Cell force mapping using a double-sided micropillar array based on the moiré fringe method

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Zhang, F.; Anderson, S.; Zheng, X.; Roberts, E.; Qiu, Y.; Liao, R.; Zhang, X.

2014-07-01

The mapping of traction forces is crucial to understanding the means by which cells regulate their behavior and physiological function to adapt to and communicate with their local microenvironment. To this end, polymeric micropillar arrays have been used for measuring cell traction force. However, the small scale of the micropillar deflections induced by cell traction forces results in highly inefficient force analyses using conventional optical approaches; in many cases, cell forces may be below the limits of detection achieved using conventional microscopy. To address these limitations, the moiré phenomenon has been leveraged as a visualization tool for cell force mapping due to its inherent magnification effect and capacity for whole-field force measurements. This Letter reports an optomechanical cell force sensor, namely, a double-sided micropillar array (DMPA) made of poly(dimethylsiloxane), on which one side is employed to support cultured living cells while the opposing side serves as a reference pattern for generating moiré patterns. The distance between the two sides, which is a crucial parameter influencing moiré pattern contrast, is predetermined during fabrication using theoretical calculations based on the Talbot effect that aim to optimize contrast. Herein, double-sided micropillar arrays were validated by mapping mouse embryo fibroblast contraction forces and the resulting force maps compared to conventional microscopy image analyses as the reference standard. The DMPA-based approach precludes the requirement for aligning two independent periodic substrates, improves moiré contrast, and enables efficient moiré pattern generation. Furthermore, the double-sided structure readily allows for the integration of moiré-based cell force mapping into microfabricated cell culture environments or lab-on-a-chip devices.

Development of admixture mapping panels for African Americans from commercial high-density SNP arrays

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Dunston Georgia M

2010-07-01

Full Text Available Abstract Background Admixture mapping is a powerful approach for identifying genetic variants involved in human disease that exploits the unique genomic structure in recently admixed populations. To use existing published panels of ancestry-informative markers (AIMs for admixture mapping, markers have to be genotyped de novo for each admixed study sample and samples representing the ancestral parental populations. The increased availability of dense marker data on commercial chips has made it feasible to develop panels wherein the markers need not be predetermined. Results We developed two panels of AIMs (~2,000 markers each based on the Affymetrix Genome-Wide Human SNP Array 6.0 for admixture mapping with African American samples. These two AIM panels had good map power that was higher than that of a denser panel of ~20,000 random markers as well as other published panels of AIMs. As a test case, we applied the panels in an admixture mapping study of hypertension in African Americans in the Washington, D.C. metropolitan area. Conclusions Developing marker panels for admixture mapping from existing genome-wide genotype data offers two major advantages: (1 no de novo genotyping needs to be done, thereby saving costs, and (2 markers can be filtered for various quality measures and replacement markers (to minimize gaps can be selected at no additional cost. Panels of carefully selected AIMs have two major advantages over panels of random markers: (1 the map power from sparser panels of AIMs is higher than that of ~10-fold denser panels of random markers, and (2 clusters can be labeled based on information from the parental populations. With current technology, chip-based genome-wide genotyping is less expensive than genotyping ~20,000 random markers. The major advantage of using random markers is the absence of ascertainment effects resulting from the process of selecting markers. The ability to develop marker panels informative for ancestry from

Mapping the fine structure of cortical activity with different micro-ECoG electrode array geometries

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Wang, Xi; Gkogkidis, C. Alexis; Iljina, Olga; Fiederer, Lukas D. J.; Henle, Christian; Mader, Irina; Kaminsky, Jan; Stieglitz, Thomas; Gierthmuehlen, Mortimer; Ball, Tonio

2017-10-01

Objective. Innovations in micro-electrocorticography (µECoG) electrode array manufacturing now allow for intricate designs with smaller contact diameters and/or pitch (i.e. inter-contact distance) down to the sub-mm range. The aims of the present study were: (i) to investigate whether frequency ranges up to 400 Hz can be reproducibly observed in µECoG recordings and (ii) to examine how differences in topographical substructure between these frequency bands and electrode array geometries can be quantified. We also investigated, for the first time, the influence of blood vessels on signal properties and assessed the influence of cortical vasculature on topographic mapping. Approach. The present study employed two µECoG electrode arrays with different contact diameters and inter-contact distances, which were used to characterize neural activity from the somatosensory cortex of minipigs in a broad frequency range up to 400 Hz. The analysed neural data were recorded in acute experiments under anaesthesia during peripheral electrical stimulation. Main results. We observed that µECoG recordings reliably revealed multi-focal cortical somatosensory response patterns, in which response peaks were often less than 1 cm apart and would thus not have been resolvable with conventional ECoG. The response patterns differed by stimulation site and intensity, they were distinct for different frequency bands, and the results of functional mapping proved independent of cortical vascular. Our analysis of different frequency bands exhibited differences in the number of activation peaks in topographical substructures. Notably, signal strength and signal-to-noise ratios differed between the two electrode arrays, possibly due to their different sensitivity for variations in spatial patterns and signal strengths. Significance. Our findings that the geometry of µECoG electrode arrays can strongly influence their recording performance can help to make informed decisions that maybe

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

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Garnier-Géré Pauline

2011-07-01

Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait., the main conifer used for commercial plantation in southwestern Europe. Results We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels. Offspring from three-generation outbred (G2 and inbred (F2 pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species. Conclusions Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using

Whole genome DNA copy number changes identified by high density oligonucleotide arrays

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Huang Jing

2004-05-01

Full Text Available Abstract Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous micro-array-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs. Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA, to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM and mismatch (MM probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number

Antibody Arrays Identify Potential Diagnostic Markers of Hepatocellular Carcinoma

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Brian J. Peter

2008-01-01

Full Text Available Hepatocellular carcinoma (HCC is the third leading cause of cancer deaths worldwide. Effective treatment of HCC patients is hampered by the lack of sensitive and specific diagnostic markers of HCC. Alpha-fetoprotein (AFP, the currently used HCC marker, misses 30%–50% of HCC patients, who therefore remain undiagnosed and untreated. In order to identify novel diagnostic markers that can be used individually or in combination with AFP, we used an antibody array platform to detect the levels of candidate proteins in the plasma of HCC patients (n = 48 and patients with chronic hepatitis B or C viral infections (n = 19 (both of which are the major risk factors of HCC. We identified 7 proteins that significantly differentiate HCC patients from hepatitis patients (p < 0.05 (AFP, CTNNB, CSF1, SELL, IGFBP6, IL6R, and VCAM1.Importantly, we also identified 8 proteins that significantly differentiate HCC patients with ‘normal’ levels of AFP (<20 ng/ml from hepatitis patients (p < 0.05 (IL1RN, IFNG, CDKN1A, RETN, CXCL14, CTNNB, FGF2, and SELL. These markers are potentially important complementary markers to AFP. Using an independent immunoassay method in an independent group of 23 HCC patients and 22 hepatitis patients, we validated that plasma levels of CTNNB were significantly higher in the HCC group (p = 0.020. In conclusion, we used an antibody array platform to identify potential circulating diagnostic markers of HCC, some of which may be valuable when used in combination with AFP. The clinical utility of these newly identified HCC diagnostic markers needs to be systematically evaluated.

A multi-frequency sparse hemispherical ultrasound phased array for microbubble-mediated transcranial therapy and simultaneous cavitation mapping.

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Deng, Lulu; O'Reilly, Meaghan A; Jones, Ryan M; An, Ran; Hynynen, Kullervo

2016-12-21

Focused ultrasound (FUS) phased arrays show promise for non-invasive brain therapy. However, the majority of them are limited to a single transmit/receive frequency and therefore lack the versatility to expose and monitor the treatment volume. Multi-frequency arrays could offer variable transmit focal sizes under a fixed aperture, and detect different spectral content on receive for imaging purposes. Here, a three-frequency (306, 612, and 1224 kHz) sparse hemispherical ultrasound phased array (31.8 cm aperture; 128 transducer modules) was constructed and evaluated for microbubble-mediated transcranial therapy and simultaneous cavitation mapping. The array is able to perform effective electronic beam steering over a volume spanning (-40, 40) and (-30, 50) mm in the lateral and axial directions, respectively. The focal size at the geometric center is approximately 0.9 (2.1) mm, 1.7 (3.9) mm, and 3.1 (6.5) mm in lateral (axial) pressure full width at half maximum (FWHM) at 1224, 612, and 306 kHz, respectively. The array was also found capable of dual-frequency excitation and simultaneous multi-foci sonication, which enables the future exploration of more complex exposure strategies. Passive acoustic mapping of dilute microbubble clouds demonstrated that the point spread function of the receive array has a lateral (axial) intensity FWHM between 0.8-3.5 mm (1.7-11.7 mm) over a volume spanning (-25, 25) mm in both the lateral and axial directions, depending on the transmit/receive frequency combination and the imaging location. The device enabled both half and second harmonic imaging through the intact skull, which may be useful for improving the contrast-to-tissue ratio or imaging resolution, respectively. Preliminary in vivo experiments demonstrated the system's ability to induce blood-brain barrier opening and simultaneously spatially map microbubble cavitation activity in a rat model. This work presents a tool to investigate optimal strategies for non

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

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Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

2014-01-01

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information. PMID:25914583

Rapid recognition of volatile organic compounds with colorimetric sensor arrays for lung cancer screening.

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Zhong, Xianhua; Li, Dan; Du, Wei; Yan, Mengqiu; Wang, You; Huo, Danqun; Hou, Changjun

2018-06-01

Volatile organic compounds (VOCs) in breath can be used as biomarkers to identify early stages of lung cancer. Herein, we report a disposable colorimetric array that has been constructed from diverse chemo-responsive colorants. Distinguishable difference maps were plotted within 4 min for specifically targeted VOCs. Through the consideration of various chemical interactions with VOCs, the arrays successfully discriminate between 20 different volatile organic compounds in breath that are related to lung cancer. VOCs were identified either with the visualized difference maps or through pattern recognition with an accuracy of at least 90%. No uncertainties or errors were observed in the hierarchical cluster analysis (HCA). Finally, good reproducibility and stability of the array was achieved against changes in humidity. Generally, this work provides fundamental support for construction of simple and rapid VOC sensors. More importantly, this approach provides a hypothesis-free array method for breath testing via VOC profiling. Therefore, this small, rapid, non-invasive, inexpensive, and visualized sensor array is a powerful and promising tool for early screening of lung cancer. Graphical abstract A disposable colorimetric array has been developed with broadly chemo-responsive dyes to incorporate various chemical interactions, through which the arrays successfully discriminate 20 VOCs that are related to lung cancer via difference maps alone or chemometrics within 4 min. The hydrophobic porous matrix provides good stability against changes in humidity.

The Use of High-Density SNP Array to Map Homozygosity in Consanguineous Families to Efficiently Identify Candidate Genes: Application to Woodhouse-Sakati Syndrome

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Molly B. Sheridan

2015-01-01

Full Text Available Two consanguineous Qatari siblings presented for evaluation: a 17-4/12-year-old male with hypogonadotropic hypogonadism, alopecia, intellectual disability, and microcephaly and his 19-year-old sister with primary amenorrhea, alopecia, and normal cognition. Both required hormone treatment to produce secondary sex characteristics and pubertal development beyond Tanner 1. SNP array analysis of both probands was performed to detect shared regions of homozygosity which may harbor homozygous mutations in a gene causing their common features of abnormal pubertal development, alopecia, and variable cognitive delay. Our patients shared multiple homozygous genomic regions; ten shared regions were >1 Mb in length and constituted 0.99% of the genome. DCAF17, encoding a transmembrane nuclear protein of uncertain function, was the only gene identified in a homozygous region known to cause hypogonadotropic hypogonadism. DCAF17 mutations are associated with Woodhouse-Sakati syndrome, a rare disorder characterized by alopecia, hypogonadotropic hypogonadism, sensorineural hearing loss, diabetes mellitus, and extrapyramidal movements. Sequencing of the coding exons and flanking intronic regions of DCAF17 in the proband revealed homozygosity for a previously described founder mutation (c.436delC. Targeted DCAF17 sequencing of his affected sibling revealed the same homozygous mutation. This family illustrates the utility of SNP array testing in consanguineous families to efficiently and inexpensively identify regions of genomic homozygosity in which genetic candidates for recessive conditions can be identified.

HARMONIC SPACE ANALYSIS OF PULSAR TIMING ARRAY REDSHIFT MAPS

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Roebber, Elinore; Holder, Gilbert, E-mail: roebbere@physics.mcgill.ca [Department of Physics and McGill Space Institute, McGill University, 3600 rue University, Montréal, QC, H3A 2T8 (Canada)

2017-01-20

In this paper, we propose a new framework for treating the angular information in the pulsar timing array (PTA) response to a gravitational wave (GW) background based on standard cosmic microwave background techniques. We calculate the angular power spectrum of the all-sky gravitational redshift pattern induced at the Earth for both a single bright source of gravitational radiation and a statistically isotropic, unpolarized Gaussian random GW background. The angular power spectrum is the harmonic transform of the Hellings and Downs curve. We use the power spectrum to examine the expected variance in the Hellings and Downs curve in both cases. Finally, we discuss the extent to which PTAs are sensitive to the angular power spectrum and find that the power spectrum sensitivity is dominated by the quadrupole anisotropy of the gravitational redshift map.

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

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Hanspers Kristina

2010-01-01

Full Text Available Abstract Background Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services. Results Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications. Conclusion By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org.

Simulated near-field mapping of ripple pattern supported metal nanoparticles arrays for SERS optimization

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Arya, Mahima; Bhatnagar, Mukul; Ranjan, Mukesh; Mukherjee, Subroto; Nath, Rabinder; Mitra, Anirban

2017-11-01

An analytical model has been developed using a modified Yamaguchi model along with the wavelength dependent plasmon line-width correction. The model has been used to calculate the near-field response of random nanoparticles on the plane surface, elongated and spherical silver nanoparticle arrays supported on ion beam produced ripple patterned templates. The calculated near-field mapping for elongated nanoparticles arrays on the ripple patterned surface shows maximum number of hot-spots with a higher near-field enhancement (NFE) as compared to the spherical nanoparticle arrays and randomly distributed nanoparticles on the plane surface. The results from the simulations show a similar trend for the NFE when compared to the far field reflection spectra. The nature of the wavelength dependent NFE is also found to be in agreement with the observed experimental results from surface enhanced Raman spectroscopy (SERS). The calculated and the measured optical response unambiguously reveal the importance of interparticle gap and ordering, where a high intensity Raman signal is obtained for ordered elongated nanoparticles arrays case as against non-ordered and the aligned configuration of spherical nanoparticles on the rippled surface.

Identifying Resistivity Anomalies of Sungai Batu Ancient River using 3D Contour Map

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Yusoh, R.; Saad, R.; Saidin, M.; Muhammad, S. B.; Anda, S. T.; Ismail, M. A. M.; Hazreek, Z. A. M.

