for the detection of CIN3+. Participation in primary screening and all subsequent follow-up visits was rigorously tracked. A 20% random sample of all women screened, in addition to all women with a positive screening test result underwent colposcopy with directed biopsy for final diagnosis. Sensitivity, specificity, positive and negative predictive values were adjusted for verification bias. HPV testing had a higher sensitivity (100%) and specificity (90.6%) compared to Pap cytology (sensitivity  =  78.2%; specificity = 86.0%) and VIA (sensitivity = 31.6%; specificity = 87.5%). Since 58% of the sample refused involvement and another 28% refused colposcopy or biopsy, we estimated that potentially 87.6% of the total underlying cases of CIN3 and cancer may have been missed due to program failures. Conclusions We conclude that despite our use of available resources, infrastructure, and guidelines for cervical cancer screening implementation in resource limited areas, community participation and non-compliance remain the major obstacles to successful reduction in cervical cancer mortality in this Indian population. HPV DNA testing was both more sensitive and specific than Pap cytology and VIA. The use of a less invasive and more user-friendly primary screening strategy (such as self-collected swabs for HPV DNA testing) may be required to achieve the coverage necessary for effective reduction in cervical cancer mortality. PMID:21060889

Quality of breast cancer early detection services conducted by well woman clinics in the district of Gampaha, Sri Lanka.

PubMed

Vithana, Palatiyana Vithanage Sajeewanie Chiranthika; Ariyaratne, May; Jayawardana, Pl

2013-01-01

Breast cancer is the most common cancer diagnosed in females in Sri Lanka and early detection can lead to reduction in morbidity and mortality. To evaluate selected aspects of breast cancer early detection services implemented through well woman clinics (WWCs) in the Gampaha District. The study consisted of two components. A retrospective descriptive arm assessed clinical breast examination (CBE) coverage of target age group women (TGW) of 35-59 years in all the WWCs in Gampaha district over 2003- 2007. A cross sectional descriptive study additionally assessed quality of breast cancer early detection services. The Lot Quality Assurance Sampling (LQAS) technique was used to decide on the lot size and threshold values, which were computed as twenty and six clinics. Checklists were employed in assessing coverage, physical facilities and clinic activities. Client satisfaction on WWC services was assessed among 200 TGW attending 20 WWCs using an interviewer-administered questionnaire. CBE coverage in the Gampaha district increased only from 1.1-2.2% over 2003-2007. With regard to physical facilities, the number of clinics that were rated substandard varied between 7-18 (35- 90%). The items that were lacking included dust bins, notice boards, stationary, furniture and linen, and cleanliness of outside premises and toilets. With regard to clinic activities, punctuality of staff, late commencement of clinics, provision of health education, supervision, CBE and breast self-examination (BSE) were substandard in 7- 20 clinics (35-100%). Client satisfaction for WWC services was 45.2% (IQR: 38.7-54.8%) and only 11% had a score of ≥70%, the cut off set for satisfaction. Breast cancer early detection service coverage in the Gampaha district remained low (2.2%) in 2007, 11 years after commencing WWCs. All 20 clinics were substandard for overall CBE and BSE.

A retrospective study of owner-requested testing as surveillance for equine infectious anemia in Canada (2009-2012).

PubMed

Higgins, Sara N; Howden, Krista J; James, Carolyn R; Epp, Tasha; Lohmann, Katharina L

2017-12-01

This retrospective study was undertaken to estimate i) the surveillance coverage for equine infectious anemia (EIA) based on owner-requested testing, and ii) the incidence of case detection from this surveillance activity to inform a review of Canada's national disease control strategy. Based on sample submissions by accredited veterinarians to laboratories CFIA-approved for EIA testing between 2009 and 2012, the estimated national surveillance coverage was 14% for all years, and 72 cases of EIA were detected. The annual national incidence of EIA detection ranged from 0.03 to 0.08 cases/1000 horses. On average, a greater proportion of the horse population was tested in eastern Canada (32%) than in western Canada (6%, P < 0.0001). The cumulative incidence of EIA detection was higher in western Canada (0.25 cases/1000 horses) than in eastern Canada (0.02 cases/1000 horses, P < 0.0001). This study identified regional differences in owner-requested EIA testing and case detection resulting from this testing activity.

Transient Faults in Computer Systems

NASA Technical Reports Server (NTRS)

Masson, Gerald M.

1993-01-01

A powerful technique particularly appropriate for the detection of errors caused by transient faults in computer systems was developed. The technique can be implemented in either software or hardware; the research conducted thus far primarily considered software implementations. The error detection technique developed has the distinct advantage of having provably complete coverage of all errors caused by transient faults that affect the output produced by the execution of a program. In other words, the technique does not have to be tuned to a particular error model to enhance error coverage. Also, the correctness of the technique can be formally verified. The technique uses time and software redundancy. The foundation for an effective, low-overhead, software-based certification trail approach to real-time error detection resulting from transient fault phenomena was developed.

Decision making with regard to antiviral intervention during an influenza pandemic.

PubMed

Shim, Eunha; Chapman, Gretchen B; Galvani, Alison P

2010-01-01

Antiviral coverage is defined by the proportion of the population that takes antiviral prophylaxis or treatment. High coverage of an antiviral drug has epidemiological and evolutionary repercussions. Antivirals select for drug resistance within the population, and individuals may experience adverse effects. To determine optimal antiviral coverage in the context of an influenza outbreak, we compared 2 perspectives: 1) the individual level (the Nash perspective), and 2) the population level (utilitarian perspective). We developed an epidemiological game-theoretic model of an influenza pandemic. The data sources were published literature and a national survey. The target population was the US population. The time horizon was 6 months. The perspective was individuals and the population overall. The interventions were antiviral prophylaxis and treatment. The outcome measures were the optimal coverage of antivirals in an influenza pandemic. At current antiviral pricing, the optimal Nash strategy is 0% coverage for prophylaxis and 30% coverage for treatment, whereas the optimal utilitarian strategy is 19% coverage for prophylaxis and 100% coverage for treatment. Subsidizing prophylaxis by $440 and treatment by $85 would bring the Nash and utilitarian strategies into alignment. For both prophylaxis and treatment, the optimal antiviral coverage decreases as pricing of antivirals increases. Our study does not incorporate the possibility of an effective vaccine and lacks probabilistic sensitivity analysis. Our survey also does not completely represent the US population. Because our model assumes a homogeneous population and homogeneous antiviral pricing, it does not incorporate heterogeneity of preference. The optimal antiviral coverage from the population perspective and individual perspectives differs widely for both prophylaxis and treatment strategies. Optimal population and individual strategies for prophylaxis and treatment might be aligned through subsidization.

Decision Making with Regard to Antiviral Intervention during an Influenza Pandemic

PubMed Central

Shim, Eunha; Chapman, Gretchen B.; Galvani, Alison P.

2012-01-01

Background Antiviral coverage is defined by the proportion of the population that takes antiviral prophylaxis or treatment. High coverage of an antiviral drug has epidemiological and evolutionary repercussions. Antivirals select for drug resistance within the population, and individuals may experience adverse effects. To determine optimal antiviral coverage in the context of an influenza outbreak, we compared 2 perspectives: 1) the individual level (the Nash perspective), and 2) the population level (utilitarian perspective). Methods We developed an epidemiological game-theoretic model of an influenza pandemic. The data sources were published literature and a national survey. The target population was the US population. The time horizon was 6 months. The perspective was individuals and the population overall. The interventions were antiviral prophylaxis and treatment. The outcome measures were the optimal coverage of antivirals in an influenza pandemic. Results At current antiviral pricing, the optimal Nash strategy is 0% coverage for prophylaxis and 30% coverage for treatment, whereas the optimal utilitarian strategy is 19% coverage for prophylaxis and 100% coverage for treatment. Subsidizing prophylaxis by $440 and treatment by $85 would bring the Nash and utilitarian strategies into alignment. For both prophylaxis and treatment, the optimal antiviral coverage decreases as pricing of antivirals increases. Our study does not incorporate the possibility of an effective vaccine and lacks probabilistic sensitivity analysis. Our survey also does not completely represent the US population. Because our model assumes a homogeneous population and homogeneous antiviral pricing, it does not incorporate heterogeneity of preference. Conclusions The optimal antiviral coverage from the population perspective and individual perspectives differs widely for both prophylaxis and treatment strategies. Optimal population and individual strategies for prophylaxis and treatment might be aligned through subsidization. PMID:20634545

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.

Profile of sterilized women in urban slums and evaluation of motivational strategies.

PubMed

Vaidya, V G; Sahasrabudhe, B G; Jogi, J A; Mitkar, R P

2003-01-01

A study undertaken in hard core pockets having C.P.R. >50% of urban slums to sensitize target couples for encouraging spacing methods and sterilizations showed 55.4% coverage of 1820 unprotected eligible couples. This coverage is attributed to involvement of Aganwadi workers, Mahila Mandals and home visits. The motivational strategies such as sensitization of Mahila Mondals, provision of MCH services and inter personal communications were found to be effective. The reasons for non-acceptance, such as desire to have male and female child in 17.8%, post insertion bleeding due to Cu-T in 13.9% and refusal by male partners in 13.36% were noted in eligible couples. These reasons could be removed by continued inter personal communications. Illiteracy rate of 76.30% in living children of sterilized women indicates need of implementing literacy programme.

Pediatric ambulatory care sensitive conditions: Birth cohorts and the socio-economic gradient.

PubMed

Roos, Leslie L; Dragan, Roxana; Schroth, Robert J

2017-09-14

This study examines the socio-economic gradient in utilization and the risk factors associated with hospitalization for four pediatric ambulatory care sensitive conditions (dental conditions, asthma, gastroenteritis, and bacterial pneumonia). Dental conditions, where much care is provided by dentists and insurance coverage varies among different population segments, present special issues. A population registry, provider registry, physician ambulatory claims, and hospital discharge abstracts from 28 398 children born in 2003-2006 in urban centres in Manitoba, Canada were the main data sources. Physician visits and hospitalizations were compared across neighbourhood income groupings using rank correlations and logistic regressions. Very strong relationships between neighbourhood income and utilization were highlighted. Additional variables - family on income assistance, mother's age at first birth, breastfeeding - helped predict the probability of hospitalization. Despite the complete insurance coverage (including visits to dentists and physicians and for hospitalizations) provided, receiving income assistance was associated with higher probabilities of hospitalization. We found a socio-economic gradient in utilization for pediatric ambulatory care sensitive conditions, with higher rates of ambulatory visits and hospitalizations in the poorest neighbourhoods. Insurance coverage which varies between different segments of the population complicates matters. Providing funding for dental care for Manitobans on income assistance has not prevented physician visits or intensive treatment in high-cost facilities, specifically treatment under general anesthesia. When services from one type of provider (dentist) are not universally insured but those from another type (physician) are, using rates of hospitalization to indicate problems in the organization of care seems particularly difficult.

Ternary Surface Monolayers for Ultrasensitive (Zeptomole) Amperometric Detection of Nucleic-Acid Hybridization without Signal Amplification

PubMed Central

Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A.; Wang, Joseph

2010-01-01

A ternary surface monolayer, consisting of co-assembled thiolated capture probe (SHCP) mercaptohexanol (MCH) and dithiothreitol (DTT), is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers (SAMs). Remarkably low detection limits down to 40 zmole (in 4 μL samples) as well as only 1 CFU E. coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3′,5,5′-tetramethylbenzidine (HRP/TMB) system. Such dramatic improvements in the detection limits (compared to common binary alkanethiol interfaces and to most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to non-specific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration ‘backfillers’ that leads to a remarkably low background noise even in the presence of complex sample matrices. A wide range of surface compositions have been investigated and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety and forensic analysis. PMID:20883023

Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification.

PubMed

Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A; Wang, Joseph

2010-11-01

A ternary surface monolayer, consisting of coassembled thiolated capture probe, mercaptohexanol and dithiothreitol, is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers. Remarkably low detection limits down to 40 zmol (in 4 μL samples) as well as only 1 CFU Escherichia coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3',5,5'-tetramethylbenzidine system. Such dramatic improvements in the detection limits (compared to those of common binary alkanethiol interfaces and to those of most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to nonspecific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration "backfillers" that leads to a remarkably low background noise even in the presence of complex sample matrixes. A wide range of surface compositions have been investigated, and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety, and forensic analysis.

Using High Spatial Resolution to Improve BOLD fMRI Detection at 3T

PubMed Central

Claise, Béatrice; Jean, Betty

2015-01-01

For different functional magnetic resonance imaging experiments using blood oxygenation level-dependent (BOLD) contrast, the acquisition of T 2*-weighted scans at a high spatial resolution may be advantageous in terms of time-course signal-to-noise ratio and of BOLD sensitivity when the regions are prone to susceptibility artifacts. In this study, we explore this solution by examining how spatial resolution influences activations elicited when appetizing food pictures are viewed. Twenty subjects were imaged at 3 T with two different voxel volumes, 3.4 μl and 27 μl. Despite the diminution of brain coverage, we found that high-resolution acquisition led to a better detection of activations. Though known to suffer to different degrees from susceptibility artifacts, the activations detected by high spatial resolution were notably consistent with those reported in published activation likelihood estimation meta-analyses, corresponding to taste-responsive regions. Furthermore, these regions were found activated bilaterally, in contrast with previous findings. Both the reduction of partial volume effect, which improves BOLD contrast, and the mitigation of susceptibility artifact, which boosts the signal to noise ratio in certain regions, explained the better detection noted with high resolution. The present study provides further evidences that high spatial resolution is a valuable solution for human BOLD fMRI, especially for studying food-related stimuli. PMID:26550990

ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification.

PubMed

Bao, Riyue; Hernandez, Kyle; Huang, Lei; Kang, Wenjun; Bartom, Elizabeth; Onel, Kenan; Volchenboum, Samuel; Andrade, Jorge

2015-01-01

Whole exome sequencing has facilitated the discovery of causal genetic variants associated with human diseases at deep coverage and low cost. In particular, the detection of somatic mutations from tumor/normal pairs has provided insights into the cancer genome. Although there is an abundance of publicly-available software for the detection of germline and somatic variants, concordance is generally limited among variant callers and alignment algorithms. Successful integration of variants detected by multiple methods requires in-depth knowledge of the software, access to high-performance computing resources, and advanced programming techniques. We present ExScalibur, a set of fully automated, highly scalable and modulated pipelines for whole exome data analysis. The suite integrates multiple alignment and variant calling algorithms for the accurate detection of germline and somatic mutations with close to 99% sensitivity and specificity. ExScalibur implements streamlined execution of analytical modules, real-time monitoring of pipeline progress, robust handling of errors and intuitive documentation that allows for increased reproducibility and sharing of results and workflows. It runs on local computers, high-performance computing clusters and cloud environments. In addition, we provide a data analysis report utility to facilitate visualization of the results that offers interactive exploration of quality control files, read alignment and variant calls, assisting downstream customization of potential disease-causing mutations. ExScalibur is open-source and is also available as a public image on Amazon cloud.

Reality of Single Circulating Tumor Cell Sequencing for Molecular Diagnostics in Pancreatic Cancer.

PubMed

Court, Colin M; Ankeny, Jacob S; Sho, Shonan; Hou, Shuang; Li, Qingyu; Hsieh, Carolyn; Song, Min; Liao, Xinfang; Rochefort, Matthew M; Wainberg, Zev A; Graeber, Thomas G; Tseng, Hsian-Rong; Tomlinson, James S

2016-09-01

To understand the potential and limitations of circulating tumor cell (CTC) sequencing for molecular diagnostics, we investigated the feasibility of identifying the ubiquitous KRAS mutation in single CTCs from pancreatic cancer (PC) patients. We used the NanoVelcro/laser capture microdissection CTC platform, combined with whole genome amplification and KRAS Sanger sequencing. We assessed both KRAS codon-12 coverage and the degree that allele dropout during whole genome amplification affected the detection of KRAS mutations from single CTCs. We isolated 385 single cells, 163 from PC cell lines and 222 from the blood of 12 PC patients, and obtained KRAS sequence coverage in 218 of 385 single cells (56.6%). For PC cell lines with known KRAS mutations, single mutations were detected in 67% of homozygous cells but only 37.4% of heterozygous single cells, demonstrating that both coverage and allele dropout are important causes of mutation detection failure from single cells. We could detect KRAS mutations in CTCs from 11 of 12 patients (92%) and 33 of 119 single CTCs sequenced, resulting in a KRAS mutation detection rate of 27.7%. Importantly, KRAS mutations were never found in the 103 white blood cells sequenced. Sequencing of groups of cells containing between 1 and 100 cells determined that at least 10 CTCs are likely required to reliably assess KRAS mutation status from CTCs. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Cloud and Aerosol Retrieval for the 2001 GLAS Satellite Lidar Mission

NASA Technical Reports Server (NTRS)

Hart, William D.; Palm, Stephen P.; Spinhirne, James D.

2000-01-01

The Geoscience Laser Altimeter System (GLAS) is scheduled for launch in July of 2001 aboard the Ice, Cloud and Land Elevation Satellite (ICESAT). In addition to being a precision altimeter for mapping the height of the Earth's icesheets, GLAS will be an atmospheric lidar, sensitive enough to detect gaseous, aerosol, and cloud backscatter signals, at horizontal and vertical resolutions of 175 and 75m, respectively. GLAS will be the first lidar to produce temporally continuous atmospheric backscatter profiles with nearly global coverage (94-degree orbital inclination). With a projected operational lifetime of five years, GLAS will collect approximately six billion lidar return profiles. The large volume of data dictates that operational analysis algorithms, which need to keep pace with the data yield of the instrument, must be efficient. So, we need to evaluate the ability of operational algorithms to detect atmospheric constituents that affect global climate. We have to quantify, in a statistical manner, the accuracy and precision of GLAS cloud and aerosol observations. Our poster presentation will show the results of modeling studies that are designed to reveal the effectiveness and sensitivity of GLAS in detecting various atmospheric cloud and aerosol features. The studies consist of analyzing simulated lidar returns. Simulation cases are constructed either from idealized renditions of atmospheric cloud and aerosol layers or from data obtained by the NASA ER-2 Cloud Lidar System (CLS). The fabricated renditions permit quantitative evaluations of operational algorithms to retrieve cloud and aerosol parameters. The use of observational data permits the evaluations of performance for actual atmospheric conditions. The intended outcome of the presentation is that climatology community will be able to use the results of these studies to evaluate and quantify the impact of GLAS data upon atmospheric modeling efforts.

Cost-effectiveness of community-based practitioner programmes in Ethiopia, Indonesia and Kenya.

PubMed

McPake, Barbara; Edoka, Ijeoma; Witter, Sophie; Kielmann, Karina; Taegtmeyer, Miriam; Dieleman, Marjolein; Vaughan, Kelsey; Gama, Elvis; Kok, Maryse; Datiko, Daniel; Otiso, Lillian; Ahmed, Rukhsana; Squires, Neil; Suraratdecha, Chutima; Cometto, Giorgio

2015-09-01

To assess the cost-effectiveness of community-based practitioner programmes in Ethiopia, Indonesia and Kenya. Incremental cost-effectiveness ratios for the three programmes were estimated from a government perspective. Cost data were collected for 2012. Life years gained were estimated based on coverage of reproductive, maternal, neonatal and child health services. For Ethiopia and Kenya, estimates of coverage before and after the implementation of the programme were obtained from empirical studies. For Indonesia, coverage of health service interventions was estimated from routine data. We used the Lives Saved Tool to estimate the number of lives saved from changes in reproductive, maternal, neonatal and child health-service coverage. Gross domestic product per capita was used as the reference willingness-to-pay threshold value. The estimated incremental cost per life year gained was 82 international dollars ($)in Kenya, $999 in Ethiopia and $3396 in Indonesia. The results were most sensitive to uncertainty in the estimates of life-years gained. Based on the results of probabilistic sensitivity analysis, there was greater than 80% certainty that each programme was cost-effective. Community-based approaches are likely to be cost-effective for delivery of some essential health interventions where community-based practitioners operate within an integrated team supported by the health system. Community-based practitioners may be most appropriate in rural poor communities that have limited access to more qualified health professionals. Further research is required to understand which programmatic design features are critical to effectiveness.

Vectorial capacity and vector control: reconsidering sensitivity to parameters for malaria elimination.

PubMed

Brady, Oliver J; Godfray, H Charles J; Tatem, Andrew J; Gething, Peter W; Cohen, Justin M; McKenzie, F Ellis; Perkins, T Alex; Reiner, Robert C; Tusting, Lucy S; Sinka, Marianne E; Moyes, Catherine L; Eckhoff, Philip A; Scott, Thomas W; Lindsay, Steven W; Hay, Simon I; Smith, David L

2016-02-01

Major gains have been made in reducing malaria transmission in many parts of the world, principally by scaling-up coverage with long-lasting insecticidal nets and indoor residual spraying. Historically, choice of vector control intervention has been largely guided by a parameter sensitivity analysis of George Macdonald's theory of vectorial capacity that suggested prioritizing methods that kill adult mosquitoes. While this advice has been highly successful for transmission suppression, there is a need to revisit these arguments as policymakers in certain areas consider which combinations of interventions are required to eliminate malaria. Using analytical solutions to updated equations for vectorial capacity we build on previous work to show that, while adult killing methods can be highly effective under many circumstances, other vector control methods are frequently required to fill effective coverage gaps. These can arise due to pre-existing or developing mosquito physiological and behavioral refractoriness but also due to additive changes in the relative importance of different vector species for transmission. Furthermore, the optimal combination of interventions will depend on the operational constraints and costs associated with reaching high coverage levels with each intervention. Reaching specific policy goals, such as elimination, in defined contexts requires increasingly non-generic advice from modelling. Our results emphasize the importance of measuring baseline epidemiology, intervention coverage, vector ecology and program operational constraints in predicting expected outcomes with different combinations of interventions. © The Author 2016. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.

Modelling the implications of moving towards universal coverage in Tanzania.

PubMed

Borghi, Josephine; Mtei, Gemini; Ally, Mariam

2012-03-01

A model was developed to assess the impact of possible moves towards universal coverage in Tanzania over a 15-year time frame. Three scenarios were considered: maintaining the current situation ('the status quo'); expanded health insurance coverage (the estimated maximum achievable coverage in the absence of premium subsidies, coverage restricted to those who can pay); universal coverage to all (government revenues used to pay the premiums for the poor). The model estimated the costs of delivering public health services and all health services to the population as a proportion of Gross Domestic Product (GDP), and forecast revenue from user fees and insurance premiums. Under the status quo, financial protection is provided to 10% of the population through health insurance schemes, with the remaining population benefiting from subsidized user charges in public facilities. Seventy-six per cent of the population would benefit from financial protection through health insurance under the expanded coverage scenario, and 100% of the population would receive such protection through a mix of insurance cover and government funding under the universal coverage scenario. The expanded and universal coverage scenarios have a significant effect on utilization levels, especially for public outpatient care. Universal coverage would require an initial doubling in the proportion of GDP going to the public health system. Government health expenditure would increase to 18% of total government expenditure. The results are sensitive to the cost of health system strengthening, the level of real GDP growth, provider reimbursement rates and administrative costs. Promoting greater cross-subsidization between insurance schemes would provide sufficient resources to finance universal coverage. Alternately, greater tax funding for health could be generated through an increase in the rate of Value-Added Tax (VAT) or expanding the income tax base. The feasibility and sustainability of efforts to promote universal coverage will depend on the ability of the system to contain costs.

HPLC-MRM relative quantification analysis of fatty acids based on a novel derivatization strategy.

PubMed

Cai, Tie; Ting, Hu; Xin-Xiang, Zhang; Jiang, Zhou; Jin-Lan, Zhang

2014-12-07

Fatty acids (FAs) are associated with a series of diseases including tumors, diabetes, and heart diseases. As potential biomarkers, FAs have attracted increasing attention from both biological researchers and the pharmaceutical industry. However, poor ionization efficiency, extreme diversity, strict dependence on internal standards and complicated multiple reaction monitoring (MRM) optimization protocols have challenged efforts to quantify FAs. In this work, a novel derivatization strategy based on 2,4-bis(diethylamino)-6-hydrazino-1,3,5-triazine was developed to enable quantification of FAs. The sensitivity of FA detection was significantly enhanced as a result of the derivatization procedure. FA quantities as low as 10 fg could be detected by high-performance liquid chromatography coupled with triple-quadrupole mass spectrometry. General MRM conditions were developed for any FA, which facilitated the quantification and extended the application of the method. The FA quantification strategy based on HPLC-MRM was carried out using deuterated derivatization reagents. "Heavy" derivatization reagents were used as internal standards (ISs) to minimize matrix effects. Prior to statistical analysis, amounts of each FA species were normalized by their corresponding IS, which guaranteed the accuracy and reliability of the method. FA changes in plasma induced by ageing were studied using this strategy. Several FA species were identified as potential ageing biomarkers. The sensitivity, accuracy, reliability, and full coverage of the method ensure that this strategy has strong potential for both biomarker discovery and lipidomic research.

A Hybrid Memetic Framework for Coverage Optimization in Wireless Sensor Networks.

PubMed

Chen, Chia-Pang; Mukhopadhyay, Subhas Chandra; Chuang, Cheng-Long; Lin, Tzu-Shiang; Liao, Min-Sheng; Wang, Yung-Chung; Jiang, Joe-Air

2015-10-01

One of the critical concerns in wireless sensor networks (WSNs) is the continuous maintenance of sensing coverage. Many particular applications, such as battlefield intrusion detection and object tracking, require a full-coverage at any time, which is typically resolved by adding redundant sensor nodes. With abundant energy, previous studies suggested that the network lifetime can be maximized while maintaining full coverage through organizing sensor nodes into a maximum number of disjoint sets and alternately turning them on. Since the power of sensor nodes is unevenly consumed over time, and early failure of sensor nodes leads to coverage loss, WSNs require dynamic coverage maintenance. Thus, the task of permanently sustaining full coverage is particularly formulated as a hybrid of disjoint set covers and dynamic-coverage-maintenance problems, and both have been proven to be nondeterministic polynomial-complete. In this paper, a hybrid memetic framework for coverage optimization (Hy-MFCO) is presented to cope with the hybrid problem using two major components: 1) a memetic algorithm (MA)-based scheduling strategy and 2) a heuristic recursive algorithm (HRA). First, the MA-based scheduling strategy adopts a dynamic chromosome structure to create disjoint sets, and then the HRA is utilized to compensate the loss of coverage by awaking some of the hibernated nodes in local regions when a disjoint set fails to maintain full coverage. The results obtained from real-world experiments using a WSN test-bed and computer simulations indicate that the proposed Hy-MFCO is able to maximize sensing coverage while achieving energy efficiency at the same time. Moreover, the results also show that the Hy-MFCO significantly outperforms the existing methods with respect to coverage preservation and energy efficiency.

Resolution Enhanced Magnetic Sensing System for Wide Coverage Real Time UXO Detection

NASA Astrophysics Data System (ADS)

Zalevsky, Zeev; Bregman, Yuri; Salomonski, Nizan; Zafrir, Hovav

2012-09-01

In this paper we present a new high resolution automatic detection algorithm based upon a Wavelet transform and then validate it in marine related experiments. The proposed approach allows obtaining an automatic detection in a very low signal to noise ratios. The amount of calculations is reduced, the magnetic trend is depressed and the probability of detection/ false alarm rate can easily be controlled. Moreover, the algorithm enables to distinguish between close targets. In the algorithm we use the physical dependence of the magnetic field of a magnetic dipole in order to define a Wavelet mother function that later on can detect magnetic targets modeled as dipoles and embedded in noisy surrounding, at improved resolution. The proposed algorithm was realized on synthesized targets and then validated in field experiments involving a marine surface-floating system for wide coverage real time unexploded ordinance (UXO) detection and mapping. The detection probability achieved in the marine experiment was above 90%. The horizontal radial error of most of the detected targets was only 16 m and two baseline targets that were immersed about 20 m one to another could easily be distinguished.

[The social representation that adolescents from Jalisco, Mexico have of early detection of breast cancer].

PubMed

Tapia Curiel, Amparo; Villaseñor Farías, Martha; Lidia Nuño Gutiérrez, Bertha; Rodríguez Carlos, Aída Araceli; Salas González, Efraín; López López, José Luis

2014-10-01

To describe the social representation that adolescents from Jalisco, Mexico, have of early detection of breast cancer. Qualitative cross, analytical interpretative and based on the theory of social representations. Non-probability sampling. Contact schools in basic education level of 7municipalities of the State of Jalisco, Mexico, through various government and educational institutions. A hundred thirty five schooled adolescents, men and women. Interview with 12 focus group 8-12participants and 1 with 18participants. The interviews were transcribed in Atlas Ti program version 4.1 for a semiotic analysis to identify components of social representation. The precocious detection linked itself to the decrease of deaths for cancer of breast, long treatments and mastectomy, but little coverage was perceived to the mammary health of the teenager. They refer as limiter elements of the precocious detection the aspects of kind, psychological and of access to the information and services of health; since facilitators there was mentioned the transition of the limiter elements to facilitators. A favorable panorama appears on the level of awareness of the teenagers on his mammary health, identifying as a sector highly sensitive to the information about cancer of breast and with disposition to effect actions of early detection; there are identified as important challenge the generation of campaigns, educational materials and spaces of health focused on the teenager. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

Clinical outcome of subchromosomal events detected by whole‐genome noninvasive prenatal testing

PubMed Central

Helgeson, J.; Wardrop, J.; Boomer, T.; Almasri, E.; Paxton, W. B.; Saldivar, J. S.; Dharajiya, N.; Monroe, T. J.; Farkas, D. H.; Grosu, D. S.