2018-04-01

Electrical resistivity method was undertaken at archeological site at Sungai Batu in Lembah Bujang, located at Sungai Merbok in northwestern of Malaysia. The survey was implemented near the excavation site. This paper shows the results of 5 ground resistivity survey line was carry out using SAS4000 equipment. The wenner-schlumberger array was applied for measurement. Resistivity data are used to obtain valuable information to identify the remain buried archeology. The ground resistivity data were presented in contour map for various depth by using Surfer 13 software visualized clearly the anomalies evidenced for every single depth section. The results from the survey has found the appearance of sedimentation formation that believe happen long time ago after ancient river was buried by sediment from weathering process due to increasing sea level. Otherwise, another anomaly was found in the middle of the survey area which shows high resistivity value about 1000 – 2000 ohm.m

Two-dimensional mapping of needle visibility with linear and curved array for ultrasound-guided interventional procedure

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Susanti, Hesty; Suprijanto, Kurniadi, Deddy

2018-02-01

Needle visibility in ultrasound-guided technique has been a crucial factor for successful interventional procedure. It has been affected by several factors, i.e. puncture depth, insertion angle, needle size and material, and imaging technology. The influences of those factors made the needle not always well visible. 20 G needles of 15 cm length (Nano Line, facet) were inserted into water bath with variation of insertion angles and depths. Ultrasound measurements are performed with BK-Medical Flex Focus 800 using 12 MHz linear array and 5 MHz curved array in Ultrasound Guided Regional Anesthesia mode. We propose 3 criteria to evaluate needle visibility, i.e. maximum intensity, mean intensity, and the ratio between minimum and maximum intensity. Those criteria were then depicted into representative maps for practical purpose. The best criterion candidate for representing the needle visibility was criterion 1. Generally, the appearance pattern of the needle from this criterion was relatively consistent, i.e. for linear array, it was relatively poor visibility in the middle part of the shaft, while for curved array, it is relatively better visible toward the end of the shaft. With further investigations, for example with the use of tissue-mimicking phantom, the representative maps can be built for future practical purpose, i.e. as a tool for clinicians to ensure better needle placement in clinical application. It will help them to avoid the "dead" area where the needle is not well visible, so it can reduce the risks of vital structures traversing and the number of required insertion, resulting in less patient morbidity. Those simple criteria and representative maps can be utilized to evaluate general visibility patterns of the needle in vast range of needle types and sizes in different insertion media. This information is also important as an early investigation for future research of needle visibility improvement, i.e. the development of beamforming strategies and

Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression

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Kote-Jarai, Zsofia; Saunders, Edward J.; Leongamornlert, Daniel A.; Tymrakiewicz, Malgorzata; Dadaev, Tokhir; Jugurnauth-Little, Sarah; Ross-Adams, Helen; Al Olama, Ali Amin; Benlloch, Sara; Halim, Silvia; Russel, Roslin; Dunning, Alison M.; Luccarini, Craig; Dennis, Joe; Neal, David E.; Hamdy, Freddie C.; Donovan, Jenny L.; Muir, Ken; Giles, Graham G.; Severi, Gianluca; Wiklund, Fredrik; Gronberg, Henrik; Haiman, Christopher A.; Schumacher, Fredrick; Henderson, Brian E.; Le Marchand, Loic; Lindstrom, Sara; Kraft, Peter; Hunter, David J.; Gapstur, Susan; Chanock, Stephen; Berndt, Sonja I.; Albanes, Demetrius; Andriole, Gerald; Schleutker, Johanna; Weischer, Maren; Canzian, Federico; Riboli, Elio; Key, Tim J.; Travis, Ruth C.; Campa, Daniele; Ingles, Sue A.; John, Esther M.; Hayes, Richard B.; Pharoah, Paul; Khaw, Kay-Tee; Stanford, Janet L.; Ostrander, Elaine A.; Signorello, Lisa B.; Thibodeau, Stephen N.; Schaid, Dan; Maier, Christiane; Vogel, Walther; Kibel, Adam S.; Cybulski, Cezary; Lubinski, Jan; Cannon-Albright, Lisa; Brenner, Hermann; Park, Jong Y.; Kaneva, Radka; Batra, Jyotsna; Spurdle, Amanda; Clements, Judith A.; Teixeira, Manuel R.; Govindasami, Koveela; Guy, Michelle; Wilkinson, Rosemary A.; Sawyer, Emma J.; Morgan, Angela; Dicks, Ed; Baynes, Caroline; Conroy, Don; Bojesen, Stig E.; Kaaks, Rudolf; Vincent, Daniel; Bacot, François; Tessier, Daniel C.; Easton, Douglas F.; Eeles, Rosalind A.

2013-01-01

Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease. PMID:23535824

Spatio-temporal dimension of lightning flashes based on three-dimensional Lightning Mapping Array

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López, Jesús A.; Pineda, Nicolau; Montanyà, Joan; Velde, Oscar van der; Fabró, Ferran; Romero, David

2017-11-01

3D mapping system like the LMA - Lightning Mapping Array - are a leap forward in lightning observation. LMA measurements has lead to an improvement on the analysis of the fine structure of lightning, allowing to characterize the duration and maximum extension of the cloud fraction of a lightning flash. During several years of operation, the first LMA deployed in Europe has been providing a large amount of data which now allows a statistical approach to compute the full duration and horizontal extension of the in-cloud phase of a lightning flash. The "Ebro Lightning Mapping Array" (ELMA) is used in the present study. Summer and winter lighting were analyzed for seasonal periods (Dec-Feb and Jun-Aug). A simple method based on an ellipse fitting technique (EFT) has been used to characterize the spatio-temporal dimensions from a set of about 29,000 lightning flashes including both summer and winter events. Results show an average lightning flash duration of 440 ms (450 ms in winter) and a horizontal maximum length of 15.0 km (18.4 km in winter). The uncertainties for summer lightning lengths were about ± 1.2 km and ± 0.7 km for the mean and median values respectively. In case of winter lightning, the level of uncertainty reaches up to 1 km and 0.7 km of mean and median value. The results of the successful correlation of CG discharges with the EFT method, represent 6.9% and 35.5% of the total LMA flashes detected in summer and winter respectively. Additionally, the median value of lightning lengths calculated through this correlative method was approximately 17 km for both seasons. On the other hand, the highest median ratios of lightning length to CG discharges in both summer and winter were reported for positive CG discharges.

Mapping Electrical Crosstalk in Pixelated Sensor Arrays

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Seshadri, Suresh (Inventor); Cole, David (Inventor); Smith, Roger M. (Inventor); Hancock, Bruce R. (Inventor)

2017-01-01

The effects of inter pixel capacitance in a pixilated array may be measured by first resetting all pixels in the array to a first voltage, where a first image is read out, followed by resetting only a subset of pixels in the array to a second voltage, where a second image is read out, where the difference in the first and second images provide information about the inter pixel capacitance. Other embodiments are described and claimed.

Transcranial passive acoustic mapping with hemispherical sparse arrays using CT-based skull-specific aberration corrections: a simulation study

International Nuclear Information System (INIS)

Jones, Ryan M; O’Reilly, Meaghan A; Hynynen, Kullervo

2013-01-01

The feasibility of transcranial passive acoustic mapping with hemispherical sparse arrays (30 cm diameter, 16 to 1372 elements, 2.48 mm receiver diameter) using CT-based aberration corrections was investigated via numerical simulations. A multi-layered ray acoustic transcranial ultrasound propagation model based on CT-derived skull morphology was developed. By incorporating skull-specific aberration corrections into a conventional passive beamforming algorithm (Norton and Won 2000 IEEE Trans. Geosci. Remote Sens. 38 1337–43), simulated acoustic source fields representing the emissions from acoustically-stimulated microbubbles were spatially mapped through three digitized human skulls, with the transskull reconstructions closely matching the water-path control images. Image quality was quantified based on main lobe beamwidths, peak sidelobe ratio, and image signal-to-noise ratio. The effects on the resulting image quality of the source’s emission frequency and location within the skull cavity, the array sparsity and element configuration, the receiver element sensitivity, and the specific skull morphology were all investigated. The system’s resolution capabilities were also estimated for various degrees of array sparsity. Passive imaging of acoustic sources through an intact skull was shown possible with sparse hemispherical imaging arrays. This technique may be useful for the monitoring and control of transcranial focused ultrasound (FUS) treatments, particularly non-thermal, cavitation-mediated applications such as FUS-induced blood–brain barrier disruption or sonothrombolysis, for which no real-time monitoring techniques currently exist. (paper)

Transcranial passive acoustic mapping with hemispherical sparse arrays using CT-based skull-specific aberration corrections: a simulation study

Science.gov (United States)

Jones, Ryan M.; O’Reilly, Meaghan A.; Hynynen, Kullervo

2013-01-01

The feasibility of transcranial passive acoustic mapping with hemispherical sparse arrays (30 cm diameter, 16 to 1372 elements, 2.48 mm receiver diameter) using CT-based aberration corrections was investigated via numerical simulations. A multi-layered ray acoustic transcranial ultrasound propagation model based on CT-derived skull morphology was developed. By incorporating skull-specific aberration corrections into a conventional passive beamforming algorithm (Norton and Won 2000 IEEE Trans. Geosci. Remote Sens. 38 1337–43), simulated acoustic source fields representing the emissions from acoustically-stimulated microbubbles were spatially mapped through three digitized human skulls, with the transskull reconstructions closely matching the water-path control images. Image quality was quantified based on main lobe beamwidths, peak sidelobe ratio, and image signal-to-noise ratio. The effects on the resulting image quality of the source’s emission frequency and location within the skull cavity, the array sparsity and element configuration, the receiver element sensitivity, and the specific skull morphology were all investigated. The system’s resolution capabilities were also estimated for various degrees of array sparsity. Passive imaging of acoustic sources through an intact skull was shown possible with sparse hemispherical imaging arrays. This technique may be useful for the monitoring and control of transcranial focused ultrasound (FUS) treatments, particularly non-thermal, cavitation-mediated applications such as FUS-induced blood-brain barrier disruption or sonothrombolysis, for which no real-time monitoring technique currently exists. PMID:23807573

Use of Microtremor Array Recordings for Mapping Subsurface Soil Structure, Singapore

Science.gov (United States)

Walling, M.

2012-12-01

Microtremor array recordings are carried out in Singapore, for different geology, to study the influence of each site in modeling the subsurface structure. The Spatial Autocorrelation (SPAC) method is utilized for the computation of the soil profiles. The array configuration of the recording consists of 7 seismometers, recording the vertical component of the ground motion, and the recording at each site is carried out for 30 minutes. The results from the analysis show that the soil structure modeled for the young alluvial of Kallang Formation (KF), in terms of shear wave velocity (Vs), gives a good correlation with borehole information, while for the older geological formation of Jurong Formation (JF) (sedimentary rock sequence) and Old Alluvial (OA) (dense alluvium formation), the correlation is not very clear due to the lack of impedance contrast. The older formation of Bukit Timah Granite (BTG) show contrasting results within the formation, with the northern BTG suggesting a low Vs upper layer of about 20m - 30m while the southern BTG reveals a dense formation. The discrepancy in the variation within BTG is confirmed from borehole data that reveals the northern BTG to have undergone intense weathering while the southern BTG have not undergone noticeable weathering. Few sites with bad recording quality could not resolve the soil structure. Microtremor array recording is good for mapping sites with soft soil formation and weathered rock formation but can be limited in the absence of subsurface velocity contrast and bad quality of microtremor records.; The correlation between the Vs30 estimated from SPAC method and borehole data for the four major geological formations of Singapore. The encircled sites are the sites with recording error.

Parallel Access of Out-Of-Core Dense Extendible Arrays

Energy Technology Data Exchange (ETDEWEB)

Otoo, Ekow J; Rotem, Doron

2007-07-26

Datasets used in scientific and engineering applications are often modeled as dense multi-dimensional arrays. For very large datasets, the corresponding array models are typically stored out-of-core as array files. The array elements are mapped onto linear consecutive locations that correspond to the linear ordering of the multi-dimensional indices. Two conventional mappings used are the row-major order and the column-major order of multi-dimensional arrays. Such conventional mappings of dense array files highly limit the performance of applications and the extendibility of the dataset. Firstly, an array file that is organized in say row-major order causes applications that subsequently access the data in column-major order, to have abysmal performance. Secondly, any subsequent expansion of the array file is limited to only one dimension. Expansions of such out-of-core conventional arrays along arbitrary dimensions, require storage reorganization that can be very expensive. Wepresent a solution for storing out-of-core dense extendible arrays that resolve the two limitations. The method uses a mapping function F*(), together with information maintained in axial vectors, to compute the linear address of an extendible array element when passed its k-dimensional index. We also give the inverse function, F-1*() for deriving the k-dimensional index when given the linear address. We show how the mapping function, in combination with MPI-IO and a parallel file system, allows for the growth of the extendible array without reorganization and no significant performance degradation of applications accessing elements in any desired order. We give methods for reading and writing sub-arrays into and out of parallel applications that run on a cluster of workstations. The axial-vectors are replicated and maintained in each node that accesses sub-array elements.

A Spatiotemporal Indexing Approach for Efficient Processing of Big Array-Based Climate Data with MapReduce

Science.gov (United States)

Li, Zhenlong; Hu, Fei; Schnase, John L.; Duffy, Daniel Q.; Lee, Tsengdar; Bowen, Michael K.; Yang, Chaowei

2016-01-01

Climate observations and model simulations are producing vast amounts of array-based spatiotemporal data. Efficient processing of these data is essential for assessing global challenges such as climate change, natural disasters, and diseases. This is challenging not only because of the large data volume, but also because of the intrinsic high-dimensional nature of geoscience data. To tackle this challenge, we propose a spatiotemporal indexing approach to efficiently manage and process big climate data with MapReduce in a highly scalable environment. Using this approach, big climate data are directly stored in a Hadoop Distributed File System in its original, native file format. A spatiotemporal index is built to bridge the logical array-based data model and the physical data layout, which enables fast data retrieval when performing spatiotemporal queries. Based on the index, a data-partitioning algorithm is applied to enable MapReduce to achieve high data locality, as well as balancing the workload. The proposed indexing approach is evaluated using the National Aeronautics and Space Administration (NASA) Modern-Era Retrospective Analysis for Research and Applications (MERRA) climate reanalysis dataset. The experimental results show that the index can significantly accelerate querying and processing (10 speedup compared to the baseline test using the same computing cluster), while keeping the index-to-data ratio small (0.0328). The applicability of the indexing approach is demonstrated by a climate anomaly detection deployed on a NASA Hadoop cluster. This approach is also able to support efficient processing of general array-based spatiotemporal data in various geoscience domains without special configuration on a Hadoop cluster.

Characteristics of Lightning Within Electrified Snowfall Events Using Lightning Mapping Arrays

Science.gov (United States)

Schultz, Christopher J.; Lang, Timothy J.; Bruning, Eric C.; Calhoun, Kristin M.; Harkema, Sebastian; Curtis, Nathan

2018-02-01

This study examined 34 lightning flashes within four separate thundersnow events derived from lightning mapping arrays (LMAs) in northern Alabama, central Oklahoma, and Washington DC. The goals were to characterize the in-cloud component of each lightning flash, as well as the correspondence between the LMA observations and lightning data taken from national lightning networks like the National Lightning Detection Network (NLDN). Individual flashes were examined in detail to highlight several observations within the data set. The study results demonstrated that the structures of these flashes were primarily normal polarity. The mean area encompassed by this set of flashes is 375 km2, with a maximum flash extent of 2,300 km2, a minimum of 3 km2, and a median of 128 km2. An average of 2.29 NLDN flashes were recorded per LMA-derived lightning flash. A maximum of 11 NLDN flashes were recorded in association with a single LMA-derived flash on 10 January 2011. Additionally, seven of the 34 flashes in the study contain zero NLDN-identified flashes. Eleven of the 34 flashes initiated from tall human-made objects (e.g., communication towers). In at least six lightning flashes, the NLDN detected a return stroke from the cloud back to the tower and not the initial upward leader. This study also discusses lightning's interaction with the human-built environment and provides an example of lightning within heavy snowfall observed by Geostationary Operational Environmental Satellite-16's Geostationary Lightning Mapper.

High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis

NARCIS (Netherlands)

Eyre, Steve; Bowes, John; Diogo, Dorothee; Lee, Annette; Barton, Anne; Martin, Paul; Zhernakova, Alexandra; Stahl, Eli; Viatte, Sebastien; McAllister, Kate; Amos, Christopher I.; Padyukov, Leonid; Toes, Rene E. M.; Huizinga, Tom W. J.; Wijmenga, Cisca; Trynka, Gosia; Franke, Lude; Westra, Harm-Jan; Alfredsson, Lars; Hu, Xinli; Sandor, Cynthia; de Bakker, Paul I. W.; Davila, Sonia; Khor, Chiea Chuen; Heng, Khai Koon; Andrews, Robert; Edkins, Sarah; Hunt, Sarah E.; Langford, Cordelia; Symmons, Deborah; Concannon, Pat; Onengut-Gumuscu, Suna; Rich, Stephen S.; Deloukas, Panos; Gonzalez-Gay, Miguel A.; Rodriguez-Rodriguez, Luis; Arlsetig, Lisbeth; Martin, Javier; Rantapaa-Dahlqvist, Solbritt; Plenge, Robert M.; Raychaudhuri, Soumya; Klareskog, Lars; Gregersen, Peter K.; Worthington, Jane

2012-01-01

Using the Immunochip custom SNP array, which was designed for dense genotyping of 186 loci identified through genome-wide association studies (GWAS), we analyzed 11,475 individuals with rheumatoid arthritis (cases) of European ancestry and 15,870 controls for 129,464 markers. We combined these data

Performance Analysis of Digital loudspeaker Arrays

DEFF Research Database (Denmark)

Pedersen, Bo Rohde; Kontomichos, Fotios; Mourjopoulos, John

2008-01-01

An analysis of digital loudspeaker arrays shows that the ways in which bits are mapped to the drivers influence the quality of the audio result. Specifically, a "bit-summed" rather than the traditional "bit-mapped" strategy greatly reduces the number of times drivers make binary transitions per...... period of the input frequency. Detailed simulations compare the results for a 32-loudspeaker array with a similar configuration with analog excitation of the drivers. Ideally, drivers in digital arrays should be very small and span a small area, but that sets limits on the low-frequency response...

Whole-Genome Sequencing and iPLEX MassARRAY Genotyping Map an EMS-Induced Mutation Affecting Cell Competition in Drosophila melanogaster

Directory of Open Access Journals (Sweden)

Chang-Hyun Lee

2016-10-01

Full Text Available Cell competition, the conditional loss of viable genotypes only when surrounded by other cells, is a phenomenon observed in certain genetic mosaic conditions. We conducted a chemical mutagenesis and screen to recover new mutations that affect cell competition between wild-type and RpS3 heterozygous cells. Mutations were identified by whole-genome sequencing, making use of software tools that greatly facilitate the distinction between newly induced mutations and other sources of apparent sequence polymorphism, thereby reducing false-positive and false-negative identification rates. In addition, we utilized iPLEX MassARRAY for genotyping recombinant chromosomes. These approaches permitted the mapping of a new mutation affecting cell competition when only a single allele existed, with a phenotype assessed only in genetic mosaics, without the benefit of complementation with existing mutations, deletions, or duplications. These techniques expand the utility of chemical mutagenesis and whole-genome sequencing for mutant identification. We discuss mutations in the Atm and Xrp1 genes identified in this screen.

Dose mapping of the rectal wall during brachytherapy with an array of scintillation dosimeters

International Nuclear Information System (INIS)

Cartwright, L. E.; Suchowerska, N.; Yin, Y.; Lambert, J.; Haque, M.; McKenzie, D. R.

2010-01-01

Purpose: In pelvic brachytherapy treatments, the rectum is an organ at risk. The authors have developed an array of scintillation dosimeters suitable for in vivo use that enables quality assurance of the treatment delivery and provides an alert to potential radiation accidents. Ultimately, this will provide evidence to direct treatment planning and dose escalation and correlate dose with the rectal response. Methods: An array of 16 scintillation dosimeters in an insertable applicator has been developed. The dosimeters were calibrated simultaneously in a custom designed circular jig before use. Each dosimeter is optically interfaced to a set of pixels on a CCD camera located outside the treatment bunker. A customized software converts pixel values into dose rate and accumulates dose for presentation during treatment delivery. The performance of the array is tested by simulating brachytherapy treatments in a water phantom. The treatment plans were designed to deliver a known dose distribution on the surface of the rectal applicator, assumed to represent the dose to the rectal wall. Results: The measured doses were compared to those predicted by the treatment plan and found to be in agreement to within the uncertainty in measurement, usually within 3%. The array was also used to track the progression of the source as it moved along the catheter. The measured position was found to agree with the position reported by the afterloader to within the measurement uncertainty, usually within 2 mm. Conclusions: This array is capable of measuring the actual dose received by each region of the rectal wall during brachytherapy treatments. It will provide real time monitoring of treatment delivery and raise an alert to a potential radiation accident. Real time dose mapping in the clinical environment will give the clinician additional confidence to carry out dose escalation to the tumor volume while avoiding rectal side effects.

Fractal-Based Lightning Channel Length Estimation from Convex-Hull Flash Areas for DC3 Lightning Mapping Array Data

Science.gov (United States)

Bruning, Eric C.; Thomas, Ronald J.; Krehbiel, Paul R.; Rison, William; Carey, Larry D.; Koshak, William; Peterson, Harold; MacGorman, Donald R.

2013-01-01

We will use VHF Lightning Mapping Array data to estimate NOx per flash and per unit channel length, including the vertical distribution of channel length. What s the best way to find channel length from VHF sources? This paper presents the rationale for the fractal method, which is closely related to the box-covering method.

The plant microtubule-associated protein AtMAP65-3/PLE is essential for cytokinetic phragmoplast function.

Science.gov (United States)

Müller, Sabine; Smertenko, Andrei; Wagner, Vera; Heinrich, Maria; Hussey, Patrick J; Hauser, Marie-Theres

2004-03-09

Directional cell expansion in interphase and nuclear and cell division in M-phase are mediated by four microtubule arrays, three of which are unique to plants: the interphase array, the preprophase band, and the phragmoplast. The plant microtubule-associated protein MAP65 has been identified as a key structural component in these arrays. The Arabidopsis genome has nine MAP65 genes, and here we show that one, AtMAP65-3/PLE, locates only to the mitotic arrays and is essential for cytokinesis. The Arabidopsis pleiade (ple) alleles are single recessive mutations, and we show that these mutations are in the AtMAP65-3 gene. Moreover, these mutations cause C-terminal truncations that abolish microtubule binding. In the ple mutants the anaphase spindle is normal, and the cytokinetic phragmoplast can form but is distorted; not only is it wider, but the midline, the region where oppositely oriented microtubules overlap, is unusually expanded. Here we present data that demonstrate an essential role for AtMAP65-3/PLE in cytokinesis in plant cells.

Testing of focal plane arrays

International Nuclear Information System (INIS)

Merriam, J.D.

1988-01-01

Problems associated with the testing of focal plane arrays are briefly examined with reference to the instrumentation and measurement procedures. In particular, the approach and instrumentation used as the Naval Ocean Systems Center is presented. Most of the measurements are made with flooded illumination on the focal plane array. The array is treated as an ensemble of individual pixels, data being taken on each pixel and array averages and standard deviations computed for the entire array. Data maps are generated, showing the pixel data in the proper spatial position on the array and the array statistics

A dual-mode hemispherical sparse array for 3D passive acoustic mapping and skull localization within a clinical MRI guided focused ultrasound device

Science.gov (United States)

Crake, Calum; Brinker, Spencer T.; Coviello, Christian M.; Livingstone, Margaret S.; McDannold, Nathan J.

2018-03-01

Previous work has demonstrated that passive acoustic imaging may be used alongside MRI for monitoring of focused ultrasound therapy. However, past implementations have generally made use of either linear arrays originally designed for diagnostic imaging or custom narrowband arrays specific to in-house therapeutic transducer designs, neither of which is fully compatible with clinical MR-guided focused ultrasound (MRgFUS) devices. Here we have designed an array which is suitable for use within an FDA-approved MR-guided transcranial focused ultrasound device, within the bore of a 3 Tesla clinical MRI scanner. The array is constructed from 5  ×  0.4 mm piezoceramic disc elements arranged in pseudorandom fashion on a low-profile laser-cut acrylic frame designed to fit between the therapeutic elements of a 230 kHz InSightec ExAblate 4000 transducer. By exploiting thickness and radial resonance modes of the piezo discs the array is capable of both B-mode imaging at 5 MHz for skull localization, as well as passive reception at the second harmonic of the therapy array for detection of cavitation and 3D passive acoustic imaging. In active mode, the array was able to perform B-mode imaging of a human skull, showing the outer skull surface with good qualitative agreement with MR imaging. Extension to 3D showed the array was able to locate the skull within  ±2 mm/2° of reference points derived from MRI, which could potentially allow registration of a patient to the therapy system without the expense of real-time MRI. In passive mode, the array was able to resolve a point source in 3D within a  ±10 mm region about each axis from the focus, detect cavitation (SNR ~ 12 dB) at burst lengths from 10 cycles to continuous wave, and produce 3D acoustic maps in a flow phantom. Finally, the array was used to detect and map cavitation associated with microbubble activity in the brain in nonhuman primates.

Hazardous industrial gases identified using a novel polymer/MWNT composite resistance sensor array

International Nuclear Information System (INIS)

Yuana, C.L.; Chang, C.P.; Song, Y.

2011-01-01

Highlights: → In this work, a silicon wafer microelectrode substrate for a resistance sensor was fabricated using the semiconductor manufacturing process. → This work developed polymer-functionalized MWNT sensor plat forms for the detection of vapors from chemical agents at different temperatures. → Applied PCA to determine the performance of as-fabricated films for exposure to three chemical agents. - Abstract: Hazardous industrial chemical gases pose a significant threat to the environment and human life. Therefore, there is an urgent need to develop a reliable sensor for identifying these hazardous gases. In this work, a silicon wafer microelectrode substrate for a resistance sensor was fabricated using the semiconductor manufacturing process. Conductive carbon nanotubes were then mixed with six different polymers with different chemical adsorption properties to produce a composite thin film for the fabrication of a chemical sensor array. This array was then utilized to identify three hazardous gases at different temperatures. Experimental results for six polymers for chemical gases, such as tetrahydrofuran (THF), chloroform (CHCl 3 ) and methanol (MeOH) at different temperatures, indicate that the variation in sensitivity resistance increased when the sensing temperature increased. The poly(ethylene adipate)/MWNT sensing film had high sensitivity, excellent selectivity, and good reproducibility in detecting all chemical agent vapors. Additionally, this study utilized a bar chart and statistical methods in principal component analysis to identify gases with the polymer/MWNT sensor.

Variants for HDL-C, LDL-C, and triglycerides identified from admixture mapping and fine-mapping analysis in African American families.

Science.gov (United States)

Shetty, Priya B; Tang, Hua; Feng, Tao; Tayo, Bamidele; Morrison, Alanna C; Kardia, Sharon L R; Hanis, Craig L; Arnett, Donna K; Hunt, Steven C; Boerwinkle, Eric; Rao, Dabeeru C; Cooper, Richard S; Risch, Neil; Zhu, Xiaofeng

2015-02-01

Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African Americans. The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. The analysis was performed in 1905 unrelated African American subjects from the National Heart, Lung and Blood Institute's Family Blood Pressure Program (FBPP). Regions showing admixture evidence were followed-up with family-based association analysis in 3556 African American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age(2), sex, body mass index, and genome-wide mean ancestry to minimize the confounding caused by population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (low-density lipoprotein cholesterol), 8 (high-density lipoprotein cholesterol), 14 (triglycerides), and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52 939 single-nucleotide polymorphisms (SNPs) were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with high-density lipoprotein cholesterol (2 SNPs), low-density lipoprotein cholesterol (4 SNPs), and triglycerides (5 SNPs). The family data were used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions, including genes with known associations for cardiovascular disease. This study identified regions on chromosomes 7, 8, 14, and 19 and 11 SNPs from the fine-mapping analysis that were associated with high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides for further studies of cardiovascular disease in African Americans. © 2014 American Heart Association, Inc.

Variants for HDL-C, LDL-C and Triglycerides Identified from Admixture Mapping and Fine-Mapping Analysis in African-American Families

Science.gov (United States)

Shetty, Priya B.; Tang, Hua; Feng, Tao; Tayo, Bamidele; Morrison, Alanna C.; Kardia, Sharon L.R.; Hanis, Craig L.; Arnett, Donna K.; Hunt, Steven C.; Boerwinkle, Eric; Rao, D.C.; Cooper, R.S.; Risch, Neil; Zhu, Xiaofeng

2015-01-01

Background Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African-Americans. Methods and Results The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglycerides. The analysis was performed in 1,905 unrelated African-American subjects from the National Heart, Lung and Blood Institute’s Family Blood Pressure Program. Regions showing admixture evidence were followed-up with family-based association analysis in 3,556 African-American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age2, sex, body-mass-index, and genome-wide mean ancestry to minimize the confounding due to population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (LDL-C), 8 (HDL-C), 14 (triglycerides) and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52,939 SNPs were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with HDL-C (2 SNPs), LDL-C (4 SNPs) and triglycerides (5 SNPs). The family data was used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions including genes with known associations for cardiovascular disease. Conclusions This study identified regions on chromosomes 7, 8, 14 and 19 and 11 SNPs from the fine-mapping analysis that were associated with HDL-C, LDL-C and triglycerides for further studies of cardiovascular disease in African-Americans. PMID:25552592

Surface analysis and mechanical behaviour mapping of vertically aligned CNT forest array through nanoindentation

Energy Technology Data Exchange (ETDEWEB)

Koumoulos, Elias P.; Charitidis, C.A., E-mail: charitidis@chemeng.ntua.gr

2017-02-28

Highlights: • Structure and wall numbers are identified through TEM. • Static contact angle measurements revealed a super-hydrophobic behavior. • Hysteresis was observed (loading–unloading) due to the local stress distribution. • Hardness and modulus mapping for a grid of 70 μm{sup 2} is conducted. • Resistance is clearly divided in 2 regions (MWCNT and MWCNT – MWCNT) interface. - Abstract: Carbon nanotube (CNT) based architectures have increased the scientific interest owning to their exceptional performance rendering them promising candidates for advanced industrial applications in the nanotechnology field. Despite individual CNTs being considered as one of the most known strong materials, much less is known about other CNT forms, such as CNT arrays, in terms of their mechanical performance (integrity). In this work, thermal chemical vapor deposition (CVD) method is employed to produce vertically aligned multiwall (VA-MW) CNT carpets. Their structural properties were studied by means of scanning electron microscopy (SEM), X-Ray diffraction (XRD) and Raman spectroscopy, while their hydrophobic behavior was investigated via contact angle measurements. The resistance to indentation deformation of VA-MWCNT carpets was investigated through nanoindentation technique. The synthesized VA-MWCNTs carpets consisted of well-aligned MWCNTs. Static contact angle measurements were performed with water and glycerol, revealing a rather super-hydrophobic behavior. The structural analysis, hydrophobic behavior and indentation response of VA-MWCNTs carpets synthesized via CVD method are clearly demonstrated. Additionally, cycle indentation load-depth curve was applied and hysteresis loops were observed in the indenter loading–unloading cycle due to the local stress distribution. Hardness (as resistance to applied load) and modulus mapping, at 200 nm of displacement for a grid of 70 μm{sup 2} is presented. Through trajection, the resistance is clearly divided in 2

Whole-Genome Sequencing and iPLEX MassARRAY Genotyping Map an EMS-Induced Mutation Affecting Cell Competition in Drosophila melanogaster.

Science.gov (United States)

Lee, Chang-Hyun; Rimesso, Gerard; Reynolds, David M; Cai, Jinlu; Baker, Nicholas E

2016-10-13

Cell competition, the conditional loss of viable genotypes only when surrounded by other cells, is a phenomenon observed in certain genetic mosaic conditions. We conducted a chemical mutagenesis and screen to recover new mutations that affect cell competition between wild-type and RpS3 heterozygous cells. Mutations were identified by whole-genome sequencing, making use of software tools that greatly facilitate the distinction between newly induced mutations and other sources of apparent sequence polymorphism, thereby reducing false-positive and false-negative identification rates. In addition, we utilized iPLEX MassARRAY for genotyping recombinant chromosomes. These approaches permitted the mapping of a new mutation affecting cell competition when only a single allele existed, with a phenotype assessed only in genetic mosaics, without the benefit of complementation with existing mutations, deletions, or duplications. These techniques expand the utility of chemical mutagenesis and whole-genome sequencing for mutant identification. We discuss mutations in the Atm and Xrp1 genes identified in this screen. Copyright © 2016 Lee et al.

Identification and mapping of linear antibody epitopes in human serum albumin using high-density Peptide arrays.

Directory of Open Access Journals (Sweden)

Lajla Bruntse Hansen

Full Text Available We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2. Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA and from rabbit serum albumin (RSA were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.

Identification and mapping of linear antibody epitopes in human serum albumin using high-density Peptide arrays.

Science.gov (United States)

Hansen, Lajla Bruntse; Buus, Soren; Schafer-Nielsen, Claus

2013-01-01

We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2). Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA) as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids) at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA) and from rabbit serum albumin (RSA) were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.

Molecular diagnosis of known recessive ataxias by homozygosity mapping with SNP arrays.

Science.gov (United States)

H'mida-Ben Brahim, D; M'zahem, A; Assoum, M; Bouhlal, Y; Fattori, F; Anheim, M; Ali-Pacha, L; Ferrat, F; Chaouch, M; Lagier-Tourenne, C; Drouot, N; Thibaut, C; Benhassine, T; Sifi, Y; Stoppa-Lyonnet, D; N'Guyen, K; Poujet, J; Hamri, A; Hentati, F; Amouri, R; Santorelli, F M; Tazir, M; Koenig, M

2011-01-01

The diagnosis of rare inherited diseases is becoming more and more complex as an increasing number of clinical conditions appear to be genetically heterogeneous. Multigenic inheritance also applies to the autosomal recessive progressive cerebellar ataxias (ARCAs), for which 14 genes have been identified and more are expected to be discovered. We used homozygosity mapping as a guide for identification of the defective locus in patients with ARCA born from consanguineous parents. Patients from 97 families were analyzed with GeneChip Mapping 10K or 50K SNP Affymetrix microarrays. We identified six families homozygous for regions containing the autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) gene, two families homozygous for the ataxia-telangiectasia gene (ATM), two families homozygous for the ataxia with oculomotor apraxia type 1 (AOA1) gene, and one family homozygous for the AOA type 2 (AOA2) gene. Upon direct gene testing, we were able to identify a disease-related mutation in all families but one of the two kindred homozygous at the ATM locus. Although linkage analyses pointed to a single locus on chromosome 11q22.1-q23.1 for this family, clinical features, normal levels of serum alpha-foetoprotein as well as absence of mutations in the ATM gene rather suggest the existence of an additional ARCA-related gene in that interval. While the use of homozygosity mapping was very effective at pointing to the correct gene, it also suggests that the majority of patients harbor mutations either in the genes of the rare forms of ARCA or in genes yet to be identified.

Using Latent Semantic Analysis to Identify Research Trends in OpenStreetMap

Directory of Open Access Journals (Sweden)

Sukhjit Singh Sehra

2017-07-01

Full Text Available OpenStreetMap (OSM, based on collaborative mapping, has become a subject of great interest to the academic community, resulting in a considerable body of literature produced by many researchers. In this paper, we use Latent Semantic Analysis (LSA to help identify the emerging research trends in OSM. An extensive corpus of 485 academic abstracts of papers published during the period 2007–2016 was used. Five core research areas and fifty research trends were identified in this study. In addition, potential future research directions have been provided to aid geospatial information scientists, technologists and researchers in undertaking future OSM research.