2015-01-01

Abstract Objective A novel algorithm to identify fetal microdeletion events in maternal plasma has been developed and used in clinical laboratory‐based noninvasive prenatal testing. We used this approach to identify the subchromosomal events 5pdel, 22q11del, 15qdel, 1p36del, 4pdel, 11qdel, and 8qdel in routine testing. We describe the clinical outcomes of those samples identified with these subchromosomal events. Methods Blood samples from high‐risk pregnant women submitted for noninvasive prenatal testing were analyzed using low coverage whole genome massively parallel sequencing. Sequencing data were analyzed using a novel algorithm to detect trisomies and microdeletions. Results In testing 175 393 samples, 55 subchromosomal deletions were reported. The overall positive predictive value for each subchromosomal aberration ranged from 60% to 100% for cases with diagnostic and clinical follow‐up information. The total false positive rate was 0.0017% for confirmed false positives results; false negative rate and sensitivity were not conclusively determined. Conclusion Noninvasive testing can be expanded into the detection of subchromosomal copy number variations, while maintaining overall high test specificity. In the current setting, our results demonstrate high positive predictive values for testing of rare subchromosomal deletions. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd. PMID:26088833

Distributed measurement of acoustic vibration location with frequency multiplexed phase-OTDR

NASA Astrophysics Data System (ADS)

Iida, Daisuke; Toge, Kunihiro; Manabe, Tetsuya

2017-07-01

All-fiber distributed vibration sensing is attracting attention in relation to structural health monitoring because it is cost effective, offers high coverage of the monitored area and can detect various structural problems. And in particular the demand for high-speed vibration sensing operating at more than 10 kHz has increased because high frequency vibration indicates high energy and severe trouble in the monitored object. Optical fiber vibration sensing with phase-sensitive optical time domain reflectometry (phase-OTDR) has long been studied because it can be used for distributed vibration sensing in optical fiber. However, pulse reflectometry such as OTDR cannot measure high-frequency vibration whose cycle is shorter than the repetition time of the OTDR. That is, the maximum detectable frequency depends on fiber length. In this paper, we describe a vibration sensing technique with frequency-multiplexed OTDR that can detect the entire distribution of a high-frequency vibration thus allowing us to locate a high-speed vibration point. We can measure the position, frequency and dynamic change of a high-frequency vibration whose cycle is shorter than the repetition time. Both frequency and position are visualized simultaneously for a 5-km fiber with an 80-kHz frequency response and a 20-m spatial resolution.

On the Ability of Space-Based Passive and Active Remote Sensing Observations of CO2 to Detect Flux Perturbations to the Carbon Cycle

NASA Astrophysics Data System (ADS)

Crowell, Sean M. R.; Randolph Kawa, S.; Browell, Edward V.; Hammerling, Dorit M.; Moore, Berrien; Schaefer, Kevin; Doney, Scott C.

2018-01-01

Space-borne observations of CO2 are vital to gaining understanding of the carbon cycle in regions of the world that are difficult to measure directly, such as the tropical terrestrial biosphere, the high northern and southern latitudes, and in developing nations such as China. Measurements from passive instruments such as GOSAT and OCO-2, however, are constrained by solar zenith angle limitations as well as sensitivity to the presence of clouds and aerosols. Active measurements such as those in development for the Active Sensing of CO2 Emissions over Nights, Days and Seasons (ASCENDS) mission show strong potential for making measurements in the high-latitude winter and in cloudy regions. In this work we examine the enhanced flux constraint provided by the improved coverage from an active measurement such as ASCENDS. The simulation studies presented here show that with sufficient precision, ASCENDS will detect permafrost thaw and fossil fuel emissions shifts at annual and seasonal time scales, even in the presence of transport errors, representativeness errors, and biogenic flux errors. While OCO-2 can detect some of these perturbations at the annual scale, the seasonal sampling provided by ASCENDS provides the stronger constraint.

Detection of HIV-1 p24 Gag in plasma by a nanoparticle-based bio-barcode-amplification method.

PubMed

Kim, Eun-Young; Stanton, Jennifer; Korber, Bette T M; Krebs, Kendall; Bogdan, Derek; Kunstman, Kevin; Wu, Samuel; Phair, John P; Mirkin, Chad A; Wolinsky, Steven M

2008-06-01

Detection of HIV-1 in patients is limited by the sensitivity and selectivity of available tests. The nanotechnology-based bio-barcode-amplification method offers an innovative approach to detect specific HIV-1 antigens from diverse HIV-1 subtypes. We evaluated the efficacy of this protein-detection method in detecting HIV-1 in men enrolled in the Chicago component of the Multicenter AIDS Cohort Study (MACS). The method relies on magnetic microparticles with antibodies that specifically bind the HIV-1 p24 Gag protein and nanoparticles that are encoded with DNA and antibodies that can sandwich the target protein captured by the microparticle-bound antibodies. The aggregate sandwich structures are magnetically separated from solution, and treated to remove the conjugated barcode DNA. The DNA barcodes (hundreds per target) were identified by a nanoparticle-based detection method that does not rely on PCR. Of 112 plasma samples from HIV-1-infected subjects, 111 were positive for HIV-1 p24 Gag protein (range: 0.11-71.5 ng/ml of plasma) by the bio-barcode-amplification method. HIV-1 p24 Gag protein was detected in only 23 out of 112 men by the conventional ELISA. A total of 34 uninfected subjects were negative by both tests. Thus, the specificity of the bio-barcode-amplification method was 100% and the sensitivity 99%. The bio-barcode-amplification method detected HIV-1 p24 Gag protein in plasma from all study subjects with less than 200 CD4(+) T cells/microl of plasma (100%) and 19 out of 20 (95%) HIV-1-infected men who had less than 50 copies/ml of plasma of HIV-1 RNA. In a separate group of 60 diverse international isolates, representative of clades A, B, C and D and circulating recombinant forms CRF01_AE and CRF02_AG, the bio-barcode-amplification method identified the presence of virus correctly. The bio-barcode-amplification method was superior to the conventional ELISA assay for the detection of HIV-1 p24 Gag protein in plasma with a breadth of coverage for diverse HIV-1 subtypes. Because the bio-barcode-amplification method does not require enzymatic amplification, this method could be translated into a robust point-of-care test.

Abnormal plasma DNA profiles in early ovarian cancer using a non-invasive prenatal testing platform: implications for cancer screening.

PubMed

Cohen, Paul A; Flowers, Nicola; Tong, Stephen; Hannan, Natalie; Pertile, Mark D; Hui, Lisa

2016-08-24

Non-invasive prenatal testing (NIPT) identifies fetal aneuploidy by sequencing cell-free DNA in the maternal plasma. Pre-symptomatic maternal malignancies have been incidentally detected during NIPT based on abnormal genomic profiles. This low coverage sequencing approach could have potential for ovarian cancer screening in the non-pregnant population. Our objective was to investigate whether plasma DNA sequencing with a clinical whole genome NIPT platform can detect early- and late-stage high-grade serous ovarian carcinomas (HGSOC). This is a case control study of prospectively-collected biobank samples comprising preoperative plasma from 32 women with HGSOC (16 'early cancer' (FIGO I-II) and 16 'advanced cancer' (FIGO III-IV)) and 32 benign controls. Plasma DNA from cases and controls were sequenced using a commercial NIPT platform and chromosome dosage measured. Sequencing data were blindly analyzed with two methods: (1) Subchromosomal changes were called using an open source algorithm WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR). Genomic gains or losses ≥ 15 Mb were prespecified as "screen positive" calls, and mapped to recurrent copy number variations reported in an ovarian cancer genome atlas. (2) Selected whole chromosome gains or losses were reported using the routine NIPT pipeline for fetal aneuploidy. We detected 13/32 cancer cases using the subchromosomal analysis (sensitivity 40.6 %, 95 % CI, 23.7-59.4 %), including 6/16 early and 7/16 advanced HGSOC cases. Two of 32 benign controls had subchromosomal gains ≥ 15 Mb (specificity 93.8 %, 95 % CI, 79.2-99.2 %). Twelve of the 13 true positive cancer cases exhibited specific recurrent changes reported in HGSOC tumors. The NIPT pipeline resulted in one "monosomy 18" call from the cancer group, and two "monosomy X" calls in the controls. Low coverage plasma DNA sequencing used for prenatal testing detected 40.6 % of all HGSOC, including 38 % of early stage cases. Our findings demonstrate the potential of a high throughput sequencing platform to screen for early HGSOC in plasma based on characteristic multiple segmental chromosome gains and losses. The performance of this approach may be further improved by refining bioinformatics algorithms and targeting selected cancer copy number variations.

Change-Based Satellite Monitoring Using Broad Coverage and Targetable Sensing

NASA Technical Reports Server (NTRS)

Chien, Steve A.; Tran, Daniel Q.; Doubleday, Joshua R.; Doggett, Thomas

2013-01-01

A generic software framework analyzes data from broad coverage sweeps or general larger areas of interest. Change detection methods are used to extract subsets of directed swath areas that intersect areas of change. These areas are prioritized and allocated to targetable assets. This method is deployed in an automatic fashion, and has operated without human monitoring or intervention for sustained periods of time (months).

What You Can Learn from the 1979 Pacemakers.

ERIC Educational Resources Information Center

Brasler, Wayne

1980-01-01

Indicates that prizewinning school publications differ from good publications in having three qualities: wide-ranging content reflecting organized, creative approaches to coverage; intelligence and sensitivity in content; and thoughtful design. Includes illustrations from prizewinners. (TJ)

Crosscutting Airborne Remote Sensing Technologies for Oil and Gas and Earth Science Applications

NASA Technical Reports Server (NTRS)

Aubrey, A. D.; Frankenberg, C.; Green, R. O.; Eastwood, M. L.; Thompson, D. R.; Thorpe, A. K.

2015-01-01

Airborne imaging spectroscopy has evolved dramatically since the 1980s as a robust remote sensing technique used to generate 2-dimensional maps of surface properties over large spatial areas. Traditional applications for passive airborne imaging spectroscopy include interrogation of surface composition, such as mapping of vegetation diversity and surface geological composition. Two recent applications are particularly relevant to the needs of both the oil and gas as well as government sectors: quantification of surficial hydrocarbon thickness in aquatic environments and mapping atmospheric greenhouse gas components. These techniques provide valuable capabilities for petroleum seepage in addition to detection and quantification of fugitive emissions. New empirical data that provides insight into the source strength of anthropogenic methane will be reviewed, with particular emphasis on the evolving constraints enabled by new methane remote sensing techniques. Contemporary studies attribute high-strength point sources as significantly contributing to the national methane inventory and underscore the need for high performance remote sensing technologies that provide quantitative leak detection. Imaging sensors that map spatial distributions of methane anomalies provide effective techniques to detect, localize, and quantify fugitive leaks. Airborne remote sensing instruments provide the unique combination of high spatial resolution (<1 m) and large coverage required to directly attribute methane emissions to individual emission sources. This capability cannot currently be achieved using spaceborne sensors. In this study, results from recent NASA remote sensing field experiments focused on point-source leak detection, will be highlighted. This includes existing quantitative capabilities for oil and methane using state-of-the-art airborne remote sensing instruments. While these capabilities are of interest to NASA for assessment of environmental impact and global climate change, industry similarly seeks to detect and localize leaks of both oil and methane across operating fields. In some cases, higher sensitivities desired for upstream and downstream applications can only be provided by new airborne remote sensing instruments tailored specifically for a given application. There exists a unique opportunity for alignment of efforts between commercial and government sectors to advance the next generation of instruments to provide more sensitive leak detection capabilities, including those for quantitative source strength determination.

Joint Sensing/Sampling Optimization for Surface Drifting Mine Detection with High-Resolution Drift Model

DTIC Science & Technology

2012-09-01

as potential tools for large area detection coverage while being moderately inexpensive (Wettergren, Performance of Search via Track - Before - Detect for...via Track - Before - Detect for Distribute 34 Sensor Networks, 2008). These statements highlight three specific needs to further sensor network research...Bay hydrography. Journal of Marine Systems, 12, 221–236. Wettergren, T. A. (2008). Performance of search via track - before - detect for distributed

in silico Surveillance: evaluating outbreak detection with simulation models

PubMed Central

2013-01-01

Background Detecting outbreaks is a crucial task for public health officials, yet gaps remain in the systematic evaluation of outbreak detection protocols. The authors’ objectives were to design, implement, and test a flexible methodology for generating detailed synthetic surveillance data that provides realistic geographical and temporal clustering of cases and use to evaluate outbreak detection protocols. Methods A detailed representation of the Boston area was constructed, based on data about individuals, locations, and activity patterns. Influenza-like illness (ILI) transmission was simulated, producing 100 years of in silico ILI data. Six different surveillance systems were designed and developed using gathered cases from the simulated disease data. Performance was measured by inserting test outbreaks into the surveillance streams and analyzing the likelihood and timeliness of detection. Results Detection of outbreaks varied from 21% to 95%. Increased coverage did not linearly improve detection probability for all surveillance systems. Relaxing the decision threshold for signaling outbreaks greatly increased false-positives, improved outbreak detection slightly, and led to earlier outbreak detection. Conclusions Geographical distribution can be more important than coverage level. Detailed simulations of infectious disease transmission can be configured to represent nearly any conceivable scenario. They are a powerful tool for evaluating the performance of surveillance systems and methods used for outbreak detection. PMID:23343523

A Distributed and Energy-Efficient Algorithm for Event K-Coverage in Underwater Sensor Networks

PubMed Central

Jiang, Peng; Xu, Yiming; Liu, Jun

2017-01-01

For event dynamic K-coverage algorithms, each management node selects its assistant node by using a greedy algorithm without considering the residual energy and situations in which a node is selected by several events. This approach affects network energy consumption and balance. Therefore, this study proposes a distributed and energy-efficient event K-coverage algorithm (DEEKA). After the network achieves 1-coverage, the nodes that detect the same event compete for the event management node with the number of candidate nodes and the average residual energy, as well as the distance to the event. Second, each management node estimates the probability of its neighbor nodes’ being selected by the event it manages with the distance level, the residual energy level, and the number of dynamic coverage event of these nodes. Third, each management node establishes an optimization model that uses expectation energy consumption and the residual energy variance of its neighbor nodes and detects the performance of the events it manages as targets. Finally, each management node uses a constrained non-dominated sorting genetic algorithm (NSGA-II) to obtain the Pareto set of the model and the best strategy via technique for order preference by similarity to an ideal solution (TOPSIS). The algorithm first considers the effect of harsh underwater environments on information collection and transmission. It also considers the residual energy of a node and a situation in which the node is selected by several other events. Simulation results show that, unlike the on-demand variable sensing K-coverage algorithm, DEEKA balances and reduces network energy consumption, thereby prolonging the network’s best service quality and lifetime. PMID:28106837

RNA-seq: technical variability and sampling

PubMed Central

2011-01-01

Background RNA-seq is revolutionizing the way we study transcriptomes. mRNA can be surveyed without prior knowledge of gene transcripts. Alternative splicing of transcript isoforms and the identification of previously unknown exons are being reported. Initial reports of differences in exon usage, and splicing between samples as well as quantitative differences among samples are beginning to surface. Biological variation has been reported to be larger than technical variation. In addition, technical variation has been reported to be in line with expectations due to random sampling. However, strategies for dealing with technical variation will differ depending on the magnitude. The size of technical variance, and the role of sampling are examined in this manuscript. Results In this study three independent Solexa/Illumina experiments containing technical replicates are analyzed. When coverage is low, large disagreements between technical replicates are apparent. Exon detection between technical replicates is highly variable when the coverage is less than 5 reads per nucleotide and estimates of gene expression are more likely to disagree when coverage is low. Although large disagreements in the estimates of expression are observed at all levels of coverage. Conclusions Technical variability is too high to ignore. Technical variability results in inconsistent detection of exons at low levels of coverage. Further, the estimate of the relative abundance of a transcript can substantially disagree, even when coverage levels are high. This may be due to the low sampling fraction and if so, it will persist as an issue needing to be addressed in experimental design even as the next wave of technology produces larger numbers of reads. We provide practical recommendations for dealing with the technical variability, without dramatic cost increases. PMID:21645359

A Distributed and Energy-Efficient Algorithm for Event K-Coverage in Underwater Sensor Networks.

PubMed

Jiang, Peng; Xu, Yiming; Liu, Jun

2017-01-19

For event dynamic K-coverage algorithms, each management node selects its assistant node by using a greedy algorithm without considering the residual energy and situations in which a node is selected by several events. This approach affects network energy consumption and balance. Therefore, this study proposes a distributed and energy-efficient event K-coverage algorithm (DEEKA). After the network achieves 1-coverage, the nodes that detect the same event compete for the event management node with the number of candidate nodes and the average residual energy, as well as the distance to the event. Second, each management node estimates the probability of its neighbor nodes' being selected by the event it manages with the distance level, the residual energy level, and the number of dynamic coverage event of these nodes. Third, each management node establishes an optimization model that uses expectation energy consumption and the residual energy variance of its neighbor nodes and detects the performance of the events it manages as targets. Finally, each management node uses a constrained non-dominated sorting genetic algorithm (NSGA-II) to obtain the Pareto set of the model and the best strategy via technique for order preference by similarity to an ideal solution (TOPSIS). The algorithm first considers the effect of harsh underwater environments on information collection and transmission. It also considers the residual energy of a node and a situation in which the node is selected by several other events. Simulation results show that, unlike the on-demand variable sensing K-coverage algorithm, DEEKA balances and reduces network energy consumption, thereby prolonging the network's best service quality and lifetime.

Hospitalizations for ambulatory care-sensitive conditions, Minas Gerais, Southeastern Brazil, 2000 and 2010

PubMed Central

Rodrigues-Bastos, Rita Maria; Campos, Estela Márcia Saraiva; Ribeiro, Luiz Cláudio; Bastos, Mauro Gomes; Bustamante-Teixeira, Maria Teresa

2014-01-01

OBJECTIVE To analyze hospitalization rates and the proportion of deaths due to ambulatory care-sensitive hospitalizations and to characterize them according to coverage by the Family Health Strategy, a primary health care guidance program. METHODS An ecological study comprising 853 municipalities in the state of Minas Gerais, under the purview of 28 regional health care units, was conducted. We used data from the Hospital Information System of the Brazilian Unified Health System. Ambulatory care-sensitive hospitalizations in 2000 and 2010 were compared. Population data were obtained from the demographic censuses. RESULTS The number of ambulatory care-sensitive hospitalizations declined from 20.75/1,000 inhabitants [standard deviation (SD) = 10.42) in 2000 to 14.92/thousand inhabitants (SD = 10.04) in 2010 Heart failure was the most frequent cause in both years. Hospitalizations rates for hypertension, asthma, and diabetes mellitus, decreased, whereas those for angina pectoris, prenatal and birth disorders, kidney and urinary tract infections, and other acute infections increased. Hospitalization durations and the proportion of deaths due to ambulatory care-sensitive hospitalizations increased significantly. CONCLUSIONS Mean hospitalization rates for sensitive conditions were significantly lower in 2010 than in 2000, but no correlation was found with regard to the expansion of the population coverage of the Family Health Strategy. Hospitalization rates and proportion of deaths were different between the various health care regions in the years evaluated, indicating a need to prioritize the primary health care with high efficiency and quality. PMID:26039399

The Advanced Pair Telescope (APT) Mission Concept

NASA Technical Reports Server (NTRS)

Hunter, Stanley; Buckley, James H.

2008-01-01

We present a mission concept for the Advanced Pair Telescope (APT), a high-energy gamma-ray instrument with an order of magnitude improvement in sensitivity, 6 sr field of view, and angular resolution a factor of 3-10 times that of GLAST. With its very wide instantaneous field-of-view and large effective area, this instrument would be capable of detecting GRBs at very large redshifts, would enable a very high resolution study of SNRs and PWN, and could provide hour-scale temporal resolution of transients from many AGN and galactic sources. The APT instrument will consist of a Xe time-projection-chamber tracker that bridges the energy regime between Compton scattering and pair production and will provide an unprecedented improvement in angular resolution; a thick scintillating-fiber trackerlcalorimeter that will provide sensitivity and energy resolution to higher energies and will possess a factor of 10 improvement in geometric factor over GLAST; and an anticoincidence detector using scintillator-tiles to reject charged particles. After the anticipated 10-years of GLAST operation , the APT instrument would provide continued coverage of the critial high-energy gamma-ray band (between 30 MeV to 100 GeV), providing an essential component of broad-band multiwavelength studies of the high-energy universe.

Enhancing the performance of coherent OTDR systems with polarization diversity complementary codes.

PubMed

Dorize, Christian; Awwad, Elie

2018-05-14

Monitoring the optical phase change in a fiber enables a wide range of applications where fast phase variations are induced by acoustic signals or by vibrations in general. However, the quality of the estimated fiber response strongly depends on the method used to modulate the light sent to the fiber and capture the variations of the optical field. In this paper, we show that distributed optical fiber sensing systems can advantageously exploit techniques from the telecommunication domain, as those used in coherent optical transmission, to enhance their performance in detecting mechanical events, while jointly offering a simpler setup than widespread pulse-cloning or spectral-sweep based schemes with acousto-optic modulators. We periodically capture an overall fiber Jones matrix estimate thanks to a novel probing technique using two mutually orthogonal complementary (Golay) pairs of binary sequences applied simultaneously in phase and quadrature on two orthogonal polarization states. A perfect channel response estimation of the sensor array is achieved, subject to conditions detailed in the paper, thus enhancing the sensitivity and bandwidth of coherent ϕ-OTDR systems. High sensitivity, linear response, and bandwidth coverage up to 18 kHz are demonstrated with a sensor array composed of 10 fiber Bragg gratings (FBGs).

Sequence investigation of 34 forensic autosomal STRs with massively parallel sequencing.

PubMed

Zhang, Suhua; Niu, Yong; Bian, Yingnan; Dong, Rixia; Liu, Xiling; Bao, Yun; Jin, Chao; Zheng, Hancheng; Li, Chengtao

2018-05-01

STRs vary not only in the length of the repeat units and the number of repeats but also in the region with which they conform to an incremental repeat pattern. Massively parallel sequencing (MPS) offers new possibilities in the analysis of STRs since they can simultaneously sequence multiple targets in a single reaction and capture potential internal sequence variations. Here, we sequenced 34 STRs applied in the forensic community of China with a custom-designed panel. MPS performance were evaluated from sequencing reads analysis, concordance study and sensitivity testing. High coverage sequencing data were obtained to determine the constitute ratios and heterozygous balance. No actual inconsistent genotypes were observed between capillary electrophoresis (CE) and MPS, demonstrating the reliability of the panel and the MPS technology. With the sequencing data from the 200 investigated individuals, 346 and 418 alleles were obtained via CE and MPS technologies at the 34 STRs, indicating MPS technology provides higher discrimination than CE detection. The whole study demonstrated that STR genotyping with the custom panel and MPS technology has the potential not only to reveal length and sequence variations but also to satisfy the demands of high throughput and high multiplexing with acceptable sensitivity.

Enhancing the performance of coherent OTDR systems with polarization diversity complementary codes

NASA Astrophysics Data System (ADS)

Dorize, Christian; Awwad, Elie

2018-05-01

Monitoring the optical phase change in a fiber enables a wide range of applications where fast phase variations are induced by acoustic signals or vibrations in general. However, the quality of the estimated fiber response strongly depends on the method used to modulate the light sent to the fiber and capture the variations of the optical field. In this paper, we show that distributed optical fiber sensing systems can advantageously exploit techniques from the telecommunication domain, as those used in coherent optical transmission, to enhance their performance in detecting mechanical events, while jointly offering a simpler setup than widespread pulse-cloning or spectral-sweep based schemes with acousto-optic modulators. We periodically capture an overall fiber Jones matrix estimate thanks to a novel probing technique using two mutually orthogonal complementary (Golay) pairs of binary sequences applied simultaneously in phase and quadrature on two orthogonal polarization states. A perfect channel response estimation of the sensor array is achieved, subject to conditions detailed in the paper, thus enhancing the sensitivity and bandwidth of coherent phase-OTDR systems. High sensitivity, linear response, and bandwidth coverage up to 18 kHz are demonstrated with a sensor array composed of 10 fiber Bragg gratings (FBGs).

COACH: profile-profile alignment of protein families using hidden Markov models.

PubMed

Edgar, Robert C; Sjölander, Kimmen

2004-05-22

Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. COACH is freely available from www.drive5.com/lobster

Fault tolerant system with imperfect coverage, reboot and server vacation

NASA Astrophysics Data System (ADS)

Jain, Madhu; Meena, Rakesh Kumar

2017-06-01

This study is concerned with the performance modeling of a fault tolerant system consisting of operating units supported by a combination of warm and cold spares. The on-line as well as warm standby units are subject to failures and are send for the repair to a repair facility having single repairman which is prone to failure. If the failed unit is not detected, the system enters into an unsafe state from which it is cleared by the reboot and recovery action. The server is allowed to go for vacation if there is no failed unit present in the system. Markov model is developed to obtain the transient probabilities associated with the system states. Runge-Kutta method is used to evaluate the system state probabilities and queueing measures. To explore the sensitivity and cost associated with the system, numerical simulation is conducted.

Material condition assessment with eddy current sensors

NASA Technical Reports Server (NTRS)

Goldfine, Neil J. (Inventor); Washabaugh, Andrew P. (Inventor); Sheiretov, Yanko K. (Inventor); Schlicker, Darrell E. (Inventor); Lyons, Robert J. (Inventor); Windoloski, Mark D. (Inventor); Craven, Christopher A. (Inventor); Tsukernik, Vladimir B. (Inventor); Grundy, David C. (Inventor)

2010-01-01

Eddy current sensors and sensor arrays are used for process quality and material condition assessment of conducting materials. In an embodiment, changes in spatially registered high resolution images taken before and after cold work processing reflect the quality of the process, such as intensity and coverage. These images also permit the suppression or removal of local outlier variations. Anisotropy in a material property, such as magnetic permeability or electrical conductivity, can be intentionally introduced and used to assess material condition resulting from an operation, such as a cold work or heat treatment. The anisotropy is determined by sensors that provide directional property measurements. The sensor directionality arises from constructs that use a linear conducting drive segment to impose the magnetic field in a test material. Maintaining the orientation of this drive segment, and associated sense elements, relative to a material edge provides enhanced sensitivity for crack detection at edges.

The S201 far-ultraviolet imaging survey - A summary of results and implications for future surveys

NASA Technical Reports Server (NTRS)

Carruthers, G. R.; Page, T.

1984-01-01

The results from all-sky surveys with the S201 FUV camera/spectrograph from the moon during the Apollo 16 mission are summarized with respect to implications for future UV all-sky surveys. The scans provided imagery of 10 fields, each 20 deg in diameter, in the wavelength ranges 1050-1600 A and 1250-1600 A. Best detection thresholds were obtained with 10 and 30 min exposures at 1400 A. Only 7 percent sky coverage was recorded, and then only down to 11th mag. A Mark II camera may be flown on the Shuttle on the Spartan 3 mission, as may be an all-reflector Schmidt telescope. An additional 20 percent of the sky will be mapped and microchannel intensification will increase the diffuse source sensitivity by two orders of magnitude. Several objects sighted with the S201 will be reviewed with the Mark II.

Nanoparticle functionalised small-core suspended-core fibre - a novel platform for efficient sensing.

PubMed

Doherty, Brenda; Csáki, Andrea; Thiele, Matthias; Zeisberger, Matthias; Schwuchow, Anka; Kobelke, Jens; Fritzsche, Wolfgang; Schmidt, Markus A

2017-02-01

Detecting small quantities of specific target molecules is of major importance within bioanalytics for efficient disease diagnostics. One promising sensing approach relies on combining plasmonically-active waveguides with microfluidics yielding an easy-to-use sensing platform. Here we introduce suspended-core fibres containing immobilised plasmonic nanoparticles surrounding the guiding core as a concept for an entirely integrated optofluidic platform for efficient refractive index sensing. Due to the extremely small optical core and the large adjacent microfluidic channels, over two orders of magnitude of nanoparticle coverage densities have been accessed with millimetre-long sample lengths showing refractive index sensitivities of 170 nm/RIU for aqueous analytes where the fibre interior is functionalised by gold nanospheres. Our concept represents a fully integrated optofluidic sensing system demanding small sample volumes and allowing for real-time analyte monitoring, both of which are highly relevant within invasive bioanalytics, particularly within molecular disease diagnostics and environmental science.

A 10 micron heterodyne receiver for ultra high resolution astronomical spectroscopy

NASA Technical Reports Server (NTRS)

Buhl, D.; Chin, G.; Faris, J.; Kostiuk, T.; Mumma, M. J.; Zipoy, D.

1980-01-01

An improved CO2 laser heterodyne spectrometer is examined. The present system uses reflective optics to eliminate refocusing at different wavelengths, and the local oscillator is a line-center-stabilized isotopic CO2 laser. A tunable diffraction grating makes possible easy and rapid selection of over 50 transitions per isotope of CO2. The IF (0 to 1.6 GHz) from the HgCdTe photomizer is analyzed by a 128-channel filter bank, consisting of 64 tunable 5-MHz filters and 64 fixed 25-MHz RF filters. These filters provide resolving powers of about 1,000,000 to 10,000,000 and velocity resolution of 50 to 250 m/sec; their output is synchronously detected, integrated, multiplexed and stored in a buffer memory for the desired integration period. Kitt Peak observations show the wide spectral coverage, wide mixer and electronics bandwidth, and high sensitivity of the system.

DNA Methyltransferase Activity Assays: Advances and Challenges

PubMed Central

Poh, Wan Jun; Wee, Cayden Pang Pee; Gao, Zhiqiang

2016-01-01

DNA methyltransferases (MTases), a family of enzymes that catalyse the methylation of DNA, have a profound effect on gene regulation. A large body of evidence has indicated that DNA MTase is potentially a predictive biomarker closely associated with genetic disorders and genetic diseases like cancer. Given the attention bestowed onto DNA MTases in molecular biology and medicine, highly sensitive detection of DNA MTase activity is essential in determining gene regulation, epigenetic modification, clinical diagnosis and therapeutics. Conventional techniques such as isotope labelling are effective, but they often require laborious sample preparation, isotope labelling, sophisticated equipment and large amounts of DNA, rendering them unsuitable for uses at point-of-care. Simple, portable, highly sensitive and low-cost assays are urgently needed for DNA MTase activity screening. In most recent technological advances, many alternative DNA MTase activity assays such as fluorescent, electrochemical, colorimetric and chemiluminescent assays have been proposed. In addition, many of them are coupled with nanomaterials and/or enzymes to significantly enhance their sensitivity. Herein we review the progress in the development of DNA MTase activity assays with an emphasis on assay mechanism and performance with some discussion on challenges and perspectives. It is hoped that this article will provide a broad coverage of DNA MTase activity assays and their latest developments and open new perspectives toward the development of DNA MTase activity assays with much improved performance for uses in molecular biology and clinical practice. PMID:26909112

Strain/species identification in metagenomes using genome-specific markers

PubMed Central

Tu, Qichao; He, Zhili; Zhou, Jizhong

2014-01-01

Shotgun metagenome sequencing has become a fast, cheap and high-throughput technology for characterizing microbial communities in complex environments and human body sites. However, accurate identification of microorganisms at the strain/species level remains extremely challenging. We present a novel k-mer-based approach, termed GSMer, that identifies genome-specific markers (GSMs) from currently sequenced microbial genomes, which were then used for strain/species-level identification in metagenomes. Using 5390 sequenced microbial genomes, 8 770 321 50-mer strain-specific and 11 736 360 species-specific GSMs were identified for 4088 strains and 2005 species (4933 strains), respectively. The GSMs were first evaluated against mock community metagenomes, recently sequenced genomes and real metagenomes from different body sites, suggesting that the identified GSMs were specific to their targeting genomes. Sensitivity evaluation against synthetic metagenomes with different coverage suggested that 50 GSMs per strain were sufficient to identify most microbial strains with ≥0.25× coverage, and 10% of selected GSMs in a database should be detected for confident positive callings. Application of GSMs identified 45 and 74 microbial strains/species significantly associated with type 2 diabetes patients and obese/lean individuals from corresponding gastrointestinal tract metagenomes, respectively. Our result agreed with previous studies but provided strain-level information. The approach can be directly applied to identify microbial strains/species from raw metagenomes, without the effort of complex data pre-processing. PMID:24523352

Mapping plastic greenhouse with medium spatial resolution satellite data: Development of a new spectral index

NASA Astrophysics Data System (ADS)

Yang, Dedi; Chen, Jin; Zhou, Yuan; Chen, Xiang; Chen, Xuehong; Cao, Xin

2017-06-01

Plastic greenhouses (PGs) are an important agriculture development technique to protect and control the growing environment for food crops. The extensive use of PGs can change the agriculture landscape and affects the local environment. Accurately mapping and estimating the coverage of PGs is a necessity to the strategic planning of modern agriculture. Unfortunately, PG mapping over large areas is methodologically challenging, as the medium spatial resolution satellite imagery (such as Landsat data) used for analysis lacks spatial details and spectral variations. To fill the gap, the paper proposes a new plastic greenhouse index (PGI) based on the spectral, sensitivity, and separability analysis of PGs using medium spatial resolution images. In the context of the Landsat Enhanced Thematic Mapper Plus (ETM+) imagery, the paper examines the effectiveness and capability of the proposed PGI. The results indicate that PGs in Landsat ETM+ image can be successfully detected by the PGI if the PG fraction is greater than 12% in a mixed pixel. A kappa coefficient of 0.83 and overall accuracy of 91.2% were achieved when applying the proposed PGI in the case of Weifang District, Shandong, China. These results show that the proposed index can be applied to identifying transparent PGs in atmospheric corrected Landsat image and has the potential for the digital mapping of plastic greenhouse coverage over a large area.

A SPR-based immunosensor for the detection of isoproturon.

PubMed

Gouzy, Marie-Françoise; Kess, Melanie; Krämer, Petra M

2009-02-15

The proof of principle of a reusable surface plasmon resonance (SPR)-based immunosensor for the monitoring of isoproturon (IPU), a selective and systemic herbicide, is presented. The detecting rat monoclonal anti-isoproturon antibody (mAb IOC 7E1) was reversibly immobilized through the use of a capture mouse anti-rat (kappa-chain) monoclonal antibody (mAb TIB 172), which was covalently immobilized on the sensor chip surface. Such strategy features a controlled binding of the captured detecting antibody as well as facilitates the surface regeneration. The capture of the anti-IPU mAb by the antibody (TIB 172) coated sensor surface could be carried out up to 120 times (immobilization/regeneration cycles) without any evidence of activity loss. With a high test midpoint and a low associated SPR signal, the direct detection format was shown to be unsuitable for the routine analysis of isoproturon. However, the limit of detection (LOD) could be easily enhanced by using a strategy based on a surface competition assay, which improved all immunosensor parameters. Moreover, the sensitivity and working range of the indirect format were found to be dependent on the surface density of the anti-IPU mAb IOC 7E1. As expected for competitive formats, the lowest surface coverage (0.5 ng/mm(2)) allowed a lower detection of the herbicide isoproturon with a calculated LOD of 0.1 microg/l, an IC(50) (50% inhibition) of 5.3+/-0.6 microg/l, and a working range (20-80% inhibition) of 1.3-16.3 microg/l.

Detection of a stellar flare at extreme ultraviolet wavelengths

NASA Technical Reports Server (NTRS)

Barstow, M. A.; Denby, M.; Pye, J. P.; Pankiewicz, G. S.; Bromage, G. E.; Gonzalez-Riestra, R.

1991-01-01

During the all-sky survey conducted by the Rosat Wide Field Camera, the binary flare star system BY Draconis was monitored with coverage by the IUE satellite far-UV and optical observations and by the Rosat X-ray telescope for part of the time. A stellar flare was detected in all four wavebands. This is the first unambiguous EUV detection of a flare and one of the widest simultaneous wavelength-range coverages obtained. The peak luminosity and total energy of this flare in the photon energy range 0.08-0.18 keV are comparable with the values obtained for a number of flares integrated over a larger energy range by Exosat satellite observations in 1983-86. It is concluded that radiation in the EUV carries away a substantial fraction of the total flare energy.

Wireless infrared computer control

NASA Astrophysics Data System (ADS)

Chen, George C.; He, Xiaofei

2004-04-01

Wireless mouse is not restricted by cable"s length and has advantage over its wired counterpart. However, all the mice available in the market have detection range less than 2 meters and angular coverage less than 180 degrees. Furthermore, commercial infrared mice are based on track ball and rollers to detect movements. This restricts them to be used in those occasions where users want to have dynamic movement, such as presentations and meetings etc. This paper presents our newly developed infrared wireless mouse, which has a detection range of 6 meters and angular coverage of 180 degrees. This new mouse uses buttons instead of traditional track ball and is developed to be a hand-held device like remote controller. It enables users to control cursor with a distance closed to computer and the mouse to be free from computer operation.

Analysis on the Change of Grassland Coverage in the Source Region of Three Rivers during 2000-2012

NASA Astrophysics Data System (ADS)

Luo, Chengfeng; Wang, Jiao; Liu, Meilin; Liu, Zhengjun

2014-03-01

The Source Region of Three Rivers (SRTR) has very important ecological functions which form an ecological security barrier for China's Qinghai-Tibet plateau. As the biggest nationally occuring nature reserve region in China, the ecological environment here is very fragile. In SRTR the grassland coverage is an effective detector to reflect the ecological environment condition, because it records the changing process of climatic and environmental sensitively. In recent years SRTR has been suffering pressures from both nature and social pressures. With MODIS data the study monitored the grassland coverage continuously in SRTR from 2000 to 2012. The density-model was adapted to estimate grassland coverage degree firstly. Then the degree of change and the change intensity, change type were used to judge the grassland coverage change trend comprehensively. For grassland coverage there was natural change annual or within the year, and the degree of change was used to judge if there was change or not. The grassland has another important characteristic, annual fluctuation, and it can be differed from sustained changes with change type. For grassland coverage, such continuous change, like improvement or degradation, and to what extent, has more guidance sense on specific production practice. On the base of change type and degree of change, change intensity was used to identify the change trend of the grassland coverage. The analysis results from our study show that steady state and fluctuation are two main change trends for the vegetation coverage in SRTR from 2000 to 2012. The conclusion of this paper can provide references in response to environment change research and in the regional ecological environmental protection project in SRTR.

Statistical-Mechanics-Inspired Optimization of Sensor Field Configuration for Detection of Mobile Targets (PREPRINT)

DTIC Science & Technology

2010-11-01

pected target motion. Along this line, Wettergren [5] analyzed the performance of the track - before - detect schemes for the sensor networks. Furthermore...dressed by Baumgartner and Ferrari [11] for the reorganization of the sensor field to achieve the maximum coverage. The track - before - detect -based optimal...confirming a target. In accordance with the track - before - detect paradigm [4], a moving target is detected if the kd (typically kd = 3 or 4) sensors detect

Experiment of constraining symmetry energy at supra-saturation density with π-/π+ at HIRFL-CSR

NASA Astrophysics Data System (ADS)

Zhang, Ming; Xiao, Zhi-Gang; Zhu, Sheng-Jiang

2010-08-01

The possibility of the experiment for constraining the symmetry energy Esym(ρ) at supra-densities via π-/π+ probe on the external target experiment of phase I (ETE(I)) with part coverage at forward angle at HIRFL-CSR is studied for the first time by using the isospin and momentum dependent hadronic transport model IBUU04. Based on the transport simulation with Au+Au collisions at 400 MeV/u, it is found that the differential π-/π+ ratios are more sensitive to Esym(ρ) at forward angles in laboratory reference, compared with the total yield ratio widely proposed. The insufficient coverage at lower transverse momentum maintains the sensitivity of the dependence of π-/π+ ratio on the Esym(ρ) at high density, indicating that the ETF (I) under construction in Lanzhou provides the possibility of performing the experiment for probing the asymmetric nuclear equation of state.

Large-scale mass spectrometric detection of variant peptides resulting from non-synonymous nucleotide differences

PubMed Central

Sheynkman, Gloria M.; Shortreed, Michael R.; Frey, Brian L.; Scalf, Mark; Smith, Lloyd M.

2013-01-01

Each individual carries thousands of non-synonymous single nucleotide variants (nsSNVs) in their genome, each corresponding to a single amino acid polymorphism (SAP) in the encoded proteins. It is important to be able to directly detect and quantify these variations at the protein level in order to study post-transcriptional regulation, differential allelic expression, and other important biological processes. However, such variant peptides are not generally detected in standard proteomic analyses, due to their absence from the generic databases that are employed for mass spectrometry searching. Here, we extend previous work that demonstrated the use of customized SAP databases constructed from sample-matched RNA-Seq data. We collected deep coverage RNA-Seq data from the Jurkat cell line, compiled the set of nsSNVs that are expressed, used this information to construct a customized SAP database, and searched it against deep coverage shotgun MS data obtained from the same sample. This approach enabled detection of 421 SAP peptides mapping to 395 nsSNVs. We compared these peptides to peptides identified from a large generic search database containing all known nsSNVs (dbSNP) and found that more than 70% of the SAP peptides from this dbSNP-derived search were not supported by the RNA-Seq data, and thus are likely false positives. Next, we increased the SAP coverage from the RNA-Seq derived database by utilizing multiple protease digestions, thereby increasing variant detection to 695 SAP peptides mapping to 504 nsSNV sites. These detected SAP peptides corresponded to moderate to high abundance transcripts (30+ transcripts per million, TPM). The SAP peptides included 192 allelic pairs; the relative expression levels of the two alleles were evaluated for 51 of those pairs, and found to be comparable in all cases. PMID:24175627

Identification of the nitrogen-based blister agents bis(2-chloroethyl)methylamine (HN-2) and tris(2-chloroethyl)amine (HN-3) and their hydrolysis products on soil using ion trap secondary ion mass spectrometry.

PubMed

Gresham, G L; Groenewold, G S; Olson, J E

2000-12-01

The nitrogen blister agents HN-2 (bis(2-chloroethyl)methylamine) and HN-3 (tris(2-chloroethyl)amine) were directly analyzed on the surface of soil samples using ion trap secondary ion mass spectrometry (SIMS). In the presence of water, HN-1 (bis(2-choroethyl)ethylamine), HN-2 and HN-3 undergo hydrolysis to form N-ethyldiethanolamine, N-methyldiethanolamine and triethanolamine (TEA), respectively; these compounds can be readily detected as adsorbed species on soil particles. When soil samples spiked with HN-3 in alcohol were analyzed, 2-alkoxyethylamine derivatives were observed on the sample surfaces. This result shows that nitrogen blister agents will undergo condensation reactions with nucleophilic compounds and emphasizes the need for an analytical methodology capable of detecting a range of degradation and condensation products on environmental surfaces. The ability of ion trap SIMS to isolate and accumulate ions, and then perform tandem mass spectrometric analysis improves the detection of low-abundance surface contaminants and the selectivity of the technique. Utilizing these techniques, the limits of detection for HN-3 were studied as a function of surface coverage. It was found that HN-3 could be detected at a surface coverage of 0.01 monolayer, which corresponds to 20 ppm (mass/mass) for a soil having a surface area of 2.2 m(2) g(-1). TEA, the exhaustive hydrolysis product of HN-3, was detected at a surface coverage of 0.001 monolayer, which corresponds to 0.86 ppm. Copyright 2000 John Wiley & Sons, Ltd.

COSPAS-SARSAT Satellite Orbit Predictor. Volume 3

NASA Technical Reports Server (NTRS)

Friedman, Morton L.; Garrett, James

1984-01-01

The satellite orbit predictor is a graphical aid for determining the relationship between the satellite (SARSAT or COSPAS) orbit, antenna coverage of the spacecraft and coverage of the LUTs. The predictor allows the user to quickly visualize if a selected position will probably be detected and is composed of a base map and a satellite track overlay for each satellite. Additionally, a table of equator crossings for each satellite is included.

Modeling the SHG activities of diverse protein crystals

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

Haupert, Levi M.; DeWalt, Emma L.; Simpson, Garth J., E-mail: gsimpson@purdue.edu

2012-11-01

The origins of the diversity in the SHG signal from protein crystals are investigated and potential protein-crystal coverage by SHG microscopy is assessed. A symmetry-additive ab initio model for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine point-group symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much ofmore » the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within the crystal lattice. Two or more orders-of-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of ∼84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices.« less

Measles in Poland in 2013.

PubMed

Rogalska, Justyna

2015-01-01

Since 1998, Poland has been actively participating in the Measles Elimination Program, coordinated by the World Health Organization (WHO). It requires achieving and maintaining very high vaccine coverage (>95%), recording all cases and suspected cases of measles, and laboratory testing of all suspected measles cases in the WHO Reference Laboratory. In Poland it is a Laboratory of Department of Virology, NIPH-NIH. In order to confirm or exclude the case of measles specific measles IgM antibodies should be measured using Elisa test, or molecular testing (PCR) should be performed to detect the presence measles virus RNA in biological material. To assess epidemiological situation of measles in Poland in 2013, including vaccination coverage in Polish population, and Measles Elimination Program implementation status. The descriptive analysis was based on data retrieved from routine mandatory surveillance system and published in the annual bulletins "Infectious diseases and poisonings in Poland in 2013" and "Vaccinations in Poland in 2013", and measles case-based reports from 2013 sent to the Department of Epidemiology NIPH-NIH by Sanitary-Epidemiological Stations. In total, there were 84 measles cases registered in Poland in 2013 (incidence 0.22 per 100,000). The highest incidence rate was observed among infants (2.18 per 100,000) and children aged 1 year (1.27 per 100,000). In 2013, 56 cases (66.7%) were hospitalized due to measles. No deaths from measles were reported. Vaccination coverage of children and youth aged 2-11 years ranged from 82.8% do 99.5% (primary vaccination in children born in 2012-2007) and from 73.6% to 93.2% (booster dose in children born in 2004-2001). In 2013, 127 measles-compatible cases were reported (67% of expected reports). Two hundred seven cases (80%) were confirmed by IgM ELISA test. In 2013, the epidemiological situation of measles deteriorated in comparison to proceding year. The sensitivity of measles surveillance improved but is still insufficient. It is necessary to further promote Measles Elimination Program in Poland, to improve measles surveillance system and to maintain the high immunisation coverage.

Global Precipitation Measurement - Report 9 Core Coverage Trade Space Analysis

NASA Technical Reports Server (NTRS)

Mailhe, Laurie; Schiff, Conrad; Mendelsohn, Chad; Everett, David; Folta, David

2002-01-01

This paper summarizes the GPM-Core coverage trade space analysis. The goal of this analysis was to determine the GPM-Core sensitivity to changes in altitude and inclination for the three onboard instruments: the radiometer, the KU band radar and the KA band radar. This study will enable a better choice of the nominal GPM-Core orbit as well as the optimal size of the maintenance box (+/-1 km, +/-5 km..). For this work, we used two different figures-of-merit: (1) the time required to cover 100% of the +/-65 deg latitude band and (2) the coverage obtained for a given propagation time (7 days and 30 days). The first figure-of-merit is used for the radiometer as it has a sensor cone half-angle between 3 to 5 times bigger than the radars. Thus, we anticipate that for this instrument the period of the orbit (i.e. altitude) will be the main driver and that the 100% coverage value will be reached within less than a week. The second figure-of-merit is used for the radar instruments as they have small sensor cone half-angle and will, in some cases, never reach the 100% coverage threshold point.

Evaluation of Dry Electrodes in Canine Heart Rate Monitoring.

PubMed

Virtanen, Juhani; Somppi, Sanni; Törnqvist, Heini; Jeyhani, Vala; Fiedler, Patrique; Gizatdinova, Yulia; Majaranta, Päivi; Väätäjä, Heli; Valldeoriola Cardó, Anna; Lekkala, Jukka; Tuukkanen, Sampo; Surakka, Veikko; Vainio, Outi; Vehkaoja, Antti

2018-05-30

The functionality of three dry electrocardiogram electrode constructions was evaluated by measuring canine heart rate during four different behaviors: Standing, sitting, lying and walking. The testing was repeated (n = 9) in each of the 36 scenarios with three dogs. Two of the electrodes were constructed with spring-loaded test pins while the third electrode was a molded polymer electrode with Ag/AgCl coating. During the measurement, a specifically designed harness was used to attach the electrodes to the dogs. The performance of the electrodes was evaluated and compared in terms of heartbeat detection coverage. The effect on the respective heart rate coverage was studied by computing the heart rate coverage from the measured electrocardiogram signal using a pattern-matching algorithm to extract the R-peaks and further the beat-to-beat heart rate. The results show that the overall coverage ratios regarding the electrodes varied between 45⁻95% in four different activity modes. The lowest coverage was for lying and walking and the highest was for standing and sitting.

Spider: Probing the Early Universe with a Large-Scale CMB Polarization Survey

NASA Astrophysics Data System (ADS)

Jones, William

The standard dark-matter and dark-energy dominated cosmological model (LCDM) has proven to be remarkably successful in describing the current state and past evolution of the Universe. However, there remain significant uncertainties regarding the physical mechanisms that established the initial conditions upon which the LCDM predictions rely. Theories of cosmic genesis - the extremely high energy mechanisms that established these conditions - should be expected to provide a natural description of the nearly flat geometry of the Universe, the existence of super-horizon density correlations, and the adiabatic, Gaussian and nearly scale-invariant nature of the observed primordial density perturbations. The primary objective of Spider is to subject models of the early Universe to observational test, probing fundamental physics at energy scales far beyond the reach of terrestrial particle accelerators. The main scientific result will be to characterize, or place stringent upper limits on the level of the odd-parity polarization of the CMB. In the context of the inflationary paradigm, Spider will confirm or exclude the predictions of the simplest single-field inflationary models near the Lyth bound, characterized by tensor to scalar ratios r 0.03. While viable alternatives to the inflationary paradigm are an active and important area of investigation, including string cosmologies and cyclic models, early Universe models described by inflationary periods are now widely accepted as the underlying cause behind much of what we observe in cosmology today. Nevertheless, we know very little about the mechanism that would drive inflation or the energy scale at which it occurred, and the paradigm faces significant questions about the viability of the framework as a scientific theory. Fortunately, inflationary paradigms and alternative theories offer distinct predictions regarding the statistical properties of the Cosmic Microwave Background radiation. Spider will use measurements of the polarization of the CMB to search for the signature of primordial gravitational waves that are predicted within the currently favored theories of inflation. A definitive detection of this signal would provide the first direct insight into the underlying physics of inflation as well as a measurement of its energy scale. A stringent limit on the amplitude of this signal would exclude the currently favored class of inflationary models, bolstering the case for alternative theories. Spider is a suborbital Long-Duration Balloon payload housing six cryogenic smallaperture (half-degree resolution) millimeter-wave polarimeters. The frequency bands of the individual polarimeters are chosen to optimize overall sensitivity to the inflationary CMB polarization signal in the presence of Galactic foregrounds. By making extremely deep, high fidelity measurements of the entire portion of the southern sky that is relatively free of Galactic emission, the Spider data complement those of Planck (in sensitivity and control of systematics) PIPER (in frequency coverage) and EBEX (in sky coverage and angular scale). The data from Spider's inaugural flight in 2015 has resulted in high signal-to-noise maps of the southern Galactic hemisphere covering 10% of the full sky at each of 94 and 150 GHz. The payload is now being fabricated and fitted with a suite of 285 GHz cameras to extend our frequency coverage, improving our ability to disentangle the Galactic and cosmological signals. If its signature is present in the CMB, Spider's frequency coverage and fidelity to a broad range of angular scales enable the experiment to take a step beyond detection, toward the characterization of the gravitational wave induced signature in the CMB. Additionally Spider serves as a training ground for young scientists, including 16 graduate students (9 female, 7 male).

Optimal survey strategies and predicted planet yields for the Korean microlensing telescope network

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

Henderson, Calen B.; Gaudi, B. Scott; Skowron, Jan

2014-10-10

The Korean Microlensing Telescope Network (KMTNet) will consist of three 1.6 m telescopes each with a 4 deg{sup 2} field of view (FoV) and will be dedicated to monitoring the Galactic Bulge to detect exoplanets via gravitational microlensing. KMTNet's combination of aperture size, FoV, cadence, and longitudinal coverage will provide a unique opportunity to probe exoplanet demographics in an unbiased way. Here we present simulations that optimize the observing strategy for and predict the planetary yields of KMTNet. We find preferences for four target fields located in the central Bulge and an exposure time of t {sub exp} = 120more » s, leading to the detection of ∼2200 microlensing events per year. We estimate the planet detection rates for planets with mass and separation across the ranges 0.1 ≤ M{sub p} /M {sub ⊕} ≤ 1000 and 0.4 ≤ a/AU ≤ 16, respectively. Normalizing these rates to the cool-planet mass function of Cassan et al., we predict KMTNet will be approximately uniformly sensitive to planets with mass 5 ≤ M{sub p} /M {sub ⊕} ≤ 1000 and will detect ∼20 planets per year per dex in mass across that range. For lower-mass planets with mass 0.1 ≤ M{sub p} /M {sub ⊕} < 5, we predict KMTNet will detect ∼10 planets per year. We also compute the yields KMTNet will obtain for free-floating planets (FFPs) and predict KMTNet will detect ∼1 Earth-mass FFP per year, assuming an underlying population of one such planet per star in the Galaxy. Lastly, we investigate the dependence of these detection rates on the number of observatories, the photometric precision limit, and optimistic assumptions regarding seeing, throughput, and flux measurement uncertainties.« less

High Throughput Transcriptomics @ USEPA (Toxicology Forum)

EPA Science Inventory

The ideal chemical testing approach will provide complete coverage of all relevant toxicological responses. It should be sensitive and specific It should identify the mechanism/mode-of-action (with dose-dependence). It should identify responses relevant to the species of interest...

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles.

PubMed

Van der Borght, Koen; Thys, Kim; Wetzels, Yves; Clement, Lieven; Verbist, Bie; Reumers, Joke; van Vlijmen, Herman; Aerssens, Jeroen

2015-11-10

Next generation sequencing enables studying heterogeneous populations of viral infections. When the sequencing is done at high coverage depth ("deep sequencing"), low frequency variants can be detected. Here we present QQ-SNV (http://sourceforge.net/projects/qqsnv), a logistic regression classifier model developed for the Illumina sequencing platforms that uses the quantiles of the quality scores, to distinguish true single nucleotide variants from sequencing errors based on the estimated SNV probability. To train the model, we created a dataset of an in silico mixture of five HIV-1 plasmids. Testing of our method in comparison to the existing methods LoFreq, ShoRAH, and V-Phaser 2 was performed on two HIV and four HCV plasmid mixture datasets and one influenza H1N1 clinical dataset. For default application of QQ-SNV, variants were called using a SNV probability cutoff of 0.5 (QQ-SNV(D)). To improve the sensitivity we used a SNV probability cutoff of 0.0001 (QQ-SNV(HS)). To also increase specificity, SNVs called were overruled when their frequency was below the 80(th) percentile calculated on the distribution of error frequencies (QQ-SNV(HS-P80)). When comparing QQ-SNV versus the other methods on the plasmid mixture test sets, QQ-SNV(D) performed similarly to the existing approaches. QQ-SNV(HS) was more sensitive on all test sets but with more false positives. QQ-SNV(HS-P80) was found to be the most accurate method over all test sets by balancing sensitivity and specificity. When applied to a paired-end HCV sequencing study, with lowest spiked-in true frequency of 0.5%, QQ-SNV(HS-P80) revealed a sensitivity of 100% (vs. 40-60% for the existing methods) and a specificity of 100% (vs. 98.0-99.7% for the existing methods). In addition, QQ-SNV required the least overall computation time to process the test sets. Finally, when testing on a clinical sample, four putative true variants with frequency below 0.5% were consistently detected by QQ-SNV(HS-P80) from different generations of Illumina sequencers. We developed and successfully evaluated a novel method, called QQ-SNV, for highly efficient single nucleotide variant calling on Illumina deep sequencing virology data.

Remote sensing observing systems of the Meteorological Service of Catalonia (SMC): application to thunderstorm surveillance

NASA Astrophysics Data System (ADS)

Argemí, O.; Bech, J.; Pineda, N.; Rigo, T.