Development and mapping of DArT markers within the Festuca - Lolium complex

Science.gov (United States)

Kopecký, David; Bartoš, Jan; Lukaszewski, Adam J; Baird, James H; Černoch, Vladimír; Kölliker, Roland; Rognli, Odd Arne; Blois, Helene; Caig, Vanessa; Lübberstedt, Thomas; Studer, Bruno; Shaw, Paul; Doležel, Jaroslav; Kilian, Andrzej

2009-01-01

Background Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT) array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum. Results The DArTFest array contains 7680 probes derived from methyl-filtered genomic representations. In a first marker discovery experiment performed on 40 genotypes from each species (with the exception of F. glaucescens for which only 7 genotypes were used), we identified 3884 polymorphic markers. The number of DArT markers identified in every single genotype varied from 821 to 1852. To test the usefulness of DArTFest array for physical mapping, DArT markers were assigned to each of the seven chromosomes of F. pratensis using single chromosome substitution lines while recombinants of F. pratensis chromosome 3 were used to allocate the markers to seven chromosome bins. Conclusion The resources developed in this project will facilitate the development of genetic maps in Festuca and Lolium, the analysis on genetic diversity, and the monitoring of the genomic constitution of the Festuca × Lolium hybrids. They will also enable marker-assisted selection for multiple traits or for specific genome regions. PMID:19832973

Magnetic field mapping of the UCNTau magneto-gravitational trap: design study

Energy Technology Data Exchange (ETDEWEB)

Libersky, Matthew Murray [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2014-09-04

The beta decay lifetime of the free neutron is an important input to the Standard Model of particle physics, but values measured using different methods have exhibited substantial disagreement. The UCN r experiment in development at Los Alamos National Laboratory (LANL) plans to explore better methods of measuring the neutron lifetime using ultracold neutrons (UCNs). In this experiment, UCNs are confined in a magneto-gravitational trap formed by a curved, asymmetric Halbach array placed inside a vacuum vessel and surrounded by holding field coils. If any defects present in the Halbach array are sufficient to reduce the local field near the surface below that needed to repel the desired energy level UCNs, loss by material interaction can occur at a rate similar to the loss by beta decay. A map of the magnetic field near the surface of the array is necessary to identify any such defects, but the array's curved geometry and placement in a vacuum vessel make conventional field mapping methods difficult. A system consisting of computer vision-based tracking and a rover holding a Hall probe has been designed to map the field near the surface of the array, and construction of an initial prototype has begun at LANL. The design of the system and initial results will be described here.

Integrated B1+ Mapping for Hyperpolarized 13C MRI in a Clinical Setup using Multi-Channel Receive Arrays

DEFF Research Database (Denmark)

Hansen, Rie Beck; Shin, Peter J.; Gordon, Jeremy W.

inhomogeneous transmit coils, and because kinetic modeling based on incorrect flip angles can lead to incorrect rate constant estimations. This study demonstrates the feasibility of integrated B1+ mapping for large volume thermal and hyperpolarized phantoms in a clinical setup using a clamshell transmit coil...... and a 16-channel receive array, and a 3D stack-of-spirals sequence. Phase-sensitive coil-combination was achieved using ESPIRiT....

Sao Paulo Lightning Mapping Array (SP-LMA): Deployment and Plans

Science.gov (United States)

Bailey, J. C.; Carey, L. D.; Blakeslee, R. J.; Albrecht, R.; Morales, C. A.; Pinto, O., Jr.

2011-01-01

An 8-10 station Lightning Mapping Array (LMA) network is being deployed in the vicinity of Sao Paulo to create the SP-LMA for total lightning measurements in association with the international CHUVA [Cloud processes of tHe main precipitation systems in Brazil: A contribUtion to cloud resolVing modeling and to the GPM (GlobAl Precipitation Measurement)] field campaign. Besides supporting CHUVA science/mission objectives and the Sao Luz Paraitinga intensive operation period (IOP) in December 2011-January 2012, the SP-LMA will support the generation of unique proxy data for the Geostationary Lightning Mapper (GLM) and Advanced Baseline Imager (ABI), both sensors on the NOAA Geostationary Operational Environmental Satellite-R (GOES-R), presently under development and scheduled for a 2015 launch. The proxy data will be used to develop and validate operational algorithms so that they will be ready for use on "day1" following the launch of GOES-R. A preliminary survey of potential sites in the vicinity of Sao Paulo was conducted in December 2009 and January 2010, followed up by a detailed survey in July 2010, with initial network deployment scheduled for October 2010. However, due to a delay in the Sa Luz Paraitinga IOP, the SP-LMA will now be installed in July 2011 and operated for one year. Spacing between stations is on the order of 15-30 km, with the network "diameter" being on the order of 30-40 km, which provides good 3-D lightning mapping 150 km from the network center. Optionally, 1-3 additional stations may be deployed in the vicinity of Sa Jos dos Campos.

Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits

DEFF Research Database (Denmark)

Chami, Nathalie; Chen, Ming-Huei; Slater, Andrew J

2016-01-01

array. After conditional analyses and replication in 27,480 independent individuals, we identified 16 new RBC variants. We found low-frequency missense variants in MAP1A (rs55707100, minor allele frequency [MAF] = 3.3%, p = 2 × 10(-10) for hemoglobin [HGB]) and HNF4A (rs1800961, MAF = 2.4%, p

The OncoArray Consortium: a Network for Understanding the Genetic Architecture of Common Cancers

Science.gov (United States)

Amos, Christopher I.; Dennis, Joe; Wang, Zhaoming; Byun, Jinyoung; Schumacher, Fredrick R.; Gayther, Simon A.; Casey, Graham; Hunter, David J.; Sellers, Thomas A.; Gruber, Stephen B.; Dunning, Alison M.; Michailidou, Kyriaki; Fachal, Laura; Doheny, Kimberly; Spurdle, Amanda B.; Li, Yafang; Xiao, Xiangjun; Romm, Jane; Pugh, Elizabeth; Coetzee, Gerhard A.; Hazelett, Dennis J.; Bojesen, Stig E.; Caga-Anan, Charlisse; Haiman, Christopher A.; Kamal, Ahsan; Luccarini, Craig; Tessier, Daniel; Vincent, Daniel; Bacot, François; Van Den Berg, David J.; Nelson, Stefanie; Demetriades, Stephen; Goldgar, David E.; Couch, Fergus J.; Forman, Judith L.; Giles, Graham G.; Conti, David V.; Bickeböller, Heike; Risch, Angela; Waldenberger, Melanie; Brüske, Irene; Hicks, Belynda D.; Ling, Hua; McGuffog, Lesley; Lee, Andrew; Kuchenbaecker, Karoline B.; Soucy, Penny; Manz, Judith; Cunningham, Julie M.; Butterbach, Katja; Kote-Jarai, Zsofia; Kraft, Peter; FitzGerald, Liesel M.; Lindström, Sara; Adams, Marcia; McKay, James D.; Phelan, Catherine M.; Benlloch, Sara; Kelemen, Linda E.; Brennan, Paul; Riggan, Marjorie; O’Mara, Tracy A.; Shen, Hongbin; Shi, Yongyong; Thompson, Deborah J.; Goodman, Marc T.; Nielsen, Sune F.; Berchuck, Andrew; Laboissiere, Sylvie; Schmit, Stephanie L.; Shelford, Tameka; Edlund, Christopher K.; Taylor, Jack A.; Field, John K.; Park, Sue K.; Offit, Kenneth; Thomassen, Mads; Schmutzler, Rita; Ottini, Laura; Hung, Rayjean J.; Marchini, Jonathan; Al Olama, Ali Amin; Peters, Ulrike; Eeles, Rosalind A.; Seldin, Michael F.; Gillanders, Elizabeth; Seminara, Daniela; Antoniou, Antonis C.; Pharoah, Paul D.; Chenevix-Trench, Georgia; Chanock, Stephen J.; Simard, Jacques; Easton, Douglas F.

2016-01-01

Background Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers and cancer related traits. Methods The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background. Results The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis. Conclusions Results from these analyses will enable researchers to identify new susceptibility loci, perform fine mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental and lifestyle related exposures. Impact Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. PMID:27697780

Genetic mapping and exome sequencing identify variants associated with five novel diseases.

Directory of Open Access Journals (Sweden)

Erik G Puffenberger

Full Text Available The Clinic for Special Children (CSC has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain children. Among the Plain people, we have used single nucleotide polymorphism (SNP microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb that contain many genes (mean = 79. For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data.

The North Alabama Lightning Mapping Array (LMA): A Network Overview

Science.gov (United States)

Blakeslee, R. J.; Bailey, J.; Buechler, D.; Goodman, S. J.; McCaul, E. W., Jr.; Hall, J.

2005-01-01

The North Alabama Lightning Mapping Array (LMA) is s a 3-D VHF regional lightning detection system that provides on-orbit algorithm validation and instrument performance assessments for the NASA Lightning Imaging Sensor, as well as information on storm kinematics and updraft evolution that offers the potential to improve severe storm warning lead time by up t o 50% and decrease te false alarm r a t e ( for non-tornado producing storms). In support of this latter function, the LMA serves as a principal component of a severe weather test bed to infuse new science and technology into the short-term forecasting of severe and hazardous weather, principally within nearby National Weather Service forecast offices. The LMA, which became operational i n November 2001, consists of VHF receivers deployed across northern Alabama and a base station located at the National Space Science and Technology Center (NSSTC), which is on t h e campus of the University of Alabama in Huntsville. The LMA system locates the sources of impulsive VHF radio signals s from lightning by accurately measuring the time that the signals aririve at the different receiving stations. Each station's records the magnitude and time of the peak lightning radiation signal in successive 80 ms intervals within a local unused television channel (channel 5, 76-82 MHz in our case ) . Typically hundreds of sources per flash can be reconstructed, which i n t u r n produces accurate 3-dimensional lightning image maps (nominally network topology and the links have an effective data throughput rate ranging from 600 kbits s -1 t o 1.5 %its s -1. This presentation provides an overview of t h e North Alabama network, the data processing (both real-time and post processing) and network statistics.

Development and mapping of DArT markers within the Festuca - Lolium complex

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Studer Bruno

2009-10-01

Full Text Available Abstract Background Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum. Results The DArTFest array contains 7680 probes derived from methyl-filtered genomic representations. In a first marker discovery experiment performed on 40 genotypes from each species (with the exception of F. glaucescens for which only 7 genotypes were used, we identified 3884 polymorphic markers. The number of DArT markers identified in every single genotype varied from 821 to 1852. To test the usefulness of DArTFest array for physical mapping, DArT markers were assigned to each of the seven chromosomes of F. pratensis using single chromosome substitution lines while recombinants of F. pratensis chromosome 3 were used to allocate the markers to seven chromosome bins. Conclusion The resources developed in this project will facilitate the development of genetic maps in Festuca and Lolium, the analysis on genetic diversity, and the monitoring of the genomic constitution of the Festuca × Lolium hybrids. They will also enable marker-assisted selection for multiple traits or for specific genome regions.

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

Science.gov (United States)

Beecham, Ashley H; Patsopoulos, Nikolaos A; Xifara, Dionysia K; Davis, Mary F; Kemppinen, Anu; Cotsapas, Chris; Shahi, Tejas S; Spencer, Chris; Booth, David; Goris, An; Oturai, Annette; Saarela, Janna; Fontaine, Bertrand; Hemmer, Bernhard; Martin, Claes; Zipp, Frauke; D’alfonso, Sandra; Martinelli-Boneschi, Filippo; Taylor, Bruce; Harbo, Hanne F; Kockum, Ingrid; Hillert, Jan; Olsson, Tomas; Ban, Maria; Oksenberg, Jorge R; Hintzen, Rogier; Barcellos, Lisa F; Agliardi, Cristina; Alfredsson, Lars; Alizadeh, Mehdi; Anderson, Carl; Andrews, Robert; Søndergaard, Helle Bach; Baker, Amie; Band, Gavin; Baranzini, Sergio E; Barizzone, Nadia; Barrett, Jeffrey; Bellenguez, Céline; Bergamaschi, Laura; Bernardinelli, Luisa; Berthele, Achim; Biberacher, Viola; Binder, Thomas M C; Blackburn, Hannah; Bomfim, Izaura L; Brambilla, Paola; Broadley, Simon; Brochet, Bruno; Brundin, Lou; Buck, Dorothea; Butzkueven, Helmut; Caillier, Stacy J; Camu, William; Carpentier, Wassila; Cavalla, Paola; Celius, Elisabeth G; Coman, Irène; Comi, Giancarlo; Corrado, Lucia; Cosemans, Leentje; Cournu-Rebeix, Isabelle; Cree, Bruce A C; Cusi, Daniele; Damotte, Vincent; Defer, Gilles; Delgado, Silvia R; Deloukas, Panos; di Sapio, Alessia; Dilthey, Alexander T; Donnelly, Peter; Dubois, Bénédicte; Duddy, Martin; Edkins, Sarah; Elovaara, Irina; Esposito, Federica; Evangelou, Nikos; Fiddes, Barnaby; Field, Judith; Franke, Andre; Freeman, Colin; Frohlich, Irene Y; Galimberti, Daniela; Gieger, Christian; Gourraud, Pierre-Antoine; Graetz, Christiane; Graham, Andrew; Grummel, Verena; Guaschino, Clara; Hadjixenofontos, Athena; Hakonarson, Hakon; Halfpenny, Christopher; Hall, Gillian; Hall, Per; Hamsten, Anders; Harley, James; Harrower, Timothy; Hawkins, Clive; Hellenthal, Garrett; Hillier, Charles; Hobart, Jeremy; Hoshi, Muni; Hunt, Sarah E; Jagodic, Maja; Jelčić, Ilijas; Jochim, Angela; Kendall, Brian; Kermode, Allan; Kilpatrick, Trevor; Koivisto, Keijo; Konidari, Ioanna; Korn, Thomas; Kronsbein, Helena; Langford, Cordelia; Larsson, Malin; Lathrop, Mark; Lebrun-Frenay, Christine; Lechner-Scott, Jeannette; Lee, Michelle H; Leone, Maurizio A; Leppä, Virpi; Liberatore, Giuseppe; Lie, Benedicte A; Lill, Christina M; Lindén, Magdalena; Link, Jenny; Luessi, Felix; Lycke, Jan; Macciardi, Fabio; Männistö, Satu; Manrique, Clara P; Martin, Roland; Martinelli, Vittorio; Mason, Deborah; Mazibrada, Gordon; McCabe, Cristin; Mero, Inger-Lise; Mescheriakova, Julia; Moutsianas, Loukas; Myhr, Kjell-Morten; Nagels, Guy; Nicholas, Richard; Nilsson, Petra; Piehl, Fredrik; Pirinen, Matti; Price, Siân E; Quach, Hong; Reunanen, Mauri; Robberecht, Wim; Robertson, Neil P; Rodegher, Mariaemma; Rog, David; Salvetti, Marco; Schnetz-Boutaud, Nathalie C; Sellebjerg, Finn; Selter, Rebecca C; Schaefer, Catherine; Shaunak, Sandip; Shen, Ling; Shields, Simon; Siffrin, Volker; Slee, Mark; Sorensen, Per Soelberg; Sorosina, Melissa; Sospedra, Mireia; Spurkland, Anne; Strange, Amy; Sundqvist, Emilie; Thijs, Vincent; Thorpe, John; Ticca, Anna; Tienari, Pentti; van Duijn, Cornelia; Visser, Elizabeth M; Vucic, Steve; Westerlind, Helga; Wiley, James S; Wilkins, Alastair; Wilson, James F; Winkelmann, Juliane; Zajicek, John; Zindler, Eva; Haines, Jonathan L; Pericak-Vance, Margaret A; Ivinson, Adrian J; Stewart, Graeme; Hafler, David; Hauser, Stephen L; Compston, Alastair; McVean, Gil; De Jager, Philip; Sawcer, Stephen; McCauley, Jacob L

2013-01-01

Using the ImmunoChip custom genotyping array, we analysed 14,498 multiple sclerosis subjects and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (p-value multiple sclerosis subjects and 26,703 healthy controls. In these 80,094 individuals of European ancestry we identified 48 new susceptibility variants (p-value multiple sclerosis risk variants in 103 discrete loci outside of the Major Histocompatibility Complex. With high resolution Bayesian fine-mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalogue of multiple sclerosis risk variants and illustrates the value of fine-mapping in the resolution of GWAS signals. PMID:24076602

Sensor array signal processing

CERN Document Server

Naidu, Prabhakar S

2009-01-01

Chapter One: An Overview of Wavefields 1.1 Types of Wavefields and the Governing Equations 1.2 Wavefield in open space 1.3 Wavefield in bounded space 1.4 Stochastic wavefield 1.5 Multipath propagation 1.6 Propagation through random medium 1.7 ExercisesChapter Two: Sensor Array Systems 2.1 Uniform linear array (ULA) 2.2 Planar array 2.3 Distributed sensor array 2.4 Broadband sensor array 2.5 Source and sensor arrays 2.6 Multi-component sensor array2.7 ExercisesChapter Three: Frequency Wavenumber Processing 3.1 Digital filters in the w-k domain 3.2 Mapping of 1D into 2D filters 3.3 Multichannel Wiener filters 3.4 Wiener filters for ULA and UCA 3.5 Predictive noise cancellation 3.6 Exercises Chapter Four: Source Localization: Frequency Wavenumber Spectrum4.1 Frequency wavenumber spectrum 4.2 Beamformation 4.3 Capon's w-k spectrum 4.4 Maximum entropy w-k spectrum 4.5 Doppler-Azimuth Processing4.6 ExercisesChapter Five: Source Localization: Subspace Methods 5.1 Subspace methods (Narrowband) 5.2 Subspace methods (B...