2009-09-01

Remote sensing observing systems of the Meteorological Service of Catalonia (SMC) have been upgraded during the last years with newer technologies and enhancements. Recent changes on the weather radar network have been motivated to improve precipitation estimates by radar as well as meteorological surveillance in the area of Catalonia. This region has approximately 32,000 square kilometres and is located in the NE of Spain, limited by the Pyrenees to the North (with mountains exceeding 3000 m) and by the Mediterranean Sea to the East and South. In the case of the total lightning (intra-cloud and cloud-to-ground lightning) detection system, the current upgrades will assure a better lightning detection efficiency and location accuracy. Both upgraded systems help to enhance the tracking and the study of thunderstorm events. Initially, the weather radar network was designed to cover the complex topography of Catalonia and surrounding areas to support the regional administration, which includes civil protection and water authorities. The weather radar network was upgraded in 2008 with the addition of a new C-band Doppler radar system, which is located in the top of La Miranda Mountain (Tivissa) in the southern part of Catalonia enhancing the coverage, particularly to the South and South-West. Technically the new radar is very similar to the last one installed in 2003 (Creu del Vent radar), using a 4 m antenna (i.e., 1 degree beam width), a Vaisala-Sigmet RVP-8 digital receiver and processor and a low power transmitter using a Travelling Wave Tube (TWT) amplifier. This design allows using pulse-compression techniques to enhance radial resolution and sensitivity. Currently, the SMC is upgrading its total lightning detection system, operational since 2003. While a fourth sensor (Amposta) was added last year to enlarge the system coverage, all sensors and central processor will be upgraded this year to the new Vaisala’s total lightning location technology. The new LS8000 sensor configuration integrates two lightning detection technologies: VHF interferometry technology provides high performance in detection of cloud lightning, while LF combined magnetic direction finding and time-of-arrival technology offers a highest detection efficiency and accurate location for cloud-to-ground lightning strokes. The presentation describes in some detail all this innovation in remote sensing observing networks and also reports some examples over Catalonia which is frequently affected by different types of convective events, including severe weather (large hail, tornadic events, etc.) and heavy rainfall episodes.

Cost-effectiveness of methadone maintenance therapy as HIV prevention in an Indonesian high-prevalence setting: a mathematical modeling study.

PubMed

Wammes, Joost J G; Siregar, Adiatma Y; Hidayat, Teddy; Raya, Reynie P; van Crevel, Reinout; van der Ven, André J; Baltussen, Rob

2012-09-01

Indonesia faces an HIV epidemic that is in rapid transition. Injecting drug users (IDUs) are among the most heavily affected risk populations, with estimated prevalence of HIV reaching 50% or more in most parts of the country. Although Indonesia started opening methadone clinics in 2003, coverage remains low. We used the Asian Epidemic Model and Resource Needs Model to evaluate the long-term population-level preventive impact of expanding Methadone Maintenance Therapy (MMT) in West Java (43 million people). We compared intervention costs and the number of incident HIV cases in the intervention scenario with current practice to establish the cost per infection averted by expanding MMT. An extensive sensitivity analysis was performed on costs and epidemiological input, as well as on the cost-effectiveness calculation itself. Our analysis shows that expanding MMT from 5% coverage now to 40% coverage in 2019 would avert approximately 2400 HIV infections, at a cost of approximately US$7000 per HIV infection averted. Sensitivity analyses demonstrate that the use of alternative assumptions does not change the study conclusions. Our analyses suggest that expanding MMT is cost-effective, and support government policies to make MMT widely available as an integrated component of HIV/AIDS control in West Java. Copyright © 2012 Elsevier B.V. All rights reserved.

Automated oil spill detection with multispectral imagery

NASA Astrophysics Data System (ADS)

Bradford, Brian N.; Sanchez-Reyes, Pedro J.

2011-06-01

In this publication we present an automated detection method for ocean surface oil, like that which existed in the Gulf of Mexico as a result of the April 20, 2010 Deepwater Horizon drilling rig explosion. Regions of surface oil in airborne imagery are isolated using red, green, and blue bands from multispectral data sets. The oil shape isolation procedure involves a series of image processing functions to draw out the visual phenomenological features of the surface oil. These functions include selective color band combinations, contrast enhancement and histogram warping. An image segmentation process then separates out contiguous regions of oil to provide a raster mask to an analyst. We automate the detection algorithm to allow large volumes of data to be processed in a short time period, which can provide timely oil coverage statistics to response crews. Geo-referenced and mosaicked data sets enable the largest identified oil regions to be mapped to exact geographic coordinates. In our simulation, multispectral imagery came from multiple sources including first-hand data collected from the Gulf. Results of the simulation show the oil spill coverage area as a raster mask, along with histogram statistics of the oil pixels. A rough square footage estimate of the coverage is reported if the image ground sample distance is available.

Effect of the Medicare Part D coverage gap on medication use among patients with hypertension and hyperlipidemia.

PubMed

Li, Pengxiang; McElligott, Sean; Bergquist, Henry; Schwartz, J Sanford; Doshi, Jalpa A

2012-06-05

Prior studies of the Medicare Part D coverage gap are limited in generalizability and scope. To determine the effect of the coverage gap on drugs used for asymptomatic (antihypertensive and lipid-lowering drugs) and symptomatic (pain relievers, acid suppressants, and antidepressants) conditions in elderly patients with hypertension and hyperlipidemia. Quasi-experimental study using pre-post design and contemporaneous control group. Medicare claims files from 2005 and 2006 for 5% random sample of Medicare beneficiaries. Part D plan enrollees with hypertension or hyperlipidemia aged 65 years or older who had no coverage, generic-only coverage, or both brand-name and generic coverage during the gap in 2006. Patients who were fully eligible for the low-income subsidy served as the control group. Monthly 30-day supply prescriptions available, medication adherence, and continuous medication gaps of 30 days or more for antihypertensive or lipid-lowering drugs; monthly 30-day supply prescriptions available for pain relievers, acid suppressants, or antidepressants before and after coverage gap entry. Patients with no gap coverage had a decrease in monthly antihypertensive and lipid-lowering drug prescriptions during the coverage gap. Nonadherence also increased in this group (antihypertensives: odds ratio [OR], 1.60 [95% CI, 1.50 to 1.71]; lipid-lowering drugs: OR, 1.59 [CI, 1.50 to 1.68]). The proportion of patients with no gap coverage who had continuous medication gaps in lipid-lowering medication use and antihypertensive use increased by an absolute 7.3% (OR, 1.38 [CI, 1.29 to 1.46]) and 3.2% (OR, 1.35 [CI, 1.25 to 1.45]), respectively, because of the coverage gap. Decreases in use were smaller for pain relievers and antidepressants and larger for acid suppressants in patients with no gap coverage. Patients with generic-only coverage had decreased use of cardiovascular medications but no change in use of drugs for symptomatic conditions. No measures changed in the brand-name and generic coverage groups. Results of sensitivity analyses were consistent with the main findings. Because this study was nonrandomized, unobserved differences may still exist between study groups. The Part D coverage gap was associated with decreased use of medications for hypertension and hyperlipidemia in patients with no gap coverage and generic-only gap coverage. The proposed phasing out of the gap by 2020 will benefit such patients; however, use of low-value medications may also increase. Penn-Pfizer Alliance and American Heart Association.

Societal Implications of Health Insurance Coverage for Medically Necessary Services in the U.S. Transgender Population: A Cost-Effectiveness Analysis.

PubMed

Padula, William V; Heru, Shiona; Campbell, Jonathan D

2016-04-01

Recently, the Massachusetts Group Insurance Commission (GIC) prioritized research on the implications of a clause expressly prohibiting the denial of health insurance coverage for transgender-related services. These medically necessary services include primary and preventive care as well as transitional therapy. To analyze the cost-effectiveness of insurance coverage for medically necessary transgender-related services. Markov model with 5- and 10-year time horizons from a U.S. societal perspective, discounted at 3% (USD 2013). Data on outcomes were abstracted from the 2011 National Transgender Discrimination Survey (NTDS). U.S. transgender population starting before transitional therapy. No health benefits compared to health insurance coverage for medically necessary services. This coverage can lead to hormone replacement therapy, sex reassignment surgery, or both. Cost per quality-adjusted life year (QALY) for successful transition or negative outcomes (e.g. HIV, depression, suicidality, drug abuse, mortality) dependent on insurance coverage or no health benefit at a willingness-to-pay threshold of $100,000/QALY. Budget impact interpreted as the U.S. per-member-per-month cost. Compared to no health benefits for transgender patients ($23,619; 6.49 QALYs), insurance coverage for medically necessary services came at a greater cost and effectiveness ($31,816; 7.37 QALYs), with an incremental cost-effectiveness ratio (ICER) of $9314/QALY. The budget impact of this coverage is approximately $0.016 per member per month. Although the cost for transitions is $10,000-22,000 and the cost of provider coverage is $2175/year, these additional expenses hold good value for reducing the risk of negative endpoints--HIV, depression, suicidality, and drug abuse. Results were robust to uncertainty. The probabilistic sensitivity analysis showed that provider coverage was cost-effective in 85% of simulations. Health insurance coverage for the U.S. transgender population is affordable and cost-effective, and has a low budget impact on U.S. society. Organizations such as the GIC should consider these results when examining policies regarding coverage exclusions.

Measuring individual-level needle and syringe coverage among people who inject drugs in Myanmar.

PubMed

O'Keefe, Daniel; Aung, Soe Moe; Pasricha, Naanki; Wun, Thu; Linn, Soe Khaing; Lin, Nay; Aitken, Campbell; Hughes, Chad; Dietze, Paul

2018-05-10

Myanmar has prioritised people who inject drugs (PWID) as a key population for HIV mitigation efforts, with targets for needle and syringe distribution set at a population level. However, individual-level coverage, defined as the percentage of an individual's injecting episodes covered by a sterile syringe, is a more sensitive measure of intervention coverage. We sought to examine individual-level coverage in a sample of PWID in Myanmar. We recruited 512 PWID through urban drop-in-centres in Yangon, Mandalay and Pyin Oo Lwin. Participants were administered a quantitative questionnaire covering five domains: demographics, drug use, treatment and coverage, and injecting risk behaviour. We calculated past fortnight individual-level syringe coverage, estimating levels of sufficient (≥100% of injecting episodes covered by a sterile syringe) and insufficient (<100%) coverage, and examined associations between key variables and insufficient coverage via logistic regression. Our sample was predominately male (97%), employed (76%), and living in stable accommodation (96%), with a median age of 27. All participants reported heroin as the drug most frequently injected, and injected a median of 27 times in the past two weeks. Nineteen per cent of participants had insufficient coverage in the two weeks before interview. Insufficient coverage was positively associated with syringe re-use (AOR: 5.19, 95% CIs: 2.57, 10.48) and acquiring sterile syringes from a location other than a formal drop-in-centre (AOR: 2.04, 95% CIs: 1.08, 3.82). Participants recruited in Mandalay (AOR: 0.30, 95% CIs: 0.11, 0.80) and Pyin Oo Lwin (AOR: 0.39, 95% CIs: 0.18, 0.87) had lower odds of insufficient coverage than those recruited in Yangon. Our study shows coverage in selected areas of Myanmar was comparable with studies in other countries. Our results inform the delivery of harm reduction services for PWID, specifically by encouraging the use of formal drop-in-centres, over other sources of syringe distribution, such as pharmacies. Copyright © 2018 Elsevier B.V. All rights reserved.

Cost-Effectiveness of Providing Full Drug Coverage to Increase Medication Adherence in Post–Myocardial Infarction Medicare Beneficiaries

PubMed Central

Choudhry, Niteesh K.; Patrick, Amanda R.; Antman, Elliott M.; Avorn, Jerry; Shrank, William H.

2009-01-01

Background Effective therapies for the secondary prevention of coronary heart disease–related events are significantly underused, and attempts to improve adherence have often yielded disappointing results. Elimination of patient out-of-pocket costs may be an effective strategy to enhance medication use. We sought to estimate the incremental cost-effectiveness of providing full coverage for aspirin, β-blockers, angiotensin-converting enzyme inhibitors or angiotensin receptor blockers, and statins (combination pharmacotherapy) to individuals enrolled in the Medicare drug benefit program after acute myocardial infarction. Methods and Results We created a Markov cost-effectiveness model to estimate the incremental cost-effectiveness of providing Medicare beneficiaries with full coverage for combination pharmacotherapy compared with current coverage under the Medicare Part D program. Our analysis was conducted from the societal perspective and considered a lifetime time horizon. In a sensitivity analysis, we repeated our analysis from the perspective of Medicare. In the model, post–myocardial infarction Medicare beneficiaries who received usual prescription drug coverage under the Part D program lived an average of 8.21 quality-adjusted life-years after their initial event, incurring coronary heart disease–related medical costs of $114 000. Those who received prescription drug coverage without deductibles or copayments lived an average of 8.56 quality-adjusted life-years and incurred $111 600 in coronary heart disease–related costs. Compared with current prescription drug coverage, full coverage for post–myocardial infarction secondary prevention therapies would result in greater functional life expectancy (0.35 quality-adjusted life-year) and less resource use ($2500). From the perspective of Medicare, full drug coverage was highly cost-effective ($7182/quality-adjusted life-year) but not cost saving. Conclusions Our analysis suggests that providing full coverage for combination therapy to post–myocardial infarction Medicare beneficiaries would save both lives and money from the societal perspective. PMID:18285564

A composite indicator to measure universal health care coverage in India: way forward for post-2015 health system performance monitoring framework.

PubMed

Prinja, Shankar; Gupta, Rakesh; Bahuguna, Pankaj; Sharma, Atul; Kumar Aggarwal, Arun; Phogat, Amit; Kumar, Rajesh

2017-02-01

There is limited work done on developing methods for measurement of universal health coverage. We undertook a study to develop a methodology and demonstrate the practical application of empirically measuring the extent of universal health coverage at district level. Additionally, we also develop a composite indicator to measure UHC. A cross-sectional survey was undertaken among 51 656 households across 21 districts of Haryana state in India. Using the WHO framework for UHC, we identified indicators of service coverage, financial risk protection, equity and quality based on the Government of India and the Haryana Government's proposed UHC benefit package. Geometric mean approach was used to compute a composite UHC index (CUHCI). Various statistical approaches to aggregate input indicators with or without weighting, along with various incremental combinations of input indicators were tested in a comprehensive sensitivity analysis. The population coverage for preventive and curative services is presented. Adjusting for inequality, the coverage for all the indicators were less than the unadjusted coverage by 0.1-6.7% in absolute term and 0.1-27% in relative term. There was low unmet need for curative care. However, about 11% outpatient consultations were from unqualified providers. About 30% households incurred catastrophic health expenditures, which rose to 38% among the poorest 20% population. Summary index (CUHCI) for UHC varied from 12% in Mewat district to 71% in Kurukshetra district. The inequality unadjusted coverage for UHC correlates highly with adjusted coverage. Our paper is an attempt to develop a methodology to measure UHC. However, careful inclusion of others indicators of service coverage is recommended for a comprehensive measurement which captures the spirit of universality. Further, more work needs to be done to incorporate quality in the measurement framework. © The Author 2016. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Search for extraterrestrial intelligence (SETI)

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

Morrison, P.; Billingham, J.; Wolfe, J.

1977-01-01

Findings are presented of a series of workshops on the existence of extraterrestrial intelligent life and ways in which extraterrestrial intelligence might be detected. The coverage includes the cosmic and cultural evolutions, search strategies, detection of other planetary systems, alternate methods of communication, and radio frequency interference. 17 references. (JFP)

Metabolomics of Small Numbers of Cells: Metabolomic Profiling of 100, 1000, and 10000 Human Breast Cancer Cells.

PubMed

Luo, Xian; Li, Liang

2017-11-07

In cellular metabolomics, it is desirable to carry out metabolomic profiling using a small number of cells in order to save time and cost. In some applications (e.g., working with circulating tumor cells in blood), only a limited number of cells are available for analysis. In this report, we describe a method based on high-performance chemical isotope labeling (CIL) nanoflow liquid chromatography mass spectrometry (nanoLC-MS) for high-coverage metabolomic analysis of small numbers of cells (i.e., ≤10000 cells). As an example, 12 C-/ 13 C-dansyl labeling of the metabolites in lysates of 100, 1000, and 10000 MCF-7 breast cancer cells was carried out using a new labeling protocol tailored to handle small amounts of metabolites. Chemical-vapor-assisted ionization in a captivespray interface was optimized for improving metabolite ionization and increasing robustness of nanoLC-MS. Compared to microflow LC-MS, the nanoflow system provided much improved metabolite detectability with a significantly reduced sample amount required for analysis. Experimental duplicate analyses of biological triplicates resulted in the detection of 1620 ± 148, 2091 ± 89 and 2402 ± 80 (n = 6) peak pairs or metabolites in the amine/phenol submetabolome from the 12 C-/ 13 C-dansyl labeled lysates of 100, 1000, and 10000 cells, respectively. About 63-69% of these peak pairs could be either identified using dansyl labeled standard library or mass-matched to chemical structures in human metabolome databases. We envisage the routine applications of this method for high-coverage quantitative cellular metabolomics using a starting material of 10000 cells. Even for analyzing 100 or 1000 cells, although the metabolomic coverage is reduced from the maximal coverage, this method can still detect thousands of metabolites, allowing the analysis of a large fraction of the metabolome and focused analysis of the detectable metabolites.

(Quickly) Testing the Tester via Path Coverage

NASA Technical Reports Server (NTRS)

Groce, Alex

2009-01-01

The configuration complexity and code size of an automated testing framework may grow to a point that the tester itself becomes a significant software artifact, prone to poor configuration and implementation errors. Unfortunately, testing the tester by using old versions of the software under test (SUT) may be impractical or impossible: test framework changes may have been motivated by interface changes in the tested system, or fault detection may become too expensive in terms of computing time to justify running until errors are detected on older versions of the software. We propose the use of path coverage measures as a "quick and dirty" method for detecting many faults in complex test frameworks. We also note the possibility of using techniques developed to diversify state-space searches in model checking to diversify test focus, and an associated classification of tester changes into focus-changing and non-focus-changing modifications.

Evaluating the Detection of Hydrocarbon-Degrading Bacteria in 16S rRNA Gene Sequencing Surveys

PubMed Central

Berry, David; Gutierrez, Tony

2017-01-01

Hydrocarbonoclastic bacteria (HCB) play a key role in the biodegradation of oil hydrocarbons in marine and other environments. A small number of taxa have been identified as obligate HCB, notably the Gammaproteobacterial genera Alcanivorax, Cycloclasticus, Marinobacter, Neptumonas, Oleiphilus, Oleispira, and Thalassolituus, as well as the Alphaproteobacterial genus Thalassospira. Detection of HCB in amplicon-based sequencing surveys relies on high coverage by PCR primers and accurate taxonomic classification. In this study, we performed a phylogenetic analysis to identify 16S rRNA gene sequence regions that represent the breadth of sequence diversity within these taxa. Using validated sequences, we evaluated 449 universal 16S rRNA gene-targeted bacterial PCR primer pairs for their coverage of these taxa. The results of this analysis provide a practical framework for selection of suitable primer sets for optimal detection of HCB in sequencing surveys. PMID:28567035

Evaluating the Detection of Hydrocarbon-Degrading Bacteria in 16S rRNA Gene Sequencing Surveys.

PubMed

Berry, David; Gutierrez, Tony

2017-01-01

Hydrocarbonoclastic bacteria (HCB) play a key role in the biodegradation of oil hydrocarbons in marine and other environments. A small number of taxa have been identified as obligate HCB, notably the Gammaproteobacterial genera Alcanivorax, Cycloclasticus, Marinobacter, Neptumonas, Oleiphilus, Oleispira , and Thalassolituus , as well as the Alphaproteobacterial genus Thalassospira . Detection of HCB in amplicon-based sequencing surveys relies on high coverage by PCR primers and accurate taxonomic classification. In this study, we performed a phylogenetic analysis to identify 16S rRNA gene sequence regions that represent the breadth of sequence diversity within these taxa. Using validated sequences, we evaluated 449 universal 16S rRNA gene-targeted bacterial PCR primer pairs for their coverage of these taxa. The results of this analysis provide a practical framework for selection of suitable primer sets for optimal detection of HCB in sequencing surveys.

Evaluating Google, Twitter, and Wikipedia as Tools for Influenza Surveillance Using Bayesian Change Point Analysis: A Comparative Analysis.

PubMed

Sharpe, J Danielle; Hopkins, Richard S; Cook, Robert L; Striley, Catherine W

2016-10-20

Traditional influenza surveillance relies on influenza-like illness (ILI) syndrome that is reported by health care providers. It primarily captures individuals who seek medical care and misses those who do not. Recently, Web-based data sources have been studied for application to public health surveillance, as there is a growing number of people who search, post, and tweet about their illnesses before seeking medical care. Existing research has shown some promise of using data from Google, Twitter, and Wikipedia to complement traditional surveillance for ILI. However, past studies have evaluated these Web-based sources individually or dually without comparing all 3 of them, and it would be beneficial to know which of the Web-based sources performs best in order to be considered to complement traditional methods. The objective of this study is to comparatively analyze Google, Twitter, and Wikipedia by examining which best corresponds with Centers for Disease Control and Prevention (CDC) ILI data. It was hypothesized that Wikipedia will best correspond with CDC ILI data as previous research found it to be least influenced by high media coverage in comparison with Google and Twitter. Publicly available, deidentified data were collected from the CDC, Google Flu Trends, HealthTweets, and Wikipedia for the 2012-2015 influenza seasons. Bayesian change point analysis was used to detect seasonal changes, or change points, in each of the data sources. Change points in Google, Twitter, and Wikipedia that occurred during the exact week, 1 preceding week, or 1 week after the CDC's change points were compared with the CDC data as the gold standard. All analyses were conducted using the R package "bcp" version 4.0.0 in RStudio version 0.99.484 (RStudio Inc). In addition, sensitivity and positive predictive values (PPV) were calculated for Google, Twitter, and Wikipedia. During the 2012-2015 influenza seasons, a high sensitivity of 92% was found for Google, whereas the PPV for Google was 85%. A low sensitivity of 50% was calculated for Twitter; a low PPV of 43% was found for Twitter also. Wikipedia had the lowest sensitivity of 33% and lowest PPV of 40%. Of the 3 Web-based sources, Google had the best combination of sensitivity and PPV in detecting Bayesian change points in influenza-related data streams. Findings demonstrated that change points in Google, Twitter, and Wikipedia data occasionally aligned well with change points captured in CDC ILI data, yet these sources did not detect all changes in CDC data and should be further studied and developed.

Infrared-enhanced TV for fire detection

NASA Technical Reports Server (NTRS)

Hall, J. R.

1978-01-01

Closed-circuit television is superior to conventional smoke or heat sensors for detecting fires in large open spaces. Single TV camera scans entire area, whereas many conventional sensors and maze of interconnecting wiring might be required to get same coverage. Camera is monitored by person who would trip alarm if fire were detected, or electronic circuitry could process camera signal for fully-automatic alarm system.

The Arecibo Pisces Perseus Supercluster Survey: Declination Strip 27

NASA Astrophysics Data System (ADS)

Ricci, Mariah; Miller, Brendan; APPSS Team; Undergraduate ALFALFA Team; ALFALFA Team

2018-01-01

The Arecibo Pisces Perseus Supercluster Survey (APPSS) is an HI survey measuring galaxy infall into the filament and clusters. Galaxies were selected for HI observations based on their location within the Pisces Perseus supercluster and SDSS and GALEX colors predictive of cold gas content. Most of the HI observations were conducted at Arecibo using the L Band Wide receiver, with some high-declination coverage provided by Green Bank. The observations provide increased sensitivity compared to ALFALFA blind survey data. For this project, we investigated a subset of 132 APPSS galaxies with declinations near 27 degrees. Using custom data reduction and analysis tools developed for the Undergraduate ALFALFA Team, we determined the following information for galaxies in our subset: systemic velocity, line width, integrated flux density, HI mass, and gas fraction (or corresponding limits for non-detections). We calculate our HI detection fraction and mean gas fraction as a function of stellar mass and compare to previous results. We investigate the distribution of systemic velocities for our galaxies with their location on the sky. Finally, we discuss several interesting sources from our subset of APPSS galaxies. This work has been supported by NSF grants AST-1211005, AST-1637299, and AST-1637339

Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography

NASA Astrophysics Data System (ADS)

Favicchio, Rosy; Psycharakis, Stylianos; Schönig, Kai; Bartsch, Dusan; Mamalaki, Clio; Papamatheakis, Joseph; Ripoll, Jorge; Zacharakis, Giannis

2016-02-01

Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture.

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

Not Available

The GEM collaboration was formed in June 1991 to develop a major detector for the SSC. The primary physics objectives of GEM are those central to the motivation for the SSC, to study high p{sub T} physics - exemplified by the search for Higgs bosons - and to search for new physics beyond the standard model. The authors present in this Technical Design Report (TDR) a detector with broad capabilities for the discovery and subsequent study of electroweak symmetry breaking, the origin of mass and flavor, and other physics requiring precise measurements of gammas, electrons, and muons - hence themore » name, GEM. In addition, as a design goal, they have taken care to provide the robustness needed to do the physics that requires high luminosity. Finally, good coverage and hermeticity allow the detection of missing transverse energy, E{sub T}. The GEM design emphasizes clean identification and high resolution measurement of the primary physics signatures for high p{sub T} physics. The approach is to make precise energy measurements that maximize the sensitivity to rare narrow resonances, to detect the elementary interaction products (quarks, leptons, and photons), and to build in the features required to reduce backgrounds.« less

Cost effectiveness of full coverage of the medical management of smoking cessation in France.

PubMed

Chevreul, Karine; Cadier, Benjamin; Durand-Zaleski, Isabelle; Chan, Elis; Thomas, Daniel

2014-05-01

To estimate the incremental cost effectiveness of full coverage of the medical management of smoking cessation from the perspective of statutory health insurance (SHI) in France. Cost-effectiveness analysis based on a Markov state-transition decision analytic model was used to compare full SHI coverage of smoking cessation and actual coverage based on an annual €50 lump sum per insured person among current French smokers aged 15-75 years. We used a scenario approach to take into account the many different behaviours of smokers and the likely variability of SHI policy choices in terms of participation rate and number and frequency of attempts covered. Drug treatments for smoking cessation combined with six medical consultations including individual counselling. The cost effectiveness of full coverage was expressed by the incremental cost-effectiveness ratio (ICER) in 2009 euros per life-year gained (LYG) at the lifetime horizon. The cost effectiveness per LYG for smokers ranged from €1786 to €2012, with an average value of €1911. The minimum value was very close to the maximum value with a difference of only €226. The cost-effectiveness ratio was only minimally sensitive to the participation rate, the number of attempts covered and the cessation rate. Compared to other health measures in primary and secondary prevention of cardiovascular disease already covered by SHI, full coverage of smoking cessation is the most cost-effective approach.

Molecular Engineering of Surfaces for Sensing and Detection

DTIC Science & Technology

2005-08-01

solution was flowed in both chambers at a concentration of 0.05 mg/mL. Biotinylated single- stranded oligonucleotides ( bDNA ) were immobilized on the layer...correspondence between surface-bound bDNA and conjugate, a theoretical minimum coverage of 1.18 × 1012 molecules/cm2 of bDNA is necessary to...immobilize a monolayer of antibody. Above this bDNA coverage a monolayer of immobilized antibody should be observed. These theoretical values are

Sensitivity of Medication Use to Formulary Controls in Medicare Beneficiaries: A Review of the Literature

PubMed Central

Shenolikar, Rahul; Bruno, Amanda Schofield; Eaddy, Michael; Cantrell, Christopher

2011-01-01

Background Several studies have examined the impact of formulary management strategies on medication use in the elderly, but little has been done to synthesize the findings to determine whether the results show consistent trends. Objective To summarize the effects of formulary controls (ie, tiered copays, step edits, prior authorization, and generic substitution) on medication use in the Medicare population to inform future Medicare Part D and other coverage decisions. Methods This systematic review included research articles (found via PubMed, Google Scholar, and specific scientific journals) that evaluated the impact of drug coverage or cost-sharing on medication use in elderly (aged ≥65 years) Medicare beneficiaries. The impact of drug coverage was assessed by comparing patients with some drug coverage to those with no drug coverage or by comparing varying levels of drug coverage (eg, full coverage vs $1000 coverage or capped benefits vs noncapped benefits). Articles that were published before 1995, were not original empirical research, were published in languages other than English, or focused on populations other than Medicare beneficiaries were excluded. All studies selected were classified as positive, negative, or neutral based on the significance of the relationship (P <.05 or as otherwise specified) between the formulary control mechanism and the medication use, and on the direction of that relationship. Results Included were a total of 47 research articles (published between 1995 and 2009) that evaluated the impact of drug coverage or cost-sharing on medication use in Medicare beneficiaries. Overall, 24 studies examined the impact of the level of drug coverage on medication use; of these, 96% (N = 23) supported the association between better drug coverage (ie, branded and generic vs generic-only coverage, capped benefit vs noncapped benefit, supplemental drug insurance vs no supplemental drug insurance) or having some drug coverage and enhanced medication use. Furthermore, 84% (N = 16) of the 19 studies that examined the effect of cost-sharing on medication use demonstrated that decreased cost-sharing was significantly associated with improved medication use. Conclusion Current evidence from the literature suggests that restricting drug coverage or increasing out-of-pocket expenses for Medicare beneficiaries may lead to decreased medication use in the elderly, with all its potential implications. PMID:25126370

Sensitivity of the orbiting JEM-EUSO mission to large-scale anisotropies

NASA Astrophysics Data System (ADS)

Weiler, Thomas; Anchordoqui, Luis; Denton, Peter

2013-04-01

Uniform sky coverage and very large apertures are advantages of future extreme-energy, space-based cosmic-ray observatories. In this talk we will quantify the advantage of an all-sky/4pi observatory such as JEM-EUSO over the one to two steradian coverage of a ground-based observatory such as Auger. We exploit the availability of spherical harmonics in the case of 4pi coverage. The resulting Y(lm) coefficients will likely become a standard analysis tool for near-future, space-based, cosmic-ray astronomy. We demonstrate the use of Y(lm)'s with extractions of simulated dipole and quadrupole anisotropies. (A dipole anisotropy is expected if a single source-region such as Cen A dominates the sky, while a quadrupole moment is expected if a 2D source region such as the Supergalactic Plane dominates the sky.)

North American Magazine Coverage of Skin Cancer and Recreational Tanning Before and After the WHO/IARC 2009 Classification of Indoor Tanning Devices as Carcinogenic.

PubMed

McWhirter, Jennifer E; Hoffman-Goetz, Laurie

2015-09-01

The mass media is an influential source of skin cancer information for the public. In 2009, the World Health Organization's International Agency for Research on Cancer classified UV radiation from tanning devices as carcinogenic. Our objective was to determine if media coverage of skin cancer and recreational tanning increased in volume or changed in nature after this classification. We conducted a directed content analysis on 29 North American popular magazines (2007-2012) to investigate the overall volume of articles on skin cancer and recreational tanning and, more specifically, the presence of skin cancer risk factors, UV behaviors, and early detection information in article text (n = 410) and images (n = 714). The volume of coverage on skin cancer and recreational tanning did not increase significantly after the 2009 classification of tanning beds as carcinogenic. Key-related messages, including that UV exposure is a risk factor for skin cancer and that indoor tanning should be avoided, were not reported more frequently after the classification, but the promotion of the tanned look as attractive was conveyed more often in images afterwards (p < .01). Content promoting high-SPF sunscreen use increased after the classification (p < .01), but there were no significant positive changes in the frequency of coverage of skin cancer risk factors, other UV behaviors, or early detection information over time. The classification of indoor tanning beds as carcinogenic had no significant impact on the volume or nature of skin cancer and recreational tanning coverage in magazines.

EPA Region 1 Environmentally Sensitive Areas

EPA Pesticide Factsheets

This coverage represents polygon equivalents of environmentally sensitive areas (ESA) in EPA Region I. ESAs were developed as part of an EPA headquarters initiative based on reviews of various regulatory and guidance documents, as well as phone interviews with federal/state/local government agencies and private organizations. ESAs include, but are not limited to, wetlands, biological resources, habitats, national parks, archaeological/historic sites, natural heritage areas, tribal lands, drinking water intakes, marinas/boat ramps, wildlife areas, etc.

Extending 'Deep Blue' aerosol retrieval coverage to cases of absorbing aerosols above clouds: sensitivity analysis and first case studies

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

Sayer, Andrew M.; Hsu, C.; Bettenhausen, Corey

Cases of absorbing aerosols above clouds (AAC), such as smoke or mineral dust, are omitted from most routinely-processed space-based aerosol optical depth (AOD) data products, including those from the Moderate Resolution Imaging Spectroradiometer (MODIS). This study presents a sensitivity analysis and preliminary algorithm to retrieve above-cloud AOD and liquid cloud optical depth (COD) for AAC cases from MODIS or similar

Expanding the bovine milk proteome through extensive fractionation.

PubMed

Nissen, Asger; Bendixen, Emøke; Ingvartsen, Klaus Lønne; Røntved, Christine Maria

2013-01-01

Bovine milk is an agricultural product of tremendous value worldwide. It contains proteins, fat, lactose, vitamins, and minerals. It provides nutrition and immunological protection (e.g., in the gastrointestinal tract) to the newborn and young calf. It also forms an important part of human nutrition. The repertoire of proteins in milk (i.e., its proteome) is vast and complex. The milk proteome can be described in detail by mass spectrometry-based proteomics. However, the high concentration of dominating proteins in milk reduces mass spectrometry detection sensitivity and limits detection of low abundant proteins. Further, the general health and udder health of the dairy cows delivering the milk may influence the composition of the milk proteome. To gain a more exhaustive and true picture of the milk proteome, we performed an extensive preanalysis fractionation of raw composite milk collected from documented healthy cows in early lactation. Four simple and industrially applicable techniques exploring the physical and chemical properties of milk, including acidification, filtration, and centrifugation, were used for separation of the proteins. This resulted in 5 different fractions, whose content of proteins were compared with the proteins of nonfractionated milk using 2-dimensional liquid chromatography tandem mass spectrometry analysis. To validate the proteome analysis, spectral counts and ELISA were performed on 7 proteins using the ELISA for estimation of the detection sensitivity limit of the 2-dimensional liquid chromatography tandem mass spectrometry analysis. Each fractionation technique resulted in identification of a unique subset of proteins. However, high-speed centrifugation of milk to whey was by far the best method to achieve high and repeatable proteome coverage. The total number of milk proteins initially detected in nonfractionated milk and the fractions were 635 in 2 replicates. Removal of dominant proteins and filtering for redundancy across the different fractions reduced the number to 376 unique proteins in 2 replicates. In addition, 366 proteins were detected by this process in 1 replicate. Hence, by applying different fractionation techniques to milk, we expanded the milk proteome. The milk proteome map may serve as a reference for scientists working in the dairy sector. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification

PubMed Central

Huang, Lei; Kang, Wenjun; Bartom, Elizabeth; Onel, Kenan; Volchenboum, Samuel; Andrade, Jorge

2015-01-01

Whole exome sequencing has facilitated the discovery of causal genetic variants associated with human diseases at deep coverage and low cost. In particular, the detection of somatic mutations from tumor/normal pairs has provided insights into the cancer genome. Although there is an abundance of publicly-available software for the detection of germline and somatic variants, concordance is generally limited among variant callers and alignment algorithms. Successful integration of variants detected by multiple methods requires in-depth knowledge of the software, access to high-performance computing resources, and advanced programming techniques. We present ExScalibur, a set of fully automated, highly scalable and modulated pipelines for whole exome data analysis. The suite integrates multiple alignment and variant calling algorithms for the accurate detection of germline and somatic mutations with close to 99% sensitivity and specificity. ExScalibur implements streamlined execution of analytical modules, real-time monitoring of pipeline progress, robust handling of errors and intuitive documentation that allows for increased reproducibility and sharing of results and workflows. It runs on local computers, high-performance computing clusters and cloud environments. In addition, we provide a data analysis report utility to facilitate visualization of the results that offers interactive exploration of quality control files, read alignment and variant calls, assisting downstream customization of potential disease-causing mutations. ExScalibur is open-source and is also available as a public image on Amazon cloud. PMID:26271043

Embedded DSP-based telehealth radar system for remote in-door fall detection.

PubMed

Garripoli, Carmine; Mercuri, Marco; Karsmakers, Peter; Jack Soh, Ping; Crupi, Giovanni; Vandenbosch, Guy A E; Pace, Calogero; Leroux, Paul; Schreurs, Dominique

2015-01-01

Telehealth systems and applications are extensively investigated nowadays to enhance the quality-of-care and, in particular, to detect emergency situations and to monitor the well-being of elderly people, allowing them to stay at home independently as long as possible. In this paper, an embedded telehealth system for continuous, automatic, and remote monitoring of real-time fall emergencies is presented and discussed. The system, consisting of a radar sensor and base station, represents a cost-effective and efficient healthcare solution. The implementation of the fall detection data processing technique, based on the least-square support vector machines, through a digital signal processor and the management of the communication between radar sensor and base station are detailed. Experimental tests, for a total of 65 mimicked fall incidents, recorded with 16 human subjects (14 men and two women) that have been monitored for 320 min, have been used to validate the proposed system under real circumstances. The subjects' weight is between 55 and 90 kg with heights between 1.65 and 1.82 m, while their age is between 25 and 39 years. The experimental results have shown a sensitivity to detect the fall events in real time of 100% without reporting false positives. The tests have been performed in an area where the radar's operation was not limited by practical situations, namely, signal power, coverage of the antennas, and presence of obstacles between the subject and the antennas.

Measuring Atmospheric Carbon Dioxide from Space: The GOSAT and OCO-2 Missions

NASA Technical Reports Server (NTRS)

Crisp, David

2011-01-01

The Japanese Greenhouse gases Observing Satellite (GOSAT) is providing new insight into atmospheric carbon dioxide trends. The NASA Orbiting Carbon Observatory-2 (OCO-2)Mission will build on this record with increased sensitivity resolution, and coverage.

SWATHtoMRM: Development of High-Coverage Targeted Metabolomics Method Using SWATH Technology for Biomarker Discovery.

PubMed

Zha, Haihong; Cai, Yuping; Yin, Yandong; Wang, Zhuozhong; Li, Kang; Zhu, Zheng-Jiang

2018-03-20

The complexity of metabolome presents a great analytical challenge for quantitative metabolite profiling, and restricts the application of metabolomics in biomarker discovery. Targeted metabolomics using multiple-reaction monitoring (MRM) technique has excellent capability for quantitative analysis, but suffers from the limited metabolite coverage. To address this challenge, we developed a new strategy, namely, SWATHtoMRM, which utilizes the broad coverage of SWATH-MS technology to develop high-coverage targeted metabolomics method. Specifically, SWATH-MS technique was first utilized to untargeted profile one pooled biological sample and to acquire the MS 2 spectra for all metabolites. Then, SWATHtoMRM was used to extract the large-scale MRM transitions for targeted analysis with coverage as high as 1000-2000 metabolites. Then, we demonstrated the advantages of SWATHtoMRM method in quantitative analysis such as coverage, reproducibility, sensitivity, and dynamic range. Finally, we applied our SWATHtoMRM approach to discover potential metabolite biomarkers for colorectal cancer (CRC) diagnosis. A high-coverage targeted metabolomics method with 1303 metabolites in one injection was developed to profile colorectal cancer tissues from CRC patients. A total of 20 potential metabolite biomarkers were discovered and validated for CRC diagnosis. In plasma samples from CRC patients, 17 out of 20 potential biomarkers were further validated to be associated with tumor resection, which may have a great potential in assessing the prognosis of CRC patients after tumor resection. Together, the SWATHtoMRM strategy provides a new way to develop high-coverage targeted metabolomics method, and facilitates the application of targeted metabolomics in disease biomarker discovery. The SWATHtoMRM program is freely available on the Internet ( http://www.zhulab.cn/software.php ).

Small unmanned aircraft system for remote contour mapping of a nuclear radiation field

NASA Astrophysics Data System (ADS)

Guss, Paul; McCall, Karen; Malchow, Russell; Fischer, Rick; Lukens, Michael; Adan, Mark; Park, Ki; Abbott, Roy; Howard, Michael; Wagner, Eric; Trainham, Clifford P.; Luke, Tanushree; Mukhopadhyay, Sanjoy; Oh, Paul; Brahmbhatt, Pareshkumar; Henderson, Eric; Han, Jinlu; Huang, Justin; Huang, Casey; Daniels, Jon

2017-09-01

For nuclear disasters involving radioactive contamination, small unmanned aircraft systems (sUASs) equipped with nuclear radiation detection and monitoring capability can be very important tools. Among the advantages of a sUAS are quick deployment, low-altitude flying that enhances sensitivity, wide area coverage, no radiation exposure health safety restriction, and the ability to access highly hazardous or radioactive areas. Additionally, the sUAS can be configured with the nuclear detecting sensor optimized to measure the radiation associated with the event. In this investigation, sUAS platforms were obtained for the installation of sensor payloads for radiation detection and electro-optical systems that were specifically developed for sUAS research, development, and operational testing. The sensor payloads were optimized for the contour mapping of a nuclear radiation field, which will result in a formula for low-cost sUAS platform operations with built-in formation flight control. Additional emphases of the investigation were to develop the relevant contouring algorithms; initiate the sUAS comprehensive testing using the Unmanned Systems, Inc. (USI) Sandstorm platforms and other acquired platforms; and both acquire and optimize the sensors for detection and localization. We demonstrated contour mapping through simulation and validated waypoint detection. We mounted a detector on a sUAS and operated it initially in the counts per second (cps) mode to perform field and flight tests to demonstrate that the equipment was functioning as designed. We performed ground truth measurements to determine the response of the detector as a function of source-to-detector distance. Operation of the radiation detector was tested using different unshielded sources.

Structure and work process in primary care and hospitalizations for sensitive conditions

PubMed Central

Araujo, Waleska Regina Machado; Queiroz, Rejane Christine de Sousa; Rocha, Thiago Augusto Hernandes; da Silva, Núbia Cristina; Thumé, Elaine; Tomasi, Elaine; Facchini, Luiz Augusto; Thomaz, Erika Barbara Abreu Fonseca

2017-01-01

ABSTRACT OBJECTIVE The objective of this study is to investigate whether the characteristics of the structure of primary health units and the work process of primary care teams are associated with the number of hospitalizations for primary care sensitive conditions. METHODS In this ecological study, we have analyzed data of Brazilian municipalities related to sociodemographic characteristics, coverage of care programs, structure of primary health units, and work process of primary care teams. We have obtained the data from the first cycle of the Brazilian Program for Improving Access and Quality of the Primary Care, of the Department of Information Technology of the Brazilian Unified Health System, the Brazilian Institute of Geography and Statistics, and the United Nations Development Programme. The associations have been estimated using negative binomial regression coefficients (β) and respective 95% confidence intervals, with a hierarchical approach in three levels (alpha = 5%). RESULTS In the adjusted analysis for the outcome in 2013, in the distal level, the coverage of the Bolsa Família Program (β = -0.001) and private insurance (β = -0.01) had a negative association, and the human development index (β = 1.13), the proportion of older adults (β = 0.05) and children under the age of five (β = 0.05), and the coverage of the Community Health Agent Strategy (β = 0.002) showed positive association with hospitalizations for primary care sensitive conditions. In the intermediate level, minimum hours (β = -0.14) and availability of vaccines (β = -0.16) showed a negative association, and availability of medications showed a positive association (β = 0.16). In the proximal level, only the variable of matrix support (β = 0.10) showed a positive association. The variables in the adjusted analysis of the number of hospitalizations for primary care sensitive conditions in 2014 presented the same association as in 2013. CONCLUSIONS The characteristics of the structure of primary health units and the work process of the primary care teams impact the number of hospitalizations for primary care sensitive conditions in Brazilian municipalities. PMID:28832757

Performance Characteristics of a New LSO PET/CT Scanner With Extended Axial Field-of-View and PSF Reconstruction

NASA Astrophysics Data System (ADS)

Jakoby, Bjoern W.; Bercier, Yanic; Watson, Charles C.; Bendriem, Bernard; Townsend, David W.

2009-06-01

A new combined lutetium oxyorthosilicate (LSO) PET/CT scanner with an extended axial field-of-view (FOV) of 21.8 cm has been developed (Biograph TruePoint PET/CT with TrueV; Siemens Molecular Imaging) and introduced into clinical practice. The scanner includes the recently announced point spread function (PSF) reconstruction algorithm. The PET components incorporate four rings of 48 detector blocks, 5.4 cm times 5.4 cm in cross-section. Each block comprises a 13 times 13 matrix of 4 times 4 times 20 mm3 elements. Data are acquired with a 4.5 ns coincidence time window and an energy window of 425-650 keV. The physical performance of the new scanner has been evaluated according to the recently revised National Electrical Manufacturers Association (NEMA) NU 2-2007 standard and the results have been compared with a previous PET/CT design that incorporates three rings of block detectors with an axial coverage of 16.2 cm (Biograph TruePoint PET/CT; Siemens Molecular Imaging). In addition to the phantom measurements, patient Noise Equivalent Count Rates (NECRs) have been estimated for a range of patients with different body weights (42-154 kg). The average spatial resolution is the same for both scanners: 4.4 mm (FWHM) and 5.0 mm (FWHM) at 1 cm and 10 cm respectively from the center of the transverse FOV. The scatter fractions of the Biograph TruePoint and Biograph TruePoint TrueV are comparable at 32%. Compared to the three ring design, the system sensitivity and peak NECR with smoothed randoms correction (1R) increase by 82% and 73%, respectively. The increase in sensitivity from the extended axial coverage of the Biograph TruePoint PET/CT with TrueV should allow a decrease in either scan time or injected dose without compromising diagnostic image quality. The contrast improvement with the PSF reconstruction potentially offers enhanced detectability for small lesions.

Using classification and NDVI differencing methods for monitoring sparse vegetation coverage: a case study of saltcedar in Nevada, USA.

USDA-ARS?s Scientific Manuscript database

A change detection experiment for an invasive species, saltcedar, near Lovelock, Nevada, was conducted with multi-date Compact Airborne Spectrographic Imager (CASI) hyperspectral datasets. Classification and NDVI differencing change detection methods were tested, In the classification strategy, a p...

Extracting foreground-obscured μ-distortion anisotropies to constrain primordial non-Gaussianity

NASA Astrophysics Data System (ADS)

Remazeilles, M.; Chluba, J.

2018-07-01

Correlations between cosmic microwave background (CMB) temperature, polarization, and spectral distortion anisotropies can be used as a probe of primordial non-Gaussianity. Here, we perform a reconstruction of μ-distortion anisotropies in the presence of Galactic and extragalactic foregrounds, applying the so-called Constrained ILC component separation method to simulations of proposed CMB space missions (PIXIE, LiteBIRD, CORE, and PICO). Our sky simulations include Galactic dust, Galactic synchrotron, Galactic free-free, thermal Sunyaev-Zeldovich effect, as well as primary CMB temperature and μ-distortion anisotropies, the latter being added as correlated field. The Constrained ILC method allows us to null the CMB temperature anisotropies in the reconstructed μ-map (and vice versa), in addition to mitigating the contaminations from astrophysical foregrounds and instrumental noise. We compute the cross-power spectrum between the reconstructed (CMB-free) μ-distortion map and the (μ-free) CMB temperature map, after foreground removal and component separations. Since the cross-power spectrum is proportional to the primordial non-Gaussianity parameter, fNL, on scales k˜eq 740 Mpc^{-1}, this allows us to derive fNL-detection limits for the aforementioned future CMB experiments. Our analysis shows that foregrounds degrade the theoretical detection limits (based mostly on instrumental noise) by more than one order of magnitude, with PICO standing the best chance at placing upper limits on scale-dependent non-Gaussianity. We also discuss the dependence of the constraints on the channel sensitivities and chosen bands. Like for B-mode polarization measurements, extended coverage at frequencies ν ≲ 40 GHz and ν ≳ 400 GHz provides more leverage than increased channel sensitivity.

Extracting foreground-obscured μ-distortion anisotropies to constrain primordial non-Gaussianity

NASA Astrophysics Data System (ADS)

Remazeilles, M.; Chluba, J.

2018-04-01

Correlations between cosmic microwave background (CMB) temperature, polarization and spectral distortion anisotropies can be used as a probe of primordial non-Gaussianity. Here, we perform a reconstruction of μ-distortion anisotropies in the presence of Galactic and extragalactic foregrounds, applying the so-called Constrained ILC component separation method to simulations of proposed CMB space missions (PIXIE, LiteBIRD, CORE, PICO). Our sky simulations include Galactic dust, Galactic synchrotron, Galactic free-free, thermal Sunyaev-Zeldovich effect, as well as primary CMB temperature and μ-distortion anisotropies, the latter being added as correlated field. The Constrained ILC method allows us to null the CMB temperature anisotropies in the reconstructed μ-map (and vice versa), in addition to mitigating the contaminations from astrophysical foregrounds and instrumental noise. We compute the cross-power spectrum between the reconstructed (CMB-free) μ-distortion map and the (μ-free) CMB temperature map, after foreground removal and component separation. Since the cross-power spectrum is proportional to the primordial non-Gaussianity parameter, fNL, on scales k˜eq 740 Mpc^{-1}, this allows us to derive fNL-detection limits for the aforementioned future CMB experiments. Our analysis shows that foregrounds degrade the theoretical detection limits (based mostly on instrumental noise) by more than one order of magnitude, with PICO standing the best chance at placing upper limits on scale-dependent non-Gaussianity. We also discuss the dependence of the constraints on the channel sensitivities and chosen bands. Like for B-mode polarization measurements, extended coverage at frequencies ν ≲ 40 GHz and ν ≳ 400 GHz provides more leverage than increased channel sensitivity.

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.

PubMed

Mohapatra, Gayatry; Engler, David A; Starbuck, Kristen D; Kim, James C; Bernay, Derek C; Scangas, George A; Rousseau, Audrey; Batchelor, Tracy T; Betensky, Rebecca A; Louis, David N

2011-04-01

Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.

Extending metabolome coverage for untargeted metabolite profiling of adherent cultured hepatic cells.

PubMed

García-Cañaveras, Juan Carlos; López, Silvia; Castell, José Vicente; Donato, M Teresa; Lahoz, Agustín

2016-02-01

MS-based metabolite profiling of adherent mammalian cells comprises several challenging steps such as metabolism quenching, cell detachment, cell disruption, metabolome extraction, and metabolite measurement. In LC-MS, the final metabolome coverage is strongly determined by the separation technique and the MS conditions used. Human liver-derived cell line HepG2 was chosen as adherent mammalian cell model to evaluate the performance of several commonly used procedures in both sample processing and LC-MS analysis. In a first phase, metabolite extraction and sample analysis were optimized in a combined manner. To this end, the extraction abilities of five different solvents (or combinations) were assessed by comparing the number and the levels of the metabolites comprised in each extract. Three different chromatographic methods were selected for metabolites separation. A HILIC-based method which was set to specifically separate polar metabolites and two RP-based methods focused on lipidome and wide-ranging metabolite detection, respectively. With regard to metabolite measurement, a Q-ToF instrument operating in both ESI (+) and ESI (-) was used for unbiased extract analysis. Once metabolite extraction and analysis conditions were set up, the influence of cell harvesting on metabolome coverage was also evaluated. Therefore, different protocols for cell detachment (trypsinization or scraping) and metabolism quenching were compared. This study confirmed the inconvenience of trypsinization as a harvesting technique, and the importance of using complementary extraction solvents to extend metabolome coverage, minimizing interferences and maximizing detection, thanks to the use of dedicated analytical conditions through the combination of HILIC and RP separations. The proposed workflow allowed the detection of over 300 identified metabolites from highly polar compounds to a wide range of lipids.

Making the case: the impetus for federally mandating insurance companies to cover colorectal cancer screening.

PubMed

Toomey, April; Menon, Usha

2010-01-01

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths per year in the U.S. The 5-year survival rate of CRC detected early is 90%, but only 39% of CRC is detected in this stage. CRC screening is effective in reducing mortality from this disease, but national screening rates are alarmingly low. Mandated CRC screening insurance coverage significantly increases screening rates. However, mandated coverage varies greatly by state. Bill H.R. 1330, which would federally mandate insurance companies to cover CRC screening for people 50 and older, is currently under consideration by the House of Representatives. Reasons to support this bill and rebuttals to arguments made against H.R. 1330 are discussed.

Chemical Isotope Labeling LC-MS for High Coverage and Quantitative Profiling of the Hydroxyl Submetabolome in Metabolomics.

PubMed

Zhao, Shuang; Luo, Xian; Li, Liang

2016-11-01

A key step in metabolomics is to perform accurate relative quantification of the metabolomes in comparative samples with high coverage. Hydroxyl-containing metabolites are an important class of the metabolome with diverse structures and physical/chemical properties; however, many of them are difficult to detect with high sensitivity. We present a high-performance chemical isotope labeling liquid chromatography mass spectrometry (LC-MS) technique for in-depth profiling of the hydroxyl submetabolome, which involves the use of acidic liquid-liquid extraction to enrich hydroxyl metabolites into ethyl acetate from an aqueous sample. After drying and then redissolving in acetonitrile, the metabolite extract is labeled using a base-activated 12 C- or 13 C-dansylation reaction. A fast step-gradient LC-UV method is used to determine the total concentration of labeled metabolites. On the basis of the concentration information, a 12 C-labeled individual sample is mixed with an equal mole amount of a 13 C-labeled pool or control for relative metabolite quantification. The 12 C-/ 13 C-labeled mixtures are individually analyzed by LC-MS, and the resultant peak pairs of labeled metabolites in MS are measured for relative quantification and metabolite identification. A standard library of 85 hydroxyl compounds containing MS, retention time, and MS/MS information was constructed for positive metabolite identification based on matches of two or all three of these parameters with those of an unknown. Using human urine as an example, we analyzed samples of 1:1 12 C-/ 13 C-labeled urine in triplicate with triplicate runs per sample and detected an average of 3759 ± 45 peak pairs or metabolites per run and 3538 ± 71 pairs per sample with 3093 pairs in common (n = 9). Out of the 3093 peak pairs, 2304 pairs (75%) could be positively or putatively identified based on metabolome database searches, including 20 pairs positively identified using the dansylated hydroxyl standards library. The majority of detected metabolites were those containing hydroxyl groups. This technique opens a new avenue for the detailed characterization of the hydroxyl submetabolome in metabolomics research.

The Genetic-Algorithm-Based Normal Boundary Intersection (GANBI) Method; An Efficient Approach to Pareto Multiobjective Optimization for Engineering Design

DTIC Science & Technology

2006-05-15

alarm performance in a cost-effective manner is the use of track - before - detect strategies, in which multiple sensor detections must occur within the...corresponding to the traditional sensor coverage problem. Also, in the track - before - detect context, reference is made to the field-level functions of...detection and false alarm as successful search and false search, respectively, because the track - before - detect process serves as a searching function

Inequalities in full immunization coverage: trends in low- and middle-income countries

PubMed Central

Barros, Aluísio JD; Wong, Kerry LM; Johnson, Hope L; Pariyo, George; França, Giovanny VA; Wehrmeister, Fernando C; Victora, Cesar G

2016-01-01

Abstract Objective To investigate disparities in full immunization coverage across and within 86 low- and middle-income countries. Methods In May 2015, using data from the most recent Demographic and Health Surveys and Multiple Indicator Cluster Surveys, we investigated inequalities in full immunization coverage – i.e. one dose of bacille Calmette-Guérin vaccine, one dose of measles vaccine, three doses of vaccine against diphtheria, pertussis and tetanus and three doses of polio vaccine – in 86 low- or middle-income countries. We then investigated temporal trends in the level and inequality of such coverage in eight of the countries. Findings In each of the World Health Organization’s regions, it appeared that about 56–69% of eligible children in the low- and middle-income countries had received full immunization. However, within each region, the mean recorded level of such coverage varied greatly. In the African Region, for example, it varied from 11.4% in Chad to 90.3% in Rwanda. We detected pro-rich inequality in such coverage in 45 of the 83 countries for which the relevant data were available and pro-urban inequality in 35 of the 86 study countries. Among the countries in which we investigated coverage trends, Madagascar and Mozambique appeared to have made the greatest progress in improving levels of full immunization coverage over the last two decades, particularly among the poorest quintiles of their populations. Conclusion Most low- and middle-income countries are affected by pro-rich and pro-urban inequalities in full immunization coverage that are not apparent when only national mean values of such coverage are reported. PMID:27821882

Estimating Contrail Climate Effects from Satellite Data

NASA Technical Reports Server (NTRS)

Minnis, Patrick; Duda, David P.; Palikonda, Rabindra; Bedka, Sarah T.; Boeke, Robyn; Khlopenkov, Konstantin; Chee, Thad; Bedka, Kristopher T.

2011-01-01

An automated contrail detection algorithm (CDA) is developed to exploit six of the infrared channels on the 1-km MODerate-resolution Imaging Spectroradiometer (MODIS) on the Terra and Aqua satellites. The CDA is refined and balanced using visual error analysis. It is applied to MODIS data taken by Terra and Aqua over the United States during 2006 and 2008. The results are consistent with flight track data, but differ markedly from earlier analyses. Contrail coverage is a factor of 4 less than other retrievals and the retrieved contrail optical depths and radiative forcing are smaller by approx.30%. The discrepancies appear to be due to the inability to detect wider, older contrails that comprise a significant amount of the contrail coverage. An example of applying the algorithm to MODIS data over the entire Northern Hemisphere is also presented. Overestimates of contrail coverage are apparent in some tropical regions. Methods for improving the algorithm are discussed and are to be implemented before analyzing large amounts of Northern Hemisphere data. The results should be valuable for guiding and validating climate models seeking to account for aviation effects on climate.

Modeling the SHG activities of diverse protein crystals

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

Haupert, Levi M.; DeWalt, Emma L.; Simpson, Garth J.

2012-10-18

A symmetry-additiveab initiomodel for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine point-group symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much of the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within themore » crystal lattice. Two or more orders-of-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of ~84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices.« less

Vaccination Coverage Disparities Between Foreign-Born and U.S.-Born Children Aged 19-35 Months, United States, 2010-2012.