Detection and Mapping of the September 2017 Mexico Earthquakes Using DAS Fiber-Optic Infrastructure Arrays

Science.gov (United States)

Karrenbach, M. H.; Cole, S.; Williams, J. J.; Biondi, B. C.; McMurtry, T.; Martin, E. R.; Yuan, S.

2017-12-01

Fiber-optic distributed acoustic sensing (DAS) uses conventional telecom fibers for a wide variety of monitoring purposes. Fiber-optic arrays can be located along pipelines for leak detection; along borders and perimeters to detect and locate intruders, or along railways and roadways to monitor traffic and identify and manage incidents. DAS can also be used to monitor oil and gas reservoirs and to detect earthquakes. Because thousands of such arrays are deployed worldwide and acquiring data continuously, they can be a valuable source of data for earthquake detection and location, and could potentially provide important information to earthquake early-warning systems. In this presentation, we show that DAS arrays in Mexico and the United States detected the M8.1 and M7.2 Mexico earthquakes in September 2017. At Stanford University, we have deployed a 2.4 km fiber-optic DAS array in a figure-eight pattern, with 600 channels spaced 4 meters apart. Data have been recorded continuously since September 2016. Over 800 earthquakes from across California have been detected and catalogued. Distant teleseismic events have also been recorded, including the two Mexican earthquakes. In Mexico, fiber-optic arrays attached to pipelines also detected these two events. Because of the length of these arrays and their proximity to the event locations, we can not only detect the earthquakes but also make location estimates, potentially in near real time. In this presentation, we review the data recorded for these two events recorded at Stanford and in Mexico. We compare the waveforms recorded by the DAS arrays to those recorded by traditional earthquake sensor networks. Using the wide coverage provided by the pipeline arrays, we estimate the event locations. Such fiber-optic DAS networks can potentially play a role in earthquake early-warning systems, allowing actions to be taken to minimize the impact of an earthquake on critical infrastructure components. While many such fiber

Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Directory of Open Access Journals (Sweden)

Rasley Amy

2006-06-01

Full Text Available Abstract Background There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. Results Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1 comparative analysis of signal versus control and (2 clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. Conclusion We have developed Array2BIO – a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

Design and Fabrication of an Experimental Microheater Array Powder Sintering Printer

Science.gov (United States)

Holt, Nicholas; Zhou, Wenchao

2018-03-01

Microheater array powder sintering (MAPS) is a novel additive manufacturing process that uses an array of microheaters to selectively sinter powder particles. MAPS shows great promise as a new method of printing flexible electronics by enabling digital curing of conductive inks on a variety of substrates. For MAPS to work effectively, a microscale air gap needs to be maintained between the heater array and the conductive ink. In this article, we present an experimental MAPS printer with air gap control for printing conductive circuits. First, we discuss design aspects necessary to implement MAPS. An analysis is performed to validate that the design can maintain the desired air gap between the microheaters and the sintering layer, which consists of a silver nanoparticle ink. The printer is tested by printing conductive lines on a flexible plastic substrate with silver nanoparticle ink. Results show MAPS performs on par with or better than the existing fabrication methods for printed electronics in terms of both the print quality (conductivity of the printed line) and print speed, which shows MAPS' great promise as a competitive new method for digital production of printed electronics.

Direction-of-Arrival Estimation for Coprime Array Using Compressive Sensing Based Array Interpolation

Directory of Open Access Journals (Sweden)

Aihua Liu

2017-01-01

Full Text Available A method of direction-of-arrival (DOA estimation using array interpolation is proposed in this paper to increase the number of resolvable sources and improve the DOA estimation performance for coprime array configuration with holes in its virtual array. The virtual symmetric nonuniform linear array (VSNLA of coprime array signal model is introduced, with the conventional MUSIC with spatial smoothing algorithm (SS-MUSIC applied on the continuous lags in the VSNLA; the degrees of freedom (DoFs for DOA estimation are obviously not fully exploited. To effectively utilize the extent of DoFs offered by the coarray configuration, a compressing sensing based array interpolation algorithm is proposed. The compressing sensing technique is used to obtain the coarse initial DOA estimation, and a modified iterative initial DOA estimation based interpolation algorithm (IMCA-AI is then utilized to obtain the final DOA estimation, which maps the sample covariance matrix of the VSNLA to the covariance matrix of a filled virtual symmetric uniform linear array (VSULA with the same aperture size. The proposed DOA estimation method can efficiently improve the DOA estimation performance. The numerical simulations are provided to demonstrate the effectiveness of the proposed method.

CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

Science.gov (United States)

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

2007-10-06

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

Directory of Open Access Journals (Sweden)

Joyce Xiuweu-Xu Gu

2007-01-01

Full Text Available With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator that matches the BAC clones from array-based comparative genomic hybridization (aCGH to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specifi c BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

SU-E-T-375: Evaluation of a MapCHECK2(tm) Planar 2-D Diode Array for High-Dose-Rate Brachytherapy Treatment Delivery Verifications

Energy Technology Data Exchange (ETDEWEB)

Macey, N; Siebert, M; Shvydka, D; Parsai, E [University of Toledo Medical Center, Toledo, OH (United States)

2015-06-15

Purpose: Despite improvements of HDR brachytherapy delivery systems, verification of source position is still typically based on the length of the wire reeled out relative to the parked position. Yet, the majority of errors leading to medical events in HDR treatments continue to be classified as missed targets or wrong treatment sites. We investigate the feasibility of using dose maps acquired with a two-dimensional diode array to independently verify the source locations, dwell times, and dose during an HDR treatment. Methods: Custom correction factors were integrated into frame-by-frame raw counts recorded for a Varian VariSource™ HDR afterloader Ir-192 source located at various distances in air and in solid water from a MapCHECK2™ diode array. The resultant corrected counts were analyzed to determine the dwell position locations and doses delivered. The local maxima of polynomial equations fitted to the extracted dwell dose profiles provided the X and Y coordinates while the distance to the source was determined from evaluation of the full width at half maximum (FWHM). To verify the approach, the experiment was repeated as the source was moved through dwell positions at various distances along an inclined plane, mimicking a vaginal cylinder treatment. Results: Dose map analysis was utilized to provide the coordinates of the source and dose delivered over each dwell position. The accuracy in determining source dwell positions was found to be +/−1.0 mm of the preset values, and doses within +/−3% of those calculated by the BrachyVision™ treatment planning system for all measured distances. Conclusion: Frame-by-frame data furnished by a 2 -D diode array can be used to verify the dwell positions and doses delivered by the HDR source over the course of treatment. Our studies have verified that measurements provided by the MapCHECK2™ can be used as a routine QA tool for HDR treatment delivery verification.

Use of a Microphone Phased Array to Determine Noise Sources in a Rocket Plume

Science.gov (United States)

Panda, J.; Mosher, R.

2010-01-01

A 70-element microphone phased array was used to identify noise sources in the plume of a solid rocket motor. An environment chamber was built and other precautions were taken to protect the sensitive condenser microphones from rain, thunderstorms and other environmental elements during prolonged stay in the outdoor test stand. A camera mounted at the center of the array was used to photograph the plume. In the first phase of the study the array was placed in an anechoic chamber for calibration, and validation of the indigenous Matlab(R) based beamform software. It was found that the "advanced" beamform methods, such as CLEAN-SC was partially successful in identifying speaker sources placed closer than the Rayleigh criteria. To participate in the field test all equipments were shipped to NASA Marshal Space Flight Center, where the elements of the array hardware were rebuilt around the test stand. The sensitive amplifiers and the data acquisition hardware were placed in a safe basement, and 100m long cables were used to connect the microphones, Kulites and the camera. The array chamber and the microphones were found to withstand the environmental elements as well as the shaking from the rocket plume generated noise. The beamform map was superimposed on a photo of the rocket plume to readily identify the source distribution. It was found that the plume made an exceptionally long, >30 diameter, noise source over a large frequency range. The shock pattern created spatial modulation of the noise source. Interestingly, the concrete pad of the horizontal test stand was found to be a good acoustic reflector: the beamform map showed two distinct source distributions- the plume and its reflection on the pad. The array was found to be most effective in the frequency range of 2kHz to 10kHz. As expected, the classical beamform method excessively smeared the noise sources at lower frequencies and produced excessive side-lobes at higher frequencies. The "advanced" beamform

The Owens Valley Millimeter Array

International Nuclear Information System (INIS)

Padin, S.; Scott, S.L.; Woody, D.P.; Scoville, N.Z.; Seling, T.V.

1991-01-01

The telescopes and signal processing systems of the Owens Valley Millimeter Array are considered, and improvements in the sensitivity and stability of the instrument are characterized. The instrument can be applied to map sources in the 85 to 115 GHz and 218 to 265 GHz bands with a resolution of about 1 arcsec in the higher frequency band. The operation of the array is fully automated. The current scientific programs for the array encompass high-resolution imaging of protoplanetary/protostellar disk structures, observations of molecular cloud complexes associated with spiral structure in nearby galaxies, and observations of molecular structures in the nuclei of spiral and luminous IRAS galaxies. 9 refs

Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean

Directory of Open Access Journals (Sweden)

Sujan Mamidi

2016-07-01

Full Text Available White mold, caused by the necrotrophic fungus (Lib. de Bary, is a major disease of common bean ( L.. WM7.1 and WM8.3 are two quantitative trait loci (QTL with major effects on tolerance to the pathogen. Advanced backcross populations segregating individually for either of the two QTL, and a recombinant inbred (RI population segregating for both QTL were used to fine map and confirm the genetic location of the QTL. The QTL intervals were physically mapped using the reference common bean genome sequence, and the physical intervals for each QTL were further confirmed by sequence-based introgression mapping. Using whole-genome sequence data from susceptible and tolerant DNA pools, introgressed regions were identified as those with significantly higher numbers of single-nucleotide polymorphisms (SNPs relative to the whole genome. By combining the QTL and SNP data, WM7.1 was located to a 660-kb region that contained 41 gene models on the proximal end of chromosome Pv07, while the WM8.3 introgression was narrowed to a 1.36-Mb region containing 70 gene models. The most polymorphic candidate gene in the WM7.1 region encodes a BEACH-domain protein associated with apoptosis. Within the WM8.3 interval, a receptor-like protein with the potential to recognize pathogen effectors was the most polymorphic gene. The use of gene and sequence-based mapping identified two candidate genes whose putative functions are consistent with the current model of pathogenicity.

BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

International Nuclear Information System (INIS)

Samuelson, Emma; Karlsson, Sara; Partheen, Karolina; Nilsson, Staffan; Szpirer, Claude; Behboudi, Afrouz

2012-01-01

Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene) in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding) and Comparative Genome Hybridization (CGH) analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome) CGH-array platform. Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO) band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve genes with a critical role in mammary tumor development. Genetic

Comparison of Computational and Experimental Microphone Array Results for an 18%-Scale Aircraft Model

Science.gov (United States)

Lockard, David P.; Humphreys, William M.; Khorrami, Mehdi R.; Fares, Ehab; Casalino, Damiano; Ravetta, Patricio A.

2015-01-01

An 18%-scale, semi-span model is used as a platform for examining the efficacy of microphone array processing using synthetic data from numerical simulations. Two hybrid RANS/LES codes coupled with Ffowcs Williams-Hawkings solvers are used to calculate 97 microphone signals at the locations of an array employed in the NASA LaRC 14x22 tunnel. Conventional, DAMAS, and CLEAN-SC array processing is applied in an identical fashion to the experimental and computational results for three different configurations involving deploying and retracting the main landing gear and a part span flap. Despite the short time records of the numerical signals, the beamform maps are able to isolate the noise sources, and the appearance of the DAMAS synthetic array maps is generally better than those from the experimental data. The experimental CLEAN-SC maps are similar in quality to those from the simulations indicating that CLEAN-SC may have less sensitivity to background noise. The spectrum obtained from DAMAS processing of synthetic array data is nearly identical to the spectrum of the center microphone of the array, indicating that for this problem array processing of synthetic data does not improve spectral comparisons with experiment. However, the beamform maps do provide an additional means of comparison that can reveal differences that cannot be ascertained from spectra alone.

Antibody repertoire profiling with mimotope arrays

OpenAIRE

Pashova, Shina; Schneider, Christoph; von Gunten, Stephan; Pashov, Anastas

2016-01-01

Large-scale profiling and monitoring of antibody repertoires is possible through next generation sequencing (NGS), phage display libraries and microarrays. These methods can be combined in a pipeline, which ultimately maps the antibody reactivities onto defined arrays of structures - peptides or carbohydrates. The arrays can help analyze the individual specificities or can be used as complex patterns. In any case, the targets recognized should formally be considered mimotopes unless they are ...

Jammed-array wideband sawtooth filter.

Science.gov (United States)

Tan, Zhongwei; Wang, Chao; Goda, Keisuke; Malik, Omer; Jalali, Bahram

2011-11-21

We present an all-optical passive low-cost spectral filter that exhibits a high-resolution periodic sawtooth spectral pattern without the need for active optoelectronic components. The principle of the filter is the partial masking of a phased array of virtual light sources with multiply jammed diffraction orders. We utilize the filter's periodic linear map between frequency and intensity to demonstrate fast sensitive interrogation of fiber Bragg grating sensor arrays and ultrahigh-frequency electrical sawtooth waveform generation. © 2011 Optical Society of America

Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes.

Science.gov (United States)

Xu, Xuewen; Yu, Ting; Xu, Ruixue; Shi, Yang; Lin, Xiaojian; Xu, Qiang; Qi, Xiaohua; Weng, Yiqun; Chen, Xuehao

2016-03-01

A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

Performance of a PET detector module utilizing an array of silicon photodiodes to identify the crystal of interaction

International Nuclear Information System (INIS)

Moses, W.W.; Derenzo, S.E.; Nutt, R.; Digby, W.M.; Williams, C.W.; Andreaco, M.

1993-01-01

The authors initial performance results for a new multi-layer PET detector module consisting of an array of 3 mm square by 30 mm deep BGO crystals coupled on one end to a single photomultiplier tube and on the opposite end to an array of 3 mm square silicon photodiodes. The photomultiplier tube provides an accurate timing pulse and energy discrimination for all the crystals in the module, while the silicon photodiodes identify the crystal of interaction. When a single BGO crystal at +25 C is excited with 511 keV photons, the authors measure a photodiode signal centered at 700 electrons (e - ) with noise of 375 e - fwhm. When a four crystal/photodiode module is excited with a collimated line source of 511 keV photons, the crystal of interaction is correctly identified 82% of the time. The misidentification rate can be greatly reduced and an 8 x 8 crystal/photodiode module constructed by using thicker depletion layer photodiodes or cooling to 0 C

Fabrication of large NbSi bolometer arrays for CMB applications

International Nuclear Information System (INIS)

Ukibe, M.; Belier, B.; Camus, Ph.; Dobrea, C.; Dumoulin, L.; Fernandez, B.; Fournier, T.; Guillaudin, O.; Marnieros, S.; Yates, S.J.C.

2006-01-01

Future cosmic microwave background experiments for high-resolution anisotropy mapping and polarisation detection require large arrays of bolometers at low temperature. We have developed a process to build arrays of antenna-coupled bolometers for that purpose. With adjustment of the Nb x Si 1-x alloy composition, the array can be made of high impedance or superconductive (TES) sensors

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

Science.gov (United States)

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

2010-12-01

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

An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

Science.gov (United States)

2014-01-01

Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. Conclusions The integrated map described herein enhances the utility of genomic tools over

An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus).

Science.gov (United States)

Ren, Yi; McGregor, Cecilia; Zhang, Yan; Gong, Guoyi; Zhang, Haiying; Guo, Shaogui; Sun, Honghe; Cai, Wantao; Zhang, Jie; Xu, Yong

2014-01-20

Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A

Limited Diffraction Maps for Pulsed Wave Annular Arrays

DEFF Research Database (Denmark)

Fox, Paul D.

2002-01-01

A procedure is provided for decomposing the linear field of flat pulsed wave annular arrays into an equivalent set of known limited diffraction Bessel beams. Each Bessel beam propagates with known characteristics, enabling good insight into the propagation of annular fields to be obtained...

Lunar UV-visible-IR mapping interferometric spectrometer

Science.gov (United States)

Smith, W. Hayden; Haskin, L.; Korotev, R.; Arvidson, R.; Mckinnon, W.; Hapke, B.; Larson, S.; Lucey, P.