PubMed

Varan, Aiden K; Rodriguez-Lainz, Alfonso; Hill, Holly A; Elam-Evans, Laurie D; Yankey, David; Li, Qian

2017-08-01

Healthy People 2020 targets high vaccination coverage among children. Although reductions in coverage disparities by race/ethnicity have been described, data by nativity are limited. The National Immunization Survey is a random-digit-dialed telephone survey that estimates vaccination coverage among U.S. children aged 19-35 months. We assessed coverage among 52,441 children from pooled 2010-2012 data for individual vaccines and the combined 4:3:1:3*:3:1:4 series (which includes ≥4 doses of diphtheria, tetanus, and acellular pertussis vaccine/diphtheria and tetanus toxoids vaccine/diphtheria, tetanus toxoids, and pertussis vaccine, ≥3 doses of poliovirus vaccine, ≥1 dose of measles-containing vaccine, ≥3 or ≥4 doses of Haemophilus influenzae type b vaccine (depending on product type of vaccine; denoted as 3* in the series name), ≥3 doses of hepatitis B vaccine, ≥1 dose of varicella vaccine, and ≥4 doses of pneumococcal conjugate vaccine). Coverage estimates controlling for sociodemographic factors and multivariable logistic regression modeling for 4:3:1:3*:3:1:4 series completion are presented. Significantly lower coverage among foreign-born children was detected for DTaP, hepatitis A, hepatitis B, Hib, pneumococcal conjugate, and rotavirus vaccines, and for the combined series. Series completion disparities persisted after control for demographic, access-to-care, poverty, and language effects. Substantial and potentially widening disparities in vaccination coverage exist among foreign-born children. Improved immunization strategies targeting this population and continued vaccination coverage monitoring by nativity are needed.

Income Eligibility Thresholds, Premium Contributions, and Children's Coverage Outcomes: A Study of CHIP Expansions

PubMed Central

Gresenz, Carole Roan; Edgington, Sarah E; Laugesen, Miriam J; Escarce, José J

2013-01-01

Objective To understand the effects of Children's Health Insurance Program (CHIP) income eligibility thresholds and premium contribution requirements on health insurance coverage outcomes among children. Data Sources 2002–2009 Annual Social and Economic Supplements of the Current Population Survey linked to data from multiple secondary data sources. Study Design We use a selection correction model to simultaneously estimate program eligibility and coverage outcomes conditional upon eligibility. We simulate the effects of three premium schedules representing a range of generosity levels and the effects of income eligibility thresholds ranging from 200 to 400 percent of the federal poverty line. Principal Findings Premium contribution requirements decrease enrollment in public coverage and increase enrollment in private coverage, with larger effects for greater contribution levels. Our simulation results suggest minimal changes in coverage outcomes from eligibility expansions to higher income families under premium schedules that require more than a modest contribution (medium or high schedules). Conclusions Our simulation results are useful counterpoints to previous research that has estimated the average effect of program expansions as they were implemented without disentangling the effects of premiums or other program features. The sensitivity to premiums observed suggests that although contribution requirements may be effective in reducing crowd-out, they also have the potential, depending on the level of contribution required, to nullify the effects of CHIP expansions entirely. The persistence of uninsurance among children under the range of simulated scenarios points to the importance of Affordable Care Act provisions designed to make the process of obtaining coverage transparent and navigable. PMID:23398477

Income eligibility thresholds, premium contributions, and children's coverage outcomes: a study of CHIP expansions.

PubMed

Gresenz, Carole Roan; Edgington, Sarah E; Laugesen, Miriam J; Escarce, José J

2013-04-01

To understand the effects of Children's Health Insurance Program (CHIP) income eligibility thresholds and premium contribution requirements on health insurance coverage outcomes among children. 2002-2009 Annual Social and Economic Supplements of the Current Population Survey linked to data from multiple secondary data sources. We use a selection correction model to simultaneously estimate program eligibility and coverage outcomes conditional upon eligibility. We simulate the effects of three premium schedules representing a range of generosity levels and the effects of income eligibility thresholds ranging from 200 to 400 percent of the federal poverty line. Premium contribution requirements decrease enrollment in public coverage and increase enrollment in private coverage, with larger effects for greater contribution levels. Our simulation results suggest minimal changes in coverage outcomes from eligibility expansions to higher income families under premium schedules that require more than a modest contribution (medium or high schedules). Our simulation results are useful counterpoints to previous research that has estimated the average effect of program expansions as they were implemented without disentangling the effects of premiums or other program features. The sensitivity to premiums observed suggests that although contribution requirements may be effective in reducing crowd-out, they also have the potential, depending on the level of contribution required, to nullify the effects of CHIP expansions entirely. The persistence of uninsurance among children under the range of simulated scenarios points to the importance of Affordable Care Act provisions designed to make the process of obtaining coverage transparent and navigable. © Health Research and Educational Trust.

How to improve the standardization and the diagnostic performance of the fecal egg count reduction test?

PubMed

Levecke, Bruno; Kaplan, Ray M; Thamsborg, Stig M; Torgerson, Paul R; Vercruysse, Jozef; Dobson, Robert J

2018-04-15

Although various studies have provided novel insights into how to best design, analyze and interpret a fecal egg count reduction test (FECRT), it is still not straightforward to provide guidance that allows improving both the standardization and the analytical performance of the FECRT across a variety of both animal and nematode species. For example, it has been suggested to recommend a minimum number of eggs to be counted under the microscope (not eggs per gram of feces), but we lack the evidence to recommend any number of eggs that would allow a reliable assessment of drug efficacy. Other aspects that need further research are the methodology of calculating uncertainty intervals (UIs; confidence intervals in case of frequentist methods and credible intervals in case of Bayesian methods) and the criteria of classifying drug efficacy into 'normal', 'suspected' and 'reduced'. The aim of this study is to provide complementary insights into the current knowledge, and to ultimately provide guidance in the development of new standardized guidelines for the FECRT. First, data were generated using a simulation in which the 'true' drug efficacy (TDE) was evaluated by the FECRT under varying scenarios of sample size, analytic sensitivity of the diagnostic technique, and level of both intensity and aggregation of egg excretion. Second, the obtained data were analyzed with the aim (i) to verify which classification criteria allow for reliable detection of reduced drug efficacy, (ii) to identify the UI methodology that yields the most reliable assessment of drug efficacy (coverage of TDE) and detection of reduced drug efficacy, and (iii) to determine the required sample size and number of eggs counted under the microscope that optimizes the detection of reduced efficacy. Our results confirm that the currently recommended criteria for classifying drug efficacy are the most appropriate. Additionally, the UI methodologies we tested varied in coverage and ability to detect reduced drug efficacy, thus a combination of UI methodologies is recommended to assess the uncertainty across all scenarios of drug efficacy estimates. Finally, based on our model estimates we were able to determine the required number of eggs to count for each sample size, enabling investigators to optimize the probability of correctly classifying a theoretical TDE while minimizing both financial and technical resources. Copyright © 2018 Elsevier B.V. All rights reserved.

Bright gamma-ray flares of the quasars 3C 279 and PKS 1222+216 observed at the highest energies with Fermi-LAT and VERITAS

NASA Astrophysics Data System (ADS)

Errando, Manel

2014-08-01

Flat spectrum radio quasars (FSRQs) are the most powerful sources continuously detected at gamma-ray energies, with luminosities exceeding 1048 erg s-1. The high-energy emission of quasars peaks in the MeV-GeV band, and only a few episodic detections have been reported at very high energies (VHE, E>100 GeV). We will present the first results from an observing campaign on the FSRQ 3C 279 in April 2014 during the brightest gamma-ray outburst ever recorded for this object, with flux exceeding the historic 1991 flare seen by EGRET. Observations include simultaneous coverage with the Fermi-LAT satellite and the VERITAS ground-based array spanning four decades in energy from 100 MeV to 1 TeV with unprecedented sensitivity. We will also report on the detection of persistent VHE emission from the quasar PKS 1222+216 over a week-long period in March 2014. These observations present strong challenges to current models of energy dissipation in relativistic jets. The implications of the absence/presence of VHE emission in connection with flaring activity in the MeV-GeV regime will be discussed, especially concerning the role of ambient photon fields in the radiation mechanisms, and the size and location of the gamma-ray emission region.

Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology.

PubMed

Debladis, Emilie; Llauro, Christel; Carpentier, Marie-Christine; Mirouze, Marie; Panaud, Olivier

2017-07-17

Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV). However, these have relied on Illumina platform that generates short reads (up to 350 nucleotides). This limitation in size of sequence reads can cause high false discovery rate (FDR) and therefore limit the power of detection of TEASVs, especially in the case of large, complex genomes. The newest sequencing technologies, such as Oxford Nanopore Technologies (ONT) can generate kilobases-long reads thus representing a promising tool for TEASV detection in plant and animals. We present the results of a pilot experiment for TEASV detection on the model plant species Arabidopsis thaliana using ONT sequencing and show that it can be used efficiently to detect TE movements. We generated a ~0.8X genome coverage of a met1-derived epigenetic recombinant inbred line (epiRIL) using a MinIon device with R7 chemistry. We were able to detect nine new copies of the LTR-retrotransposon Evadé (EVD). We also evidenced the activity of the DNA transposon CACTA, CAC1. Even at a low sequence coverage (0.8X), ONT sequencing allowed us to reliably detect several TE insertions in Arabidopsis thaliana genome. The long read length allowed a precise and un-ambiguous mapping of the structural variations caused by the activity of TEs. This suggests that the trade-off between read length and genome coverage for TEASV detection may be in favor of the former. Should the technology be further improved both in terms of lower error rate and operation costs, it could be efficiently used in diversity studies at population level.

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

Bockris, J.O.; Devanathan, M.A.V.

The galvanostatic double charging method was applied to determine the coverage of Ni cathodes with adsorbed atomic H in 2 N NaOH solutions. Anodic current densities were varied from 0.05 to 1.8 amp/sq cm. The plateau indicating absence of readsorption was between 0.6 and 1.8 amp/sq cm, for a constant cathodic c.d. of 1/10,000 amp/sq cm. The variation of the adsorbed H over cathodic c.d.'s ranging from 10 to the -6th power to 1/10 at a constant anodic c.d. of 1 amp/sq cm were calculated and the coverage calculated. The mechanism of the H evolution reaction was elucidated. The ratemore » determining step is discharge from a water molecules followed by rapid Tafel recombination. The rate constants for these processes and the rate constant for the ionisation, calculated with the extrapolated value of coverage for the reversible H electrode, were determined. A modification of the Tafel equation which takes into account both coverage and ionisation is in harmony with the results. A new method for the determination of coverage suitable for corrodible metals is described which involves the measurement of the rate of permeation of H by electrochemical techniques which enhances the sensitivity of the method. (Author)« less

Comparison of Three Information Sources for Smoking Information in Electronic Health Records

PubMed Central

Wang, Liwei; Ruan, Xiaoyang; Yang, Ping; Liu, Hongfang

2016-01-01

OBJECTIVE The primary aim was to compare independent and joint performance of retrieving smoking status through different sources, including narrative text processed by natural language processing (NLP), patient-provided information (PPI), and diagnosis codes (ie, International Classification of Diseases, Ninth Revision [ICD-9]). We also compared the performance of retrieving smoking strength information (ie, heavy/light smoker) from narrative text and PPI. MATERIALS AND METHODS Our study leveraged an existing lung cancer cohort for smoking status, amount, and strength information, which was manually chart-reviewed. On the NLP side, smoking-related electronic medical record (EMR) data were retrieved first. A pattern-based smoking information extraction module was then implemented to extract smoking-related information. After that, heuristic rules were used to obtain smoking status-related information. Smoking information was also obtained from structured data sources based on diagnosis codes and PPI. Sensitivity, specificity, and accuracy were measured using patients with coverage (ie, the proportion of patients whose smoking status/strength can be effectively determined). RESULTS NLP alone has the best overall performance for smoking status extraction (patient coverage: 0.88; sensitivity: 0.97; specificity: 0.70; accuracy: 0.88); combining PPI with NLP further improved patient coverage to 0.96. ICD-9 does not provide additional improvement to NLP and its combination with PPI. For smoking strength, combining NLP with PPI has slight improvement over NLP alone. CONCLUSION These findings suggest that narrative text could serve as a more reliable and comprehensive source for obtaining smoking-related information than structured data sources. PPI, the readily available structured data, could be used as a complementary source for more comprehensive patient coverage. PMID:27980387

Progress Toward Measles Elimination - Bangladesh, 2000-2016.

PubMed

Khanal, Sudhir; Bohara, Rajendra; Chacko, Stephen; Sharifuzzaman, Mohammad; Shamsuzzaman, Mohammad; Goodson, James L; Dabbagh, Alya; Kretsinger, Katrina; Dhongde, Deepak; Liyanage, Jayantha; Bahl, Sunil; Thapa, Arun

2017-07-21

In 2013, at the 66th session of the Regional Committee of the World Health Organization (WHO) South-East Asia Region (SEAR), a regional goal was established to eliminate measles and control rubella and congenital rubella syndrome* by 2020 (1). WHO-recommended measles elimination strategies in SEAR countries include 1) achieving and maintaining ≥95% coverage with 2 doses of measles-containing vaccine (MCV) in every district, delivered through the routine immunization program or through supplementary immunization activities (SIAs) † ; 2) developing and sustaining a sensitive and timely measles case-based surveillance system that meets targets for recommended performance indicators; and 3) developing and maintaining an accredited measles laboratory network (2). In 2014, Bangladesh, one of 11 countries in SEAR, adopted a national goal for measles elimination by 2018 (2,3). This report describes progress and challenges toward measles elimination in Bangladesh during 2000-2016. Estimated coverage with the first MCV dose (MCV1) increased from 74% in 2000 to 94% in 2016. The second MCV dose (MCV2) was introduced in 2012, and MCV2 coverage increased from 35% in 2013 to 93% in 2016. During 2000-2016, approximately 108.9 million children received MCV during three nationwide SIAs conducted in phases. During 2000-2016, reported confirmed measles incidence decreased 82%, from 34.2 to 6.1 per million population. However, in 2016, 56% of districts did not meet the surveillance performance target of ≥2 discarded nonmeasles, nonrubella cases § per 100,000 population. Additional measures that include increasing MCV1 and MCV2 coverage to ≥95% in all districts with additional strategies for hard-to-reach populations, increasing sensitivity of measles case-based surveillance, and ensuring timely transport of specimens to the national laboratory will help achieve measles elimination.

Occupational contact dermatitis in the wind energy industry.

PubMed

Lárraga-Piñones, G; Heras-Mendaza, F; Conde-Salazar, L

2012-12-01

In 2010, wind energy coverage in Spain increased by 16%, making the country the world's fourth largest producer in a fast-developing industry that is also a source of employment. Occupational skin diseases in this field have received little attention. The present study aims to describe the main characteristics of skin diseases affecting workers in the wind energy industry and the allergens involved. We performed a descriptive, observational study of workers from the wind energy industry with suspected contact dermatitis who were referred to the occupational dermatology clinic of the National School of Occupational Medicine (Escuela Nacional de Medicina del Trabajo) between 2009 and 2011. We took both a clinical history and an occupational history, and patients underwent a physical examination and patch testing with the materials used in their work. We studied 10 workers (8 men, 2 women), with a mean age of 33.7 years. The main finding was dermatitis, which affected the face, eyelids, forearms, and hands. Sensitization to epoxy resins was detected in 4 workers, 1 of whom was also sensitized to epoxy curing agents. One worker was sensitized to bisphenol F resin but had a negative result with epoxy resin from the standard series. In the 5 remaining cases, the final diagnosis was irritant contact dermatitis due to fiberglass. Occupational skin diseases are increasingly common in the wind energy industry. The main allergens are epoxy resins. Fiberglass tends to produce irritation. Copyright © 2012 Elsevier España, S.L. and AEDV. All rights reserved.

Optimization of flow-sensitive alternating inversion recovery (FAIR) for perfusion functional MRI of rodent brain.

PubMed

Nasrallah, Fatima A; Lee, Eugene L Q; Chuang, Kai-Hsiang

2012-11-01

Arterial spin labeling (ASL) MRI provides a noninvasive method to image perfusion, and has been applied to map neural activation in the brain. Although pulsed labeling methods have been widely used in humans, continuous ASL with a dedicated neck labeling coil is still the preferred method in rodent brain functional MRI (fMRI) to maximize the sensitivity and allow multislice acquisition. However, the additional hardware is not readily available and hence its application is limited. In this study, flow-sensitive alternating inversion recovery (FAIR) pulsed ASL was optimized for fMRI of rat brain. A practical challenge of FAIR is the suboptimal global inversion by the transmit coil of limited dimensions, which results in low effective labeling. By using a large volume transmit coil and proper positioning to optimize the body coverage, the perfusion signal was increased by 38.3% compared with positioning the brain at the isocenter. An additional 53.3% gain in signal was achieved using optimized repetition and inversion times compared with a long TR. Under electrical stimulation to the forepaws, a perfusion activation signal change of 63.7 ± 6.3% can be reliably detected in the primary somatosensory cortices using single slice or multislice echo planar imaging at 9.4 T. This demonstrates the potential of using pulsed ASL for multislice perfusion fMRI in functional and pharmacological applications in rat brain. Copyright © 2012 John Wiley & Sons, Ltd.

Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project.

PubMed

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Kim, Kwang-Youl; Kwon, Kyung-Hoon; Yoo, Jong Shin; Omenn, Gilbert S; Baker, Mark S; Hancock, William S; Paik, Young-Ki

2015-12-04

Approximately 2.9 billion long base-pair human reference genome sequences are known to encode some 20 000 representative proteins. However, 3000 proteins, that is, ~15% of all proteins, have no or very weak proteomic evidence and are still missing. Missing proteins may be present in rare samples in very low abundance or be only temporarily expressed, causing problems in their detection and protein profiling. In particular, some technical limitations cause missing proteins to remain unassigned. For example, current mass spectrometry techniques have high limits and error rates for the detection of complex biological samples. An insufficient proteome coverage in a reference sequence database and spectral library also raises major issues. Thus, the development of a better strategy that results in greater sensitivity and accuracy in the search for missing proteins is necessary. To this end, we used a new strategy, which combines a reference spectral library search and a simulated spectral library search, to identify missing proteins. We built the human iRefSPL, which contains the original human reference spectral library and additional peptide sequence-spectrum match entries from other species. We also constructed the human simSPL, which contains the simulated spectra of 173 907 human tryptic peptides determined by MassAnalyzer (version 2.3.1). To prove the enhanced analytical performance of the combination of the human iRefSPL and simSPL methods for the identification of missing proteins, we attempted to reanalyze the placental tissue data set (PXD000754). The data from each experiment were analyzed using PeptideProphet, and the results were combined using iProphet. For the quality control, we applied the class-specific false-discovery rate filtering method. All of the results were filtered at a false-discovery rate of <1% at the peptide and protein levels. The quality-controlled results were then cross-checked with the neXtProt DB (2014-09-19 release). The two spectral libraries, iRefSPL and simSPL, were designed to ensure no overlap of the proteome coverage. They were shown to be complementary to spectral library searching and significantly increased the number of matches. From this trial, 12 new missing proteins were identified that passed the following criterion: at least 2 peptides of 7 or more amino acids in length or one of 9 or more amino acids in length with one or more unique sequences. Thus, the iRefSPL and simSPL combination can be used to help identify peptides that have not been detected by conventional sequence database searches with improved sensitivity and a low error rate.

Experimental and Numerical Analysis of Microstructures and Stress States of Shot-Peened GH4169 Superalloys

NASA Astrophysics Data System (ADS)

Hu, Dianyin; Gao, Ye; Meng, Fanchao; Song, Jun; Wang, Rongqiao

2018-04-01

Combining experiments and finite element analysis (FEA), a systematic study was performed to analyze the microstructural evolution and stress states of shot-peened GH4169 superalloy over a variety of peening intensities and coverages. A dislocation density evolution model was integrated into the representative volume FEA model to quantitatively predict microstructural evolution in the surface layers and compared with experimental results. It was found that surface roughness and through-depth residual stress profile are more sensitive to shot-peening intensity compared to coverage due to the high kinetic energy involved. Moreover, a surface nanocrystallization layer was discovered in the top surface region of GH4169 for all shot-peening conditions. However, the grain refinement was more intensified under high shot-peening coverage, under which enough time was permitted for grain refinement. The grain size gradient predicted by the numerical framework showed good agreement with experimental observations.

HERA: Illuminating Our Early Universe

NASA Astrophysics Data System (ADS)

DeBoer, David

2014-06-01

The Hydrogen Epoch of Reionization Arrays (HERA) roadmap is a staged plan for using the unique properties of the 21cm line from neutral hydrogen to probe our cosmic dawn, from the birth of the first stars and black holes, through the full reionization of the primordial intergalactic medium (IGM). HERA is a collaboration between the Precision Array Probing the Epoch of Reionization (PAPER), US-Murchison Widefield Array (MWA), and MIT Epoch of Reionization (MITEOR) teams.The first phase of the HERA roadmap entailed the operation of the PAPER and MWA telescopes to explore techniques and designs required to detect the primordial HI signal in the presence of radio continuum foreground emission some four orders of magnitude brighter. Studies with PAPER and the MWA have led to a new understanding of the interplay of foreground and instrumental systematics in the context of a three-dimensional cosmological intensity-mapping experiment. We are now able to remove foregrounds to the limits of our sensitivity with these instruments, culminating in the first physically meaningful upper limits on the power spectrum of 2 cm emission from reionization.Building on this understanding, the next stage of HERA entails a new 14m diameter antenna element that is optimized both for sensitivity and for minimizing foreground systematics. Arranging these elements in a compact hexagonal grid yields an array that facilitates calibration, leverages proven foreground removal techniques, and is scalable to large collecting areas. The HERA phase II will be located in the radio quiet environment of the SKA site in Karoo, South Africa, and have a sensitivity close to two orders of magnitude better than PAPER and the MWA, with broader frequency coverage, HERA can paint an uninterrupted picture through reionization, back to the end of the Dark Ages.This paper will present a summary of the current understanding of the signal characteristics and measurements and describe this planned HERA telescope to be built to detect and characterize the EoR power spectrum.

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

Golbus, Jessica R.; Puckelwartz, Megan J.; Dellefave-Castillo, Lisa

Background—Cardiomyopathy is highly heritable but genetically diverse. At present, genetic testing for cardiomyopathy uses targeted sequencing to simultaneously assess the coding regions of more than 50 genes. New genes are routinely added to panels to improve the diagnostic yield. With the anticipated $1000 genome, it is expected that genetic testing will shift towards comprehensive genome sequencing accompanied by targeted gene analysis. Therefore, we assessed the reliability of whole genome sequencing and targeted analysis to identify cardiomyopathy variants in 11 subjects with cardiomyopathy. Methods and Results—Whole genome sequencing with an average of 37× coverage was combined with targeted analysis focused onmore » 204 genes linked to cardiomyopathy. Genetic variants were scored using multiple prediction algorithms combined with frequency data from public databases. This pipeline yielded 1-14 potentially pathogenic variants per individual. Variants were further analyzed using clinical criteria and/or segregation analysis. Three of three previously identified primary mutations were detected by this analysis. In six subjects for whom the primary mutation was previously unknown, we identified mutations that segregated with disease, had clinical correlates, and/or had additional pathological correlation to provide evidence for causality. For two subjects with previously known primary mutations, we identified additional variants that may act as modifiers of disease severity. In total, we identified the likely pathological mutation in 9 of 11 (82%) subjects. We conclude that these pilot data demonstrate that ~30-40× coverage whole genome sequencing combined with targeted analysis is feasible and sensitive to identify rare variants in cardiomyopathy-associated genes.« less

Protein family clustering for structural genomics.

PubMed

Yan, Yongpan; Moult, John

2005-10-28

A major goal of structural genomics is the provision of a structural template for a large fraction of protein domains. The magnitude of this task depends on the number and nature of protein sequence families. With a large number of bacterial genomes now fully sequenced, it is possible to obtain improved estimates of the number and diversity of families in that kingdom. We have used an automated clustering procedure to group all sequences in a set of genomes into protein families. Bench-marking shows the clustering method is sensitive at detecting remote family members, and has a low level of false positives. This comprehensive protein family set has been used to address the following questions. (1) What is the structure coverage for currently known families? (2) How will the number of known apparent families grow as more genomes are sequenced? (3) What is a practical strategy for maximizing structure coverage in future? Our study indicates that approximately 20% of known families with three or more members currently have a representative structure. The study indicates also that the number of apparent protein families will be considerably larger than previously thought: We estimate that, by the criteria of this work, there will be about 250,000 protein families when 1000 microbial genomes have been sequenced. However, the vast majority of these families will be small, and it will be possible to obtain structural templates for 70-80% of protein domains with an achievable number of representative structures, by systematically sampling the larger families.

Silver nanocube aggregation gradient materials in search for total internal reflection with high phase sensitivity

NASA Astrophysics Data System (ADS)

König, Tobias A. F.; Ledin, Petr A.; Russell, Michael; Geldmeier, Jeffrey A.; Mahmoud, Mahmoud. A.; El-Sayed, Mostafa A.; Tsukruk, Vladimir V.

2015-03-01

We fabricated monolayer coatings of a silver nanocube aggregation to create a step-wise optical strip by applying different surface pressures during slow Langmuir-Blodgett deposition. The varying amount of randomly distributed nanocube aggregates with different surface coverages in gradient manner due to changes in surface pressure allows for continuous control of the polarization sensitive absorption of the incoming light over a broad optical spectrum. Optical characterization under total internal reflection conditions combined with electromagnetic simulations reveal that the broadband light absorption depends on the relative orientation of the nanoparticles to the polarization of the incoming light. By using computer simulations, we found that the electric field vector of the s-polarized light interacts with the different types of silver nanocube aggregations to excite different plasmonic resonances. The s-polarization shows dramatic changes of the plasmonic resonances at different angles of incidence (shift of 64 nm per 10° angle of incidence). With a low surface nanocube coverage (from 5% to 20%), we observed a polarization-selective high absorption of 80% (with an average 75%) of the incoming light over a broad optical range in the visible region from 400 nm to 700 nm. This large-area gradient material with location-dependent optical properties can be of particular interest for broadband light absorption, phase-sensitive sensors, and imaging.We fabricated monolayer coatings of a silver nanocube aggregation to create a step-wise optical strip by applying different surface pressures during slow Langmuir-Blodgett deposition. The varying amount of randomly distributed nanocube aggregates with different surface coverages in gradient manner due to changes in surface pressure allows for continuous control of the polarization sensitive absorption of the incoming light over a broad optical spectrum. Optical characterization under total internal reflection conditions combined with electromagnetic simulations reveal that the broadband light absorption depends on the relative orientation of the nanoparticles to the polarization of the incoming light. By using computer simulations, we found that the electric field vector of the s-polarized light interacts with the different types of silver nanocube aggregations to excite different plasmonic resonances. The s-polarization shows dramatic changes of the plasmonic resonances at different angles of incidence (shift of 64 nm per 10° angle of incidence). With a low surface nanocube coverage (from 5% to 20%), we observed a polarization-selective high absorption of 80% (with an average 75%) of the incoming light over a broad optical range in the visible region from 400 nm to 700 nm. This large-area gradient material with location-dependent optical properties can be of particular interest for broadband light absorption, phase-sensitive sensors, and imaging. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr06430e

Forecasting Lightning Threat Using WRF Proxy Fields

NASA Technical Reports Server (NTRS)

McCaul, E. W., Jr.

2010-01-01

Objectives: Given that high-resolution WRF forecasts can capture the character of convective outbreaks, we seek to: 1. Create WRF forecasts of LTG threat (1-24 h), based on 2 proxy fields from explicitly simulated convection: - graupel flux near -15 C (captures LTG time variability) - vertically integrated ice (captures LTG threat area). 2. Calibrate each threat to yield accurate quantitative peak flash rate densities. 3. Also evaluate threats for areal coverage, time variability. 4. Blend threats to optimize results. 5. Examine sensitivity to model mesh, microphysics. Methods: 1. Use high-resolution 2-km WRF simulations to prognose convection for a diverse series of selected case studies. 2. Evaluate graupel fluxes; vertically integrated ice (VII). 3. Calibrate WRF LTG proxies using peak total LTG flash rate densities from NALMA; relationships look linear, with regression line passing through origin. 4. Truncate low threat values to make threat areal coverage match NALMA flash extent density obs. 5. Blend proxies to achieve optimal performance 6. Study CAPS 4-km ensembles to evaluate sensitivities.

Next-generation Event Horizon Telescope developments: new stations for enhanced imaging

NASA Astrophysics Data System (ADS)

Palumbo, Daniel; Johnson, Michael; Doeleman, Sheperd; Chael, Andrew; Bouman, Katherine

2018-01-01

The Event Horizon Telescope (EHT) is a multinational Very Long Baseline Interferometry (VLBI) network of dishes joined to resolve general relativistic behavior near a supermassive black hole. The imaging quality of the EHT is largely dependent upon the sensitivity and spatial frequency coverage of the many baselines between its constituent telescopes. The EHT already contains many highly sensitive dishes, including the crucial Atacama Large Millimeter/Submillimeter Array (ALMA), making it viable to add smaller, cheaper telescopes to the array, greatly improving future capabilities of the EHT. We develop tools for optimizing the positions of new dishes in planned arrays. We also explore the feasibility of adding small orbiting dishes to the EHT, and develop orbital optimization tools for space-based VLBI imaging. Unlike the Millimetron mission planned to be at L2, we specifically treat near-earth orbiters, and find rapid filling of spatial frequency coverage across a large range of baseline lengths. Finally, we demonstrate significant improvement in image quality when adding small dishes to planned arrays in simulated observations.

Intervals for posttest probabilities: a comparison of 5 methods.

PubMed

Mossman, D; Berger, J O

2001-01-01

Several medical articles discuss methods of constructing confidence intervals for single proportions and the likelihood ratio, but scant attention has been given to the systematic study of intervals for the posterior odds, or the positive predictive value, of a test. The authors describe 5 methods of constructing confidence intervals for posttest probabilities when estimates of sensitivity, specificity, and the pretest probability of a disorder are derived from empirical data. They then evaluate each method to determine how well the intervals' coverage properties correspond to their nominal value. When the estimates of pretest probabilities, sensitivity, and specificity are derived from more than 80 subjects and are not close to 0 or 1, all methods generate intervals with appropriate coverage properties. When these conditions are not met, however, the best-performing method is an objective Bayesian approach implemented by a simple simulation using a spreadsheet. Physicians and investigators can generate accurate confidence intervals for posttest probabilities in small-sample situations using the objective Bayesian approach.

Contrails and Climate Change: An Investigation of the Role of Aviation-Induced-Cloudiness on the Ireland Climate Using AATSR Imagery

NASA Astrophysics Data System (ADS)

Whelan, Gillian M.; Cawkwell, Fiona; Mannstein, Hermann; Minnis, Patrick

2010-12-01

Contrails, or 'condensation trails', produced in the wake of jet aircraft have been found to have a small but significant global net climate-warming effect [1]. When atmospheric conditions are favorable (i.e. when ambient atmospheric humidity is high and temperature is below a threshold value of typically less than -40oC), contrails can persist for several hours, grow to become several kilometers long and can also trigger additional cirrus- cloud formation as they spread - which can further impact climate! Due to Ireland's proximity to the North Atlantic Flight Corridor, large volumes of high-altitude overflights cross Ireland daily. Contrails are essentially artificial-linear-ice-clouds at a lower temperature than the surrounding atmosphere and so are visible in 1 Km satellite imagery at the 11 and 12 μm wavelengths; but are better detected in the temperature difference image between these two thermal channels. An automated Contrail Detection Algorithm (CDA) is applied to AATSR thermal imagery over Ireland, and the percentage contrail-coverage of each scene determined. Preliminary results, based on 2008 morning and evening AATSR overpasses show a similar annual average contrail-coverage when present of 0.25% and 0.19% respectively, even though air-traffic density is typically several times higher during the morning overpasses. Cases of excessive contrail-coverage, of up to 2.06% have been observed in combination with extensive cirrus-coverage over Ireland. Results from meteorological data indicate more highly favorable atmospheric conditions for contrail formation and persistence in 00h00 and 06h00 radiosonde ascents; which corresponds to a night-time peak in high-altitude flights over Ireland. Furthermore, exceptionally thick contrail-susceptible-atmospheric layers are found in conjunction with cases of excessive satellite-derived- contrail-coverage.

Progress Toward Measles Elimination - Western Pacific Region, 2013-2017.

PubMed

Hagan, José E; Kriss, Jennifer L; Takashima, Yoshihiro; Mariano, Kayla Mae L; Pastore, Roberta; Grabovac, Varja; Dabbagh, Alya J; Goodson, James L

2018-05-04

In 2005, the Regional Committee for the World Health Organization (WHO) Western Pacific Region (WPR)* established a goal for measles elimination † by 2012 (1). To achieve this goal, the 37 WPR countries and areas implemented the recommended strategies in the WPR Plan of Action for Measles Elimination (2) and the Field Guidelines for Measles Elimination (3). The strategies include 1) achieving and maintaining ≥95% coverage with 2 doses of measles-containing vaccine (MCV) through routine immunization services and supplementary immunization activities (SIAs), when required; 2) conducting high-quality case-based measles surveillance, including timely and accurate testing of specimens to confirm or discard suspected cases and detect measles virus for genotyping and molecular analysis; and 3) establishing and maintaining measles outbreak preparedness to ensure rapid response and appropriate case management. This report updates the previous report (4) and describes progress toward measles elimination in WPR during 2013-2017. During 2013-2016, estimated regional coverage with the first MCV dose (MCV1) decreased from 97% to 96%, and coverage with the routine second MCV dose (MCV2) increased from 91% to 93%. Eighteen (50%) countries achieved ≥95% MCV1 coverage in 2016. Seven (39%) of 18 nationwide SIAs during 2013-2017 reported achieving ≥95% administrative coverage. After a record low of 5.9 cases per million population in 2012, measles incidence increased during 2013-2016 to a high of 68.9 in 2014, because of outbreaks in the Philippines and Vietnam, as well as increased incidence in China, and then declined to 5.2 in 2017. To achieve measles elimination in WPR, additional measures are needed to strengthen immunization programs to achieve high population immunity, maintain high-quality surveillance for rapid case detection and confirmation, and ensure outbreak preparedness and prompt response to contain outbreaks.

Hitting the Optimal Vaccination Percentage and the Risks of Error: Why to Miss Right.

PubMed

Harvey, Michael J; Prosser, Lisa A; Messonnier, Mark L; Hutton, David W

2016-01-01

To determine the optimal level of vaccination coverage defined as the level that minimizes total costs and explore how economic results change with marginal changes to this level of coverage. A susceptible-infected-recovered-vaccinated model designed to represent theoretical infectious diseases was created to simulate disease spread. Parameter inputs were defined to include ranges that could represent a variety of possible vaccine-preventable conditions. Costs included vaccine costs and disease costs. Health benefits were quantified as monetized quality adjusted life years lost from disease. Primary outcomes were the number of infected people and the total costs of vaccination. Optimization methods were used to determine population vaccination coverage that achieved a minimum cost given disease and vaccine characteristics. Sensitivity analyses explored the effects of changes in reproductive rates, costs and vaccine efficacies on primary outcomes. Further analysis examined the additional cost incurred if the optimal coverage levels were not achieved. Results indicate that the relationship between vaccine and disease cost is the main driver of the optimal vaccination level. Under a wide range of assumptions, vaccination beyond the optimal level is less expensive compared to vaccination below the optimal level. This observation did not hold when the cost of the vaccine cost becomes approximately equal to the cost of disease. These results suggest that vaccination below the optimal level of coverage is more costly than vaccinating beyond the optimal level. This work helps provide information for assessing the impact of changes in vaccination coverage at a societal level.

The Primordial Inflation Explorer (PIXIE) Mission

NASA Technical Reports Server (NTRS)

Kogut, Alan J.; Chuss, David T.; Dotson, Jessie L.; Fixsen, Dale J.; Halpern, Mark; Hinshaw, Gary F.; Meyer, Stephan M.; Moseley, S. Harvey; Seiffert, Michael D.; Spergel, David N.;

A study on the prenatal zone of ultrasonic guided waves in plates

NASA Astrophysics Data System (ADS)

Thomas, Tibin; Balasubramaniam, Krishnan

2017-02-01

Low frequency guided wave based inspection is an extensively used method for asset management with the advantage of wide area coverage from a single location at the cost of spatial resolution. With the advent of high frequency guided waves, short range inspections with high spatial resolution for monitoring corrosion under pipe supports and tank annular plates has gained widespread interest and acceptance. One of the major challenges in the application of high frequency guided waves in a short range inspection is to attain the desired modal displacements with respect to the application. In this paper, an investigation on the generation and formation of fundamental S0 mode is carried out through numerical simulation and experiments to establish a prenatal zone for guided waves. The effect of frequency, thickness of the plate and frequency-thickness (f*d) is studied. The investigation reveals the existence of a rudimentary form with similar modal features to the fully developed mode. This study helps in the design and development of a high frequency guided wave generator for particular applications which demands waves with very less sensitivity to the surface and loading during the initial phase which immediately evolves to a more sensitive wave towards the surface on propagation for the detection of shallow defects.

Analytical methodologies for broad metabolite coverage of exhaled breath condensate.

PubMed

Aksenov, Alexander A; Zamuruyev, Konstantin O; Pasamontes, Alberto; Brown, Joshua F; Schivo, Michael; Foutouhi, Soraya; Weimer, Bart C; Kenyon, Nicholas J; Davis, Cristina E

2017-09-01

Breath analysis has been gaining popularity as a non-invasive technique that is amenable to a broad range of medical uses. One of the persistent problems hampering the wide application of the breath analysis method is measurement variability of metabolite abundances stemming from differences in both sampling and analysis methodologies used in various studies. Mass spectrometry has been a method of choice for comprehensive metabolomic analysis. For the first time in the present study, we juxtapose the most commonly employed mass spectrometry-based analysis methodologies and directly compare the resultant coverages of detected compounds in exhaled breath condensate in order to guide methodology choices for exhaled breath condensate analysis studies. Four methods were explored to broaden the range of measured compounds across both the volatile and non-volatile domain. Liquid phase sampling with polyacrylate Solid-Phase MicroExtraction fiber, liquid phase extraction with a polydimethylsiloxane patch, and headspace sampling using Carboxen/Polydimethylsiloxane Solid-Phase MicroExtraction (SPME) followed by gas chromatography mass spectrometry were tested for the analysis of volatile fraction. Hydrophilic interaction liquid chromatography and reversed-phase chromatography high performance liquid chromatography mass spectrometry were used for analysis of non-volatile fraction. We found that liquid phase breath condensate extraction was notably superior compared to headspace extraction and differences in employed sorbents manifested altered metabolite coverages. The most pronounced effect was substantially enhanced metabolite capture for larger, higher-boiling compounds using polyacrylate SPME liquid phase sampling. The analysis of the non-volatile fraction of breath condensate by hydrophilic and reverse phase high performance liquid chromatography mass spectrometry indicated orthogonal metabolite coverage by these chromatography modes. We found that the metabolite coverage could be enhanced significantly with the use of organic solvent as a device rinse after breath sampling to collect the non-aqueous fraction as opposed to neat breath condensate sample. Here, we show the detected ranges of compounds in each case and provide a practical guide for methodology selection for optimal detection of specific compounds. Copyright © 2017 Elsevier B.V. All rights reserved.

Heart failure disease management programs: a cost-effectiveness analysis.

PubMed

Chan, David C; Heidenreich, Paul A; Weinstein, Milton C; Fonarow, Gregg C

2008-02-01

Heart failure (HF) disease management programs have shown impressive reductions in hospitalizations and mortality, but in studies limited to short time frames and high-risk patient populations. Current guidelines thus only recommend disease management targeted to high-risk patients with HF. This study applied a new technique to infer the degree to which clinical trials have targeted patients by risk based on observed rates of hospitalization and death. A Markov model was used to assess the incremental life expectancy and cost of providing disease management for high-risk to low-risk patients. Sensitivity analyses of various long-term scenarios and of reduced effectiveness in low-risk patients were also considered. The incremental cost-effectiveness ratio of extending coverage to all patients was $9700 per life-year gained in the base case. In aggregate, universal coverage almost quadrupled life-years saved as compared to coverage of only the highest quintile of risk. A worst case analysis with simultaneous conservative assumptions yielded an incremental cost-effectiveness ratio of $110,000 per life-year gained. In a probabilistic sensitivity analysis, 99.74% of possible incremental cost-effectiveness ratios were <$50,000 per life-year gained. Heart failure disease management programs are likely cost-effective in the long-term along the whole spectrum of patient risk. Health gains could be extended by enrolling a broader group of patients with HF in disease management.

MicroCantilever (MC) based nanomechanical sensor for detection of molecular interactions

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

Kang, Kyung

Specific aims of this study are to investigate the mechanism governing surface stress generation associated with chemical or molecular binding on functionalized microcantilevers. Formation of affinity complexes on cantilever surfaces leads to charge redistribution, configurational change and steric hindrance between neighboring molecules resulting in surface stress change and measureable cantilever deformation. A novel interferometry technique employing two adjacent micromachined cantilevers (a sensing/reference pair) was utilized to measure the cantilever deformation. The sensing principle is that binding/reaction of specific chemical or biological species on the sensing cantilever transduces to mechanical deformation. The differential bending of the sensing cantilever respect to themore » reference cantilever ensures that measured response is insensitive to environmental disturbances. As a proof of principle for the measurement technique, surface stress changes associated with: self-assembly of alkanethiol, hybridization of ssDNA, and the formation of cocaine-aptamer complexes were measured. Dissociation constant (K d) for each molecular reaction was utilized to estimate the surface coverage of affinity complexes. In the cases of DNA hybridization and cocaine-aptamer binding, measured surface stress was found to be dependent on the surface coverage of the affinity complexes. In order to achieve a better sensitivity for DNA hybridization, immobilization of receptor molecules was modified to enhance the deformation of underlying surface. Single-stranded DNA (ssDNA) strands with thiol-modification on both 3-foot and 5-foot ends were immobilized on the gold surface such that both ends are attached to the gold surface. Immobilization condition was controlled to obtain similar receptor density as single-thiolated DNA strands. Hybridization of double-thiolated DNA strands leads to an almost two orders of magnitude increase in cantilever deformation. In both DNA hybridization and the conventional mode for cocaine detection, the lowest detectable concentration was determined by binding activity between the ligand and receptor molecules. In order to overcome this limitation for cocaine detection, a novel competition sensing mode that relies on rate of aptamers unbinding from the cantilever due to either diffusion or reaction with cocaine as target ligands in solution was investigated. The rate of unbinding is found to be dependent on the concentration of cocaine molecules. A model based on diffusion-reaction equation was developed to explain the experimental observation. Experimental results indicate that the competition mode reduces the lowest detectable threshold to 200 nM which is comparable to that achieved analytical techniques such as mass spectrometry.« less

Cloud Statistics and Discrimination in the Polar Regions

NASA Astrophysics Data System (ADS)

Chan, M.; Comiso, J. C.

2012-12-01

Despite their important role in the climate system, cloud cover and their statistics are poorly known, especially in the polar regions, where clouds are difficult to discriminate from snow covered surfaces. The advent of the A-train, which included Aqua/MODIS, CALIPSO/CALIOP and CloudSat/CPR sensors has provided an opportunity to improve our ability to accurately characterize the cloud cover. MODIS provides global coverage at a relatively good temporal and spatial resolution while CALIOP and CPR provide limited nadir sampling but accurate characterization of the vertical structure and phase of the cloud cover. Over the polar regions, cloud detection from a passive sensors like MODIS is challenging because of the presence of cold and highly reflective surfaces such as snow, sea-ice, glaciers, and ice-sheet, which have surface signatures similar to those of clouds. On the other hand, active sensors such as CALIOP and CPR are not only very sensitive to the presence of clouds but can also provide information about its microphysical characteristics. However, these nadir-looking sensors have sparse spatial coverage and their global data can have data spatial gaps of up to 100 km. We developed a polar cloud detection system for MODIS that is trained using collocated data from CALIOP and CPR. In particular, we employ a machine learning system that reads the radiative profile observed by MODIS and determine whether the field of view is cloudy or clear. Results have shown that the improved cloud detection scheme performs better than typical cloud mask algorithms using a validation data set not used for training. A one-year data set was generated and results indicate that daytime cloud detection accuracies improved from 80.1% to 92.6% (over sea-ice) and 71.2% to 87.4% (over ice-sheet) with CALIOP data used as the baseline. Significant improvements are also observed during nighttime, where cloud detection accuracies increase by 19.8% (over sea-ice) and 11.6% (over ice-sheet). The immediate impact of the new algorithm is that it can minimize large biases of MODIS-derived cloud amount over the Polar Regions and thus a more realistic and high quality global cloud statistics. In particular, our results show that cloud fraction in the Arctic is typically 81.2 % during daytime and 84.0% during nighttime. This is significantly higher than the 71.8% and 58.5%, respectively, derived from standard MODIS cloud product.

On the Power and the Systematic Biases of the Detection of Chromosomal Inversions by Paired-End Genome Sequencing

PubMed Central

Lucas Lledó, José Ignacio; Cáceres, Mario

2013-01-01

One of the most used techniques to study structural variation at a genome level is paired-end mapping (PEM). PEM has the advantage of being able to detect balanced events, such as inversions and translocations. However, inversions are still quite difficult to predict reliably, especially from high-throughput sequencing data. We simulated realistic PEM experiments with different combinations of read and library fragment lengths, including sequencing errors and meaningful base-qualities, to quantify and track down the origin of false positives and negatives along sequencing, mapping, and downstream analysis. We show that PEM is very appropriate to detect a wide range of inversions, even with low coverage data. However, % of inversions located between segmental duplications are expected to go undetected by the most common sequencing strategies. In general, longer DNA libraries improve the detectability of inversions far better than increments of the coverage depth or the read length. Finally, we review the performance of three algorithms to detect inversions —SVDetect, GRIAL, and VariationHunter—, identify common pitfalls, and reveal important differences in their breakpoint precisions. These results stress the importance of the sequencing strategy for the detection of structural variants, especially inversions, and offer guidelines for the design of future genome sequencing projects. PMID:23637806

Validation and Application of a PCR Primer Set to Quantify Fungal Communities in the Soil Environment by Real-Time Quantitative PCR

PubMed Central

Chemidlin Prévost-Bouré, Nicolas; Christen, Richard; Dequiedt, Samuel; Mougel, Christophe; Lelièvre, Mélanie; Jolivet, Claudy; Shahbazkia, Hamid Reza; Guillou, Laure; Arrouays, Dominique; Ranjard, Lionel

2011-01-01

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1 / FF390. This in silico analysis of the specificity of FR1 / FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1 / FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils. PMID:21931659

What is the limit to case detection under the DOTS strategy for tuberculosis control?

PubMed

Dye, Christopher; Watt, Catherine J; Bleed, Daniel M; Williams, Brian G

2003-01-01

In year 2000, the WHO DOTS strategy for tuberculosis (TB) control had been adopted by 148 out of 212 countries, but only 27% of all estimated sputum smear-positive patients were notified under DOTS in that year. Here we investigate the way in which gains in case detection under DOTS were made up until 2000 in an attempt to anticipate future progress towards the global target of 70% case detection. The analysis draws on annual reports of DOTS geographical coverage and case notifications, and focuses on the 22 high-burden countries (HBCs) that account for about 80% of new TB cases arising globally each year. Our principal observation is that, as TB programmes in the 22 HBCs have expanded geographically, the fraction of the estimated number of sputum smear-positive cases detected within designated DOTS areas has remained constant at 40-50% although there are significant differences between countries. This fraction is about the same as the percentage of all smear-positive cases notified annually to WHO via public health systems worldwide. The implication is that, unless the DOTS strategy can reach beyond traditional public health reporting systems, or unless these systems can be improved, case detection will not rise much above 40% in the 22 HBCs, or in the world as a whole, even when the geographical coverage of DOTS is nominally 100%. We estimate that, under full DOTS coverage, three-quarters of the undetected smear-positive cases will be living in India, China, Indonesia, Nigeria, Bangladesh and Pakistan. But case detection could also remain low in countries with smaller populations: in year 2000, over half of all smear-positive TB cases were living in 49 countries that detected less than 40% of cases within DOTS areas. Substantial efforts are therefore needed (a) to develop new case finding and management methods to bridge the gap between current and target case detection, and (b) to improve the accuracy of national estimates of TB incidence, above all by reinforcing and expanding routine surveillance.

Dynamics of distribution and density of phreatophytes and other arid-land plant communities

NASA Technical Reports Server (NTRS)

Turner, R. M. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Six ERTS-1 images of the Tucson area, Arizona were analyzed to detect seasonal flushes of plant growth. Paired MSS-6 and MSS-5 bulk images were analyzed, using a ratioing technique, on the Electronic Satellite Image Analysis Console at Stanford Research Institute. Because of unique phenology, desert areas, covered only briefly by dense growths of ephemeral plants, are readily discerned. Grassland, evergreen forest, and riparian communities are also uniquely defined by their phenologies. Relatively sterile areas with little or no plant growth are easily discerned as are areas with varying degrees of plant productivity. The ratioing procedure detects plant coverage in excess of a threshold lying between 25% and 50%. The method is flexible and other coverage thresholds can be used.

Oil adsorption ability of three-dimensional epicuticular wax coverages in plants

NASA Astrophysics Data System (ADS)

Gorb, Elena V.; Hofmann, Philipp; Filippov, Alexander E.; Gorb, Stanislav N.

2017-04-01

Primary aerial surfaces of terrestrial plants are very often covered with three-dimensional epicuticular waxes. Such wax coverages play an important role in insect-plant interactions. Wax blooms have been experimentally shown in numerous previous studies to be impeding locomotion and reducing attachment of insects. Among the mechanisms responsible for these effects, a possible adsorption of insect adhesive fluid by highly porous wax coverage has been proposed (adsorption hypothesis). Recently, a great decrease in insect attachment force on artificial adsorbing materials was revealed in a few studies. However, adsorption ability of plant wax blooms was still not tested. Using a cryo scanning electron microscopy approach and high-speed video recordings of fluid drops behavior, followed by numerical analysis of experimental data, we show here that the three-dimensional epicuticular wax coverage in the waxy zone of Nepenthes alata pitcher adsorbs oil: we detected changes in the base, height, and volume of the oil drops. The wax layer thickness, differing in samples with untreated two-layered wax coverage and treated one-layered wax, did not significantly affect the drop behavior. These results provide strong evidence that three-dimensional plant wax coverages due to their adsorption capability are in general anti-adhesive for insects, which rely on wet adhesion.

Comparison of Mass Azithromycin Coverage Targets of Children in Niger: A Cluster-Randomized Trachoma Trial.

PubMed

Oldenburg, Catherine E; Amza, Abdou; Kadri, Boubacar; Nassirou, Beido; Cotter, Sun Y; Stoller, Nicole E; West, Sheila K; Bailey, Robin L; Porco, Travis C; Gaynor, Bruce D; Keenan, Jeremy D; Lietman, Thomas M

2018-02-01

Repeated oral azithromycin distribution targeted only to children has proven effective in reducing the ocular Chlamydia that causes trachoma. Here, we assess whether an enhanced coverage target of at least 90% of children is superior to the World Health Organization recommendation of at least 80%. Twenty-four trachoma-endemic communities in Matamèye, Niger, were randomized to a single day of azithromycin distribution aiming for at least 80% coverage or up to 4 days of treatment and > 90% coverage of children under age 12. All distributions were biannual. Children < 5 years of age and adults > 15 years were monitored for ocular Chlamydia infection by polymerase chain reaction every 6 months for 36 months in children and at baseline and 36 months in adults. Ocular Chlamydia prevalence in children decreased from 24.9% (95% confidence interval [CI] 15.9-33.8%) to 4.4% (95% CI 0.6-8.2%, P < 0.001) at 36 months in the standard coverage arm and from 15.6% (95% CI 10.0-21.2%) to 3.3% (95% CI 1.0-5.5%; P < 0.001) in the enhanced coverage arm. Enhanced coverage reduced ocular Chlamydia prevalence in children more quickly over time compared with standard ( P = 0.04). There was no difference between arms at 36 months in children (2.4% lower with enhanced coverage, 95% CI 7.7-12.5%; P = 0.60). No infection was detected in adults at 36 months. Increasing antibiotic coverage among children from 80% to 90% may yield only short term improvements for trachoma control programs. Targeting treatment to children alone may be sufficient for trachoma control in this setting.

Performance evaluation of a newly developed variable rate sprayer for nursery liner applications

USDA-ARS?s Scientific Manuscript database

An experimental variable-rate sprayer designed for liner applications was tested by comparing its spray deposit, coverage, and droplet density inside canopies of six nursery liner varieties with constant-rate applications. Spray samplers, including water sensitive papers (WSP) and nylon screens, wer...

Effects of loss on the phase sensitivity with parity detection in an SU(1,1) interferometer

NASA Astrophysics Data System (ADS)

Li, Dong; Yuan, Chun-Hua; Yao, Yao; Jiang, Wei; Li, Mo; Zhang, Weiping

2018-05-01

We theoretically study the effects of loss on the phase sensitivity of an SU(1,1) interferometer with parity detection with various input states. We show that although the sensitivity of phase estimation decreases in the presence of loss, it can still beat the shot-noise limit with small loss. To examine the performance of parity detection, the comparison is performed among homodyne detection, intensity detection, and parity detection. Compared with homodyne detection and intensity detection, parity detection has a slight better optimal phase sensitivity in the absence of loss, but has a worse optimal phase sensitivity with a significant amount of loss with one-coherent state or coherent $\\otimes$ squeezed state input.

Intentional ethylene glycol poisoning increase after media coverage of antifreeze murders.

PubMed

Morgan, Brent W; Geller, Robert J; Kazzi, Ziad N

2011-07-01

The media can have a profound impact on human behavior. A sensational murder by ethylene glycol (EG) poisoning occurred in our state. The regional media provided extensive coverage of the murder. We undertook this investigation to evaluate our incidence of EG poisoning during the timeframe of before the first report linking a death to ethylene glycol to shortly after the first murder trial. Descriptive statistics and linear regression were used to describe and analyze the number of EG cases over time. A search of the leading regional newspaper's archives established the media coverage timeline. Between 2000 and 2004, our poison center (PC) handled a steady volume of unintentional exposures to EG [range: 105-123 per year, standard deviation (SD)=7.22]. EG exposures thought to be suicidal in intent increased from 12 cases in 2000 to 121 cases in 2004. In the 19 months prior to the first media report of this story, our PC handled a mean of 1 EG case with suicidal intent per month [range: 0-2, SD=.69]. In the month after the first media report, our PC handled 5 EG cases with suicidal intent. When media coverage was most intense (2004), our PC received a mean of 10 EG suicidal-intent calls per month [range: 5-17, SD=3.55]. Although uncommon, reports of malicious EG poisonings also increased during this same period from 2 in 2000 to 14 in 2004. Media coverage of stories involving poisonings may result in copycat events, applicable to both self-poisonings and concern for malicious poisonings. Poison centers should be aware of this phenomenon, pay attention to local media and plan accordingly if a poisoning event receives significant media coverage. The media should be more sensitive to the content of their coverage and avoid providing "how to" poisoning information.

A simple model for the evolution of melt pond coverage on permeable Arctic sea ice

NASA Astrophysics Data System (ADS)

Popović, Predrag; Abbot, Dorian

2017-05-01

As the melt season progresses, sea ice in the Arctic often becomes permeable enough to allow for nearly complete drainage of meltwater that has collected on the ice surface. Melt ponds that remain after drainage are hydraulically connected to the ocean and correspond to regions of sea ice whose surface is below sea level. We present a simple model for the evolution of melt pond coverage on such permeable sea ice floes in which we allow for spatially varying ice melt rates and assume the whole floe is in hydrostatic balance. The model is represented by two simple ordinary differential equations, where the rate of change of pond coverage depends on the pond coverage. All the physical parameters of the system are summarized by four strengths that control the relative importance of the terms in the equations. The model both fits observations and allows us to understand the behavior of melt ponds in a way that is often not possible with more complex models. Examples of insights we can gain from the model are that (1) the pond growth rate is more sensitive to changes in bare sea ice albedo than changes in pond albedo, (2) ponds grow slower on smoother ice, and (3) ponds respond strongest to freeboard sinking on first-year ice and sidewall melting on multiyear ice. We also show that under a global warming scenario, pond coverage would increase, decreasing the overall ice albedo and leading to ice thinning that is likely comparable to thinning due to direct forcing. Since melt pond coverage is one of the key parameters controlling the albedo of sea ice, understanding the mechanisms that control the distribution of pond coverage will help improve large-scale model parameterizations and sea ice forecasts in a warming climate.

Zn2+ and Sr2+ Adsorption at the TiO2 (110)-Electrolyte Interface: Influence of Ionic Strength, Coverage, and Anions

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

Zhang,Z.; Fenter, P.; Cheng, L.

2006-01-01

The X-ray standing wave technique was used to probe the sensitivity of Zn{sup 2+} and Sr{sup 2+} ion adsorption to changes in both the adsorbed ion coverage and the background electrolyte species and concentrations at the rutile ({alpha}-TiO{sub 2}) (110)-aqueous interface. Measurements were made with various background electrolytes (NaCl, NaTr, RbCl, NaBr) at concentrations as high as 1 m. The results demonstrate that Zn{sub 2+} and Sr{sub 2+} reside primarily in the condensed layer and that the ion heights above the Ti-O surface plane are insensitive to ionic strength and the choice of background electrolyte (with <0.1 Angstroms changes overmore » the full compositional range). The lack of any specific anion coadsorption upon probing with Br{sup -}, coupled with the insensitivity of Zn{sup 2+} and Sr{sup 2+} cation heights to changes in the background electrolyte, implies that anions do not play a significant role in the adsorption of these divalent metal ions to the rutile (110) surface. Absolute ion coverage measurements for Zn{sup 2+} and Sr{sup 2+} show a maximum Stern-layer coverage of {approx}0.5 monolayer, with no significant variation in height as a function of Stern-layer coverage. These observations are discussed in the context of Gouy-Chapman-Stern models of the electrical double layer developed from macroscopic sorption and pH-titration studies of rutile powder suspensions. Direct comparison between these experimental observations and the MUltiSIte Complexation (MUSIC) model predictions of cation surface coverage as a function of ionic strength revealed good agreement between measured and predicted surface coverages with no adjustable parameters.« less

Early Science Planning of Protoplanetary Disks and Protostars in the Orion Nebula Cluster Using SOFIA/FORCAST

NASA Astrophysics Data System (ADS)

Hoadley, Keri; Adams, J. D.; Herter, T. L.; Gull, G.; Henderson, C.; Schoenwald, J.; Keller, L.; Megeath, T. S.