1992-01-01

Ultraviolet-visible-infrared mapping digital array scanned interferometers for lunar compositional surveys was developed. The research has defined a no-moving-parts, low-weight and low-power, high-throughput, and electronically adaptable digital array scanned interferometer that achieves measurement objectives encompassing and improving upon all the requirements defined by the LEXSWIG for lunar mineralogical investigation. In addition, LUMIS provides a new, important, ultraviolet spectral mapping, high-spatial-resolution line scan camera, and multispectral camera capabilities. An instrument configuration optimized for spectral mapping and imaging of the lunar surface and provide spectral results in support of the instrument design are described.

Overlapping structures in sensory-motor mappings.

Directory of Open Access Journals (Sweden)

Kevin Earland

Full Text Available This paper examines a biologically-inspired representation technique designed for the support of sensory-motor learning in developmental robotics. An interesting feature of the many topographic neural sheets in the brain is that closely packed receptive fields must overlap in order to fully cover a spatial region. This raises interesting scientific questions with engineering implications: e.g. is overlap detrimental? does it have any benefits? This paper examines the effects and properties of overlap between elements arranged in arrays or maps. In particular we investigate how overlap affects the representation and transmission of spatial location information on and between topographic maps. Through a series of experiments we determine the conditions under which overlap offers advantages and identify useful ranges of overlap for building mappings in cognitive robotic systems. Our motivation is to understand the phenomena of overlap in order to provide guidance for application in sensory-motor learning robots.

Fabrication of large NbSi bolometer arrays for CMB applications

Energy Technology Data Exchange (ETDEWEB)

Ukibe, M. [AIST, Tsukuba Central 2, Tsukuba, Ibaraki 305-8568 (Japan); CNRS-CSNSM, Bat 104, Orsay Campus F-91405 (France); Belier, B. [CNRS-IEF, Bat 220, Orsay Campus F-91405 (France); Camus, Ph. [CNRS-CRTBT, 25 avenue des Martyrs, Grenoble F-38042 (France)]. E-mail: philippe.camus@grenoble.cnrs.fr; Dobrea, C. [CNRS-CSNSM, Bat 104, Orsay Campus F-91405 (France); Dumoulin, L. [CNRS-CSNSM, Bat 104, Orsay Campus F-91405 (France); Fernandez, B. [CNRS-CRTBT, 25 avenue des Martyrs, Grenoble F-38042 (France); Fournier, T. [CNRS-CRTBT, 25 avenue des Martyrs, Grenoble F-38042 (France); Guillaudin, O. [CNRS-LPSC, 53 avenue des Martyrs, Grenoble F-38042 (France); Marnieros, S. [CNRS-CSNSM, Bat 104, Orsay Campus F-91405 (France); Yates, S.J.C. [CNRS-CSNSM, Bat 104, Orsay Campus F-91405 (France)

2006-04-15

Future cosmic microwave background experiments for high-resolution anisotropy mapping and polarisation detection require large arrays of bolometers at low temperature. We have developed a process to build arrays of antenna-coupled bolometers for that purpose. With adjustment of the Nb{sub x}Si{sub 1-x} alloy composition, the array can be made of high impedance or superconductive (TES) sensors.

A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd (Momordica charantia)

Science.gov (United States)

Cui, Junjie; Luo, Shaobo; Niu, Yu; Huang, Rukui; Wen, Qingfang; Su, Jianwen; Miao, Nansheng; He, Weiming; Dong, Zhensheng; Cheng, Jiaowen; Hu, Kailin

2018-01-01

Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd (Momordica charantia) is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD)-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line ‘K44’ and the monoecious line ‘Dali-11.’ This map comprised 1,009 SNP markers and spanned a total genetic distance of 2,203.95 cM across the 11 linkage groups. It anchored a total of 113 assembled scaffolds that covered about 251.32 Mb (85.48%) of the 294.01 Mb assembled genome. In addition, three horticulturally important traits including sex expression, fruit epidermal structure, and immature fruit color were evaluated using a combination of qualitative and quantitative data. As a result, we identified three QTL/gene loci responsible for these traits in three environments. The QTL/gene gy/fffn/ffn, controlling sex expression involved in gynoecy, first female flower node, and female flower number was detected in the reported region. Particularly, two QTLs/genes, Fwa/Wr and w, were found to be responsible for fruit epidermal structure and white immature fruit color, respectively. This RAD-based genetic map promotes the assembly of the bitter gourd genome and the identified genetic loci will accelerate the cloning of relevant genes in the future. PMID:29706980

A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd (Momordica charantia

Directory of Open Access Journals (Sweden)

Junjie Cui

2018-04-01

Full Text Available Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd (Momordica charantia is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line ‘K44’ and the monoecious line ‘Dali-11.’ This map comprised 1,009 SNP markers and spanned a total genetic distance of 2,203.95 cM across the 11 linkage groups. It anchored a total of 113 assembled scaffolds that covered about 251.32 Mb (85.48% of the 294.01 Mb assembled genome. In addition, three horticulturally important traits including sex expression, fruit epidermal structure, and immature fruit color were evaluated using a combination of qualitative and quantitative data. As a result, we identified three QTL/gene loci responsible for these traits in three environments. The QTL/gene gy/fffn/ffn, controlling sex expression involved in gynoecy, first female flower node, and female flower number was detected in the reported region. Particularly, two QTLs/genes, Fwa/Wr and w, were found to be responsible for fruit epidermal structure and white immature fruit color, respectively. This RAD-based genetic map promotes the assembly of the bitter gourd genome and the identified genetic loci will accelerate the cloning of relevant genes in the future.

Parallel algorithms for mapping pipelined and parallel computations

Science.gov (United States)

Nicol, David M.

1988-01-01

Many computational problems in image processing, signal processing, and scientific computing are naturally structured for either pipelined or parallel computation. When mapping such problems onto a parallel architecture it is often necessary to aggregate an obvious problem decomposition. Even in this context the general mapping problem is known to be computationally intractable, but recent advances have been made in identifying classes of problems and architectures for which optimal solutions can be found in polynomial time. Among these, the mapping of pipelined or parallel computations onto linear array, shared memory, and host-satellite systems figures prominently. This paper extends that work first by showing how to improve existing serial mapping algorithms. These improvements have significantly lower time and space complexities: in one case a published O(nm sup 3) time algorithm for mapping m modules onto n processors is reduced to an O(nm log m) time complexity, and its space requirements reduced from O(nm sup 2) to O(m). Run time complexity is further reduced with parallel mapping algorithms based on these improvements, which run on the architecture for which they create the mappings.

Low-frequency synthesis array in earth orbit

International Nuclear Information System (INIS)

Jones, D.L.; Preston, R.A.; Kuiper, T.B.H.

1987-01-01

The scientific objectives and design concept of a space-based VLBI array for high-resolution astronomical observations at 1-30 MHz are discussed. The types of investigations calling for such an array include radio spectroscopy of individual objects, measurement of the effects of scattering and refraction by the interplanetary medium (IPM) and the ISM, mapping the distribution of low-energy cosmic-ray electrons, and determining the extent of the Galactic halo. Consideration is given to the limitations imposed on an LF VLBI array by the ionosphere, the IPM, and the ISM; the calibration advantages offered by circular polar orbits of slightly differing ascending-node longitude for the array satellites; and collection of the IF data streams from the array satellites by one master satellite prior to transmission to the ground. It is shown that determination of the three-dimensional array geometry by means of intersatellite radio links is feasible if there are at least seven spacecraft in the array

A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly

Directory of Open Access Journals (Sweden)

Wang Zhiquan

2007-07-01

Full Text Available Abstract Background Radiation hybrid (RH maps are considered to be a tool of choice for fine mapping closely linked loci, considering that the resolution of linkage maps is determined by the number of informative meiosis and recombination events which may require very large mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL, haplotype map construction and refinement of candidate gene searches. Results A 12 k Radiation hybrid map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting map was aligned with the latest version of the bovine assembly (Btau_3.1 as well as other previously published RH maps. The resulting map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH map presented here and the latest sequence assembly are in very good agreement. Conclusion The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.

LOFAR for lightning-interferometery and mapping

NARCIS (Netherlands)

Scholten, Olaf; Buitink, Stijn; trinh, Gia; Bonardi, Antonio; Corstanje, Arthur; Ebert, Ute; Falcke, Heino; Hoerandel, Joerg; Mitra, Pragati; Mulrey, Katherine; Nelles, Anna; Rachen, Joerg; Rossetto, Laura; Rutjes, Casper; Schellart, Pim; Thoudam, Satayendra; ter Veen, Sander; Winchen, Tobias; Hare, Brian

2017-01-01

We show that a new observation mode at the Low Frequency Array (LOFAR) for Lightning-Interferometery and Mapping (LIM) allows for lightning observations with a resolution that is at least an order of magnitude better than presently operating Lightning Napping Arrays LMAs. Furthermore the

Mapping industrial networks as an approach to identify inter-organisational collaborative potential in new product development

DEFF Research Database (Denmark)

Parraguez, Pedro; Maier, Anja

2012-01-01

. Consequently, identifying and selecting potential partners to establish collaboration agreements can be a key activity in the new product development process. This paper explores the implications of mapping industrial networks with the purpose of identifying inter-organisational collaborative potential...

A pair of seamount chains in the Central Indian Basin, identified from multibeam mapping

Digital Repository Service at National Institute of Oceanography (India)

Kodagali, V.N.

Seamounts are major physiographic features on the ocean floor. Their study is important to the understanding of the tectonic history of the seafloor. Over 150 seamounts were identified during the multibeam (Hydrosweep system) mapping of the Central...

Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes.

Directory of Open Access Journals (Sweden)

Martin Poot

2011-05-01

Full Text Available Understanding complex networks that modulate development in humans is hampered by genetic and phenotypic heterogeneity within and between populations. Here we present a method that exploits natural variation in highly diverse mouse genetic reference panels in which genetic and environmental factors can be tightly controlled. The aim of our study is to test a cross-species genetic mapping strategy, which compares data of gene mapping in human patients with functional data obtained by QTL mapping in recombinant inbred mouse strains in order to prioritize human disease candidate genes.We exploit evolutionary conservation of developmental phenotypes to discover gene variants that influence brain development in humans. We studied corpus callosum volume in a recombinant inbred mouse panel (C57BL/6J×DBA/2J, BXD strains using high-field strength MRI technology. We aligned mouse mapping results for this neuro-anatomical phenotype with genetic data from patients with abnormal corpus callosum (ACC development.From the 61 syndromes which involve an ACC, 51 human candidate genes have been identified. Through interval mapping, we identified a single significant QTL on mouse chromosome 7 for corpus callosum volume with a QTL peak located between 25.5 and 26.7 Mb. Comparing the genes in this mouse QTL region with those associated with human syndromes (involving ACC and those covered by copy number variations (CNV yielded a single overlap, namely HNRPU in humans and Hnrpul1 in mice. Further analysis of corpus callosum volume in BXD strains revealed that the corpus callosum was significantly larger in BXD mice with a B genotype at the Hnrpul1 locus than in BXD mice with a D genotype at Hnrpul1 (F = 22.48, p<9.87*10(-5.This approach that exploits highly diverse mouse strains provides an efficient and effective translational bridge to study the etiology of human developmental disorders, such as autism and schizophrenia.

Isthmus sites identified by Ripple Mapping are usually anatomically stable: A novel method to guide atrial substrate ablation?

Science.gov (United States)

Luther, Vishal; Qureshi, Norman; Lim, Phang Boon; Koa-Wing, Michael; Jamil-Copley, Shahnaz; Ng, Fu Siong; Whinnett, Zachary; Davies, D Wyn; Peters, Nicholas S; Kanagaratnam, Prapa; Linton, Nick

2018-03-01

Postablation reentrant ATs depend upon conducting isthmuses bordered by scar. Bipolar voltage maps highlight scar as sites of low voltage, but the voltage amplitude of an electrogram depends upon the myocardial activation sequence. Furthermore, a voltage threshold that defines atrial scar is unknown. We used Ripple Mapping (RM) to test whether these isthmuses were anatomically fixed between different activation vectors and atrial rates. We studied post-AF ablation ATs where >1 rhythm was mapped. Multipolar catheters were used with CARTO Confidense for high-density mapping. RM visualized the pattern of activation, and the voltage threshold below which no activation was seen. Isthmuses were characterized at this threshold between maps for each patient. Ten patients were studied (Map 1 was AT1; Map 2: sinus 1/10, LA paced 2/10, AT2 with reverse CS activation 3/10; AT2 CL difference 50 ± 30 ms). Point density was similar between maps (Map 1: 2,589 ± 1,330; Map 2: 2,214 ± 1,384; P  =  0.31). RM activation threshold was 0.16 ± 0.08 mV. Thirty-one isthmuses were identified in Map 1 (median 3 per map; width 27 ± 15 mm; 7 anterior; 6 roof; 8 mitral; 9 septal; 1 posterior). Importantly, 7 of 31 (23%) isthmuses were unexpectedly identified within regions without prior ablation. AT1 was treated following ablation of 11/31 (35%) isthmuses. Of the remaining 20 isthmuses, 14 of 16 isthmuses (88%) were consistent between the two maps (four were inadequately mapped). Wavefront collision caused variation in low voltage distribution in 2 of 16 (12%). The distribution of isthmuses and nonconducting tissue within the ablated left atrium, as defined by RM, appear concordant between rhythms. This could guide a substrate ablative approach. © 2018 Wiley Periodicals, Inc.

Complementary standoff chemical imaging to map and identify artist materials in an early Italian Renaissance panel painting.

Science.gov (United States)

Dooley, Kathryn A; Conover, Damon M; Glinsman, Lisha Deming; Delaney, John K

2014-12-08

Two imaging modalities based on molecular and elemental spectroscopy were used to characterize a painting by Cosimo Tura. Visible-to-near-infrared (400-1680 nm) reflectance imaging spectroscopy (RIS) and X-ray fluorescence (XRF) imaging spectroscopy were employed to identify pigments and determine their spatial distribution with higher confidence than from either technique alone. For example, Mary's red robe was modeled through the distribution of an insect-derived red lake (RIS map) and lead white (XRF lead map), rather than a layer of red lake on vermilion. The RIS image cube was also used to isolate the preparatory design by mapping the reflectance spectra associated with it. In conjunction with results from an earlier RIS study (1650-2500 nm) to map and identify the binding media, a more thorough understanding was gained of the materials and techniques used in the painting. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sao Paulo Lightning Mapping Array (SP-LMA): Deployment, Operation and Initial Data Analysis

Science.gov (United States)

Blakeslee, R.; Bailey, J. C.; Carey, L. D.; Rudlosky, S.; Goodman, S. J.; Albrecht, R.; Morales, C. A.; Anseimo, E. M.; Pinto, O.

2012-01-01

An 8-10 station Lightning Mapping Array (LMA) network is being deployed in the vicinity of Sao Paulo to create the SP-LMA for total lightning measurements in association with the international CHUVA [Cloud processes of the main precipitation systems in Brazil: A contribution to cloud resolving modeling and to the GPM (Global Precipitation Measurement)] field campaign. Besides supporting CHUVA science/mission objectives and the Sao Luiz do Paraitinga intensive operation period (IOP) in November-December 2011, the SP-LMA will support the generation of unique proxy data for the Geostationary Lightning Mapper (GLM) and Advanced Baseline Imager (ABI), both sensors on the NOAA Geostationary Operational Environmental Satellite-R (GOES-R), presently under development and scheduled for a 2015 launch. The proxy data will be used to develop and validate operational algorithms so that they will be ready for use on "day1" following the launch of GOES-R. A preliminary survey of potential sites in the vicinity of Sao Paulo was conducted in December 2009 and January 2010, followed up by a detailed survey in July 2010, with initial network deployment scheduled for October 2010. However, due to a delay in the Sao Luiz do Paraitinga IOP, the SP-LMA will now be installed in July 2011 and operated for one year. Spacing between stations is on the order of 15-30 km, with the network "diameter" being on the order of 30-40 km, which provides good 3-D lightning mapping 150 km from the network center. Optionally, 1-3 additional stations may be deployed in the vicinity of Sao Jos dos Campos.

Comprehensive survey of SNPs in the Affymetrix exon array using the 1000 Genomes dataset.

Directory of Open Access Journals (Sweden)

Eric R Gamazon

Full Text Available Microarray gene expression data has been used in genome-wide association studies to allow researchers to study gene regulation as well as other complex phenotypes including disease risks and drug response. To reach scientifically sound conclusions from these studies, however, it is necessary to get reliable summarization of gene expression intensities. Among various factors that could affect expression profiling using a microarray platform, single nucleotide polymorphisms (SNPs in target mRNA may lead to reduced signal intensity measurements and result in spurious results. The recently released 1000 Genomes Project dataset provides an opportunity to evaluate the distribution of both known and novel SNPs in the International HapMap Project lymphoblastoid cell lines (LCLs. We mapped the 1000 Genomes Project genotypic data to the Affymetrix GeneChip Human Exon 1.0ST array (exon array, which had been used in our previous studies and for which gene expression data had been made publicly available. We also evaluated the potential impact of these SNPs on the differentially spliced probesets we had identified previously. Though the 1000 Genomes Project data allowed a comprehensive survey of the SNPs in this particular array, the same approach can certainly be applied to other microarray platforms. Furthermore, we present a detailed catalogue of SNP-containing probesets (exon-level and transcript clusters (gene-level, which can be considered in evaluating findings using the exon array as well as benefit the design of follow-up experiments and data re-analysis.