2011-01-01

The Faint Object Camera for the SOFIA Telescope (FORCAST) is a mid-infrared facility instrument for the Stratospheric Observatory For Infrared Astronomy (SOFIA). In late May of this year, FORCAST achieved first light on SOFIA during a Telescope Assembly characterization flight, successfully taking photometry of Jupiter, its moons, and M82 from an altitude of 35,000 ft. Analysis of images of Jupiter and one of its moons, Ganymede, show the in-flight sensitivity to be comparable to that expected from preflight (lab) measurements and models. In preparation for SOFIA Short Science, we constructed Spectral Energy Distributions (SEDs) for known proplyds and protostars (Smith et al. 2005) in the core of the Orion molecular cloud using 2MASS (Skrutskie et al. 2006), IRAC on Spitzer, TReCS on Gemini South (Smith et al. 2005), and 880mm SCUBA data (Mann and Williams 2009). FORCAST will provide important wavelength coverage (20 - 40 microns) which when used in conjunction with previous data will constrain the physical properties of the proplyds and protostars. We fit the observed SEDs with those from radiative transfer models for circumstellar disks and protostars from Robitaille et al (2006, 2007). With these models, we can extrapolate into the 20 - 40 micron region of FORCAST and determine the range of models that FORCAST is capable of detecting. Using the FORCAST sensitivity model and the SEDs of known proplyds, we expect to detect 67% of the proplyds found by other investigations. However, detectability will be greatly influenced by the presence of structures in the diffuse dust emission associated with the HII region complex. Comparing FORCAST observations with the radiative transfer models will help to understand the physical properties of proplyds and protostars, and perhaps illuminate the impact of their environments, such as photoevaporation of disks and effects from crowding.

On the Ability of Space- Based Passive and Active Remote Sensing Observations of CO2 to Detect Flux Perturbations to the Carbon Cycle

NASA Technical Reports Server (NTRS)

Crowell, Sean M. R.; Kawa, S. Randolph; Browell, Edward V.; Hammerling, Dorit M.; Moore, Berrien; Schaefer, Kevin; Doney, Scott C.

2018-01-01

Space-borne observations of CO2 are vital to gaining understanding of the carbon cycle in regions of the world that are difficult to measure directly, such as the tropical terrestrial biosphere, the high northern and southern latitudes, and in developing nations such as China. Measurements from passive instruments such as GOSAT (Greenhouse Gases Observing Satellite) and OCO-2 (Orbiting Carbon Observatory 2), however, are constrained by solar zenith angle limitations as well as sensitivity to the presence of clouds and aerosols. Active measurements such as those in development for the Active Sensing of CO2 Emissions over Nights, Days and Seasons (ASCENDS) mission show strong potential for making measurements in the high-latitude winter and in cloudy regions. In this work we examine the enhanced flux constraint provided by the improved coverage from an active measurement such as ASCENDS. The simulation studies presented here show that with sufficient precision, ASCENDS will detect permafrost thaw and fossil fuel emissions shifts at annual and seasonal time scales, even in the presence of transport errors, representativeness errors, and biogenic flux errors. While OCO-2 can detect some of these perturbations at the annual scale, the seasonal sampling provided by ASCENDS provides the stronger constraint. Plain Language Summary: Active and passive remote sensors show the potential to provide unprecedented information on the carbon cycle. With the all-season sampling, active remote sensors are more capable of constraining high-latitude emissions. The reduced sensitivity to cloud and aerosol also makes active sensors more capable of providing information in cloudy and polluted scenes with sufficient accuracy. These experiments account for errors that are fundamental to the top-down approach for constraining emissions, and even including these sources of error, we show that satellite remote sensors are critical for understanding the carbon cycle.

Attack Coverage in High-Level Men’s Volleyball: Organization on the Edge of Chaos?

PubMed Central

Laporta, Lorenzo; Nikolaidis, Pantelis; Thomas, Luke; Afonso, José

2015-01-01

Change is pervasive, but emerging patterns are occasionally detectable through analysis of systemic behaviors. Match analysis uses these patterns in order to reduce the degree of improvisation and to optimize the training process. However, it is possible that certain game phases elude systematic patterning. In this vein, our aim was to analyze the case of attack coverage in men’s volleyball, as we suspected it would elude systematic patterning and has received negligible attention in scientific research. We analyzed the occurrence of attack coverage in 4544 plays of the 2011 Volleyball World League. A Chi-square test with residual adjusted values was applied to explore significant associations between variables. A Monte Carlo correction was applied, as some cells had n<5. Effect sizes were determined using Cramer’s V. Overall, attack coverage occurred in 3.89% of ball possessions, and 23 distinct structures emerged. These structures lacked significant associations with the game complex, setting zone, and effect of attack coverage. Conversely, attack coverage structures showed significant associations with the attack zone and tempo, with very strong effect sizes (V=0.472 and V=0.521, respectively). As certain attack zones are deeply associated with attack tempo, it is apparent that quicker attack plays affect attack coverage structuring, promoting the formation of less complex structures. Ultimately, attack coverage structures seem to depend on momentary constraints, thereby rendering rigid systematization impracticable. Still, we contended that a principle-based approach might be suitable. This invites researchers to rethink how to interpret game regularities. PMID:26557208

Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis

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

Shi, Tujin; Fillmore, Thomas L.; Gao, Yuqian

2013-10-01

Long-gradient separations coupled to tandem MS were recently demonstrated to provide a deep proteome coverage for global proteomics; however, such long-gradient separations have not been explored for targeted proteomics. Herein, we investigate the potential performance of the long-gradient separations coupled with selected reaction monitoring (LG-SRM) for targeted protein quantification. Direct comparison of LG-SRM (5 h gradient) and conventional LC-SRM (45 min gradient) showed that the long-gradient separations significantly reduced background interference levels and provided an 8- to 100-fold improvement in LOQ for target proteins in human female serum. Based on at least one surrogate peptide per protein, an LOQ ofmore » 10 ng/mL was achieved for the two spiked proteins in non-depleted human serum. The LG-SRM detection of seven out of eight endogenous plasma proteins expressed at ng/mL or sub-ng/mL levels in clinical patient sera was also demonstrated. A correlation coefficient of >0.99 was observed for the results of LG-SRM and ELISA measurements for prostate-specific antigen (PSA) in selected patient sera. Further enhancement of LG-SRM sensitivity was achieved by applying front-end IgY14 immunoaffinity depletion. Besides improved sensitivity, LG-SRM offers at least 3 times higher multiplexing capacity than conventional LC-SRM due to ~3-fold increase in average peak widths for a 300-min gradient compared to a 45-min gradient. Therefore, LG-SRM holds great potential for bridging the gap between global and targeted proteomics due to its advantages in both sensitivity and multiplexing capacity.« less

Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

PubMed Central

Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

2011-01-01

As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms. PMID:21359231

Cosmic ray muon computed tomography of spent nuclear fuel in dry storage casks

DOE PAGES

Poulson, Daniel Cris; Durham, J. Matthew; Guardincerri, Elena; ...

2016-10-22

Radiography with cosmic ray muon scattering has proven to be a successful method of imaging nuclear material through heavy shielding. Of particular interest is monitoring dry storage casks for diversion of plutonium contained in spent reactor fuel. Using muon tracking detectors that surround a cylindrical cask, cosmic ray muon scattering can be simultaneously measured from all azimuthal angles, giving complete tomographic coverage of the cask interior. This article describes the first application of filtered back projection algorithms, typically used in medical imaging, to cosmic ray muon scattering imaging. The specific application to monitoring spent nuclear fuel in dry storage casksmore » is investigated via GEANT4 simulations. With a cylindrical muon tracking detector surrounding a typical spent fuel cask, simulations indicate that missing fuel bundles can be detected with a statistical significance of ~18σ in less than two days exposure and a sensitivity at 1σ to a 5% missing portion of a fuel bundle. Finally, we discuss potential detector technologies and geometries.« less

Forest Attributes from Radar Interferometric Structure and its Fusion with Optical Remote Sensing

NASA Technical Reports Server (NTRS)

Treuhaft, Robert N.; Law, Beverly E.; Asner, Gregory P.

2004-01-01

The possibility of global, three-dimensional remote sensing of forest structure with interferometric synthetic aperture radar (InSAR) bears on important forest ecological processes, particularly the carbon cycle. InSAR supplements two-dimensional remote sensing with information in the vertical dimension. Its strengths in potential for global coverage complement those of lidar (light detecting and ranging), which has the potential for high-accuracy vertical profiles over small areas. InSAR derives its sensitivity to forest vertical structure from the differences in signals received by two, spatially separate radar receivers. Estimation of parameters describing vertical structure requires multiple-polarization, multiple-frequency, or multiple-baseline InSAR. Combining InSAR with complementary remote sensing techniques, such as hyperspectral optical imaging and lidar, can enhance vertical-structure estimates and consequent biophysical quantities of importance to ecologists, such as biomass. Future InSAR experiments will supplement recent airborne and spaceborne demonstrations, and together with inputs from ecologists regarding structure, they will suggest designs for future spaceborne strategies for measuring global vegetation structure.

Determination of boron in uranium aluminum silicon alloy by spectrophotometry and estimation of expanded uncertainty in measurement

NASA Astrophysics Data System (ADS)

Ramanjaneyulu, P. S.; Sayi, Y. S.; Ramakumar, K. L.

2008-08-01

Quantification of boron in diverse materials of relevance in nuclear technology is essential in view of its high thermal neutron absorption cross section. A simple and sensitive method has been developed for the determination of boron in uranium-aluminum-silicon alloy, based on leaching of boron with 6 M HCl and H 2O 2, its selective separation by solvent extraction with 2-ethyl hexane 1,3-diol and quantification by spectrophotometry using curcumin. The method has been evaluated by standard addition method and validated by inductively coupled plasma-atomic emission spectroscopy. Relative standard deviation and absolute detection limit of the method are 3.0% (at 1 σ level) and 12 ng, respectively. All possible sources of uncertainties in the methodology have been individually assessed, following the International Organization for Standardization guidelines. The combined uncertainty is calculated employing uncertainty propagation formulae. The expanded uncertainty in the measurement at 95% confidence level (coverage factor 2) is 8.840%.

The Mobile Laboratory for Radio-Frequency Interference Monitoring at the Sardinia Radio Telescope

NASA Astrophysics Data System (ADS)

Bolli, Pietro; Gaudiomonte, Francesco; Ambrosini, Roberto; Bortolotti, Claudio; Roma, Mauro; Barberi, Carlo; Piccoli, Fabrizio

2013-10-01

In this paper, a quite unique mobile laboratory for monitoring radio-frequency interference with a radio-astronomical observatory is described. The unit is fully operational at the new Sardinia Radio Telescope, a 64-m antenna now in the commissioning phase in Italy. The mobile laboratory is mainly used to identify the source of interference with the radio astronomy service using iterative triangulations in the azimuth directions. Both the design and realization of this prototype were handled with outstanding care to limit the emission of self-interference as much as possible. The laboratory was equipped with excellent microwave instruments in terms of sensitivity, frequency coverage, dynamic range, and various demodulation and signal-analysis facilities. The unit can be quickly switched to different RF and power-supply configurations, while offering operators a safe and efficient workplace, even in adverse meteorological and driving conditions. In the past months, the mobile laboratory has proven to be successful in detecting and identifying many radio interferers. Two examples of measurement campaigns are described.

Cosmic ray muon computed tomography of spent nuclear fuel in dry storage casks

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

Poulson, Daniel Cris; Durham, J. Matthew; Guardincerri, Elena

Radiography with cosmic ray muon scattering has proven to be a successful method of imaging nuclear material through heavy shielding. Of particular interest is monitoring dry storage casks for diversion of plutonium contained in spent reactor fuel. Using muon tracking detectors that surround a cylindrical cask, cosmic ray muon scattering can be simultaneously measured from all azimuthal angles, giving complete tomographic coverage of the cask interior. This article describes the first application of filtered back projection algorithms, typically used in medical imaging, to cosmic ray muon scattering imaging. The specific application to monitoring spent nuclear fuel in dry storage casksmore » is investigated via GEANT4 simulations. With a cylindrical muon tracking detector surrounding a typical spent fuel cask, simulations indicate that missing fuel bundles can be detected with a statistical significance of ~18σ in less than two days exposure and a sensitivity at 1σ to a 5% missing portion of a fuel bundle. Finally, we discuss potential detector technologies and geometries.« less

Cosmic ray muon computed tomography of spent nuclear fuel in dry storage casks

NASA Astrophysics Data System (ADS)

Poulson, D.; Durham, J. M.; Guardincerri, E.; Morris, C. L.; Bacon, J. D.; Plaud-Ramos, K.; Morley, D.; Hecht, A. A.

2017-01-01

Radiography with cosmic ray muon scattering has proven to be a successful method of imaging nuclear material through heavy shielding. Of particular interest is monitoring dry storage casks for diversion of plutonium contained in spent reactor fuel. Using muon tracking detectors that surround a cylindrical cask, cosmic ray muon scattering can be simultaneously measured from all azimuthal angles, giving complete tomographic coverage of the cask interior. This paper describes the first application of filtered back projection algorithms, typically used in medical imaging, to cosmic ray muon scattering imaging. The specific application to monitoring spent nuclear fuel in dry storage casks is investigated via GEANT4 simulations. With a cylindrical muon tracking detector surrounding a typical spent fuel cask, simulations indicate that missing fuel bundles can be detected with a statistical significance of ∼ 18 σ in less than two days exposure and a sensitivity at 1σ to a 5% missing portion of a fuel bundle. Potential detector technologies and geometries are discussed.

Novel epoxy-silica nanoparticles to develop non-enzymatic colorimetric probe for analytical immuno/bioassays.

PubMed

Dixit, Chandra K; Bhakta, Snehasis; Macharia, John; Furtado, Jared; Suib, Steven L; Rusling, James F

2018-10-22

We have developed a novel method to develop epoxy silica nanoparticles (EfSiNP) in a single pot. High surface coverage of epoxy functional groups between 150 and 57000 molecules per particles (∼10 13 -10 16 molecules/mL of 200 nm EfSiNPs) was achieved for different preparation conditions. We then created a red colored probe by conjugating Fuchsin dye to the epoxy functionalities of EfSINPs. Anti-mouse IgG was co-immobilized with Fuchsin and their ratios were optimized for achieving optimum ratios by testing those in functional assays. Dye to antibody ratios were in good negative correlation with a coefficient of -1.00 measured at a confidence level of over 99%. We employed the developed non-enzymatic colorimetric immunonanoprobe for detecting mouse IgG in a direct immunoassay format. We achieved a sensitivity of 427 pg/mL with the assay. Copyright © 2018 Elsevier B.V. All rights reserved.

Antipsychotic treatment in schizophrenia: the role of computerized neuropsychological assessment.

PubMed

Kertzman, Semion; Reznik, Ilya; Grinspan, Haim; Weizman, Abraham; Kotler, Moshe

2008-01-01

The present study analyzes the role of neurocognitive assessment instruments in the detection of the contribution of antipsychotic treatment to cognitive functioning. Recently, a panel of experts suggested six main domains (working memory; attention/vigilance; verbal/visual learning and memory; reasoning and problem solving; speed of processing) implicated in schizophrenia-related cognitive deficits, which serve as a theoretical base for creation of real-time computerized neurocognitive batteries. The high sensitivity of computerized neuropsychological testing is based on their ability to adopt the reaction time (RT) paradigm for the assessment of brain function in a real-time regime. This testing is highly relevant for the monitoring of the cognitive effects of antipsychotics. Computerized assessment assists in the identification of state- and trait-related cognitive impairments. The optimal real-time computerized neurocognitive battery should composite balance between broad and narrow coverage of cognitive domains relevant to the beneficial effects of antipsychotics and will enable better planning of treatment and rehabilitation programs.

Performance of rapid test kits to assess household coverage of iodized salt.

PubMed

Gorstein, Jonathan; van der Haar, Frits; Codling, Karen; Houston, Robin; Knowles, Jacky; Timmer, Arnold

2016-10-01

The main indicator adopted to track universal salt iodization has been the coverage of adequately iodized salt in households. Rapid test kits (RTK) have been included in household surveys to test the iodine content in salt. However, laboratory studies of their performance have concluded that RTK are reliable only to distinguish between the presence and absence of iodine in salt, but not to determine whether salt is adequately iodized. The aim of the current paper was to examine the performance of RTK under field conditions and to recommend their most appropriate use in household surveys. Standard performance characteristics of the ability of RTK to detect the iodine content in salt at 0 mg/kg (salt with no iodine), 5 mg/kg (salt with any added iodine) and 15 mg/kg ('adequately' iodized salt) were calculated. Our analysis employed the agreement rate (AR) as a preferred metric of RTK performance. Setting/Subjects Twenty-five data sets from eighteen population surveys which assessed household iodized salt by both the RTK and a quantitative method (i.e. titration or WYD Checker) were obtained from Asian (nineteen data sets), African (five) and European (one) countries. In detecting iodine in salt at 0 mg/kg, the RTK had an AR>90 % in eight of twenty-three surveys, while eight surveys had an AR90 %. The RTK is not suited for assessment of adequately iodized salt coverage. Quantitative assessment, such as by titration or WYD Checker, is necessary for estimates of adequately iodized salt coverage.

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

PubMed Central

2012-01-01

Background High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). Results We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. Conclusion By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously. PMID:22583801

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.).

PubMed

Stoffel, Kevin; van Leeuwen, Hans; Kozik, Alexander; Caldwell, David; Ashrafi, Hamid; Cui, Xinping; Tan, Xiaoping; Hill, Theresa; Reyes-Chin-Wo, Sebastian; Truco, Maria-Jose; Michelmore, Richard W; Van Deynze, Allen

2012-05-14

High-resolution genetic maps are needed in many crops to help characterize the genetic diversity that determines agriculturally important traits. Hybridization to microarrays to detect single feature polymorphisms is a powerful technique for marker discovery and genotyping because of its highly parallel nature. However, microarrays designed for gene expression analysis rarely provide sufficient gene coverage for optimal detection of nucleotide polymorphisms, which limits utility in species with low rates of polymorphism such as lettuce (Lactuca sativa). We developed a 6.5 million feature Affymetrix GeneChip® for efficient polymorphism discovery and genotyping, as well as for analysis of gene expression in lettuce. Probes on the microarray were designed from 26,809 unigenes from cultivated lettuce and an additional 8,819 unigenes from four related species (L. serriola, L. saligna, L. virosa and L. perennis). Where possible, probes were tiled with a 2 bp stagger, alternating on each DNA strand; providing an average of 187 probes covering approximately 600 bp for each of over 35,000 unigenes; resulting in up to 13 fold redundancy in coverage per nucleotide. We developed protocols for hybridization of genomic DNA to the GeneChip® and refined custom algorithms that utilized coverage from multiple, high quality probes to detect single position polymorphisms in 2 bp sliding windows across each unigene. This allowed us to detect greater than 18,000 polymorphisms between the parental lines of our core mapping population, as well as numerous polymorphisms between cultivated lettuce and wild species in the lettuce genepool. Using marker data from our diversity panel comprised of 52 accessions from the five species listed above, we were able to separate accessions by species using both phylogenetic and principal component analyses. Additionally, we estimated the diversity between different types of cultivated lettuce and distinguished morphological types. By hybridizing genomic DNA to a custom oligonucleotide array designed for maximum gene coverage, we were able to identify polymorphisms using two approaches for pair-wise comparisons, as well as a highly parallel method that compared all 52 genotypes simultaneously.

Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.

PubMed

Xu, Chang; Nezami Ranjbar, Mohammad R; Wu, Zhong; DiCarlo, John; Wang, Yexun

2017-01-03

Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models. We present here a highly efficient, simple and scalable enrichment protocol that integrates molecular barcodes in multiplex PCR amplification. In addition, we developed smCounter, an open source, generic, barcode-aware variant caller based on a Bayesian probabilistic model. smCounter was optimized and benchmarked on two independent read sets with SNVs and indels at 5 and 1% allele fractions. Variants were called with very good sensitivity and specificity within coding regions. We demonstrated that we can accurately detect somatic mutations with allele fractions as low as 1% in coding regions using our enrichment protocol and variant caller.

Calibrating genomic and allelic coverage bias in single-cell sequencing.

PubMed

Zhang, Cheng-Zhong; Adalsteinsson, Viktor A; Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L; Meyerson, Matthew; Love, J Christopher

2015-04-16

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.

Calibrating genomic and allelic coverage bias in single-cell sequencing

PubMed Central

Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L.; Meyerson, Matthew; Love, J. Christopher

2016-01-01

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1–10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (~0.1 ×) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples. PMID:25879913

ReadXplorer—visualization and analysis of mapped sequences

PubMed Central

Hilker, Rolf; Stadermann, Kai Bernd; Doppmeier, Daniel; Kalinowski, Jörn; Stoye, Jens; Straube, Jasmin; Winnebald, Jörn; Goesmann, Alexander

2014-01-01

Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data. Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion–insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets. Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual. Contact: rhilker@mikrobio.med.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24790157

Altools: a user friendly NGS data analyser.

PubMed

Camiolo, Salvatore; Sablok, Gaurav; Porceddu, Andrea

2016-02-17

Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to address geographical population genomics of several model species. To access core SNPs and insertion/deletion polymorphisms (indels), and to infer the phyletic patterns of speciation, most such approaches map short reads to the reference genome. Variant calling is important to establish patterns of genome-wide association studies (GWAS) for quantitative trait loci (QTLs), and to determine the population and haplotype structure based on SNPs, thus allowing content-dependent trait and evolutionary analysis. Several tools have been developed to investigate such polymorphisms as well as more complex genomic rearrangements such as copy number variations, presence/absence variations and large deletions. The programs available for this purpose have different strengths (e.g. accuracy, sensitivity and specificity) and weaknesses (e.g. low computation speed, complex installation procedure and absence of a user-friendly interface). Here we introduce Altools, a software package that is easy to install and use, which allows the precise detection of polymorphisms and structural variations. Altools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations. It also uses insert size information from the alignment of paired-end reads and detects potential large deletions. A double mapping approach (BWA/BLASTn) identifies precise breakpoints while ensuring rapid elaboration. Finally, Altools implements several processes that yield deeper insight into the genes affected by the detected polymorphisms. Altools was used to analyse both simulated and real next-generation sequencing (NGS) data and performed satisfactorily in terms of positive predictive values, sensitivity, the identification of large deletion breakpoints and copy number detection. Altools is fast, reliable and easy to use for the mining of NGS data. The software package also attempts to link identified polymorphisms and structural variants to their biological functions thus providing more valuable information than similar tools.

Evaluating PRISM precipitation grid data as possible surrogates for station data at four sites in Oklahoma

USDA-ARS?s Scientific Manuscript database

The development of climate-sensitive decision support for agriculture or water resource management requires long time series of monthly precipitation for specific locations. Archived station data for many locations is available, but time continuity, quality, and spatial coverage of station data rem...

Influence of travel speed on spray deposition uniformity from an air-assisted variable-rate sprayer

USDA-ARS?s Scientific Manuscript database

A newly developed LiDAR-guided air-assisted variable-rate sprayer for nursery and orchard applications was tested at various travel speeds to compare its spray deposition and coverage uniformity with constant-rate applications. Spray samplers, including nylon screens and water-sensitive papers (WSP)...

Measles in Poland in 2014

PubMed

Paradowska-Stankiewicz, Iwona; Rogalska, Justyna

Since 1998, Poland has been actively participating in the Measles Elimination Program, coordinated by the World Health Organization (WHO). It requires achieving and maintaining very high vaccine coverage (>95%), recording all cases and suspected cases of measles, and laboratory testing of all suspected measles cases in the WHO Reference Laboratory. In Poland it is a Laboratory of Department of Virology, NIPHNIH. In order to confirm or exclude the case of measles specific measles IgM antibodies should be measured using Elisa test, or molecular testing (PCR) should be performed to detect the presence measles virus RNA in biological material. To assess epidemiological situation of measles in Poland in 2014, including vaccination coverage in Polish population, and Measles Elimination Program implementation status. The descriptive analysis was based on data retrieved from routine mandatory surveillance system, measles case-based reports from 2014 sent to the Department of Epidemiology NIPH-NIH by Sanitary-Epidemiological Stations and data published in the annual bulletins “Infectious diseases and poisonings in Poland in 2014” and “Vaccinations in Poland in 2014” (MP Czarkowski et all., Warszawa 2015, NIZP-PZH, GIS). In total, there were 110 measles cases registered in Poland in 2014 (incidence 0.29 per 100,000), from which 87 cases (79%) were confirmed with laboratory test. That was more than in 2013 - when 84 cases were reported and incidence was 0,22. The highest incidence rate was observed among children aged 1 year (3,43 per 100,000). In 2014, 76 cases (69%) were hospitalized due to measles. No deaths from measles were reported. Vaccination coverage of children and youth aged 2-11 years ranged from 79.7% do 94.8% (primary vaccination in children born in 2004-2013) and from 77.7% to 85.8% (booster dose in children born in 2005-2011). In 2013, 127 measles-compatible cases were reported (67% of expected reports). In whole country the total number of suspects decreased form 258 in 2013 to 182 in 2014 r. In 2014, the epidemiological situation of measles deteriorated incomparison to proceeding year. The sensitivity of measles surveillance improved but is still insufficient. It is necessary to further promote Measles Elimination Program in Poland, to improve measles surveillance system and to maintain the high immunisation coverage.

A Nested Phosphorus and Proton Coil Array for Brain Magnetic Resonance Imaging and Spectroscopy

PubMed Central

Brown, Ryan; Lakshmanan, Karthik; Madelin, Guillaume; Parasoglou, Prodromos

2015-01-01

A dual-nuclei radiofrequency coil array was constructed for phosphorus and proton magnetic resonance imaging and spectroscopy of the human brain at 7 Tesla. An eight-channel transceive degenerate birdcage phosphorus module was implemented to provide whole-brain coverage and significant sensitivity improvement over a standard dual-tuned loop coil. A nested eight-channel proton module provided adequate sensitivity for anatomical localization without substantially sacrificing performance on the phosphorus module. The developed array enabled phosphorus spectroscopy, a saturation transfer technique to calculate the global creatine kinase forward reaction rate, and single-metabolite whole-brain imaging with 1.4 cm nominal isotropic resolution in 15 min (2.3 cm actual resolution), while additionally enabling 1 mm isotropic proton imaging. This study demonstrates that a multi-channel array can be utilized for phosphorus and proton applications with improved coverage and/or sensitivity over traditional single-channel coils. The efficient multi-channel coil array, time-efficient pulse sequences, and the enhanced signal strength available at ultra-high fields can be combined to allow volumetric assessment of the brain and could provide new insights into the underlying energy metabolism impairment in several neurodegenerative conditions, such as Alzheimer’s and Parkinson’s diseases, as well as mental disorders such as schizophrenia. PMID:26375209

A nested phosphorus and proton coil array for brain magnetic resonance imaging and spectroscopy.

PubMed

Brown, Ryan; Lakshmanan, Karthik; Madelin, Guillaume; Parasoglou, Prodromos

2016-01-01

A dual-nuclei radiofrequency coil array was constructed for phosphorus and proton magnetic resonance imaging and spectroscopy of the human brain at 7T. An eight-channel transceive degenerate birdcage phosphorus module was implemented to provide whole-brain coverage and significant sensitivity improvement over a standard dual-tuned loop coil. A nested eight-channel proton module provided adequate sensitivity for anatomical localization without substantially sacrificing performance on the phosphorus module. The developed array enabled phosphorus spectroscopy, a saturation transfer technique to calculate the global creatine kinase forward reaction rate, and single-metabolite whole-brain imaging with 1.4cm nominal isotropic resolution in 15min (2.3cm actual resolution), while additionally enabling 1mm isotropic proton imaging. This study demonstrates that a multi-channel array can be utilized for phosphorus and proton applications with improved coverage and/or sensitivity over traditional single-channel coils. The efficient multi-channel coil array, time-efficient pulse sequences, and the enhanced signal strength available at ultra-high fields can be combined to allow volumetric assessment of the brain and could provide new insights into the underlying energy metabolism impairment in several neurodegenerative conditions, such as Alzheimer's and Parkinson's diseases, as well as mental disorders such as schizophrenia. Copyright © 2015 Elsevier Inc. All rights reserved.