Analysis of aneuploid lines of bread wheat to map chromosomal locations of genes controlling root hair length.

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Liu, Miao; Rathjen, Tina; Weligama, Kumara; Forrest, Kerrie; Hayden, Matthew; Delhaize, Emmanuel

2017-06-01

Long root hairs enable the efficient uptake of poorly mobile nutrients such as phosphorus. Mapping the chromosomal locations of genes that control root hair length can help exploit the natural variation within crops to develop improved cultivars. Genetic stocks of the wheat cultivar 'Chinese Spring' were used to map genes that control root hair length. Aneuploid stocks of 'Chinese Spring' were screened using a rapid method based on rhizosheath size and then selected lines were assayed for root hair length to identify chromosomes harbouring genes controlling root hair length. A series of lines with various fractional deletions of candidate chromosomes were then screened to map the root hair loci more accurately. A line with a deletion in chromosome 5A was analysed with a 90 000 single nucleotide polymorphism (SNP) array. The phosphorus acquisition efficiency (PAE) of one deletion line was compared with that of euploid 'Chinese Spring' by growing the seedlings in pots at low and luxury phosphorus supplies. Chromosomes 1A, 1D and 5A were found to harbour genes controlling root hair length. The 90 000 SNP array identified two candidate genes controlling root hair length located on chromosome 5A. The line with a deletion in chromosome 5A had root hairs that were approx. 20 % shorter than euploid 'Chinese Spring', but this was insufficient to reduce its PAE. A rapid screen for rhizosheath size enabled chromosomal regions controlling root hair length to be mapped in the wheat cultivar 'Chinese Spring' and subsequent analysis with an SNP array identified candidate genes controlling root hair length. The difference in root hair length between euploid 'Chinese Spring' and a deletion line identified in the rapid screen was still apparent, albeit attenuated, when the seedlings were grown on a fully fertilized soil. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Argus: A W-band 16-pixel focal plane array for the Green Bank Telescope

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Devaraj, Kiruthika; Church, Sarah; Cleary, Kieran; Frayer, David; Gawande, Rohit; Goldsmith, Paul; Gundersen, Joshua; Harris, Andrew; Kangaslahti, Pekka; Readhead, Tony; Reeves, Rodrigo; Samoska, Lorene; Sieth, Matt; Voll, Patricia

2015-05-01

We are building Argus, a 16-pixel square-packed focal plane array that will cover the 75-115.3 GHz frequency range on the Robert C. Byrd Green Bank Telescope (GBT). The primary research area for Argus is the study of star formation within our Galaxy and nearby galaxies. Argus will map key molecules that trace star formation, including carbon monoxide (CO) and hydrogen cyanide (HCN). An additional key science area is astrochemistry, which will be addressed by observing complex molecules in the interstellar medium, and the study of formation of solar systems, which will be addressed by identifying dense pre-stellar cores and by observing comets in our solar system. Argus has a highly scalable architecture and will be a technology path finder for larger arrays. The array is modular in construction, which will allow easy replacement of malfunctioning and poorly performing components.

Contig Maps and Genomic Sequencing Identify Candidate Genes in the Usher 1C Locus

Science.gov (United States)

Higgins, Michael J.; Day, Colleen D.; Smilinich, Nancy J.; Ni, L.; Cooper, Paul R.; Nowak, Norma J.; Davies, Chris; de Jong, Pieter J.; Hejtmancik, Fielding; Evans, Glen A.; Smith, Richard J.H.; Shows, Thomas B.

1998-01-01

Usher syndrome 1C (USH1C) is a congenital condition manifesting profound hearing loss, the absence of vestibular function, and eventual retinal degeneration. The USH1C locus has been mapped genetically to a 2- to 3-cM interval in 11p14–15.1 between D11S899 and D11S861. In an effort to identify the USH1C disease gene we have isolated the region between these markers in yeast artificial chromosomes (YACs) using a combination of STS content mapping and Alu–PCR hybridization. The YAC contig is ∼3.5 Mb and has located several other loci within this interval, resulting in the order CEN-LDHA-SAA1-TPH-D11S1310-(D11S1888/KCNC1)-MYOD1-D11S902D11S921-D11S1890-TEL. Subsequent haplotyping and homozygosity analysis refined the location of the disease gene to a 400-kb interval between D11S902 and D11S1890 with all affected individuals being homozygous for the internal marker D11S921. To facilitate gene identification, the critical region has been converted into P1 artificial chromosome (PAC) clones using sequence-tagged sites (STSs) mapped to the YAC contig, Alu–PCR products generated from the YACs, and PAC end probes. A contig of >50 PAC clones has been assembled between D11S1310 and D11S1890, confirming the order of markers used in haplotyping. Three PAC clones representing nearly two-thirds of the USH1C critical region have been sequenced. PowerBLAST analysis identified six clusters of expressed sequence tags (ESTs), two known genes (BIR,SUR1) mapped previously to this region, and a previously characterized but unmapped gene NEFA (DNA binding/EF hand/acidic amino-acid-rich). GRAIL analysis identified 11 CpG islands and 73 exons of excellent quality. These data allowed the construction of a transcription map for the USH1C critical region, consisting of three known genes and six or more novel transcripts. Based on their map location, these loci represent candidate disease loci for USH1C. The NEFA gene was assessed as the USH1C locus by the sequencing of an amplified NEFA

A pattern recognition approach to transistor array parameter variance

Science.gov (United States)

da F. Costa, Luciano; Silva, Filipi N.; Comin, Cesar H.

2018-06-01

The properties of semiconductor devices, including bipolar junction transistors (BJTs), are known to vary substantially in terms of their parameters. In this work, an experimental approach, including pattern recognition concepts and methods such as principal component analysis (PCA) and linear discriminant analysis (LDA), was used to experimentally investigate the variation among BJTs belonging to integrated circuits known as transistor arrays. It was shown that a good deal of the devices variance can be captured using only two PCA axes. It was also verified that, though substantially small variation of parameters is observed for BJT from the same array, larger variation arises between BJTs from distinct arrays, suggesting the consideration of device characteristics in more critical analog designs. As a consequence of its supervised nature, LDA was able to provide a substantial separation of the BJT into clusters, corresponding to each transistor array. In addition, the LDA mapping into two dimensions revealed a clear relationship between the considered measurements. Interestingly, a specific mapping suggested by the PCA, involving the total harmonic distortion variation expressed in terms of the average voltage gain, yielded an even better separation between the transistor array clusters. All in all, this work yielded interesting results from both semiconductor engineering and pattern recognition perspectives.

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

NARCIS (Netherlands)

Schouten, H.J.; Weg, van de W.E.; Carling, J.; Khan, S.A.; McKay, S.J.; Kaauwen, van M.P.W.

2012-01-01

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

Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles

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Lee Yun-Shien

2008-03-01

Full Text Available Abstract Background The hierarchical clustering tree (HCT with a dendrogram 1 and the singular value decomposition (SVD with a dimension-reduced representative map 2 are popular methods for two-way sorting the gene-by-array matrix map employed in gene expression profiling. While HCT dendrograms tend to optimize local coherent clustering patterns, SVD leading eigenvectors usually identify better global grouping and transitional structures. Results This study proposes a flipping mechanism for a conventional agglomerative HCT using a rank-two ellipse (R2E, an improved SVD algorithm for sorting purpose seriation by Chen 3 as an external reference. While HCTs always produce permutations with good local behaviour, the rank-two ellipse seriation gives the best global grouping patterns and smooth transitional trends. The resulting algorithm automatically integrates the desirable properties of each method so that users have access to a clustering and visualization environment for gene expression profiles that preserves coherent local clusters and identifies global grouping trends. Conclusion We demonstrate, through four examples, that the proposed method not only possesses better numerical and statistical properties, it also provides more meaningful biomedical insights than other sorting algorithms. We suggest that sorted proximity matrices for genes and arrays, in addition to the gene-by-array expression matrix, can greatly aid in the search for comprehensive understanding of gene expression structures. Software for the proposed methods can be obtained at http://gap.stat.sinica.edu.tw/Software/GAP.

The use of concept mapping to identify community-driven intervention strategies for physical and mental health.

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Vaughn, Lisa M; Jacquez, Farrah; McLinden, Daniel

2013-09-01

Research that partners with youth and community stakeholders increases contextual relevance and community buy-in and therefore maximizes the chance for intervention success. Concept mapping is a mixed-method participatory research process that accesses the input of the community in a collaborative manner. After a school-wide health needs assessment at a low-income, minority/immigrant K-8 school identified bullying and obesity as the most important health issues, concept mapping was used to identify and prioritize specific strategies to address these two areas. Stakeholders including 160 K-8 students, 33 college students working in the school, 35 parents, 20 academic partners, and 22 teachers/staff brainstormed strategies to reduce and prevent obesity and bullying. A smaller group of stakeholders worked individually to complete an unstructured sorting of these strategies into groups of similar ideas, once for obesity and again for bullying. Multidimensional scaling and cluster analysis was applied to the sorting data to produce a series of maps that illustrated the stakeholders' conceptual thinking about obesity and bullying prevention strategies. The maps for both obesity and bullying organized specific strategies into themes that included education, parental role, teacher/school supervision, youth role, expert/professional role, and school structure/support.

Nanoparticle sorting in silicon waveguide arrays

Science.gov (United States)

Zhao, H. T.; Zhang, Y.; Chin, L. K.; Yap, P. H.; Wang, K.; Ser, W.; Liu, A. Q.

2017-08-01

This paper presents the optical fractionation of nanoparticles in silicon waveguide arrays. The optical lattice is generated by evanescent coupling in silicon waveguide arrays. The hotspot size is tunable by changing the refractive index of surrounding liquids. In the experiment, 0.2-μm and 0.5-μm particles are separated with a recovery rate of 95.76%. This near-field approach is a promising candidate for manipulating nanoscale biomolecules and is anticipated to benefit the biomedical applications such as exosome purification, DNA optical mapping, cell-cell interaction, etc.

Development of flexible array tactile sensors

DEFF Research Database (Denmark)

Drimus, Alin; Marian, Nicolae; Bilberg, Arne

2010-01-01

time data acquisition system scans all the cells and converts electrical resistance to tactile pressure maps. We validate that this information can be used to improve grasping and perform object recognition. Key words: piezoresistivity, tactile, sensor, pressure, robotics......In this paper we describe the development of an array tactile sensor for use in robotic grippers based on a flexible piezoresistive material. We start by comparing different cell structures in terms of output characteristics and we construct an array of cells in a row and columns layout. A real...

Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants.

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Mengmeng Du

Full Text Available Genome-wide association studies (GWAS have identified many common single nucleotide polymorphisms (SNPs associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs. We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33. We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s.

Novel candidate genes and regions for childhood apraxia of speech identified by array comparative genomic hybridization.

Science.gov (United States)

Laffin, Jennifer J S; Raca, Gordana; Jackson, Craig A; Strand, Edythe A; Jakielski, Kathy J; Shriberg, Lawrence D

2012-11-01

The goal of this study was to identify new candidate genes and genomic copy-number variations associated with a rare, severe, and persistent speech disorder termed childhood apraxia of speech. Childhood apraxia of speech is the speech disorder segregating with a mutation in FOXP2 in a multigenerational London pedigree widely studied for its role in the development of speech-language in humans. A total of 24 participants who were suspected to have childhood apraxia of speech were assessed using a comprehensive protocol that samples speech in challenging contexts. All participants met clinical-research criteria for childhood apraxia of speech. Array comparative genomic hybridization analyses were completed using a customized 385K Nimblegen array (Roche Nimblegen, Madison, WI) with increased coverage of genes and regions previously associated with childhood apraxia of speech. A total of 16 copy-number variations with potential consequences for speech-language development were detected in 12 or half of the 24 participants. The copy-number variations occurred on 10 chromosomes, 3 of which had two to four candidate regions. Several participants were identified with copy-number variations in two to three regions. In addition, one participant had a heterozygous FOXP2 mutation and a copy-number variation on chromosome 2, and one participant had a 16p11.2 microdeletion and copy-number variations on chromosomes 13 and 14. Findings support the likelihood of heterogeneous genomic pathways associated with childhood apraxia of speech.

Using Landsat 5 TM Data to Identify and Map Areas of Mangrove in Tulum, Quintana Roo, Mexico

Science.gov (United States)

Meachum, Samuel Standish

Mangroves are recognized worldwide as a major ecosystem that provides significant ecosystem services. They are threatened due to rising pressures from human overpopulation and economic development. The Caribbean Coast of Mexico's Yucatan Peninsula contains mangrove habitat that have been negatively impacted by the development of the region's tourist industry. However, little research has been done to map and quantify the extent of mangrove in the region. This study used remote sensing techniques to identify mangrove in the Municipality of Tulum located in Quintana Roo, and to produce an accurate vector based thematic map that inventories these areas. Anatomical differences were analyzed and related to high-resolution field spectral data for each mangrove species. A vector map of mangrove habitat, including areas of inland mangrove, was produced with an overall accuracy of 88%. The 19,262 ha. of mangrove identified by this study represents a 140% increase in area over previous studies.

Association Mapping of Malting Quality Quantitative Trait Loci in Winter Barley: Positive Signals from Small Germplasm Arrays

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Lucía Gutiérrez

2011-11-01

Full Text Available Malting quality comprises one of the most economically relevant set of traits in barley ( L.. It is a complex phenotype, expensive and difficult to measure, that would benefit from a marker-assisted selection strategy. Malting quality is a target of the U.S. Barley Coordinated Agricultural Project (CAP and development of winter habit malting barley varieties is a key objective of the U.S. barley research community. The objective of this work was to detect quantitative trait loci (QTL for malting quality traits in a winter breeding program that is a component of the U.S. Barley CAP. We studied the association between five malting quality traits and 3072 single nucleotide polymorphisms (SNPs from the barley oligonucleotide pool assay (BOPA 1 and 2, assayed in advanced inbred lines from the Oregon State University (OSU breeding program from three germplasm arrays (CAP I, CAP II, and CAP III. After comparing 16 models we selected a structured association model with posterior probabilities inferred from software STRUCTURE (QK approach to use on all germplasm arrays. Most of the marker-trait associations are germplasm- and environment-specific and close to previously mapped genes and QTL relevant for malt and beer quality. We found alleles fixed by random genetic drift, novel unmasked alleles, and genetic-background interaction. In a relatively small population size study we provide strong evidence for detecting true QTL.

Advanced ACTPol Cryogenic Detector Arrays and Readout

Science.gov (United States)

Henderson, S. W.; Allison, R.; Austermann, J.; Baildon, T.; Battaglia, N.; Beall, J. A.; Becker, D.; De Bernardis, F.; Bond, J. R.; Calabrese, E.; Choi, S. K.; Coughlin, K. P.; Crowley, K. T.; Datta, R.; Devlin, M. J.; Duff, S. M.; Dunkley, J.; Dünner, R.; van Engelen, A.; Gallardo, P. A.; Grace, E.; Hasselfield, M.; Hills, F.; Hilton, G. C.; Hincks, A. D.; Hloẑek, R.; Ho, S. P.; Hubmayr, J.; Huffenberger, K.; Hughes, J. P.; Irwin, K. D.; Koopman, B. J.; Kosowsky, A. B.; Li, D.; McMahon, J.; Munson, C.; Nati, F.; Newburgh, L.; Niemack, M. D.; Niraula, P.; Page, L. A.; Pappas, C. G.; Salatino, M.; Schillaci, A.; Schmitt, B. L.; Sehgal, N.; Sherwin, B. D.; Sievers, J. L.; Simon, S. M.; Spergel, D. N.; Staggs, S. T.; Stevens, J. R.; Thornton, R.; Van Lanen, J.; Vavagiakis, E. M.; Ward, J. T.; Wollack, E. J.

2016-08-01

Advanced ACTPol is a polarization-sensitive upgrade for the 6 m aperture Atacama Cosmology Telescope, adding new frequencies and increasing sensitivity over the previous ACTPol receiver. In 2016, Advanced ACTPol will begin to map approximately half the sky in five frequency bands (28-230 GHz). Its maps of primary and secondary cosmic microwave background anisotropies—imaged in intensity and polarization at few arcminute-scale resolution—will enable precision cosmological constraints and also a wide array of cross-correlation science that probes the expansion history of the universe and the growth of structure via gravitational collapse. To accomplish these scientific goals, the Advanced ACTPol receiver will be a significant upgrade to the ACTPol receiver, including four new multichroic arrays of cryogenic, feedhorn-coupled AlMn transition edge sensor polarimeters (fabricated on 150 mm diameter wafers); a system of continuously rotating meta-material silicon half-wave plates; and a new multiplexing readout architecture which uses superconducting quantum interference devices and time division to achieve a 64-row multiplexing factor. Here we present the status and scientific goals of the Advanced ACTPol instrument, emphasizing the design and implementation of the Advanced ACTPol cryogenic detector arrays.

Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk

Science.gov (United States)

Permuth, Jennifer B.; Pirie, Ailith; Ann Chen, Y.; Lin, Hui-Yi; Reid, Brett M.; Chen, Zhihua; Monteiro, Alvaro; Dennis, Joe; Mendoza-Fandino, Gustavo; Anton-Culver, Hoda; Bandera, Elisa V.; Bisogna, Maria; Brinton, Louise; Brooks-Wilson, Angela; Carney, Michael E.; Chenevix-Trench, Georgia; Cook, Linda S.; Cramer, Daniel W.; Cunningham, Julie M.; Cybulski, Cezary; D’Aloisio, Aimee A.; Anne Doherty, Jennifer; Earp, Madalene; Edwards, Robert P.; Fridley, Brooke L.; Gayther, Simon A.; Gentry-Maharaj, Aleksandra; Goodman, Marc T.; Gronwald, Jacek; Hogdall, Estrid; Iversen, Edwin S.; Jakubowska, Anna; Jensen, Allan; Karlan, Beth Y.; Kelemen, Linda E.; Kjaer, Suzanne K.; Kraft, Peter; Le, Nhu D.; Levine, Douglas A.; Lissowska, Jolanta; Lubinski, Jan; Matsuo, Keitaro; Menon, Usha; Modugno, Rosemary; Moysich, Kirsten B.; Nakanishi, Toru; Ness, Roberta B.; Olson, Sara; Orlow, Irene; Pearce, Celeste L.; Pejovic, Tanja; Poole, Elizabeth M.; Ramus, Susan J.; Anne Rossing, Mary; Sandler, Dale P.; Shu, Xiao-Ou; Song, Honglin; Taylor, Jack A.; Teo, Soo-Hwang; Terry, Kathryn L.; Thompson, Pamela J.; Tworoger, Shelley S.; Webb, Penelope M.; Wentzensen, Nicolas; Wilkens, Lynne R.; Winham, Stacey; Woo, Yin-Ling; Wu, Anna H.; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Phelan, Catherine M.; Schildkraut, Joellen M.; Berchuck, Andrew; Goode, Ellen L.; Pharoah, Paul D. P.; Sellers, Thomas A.

2016-01-01

Rare and low frequency variants are not well covered in most germline genotyping arrays and are understudied in relation to epithelial ovarian cancer (EOC) risk. To address this gap, we used genotyping arrays targeting rarer protein-coding variation in 8,165 EOC cases and 11,619 controls from the international Ovarian Cancer Association Consortium (OCAC). Pooled association analyses were conducted at the variant and gene level for 98,543 variants directly genotyped through two exome genotyping projects. Only common variants that represent or are in strong linkage disequilibrium (LD) with previously-identified signals at established loci reached traditional thresholds for exome-wide significance (P  P≥5.0 ×10 − 7) were detected for rare and low-frequency variants at 16 novel loci. Four rare missense variants were identified (ACTBL2 rs73757391 (5q11.2), BTD rs200337373 (3p25.1), KRT13 rs150321809 (17q21.2) and MC2R rs104894658 (18p11.21)), but only MC2R rs104894668 had a large effect size (OR = 9.66). Genes most strongly associated with EOC risk included ACTBL2 (PAML = 3.23 × 10 − 5; PSKAT-o = 9.23 × 10 − 4) and KRT13 (PAML = 1.67 × 10 − 4; PSKAT-o = 1.07 × 10 − 5), reaffirming variant-level analysis. In summary, this large study identified several rare and low-frequency variants and genes that may contribute to EOC susceptibility, albeit with possible small effects. Future studies that integrate epidemiology, sequencing, and functional assays are needed to further unravel the unexplained heritability and biology of this disease. PMID:27378695

A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis.

Science.gov (United States)

King, Julie; Thomas, Ann; James, Caron; King, Ian; Armstead, Ian

2013-07-03

Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.

Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean.

Science.gov (United States)

Galeano, Carlos H; Cortés, Andrés J; Fernández, Andrea C; Soler, Álvaro; Franco-Herrera, Natalia; Makunde, Godwill; Vanderleyden, Jos; Blair, Matthew W

2012-06-26

In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. In short, this study illustrates the power of intron-based markers for linkage and association mapping in

Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

DEFF Research Database (Denmark)

Orr, Nick; Dudbridge, Frank; Dryden, Nicola

2015-01-01

We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further...

Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

NARCIS (Netherlands)

N. Orr (Nick); F. Dudbridge (Frank); N. Dryden (Nicola); S. Maguire (Sarah); D. Novo (Daniela); E. Perrakis (Eleni); N. Johnson (Nichola); M. Ghoussaini (Maya); J. Hopper (John); M.C. Southey (Melissa); C. Apicella (Carmel); J. Stone (Jennifer); M.K. Schmidt (Marjanka); A. Broeks (Annegien); L.J. van 't Veer (Laura); F.B.L. Hogervorst (Frans); P.A. Fasching (Peter); L. Haeberle (Lothar); A.B. Ekici (Arif); M.W. Beckmann (Matthias); L.J. Gibson (Lorna); A. Aitken; H. Warren (Helen); E.J. Sawyer (Elinor); I.P. Tomlinson (Ian); M. Kerin (Michael); N. Miller (Nicola); B. Burwinkel (Barbara); F. Marme (Federick); A. Schneeweiss (Andreas); C. Sohn (Chistof); P. Guénel (Pascal); T. Truong (Thérèse); E. Cordina-Duverger (Emilie); M. Sanchez (Marie); S.E. Bojesen (Stig); B.G. Nordestgaard (Børge); S.F. Nielsen (Sune); H. Flyger (Henrik); J. Benítez (Javier); M.P. Zamora (Pilar); J.I.A. Perez (Jose Ignacio Arias); P. Menéndez (Primitiva); H. Anton-Culver (Hoda); S.L. Neuhausen (Susan); H. Brenner (Hermann); A.K. Dieffenbach (Aida Karina); V. Arndt (Volker); C. Stegmaier (Christa); U. Hamann (Ute); H. Brauch (Hiltrud); C. Justenhoven (Christina); T. Brüning (Thomas); Y.-D. Ko (Yon-Dschun); H. Nevanlinna (Heli); K. Aittomäki (Kristiina); C. Blomqvist (Carl); S. Khan (Sofia); N.V. Bogdanova (Natalia); T. Dörk (Thilo); A. Lindblom (Annika); S. Margolin (Sara); A. Mannermaa (Arto); V. Kataja (Vesa); V-M. Kosma (Veli-Matti); J.M. Hartikainen (J.); G. Chenevix-Trench (Georgia); J. Beesley (Jonathan); D. Lambrechts (Diether); M. Moisse (Matthieu); O.A.M. Floris; B. Beuselinck (B.); J. Chang-Claude (Jenny); A. Rudolph (Anja); P. Seibold (Petra); D. Flesch-Janys (Dieter); P. Radice (Paolo); P. Peterlongo (Paolo); B. Peissel (Bernard); V. Pensotti (Valeria); F.J. Couch (Fergus); J.E. Olson (Janet); S. Slettedahl (Seth); C. Vachon (Celine); G.G. Giles (Graham G.); R.L. Milne (Roger L.); C.A. McLean (Catriona Ann); C.A. Haiman (Christopher); B.E. Henderson (Brian); F.R. Schumacher (Fredrick); L. Le Marchand (Loic); J. Simard (Jacques); M.S. Goldberg (Mark); F. Labrèche (France); M. Dumont (Martine); V. Kristensen (Vessela); G.G. Alnæs (Grethe); S. Nord (Silje); A.-L. Borresen-Dale (Anne-Lise); W. Zheng (Wei); S.L. Deming-Halverson (Sandra); M. Shrubsole (Martha); J. Long (Jirong); R. Winqvist (Robert); K. Pykäs (Katri); A. Jukkola-Vuorinen (Arja); M. Grip (Mervi); I.L. Andrulis (Irene); J.A. Knight (Julia); G. Glendon (Gord); S. Tchatchou (Sandrine); P. Devilee (Peter); R.A.E.M. Tollenaar (Robertus A. E. M.); C.M. Seynaeve (Caroline); C.J. van Asperen (Christi); M. García-Closas (Montserrat); J.D. Figueroa (Jonine); S.J. Chanock (Stephen); J. Lissowska (Jolanta); K. Czene (Kamila); H. Darabi (Hatef); M. Eriksson (Mikael); D. Klevebring (Daniel); M.J. Hooning (Maartje); A. Hollestelle (Antoinette); C.H.M. van Deurzen (Carolien); M. Kriege (Mieke); P. Hall (Per); J. Li (Jingmei); J. Liu (Jianjun); M.K. Humphreys (Manjeet); A. Cox (Angela); S.S. Cross (Simon); M.W.R. Reed (Malcolm); P.D.P. Pharoah (Paul); A.M. Dunning (Alison); M. Shah (Mitul); B. Perkins (Barbara); A. Jakubowska (Anna); J. Lubinski (Jan); K. Jaworska-Bieniek (Katarzyna); K. Durda (Katarzyna); A. Ashworth (Alan); A.J. Swerdlow (Anthony ); M. Jones (Michael); M. Schoemaker (Minouk); A. Meindl (Alfons); R.K. Schmutzler (Rita); C. Olswold (Curtis); S. Slager (Susan); A.E. Toland (Amanda); D. Yannoukakos (Drakoulis); K.R. Muir (K.); A. Lophatananon (Artitaya); S. Stewart-Brown (Sarah); P. Siriwanarangsan (Pornthep); K. Matsuo (Keitaro); H. Ito (Hidema); H. Iwata (Hisato); J. Ishiguro (Junko); A.H. Wu (Anna H.); C.-C. Tseng (Chiu-chen); D. Van Den Berg (David); D.O. Stram (Daniel O.); S.-H. Teo (Soo-Hwang); C.H. Yip (Cheng Har); P. Kang (Peter); M.K. Ikram (Kamran); X.-O. Shu (Xiao-Ou); W. Lu (Wei); Y. Gao; H. Cai (Hui); D. Kang (Daehee); J.-Y. Choi (J.); S.K. Park (Sue); D-Y. Noh (Dong-Young); J.M. Hartman (Joost); X. Miao; W.-Y. Lim (Wei-Yen); S.C. Lee (Soo Chin); S. Sangrajrang (Suleeporn); V. Gaborieau (Valerie); P. Brennan (Paul); J.D. McKay (James); P.-E. Wu (Pei-Ei); M.-F. Hou (Ming-Feng); J-C. Yu (Jyh-Cherng); C-Y. Shen (Chen-Yang); W.J. Blot (William); Q. Cai (Qiuyin); L.B. Signorello (Lisa B.); C. Luccarini (Craig); C. Bayes (Caroline); S. Ahmed (Shahana); M. Maranian (Melanie); S. Healey (Sue); A. González-Neira (Anna); G. Pita (Guillermo); M. Rosario Alonso; N. Álvarez (Nuria); D. Herrero (Daniel); D.C. Tessier (Daniel C.); D. Vincent (Daniel); F. Bacot (Francois); D. Hunter (David); S. Lindstrom (Stephen); J. Dennis (Joe); K. Michailidou (Kyriaki); M.K. Bolla (Manjeet); D.F. Easton (Douglas); I. dos Santos Silva (Isabel); O. Fletcher (Olivia); J. Peto (Julian)

2015-01-01

textabstractWe recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and

Genome-Wide Mapping of 5mC and 5hmC Identified Differentially Modified Genomic Regions in Late-Onset Severe Preeclampsia: A Pilot Study.

Directory of Open Access Journals (Sweden)

Lisha Zhu

Full Text Available Preeclampsia (PE is a leading cause of perinatal morbidity and mortality. However, as a common form of PE, the etiology of late-onset PE is elusive. We analyzed 5-methylcytosine (5mC and 5-hydroxymethylcytosine (5hmC levels in the placentas of late-onset severe PE patients (n = 4 and normal controls (n = 4 using a (hydroxymethylated DNA immunoprecipitation approach combined with deep sequencing ([h]MeDIP-seq, and the results were verified by (hMeDIP-qPCR. The most significant differentially methylated regions (DMRs were verified by MassARRAY EppiTYPER in an enlarged sample size (n = 20. Bioinformatics analysis identified 714 peaks of 5mC that were associated with 403 genes and 119 peaks of 5hmC that were associated with 61 genes, thus showing significant differences between the PE patients and the controls (>2-fold, p<0.05. Further, only one gene, PTPRN2, had both 5mC and 5hmC changes in patients. The ErbB signaling pathway was enriched in those 403 genes that had significantly different 5mC level between the groups. This genome-wide mapping of 5mC and 5hmC in late-onset severe PE and normal controls demonstrates that both 5mC and 5hmC play epigenetic roles in the regulation of the disease, but work independently. We reveal the genome-wide mapping of DNA methylation and DNA hydroxymethylation in late-onset PE placentas for the first time, and the identified ErbB signaling pathway and the gene PTPRN2 may be relevant to the epigenetic pathogenesis of late-onset PE.

Degree-of-Freedom Strengthened Cascade Array for DOD-DOA Estimation in MIMO Array Systems.

Science.gov (United States)

Yao, Bobin; Dong, Zhi; Zhang, Weile; Wang, Wei; Wu, Qisheng

2018-05-14

In spatial spectrum estimation, difference co-array can provide extra degrees-of-freedom (DOFs) for promoting parameter identifiability and parameter estimation accuracy. For the sake of acquiring as more DOFs as possible with a given number of physical sensors, we herein design a novel sensor array geometry named cascade array. This structure is generated by systematically connecting a uniform linear array (ULA) and a non-uniform linear array, and can provide more DOFs than some exist array structures but less than the upper-bound indicated by minimum redundant array (MRA). We further apply this cascade array into multiple input multiple output (MIMO) array systems, and propose a novel joint direction of departure (DOD) and direction of arrival (DOA) estimation algorithm, which is based on a reduced-dimensional weighted subspace fitting technique. The algorithm is angle auto-paired and computationally efficient. Theoretical analysis and numerical simulations prove the advantages and effectiveness of the proposed array structure and the related algorithm.

High resolution array-based comparative genomic hybridisation of medulloblastomas and supra-tentorial primitive neuroectodermal tumours

Science.gov (United States)

McCabe, Martin Gerard; Ichimura, Koichi; Liu, Lu; Plant, Karen; Bäcklund, L Magnus; Pearson, Danita M; Collins, Vincent Peter

2010-01-01

Medulloblastomas and supratentorial primitive neuroectodermal tumours are aggressive childhood tumours. We report our findings using array comparative genomic hybridisation (CGH) on a whole-genome BAC/PAC/cosmid array with a median clone separation of 0.97Mb to study 34 medulloblastomas and 7 supratentorial primitive neuroectodermal tumours. Array CGH allowed identification and mapping of numerous novel small regions of copy number change to genomic sequence, in addition to the large regions already known from previous studies. Novel amplifications were identified, some encompassing oncogenes, MYCL1, PDGFRA, KIT and MYB, not previously reported to show amplification in these tumours. In addition, one supratentorial primitive neuroectodermal tumour had lost both copies of the tumour suppressor genes CDKN2A & CDKN2B. Ten medulloblastomas had findings suggestive of isochromosome 17q. In contrast to previous reports using conventional CGH, array CGH identified three distinct breakpoints in these cases: Ch 17: 17940393-19251679 (17p11.2, n=6), Ch 17: 20111990-23308272 (17p11.2-17q11.2, n=4) and Ch 17: 38425359-39091575 (17q21.31, n=1). Significant differences were found in the patterns of copy number change between medulloblastomas and supratentorial primitive neuroectodermal tumours, providing further evidence that these tumours are genetically distinct despite their morphological and behavioural similarities. PMID:16783165

A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress

DEFF Research Database (Denmark)

Surma, Michal A; Klose, Christian; Peng, Debby

2013-01-01

Biological membranes are complex, and the mechanisms underlying their homeostasis are incompletely understood. Here, we present a quantitative genetic interaction map (E-MAP) focused on various aspects of lipid biology, including lipid metabolism, sorting, and trafficking. This E-MAP contains ∼250......,000 negative and positive genetic interaction scores and identifies a molecular crosstalk of protein quality control pathways with lipid bilayer homeostasis. Ubx2p, a component of the endoplasmic-reticulum-associated degradation pathway, surfaces as a key upstream regulator of the essential fatty acid (FA...

Mobile and replicated alignment of arrays in data-parallel programs

Science.gov (United States)

Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

1993-01-01

When a data-parallel language like FORTRAN 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: first, an alignment that maps all the objects to an abstract template, and then a distribution that maps the template to the processors. We solve two facets of the problem of finding alignments that reduce residual communication: we determine alignments that vary in loops, and objects that should have replicated alignments. We show that loop-dependent mobile alignment is sometimes necessary for optimum performance, and we provide algorithms with which a compiler can determine good mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself (via spread operations) or can be used to improve performance. We propose an algorithm based on network flow that determines which objects to replicate so as to minimize the total amount of broadcast communication in replication. This work on mobile and replicated alignment extends our earlier work on determining static alignment.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

Science.gov (United States)

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

Science.gov (United States)

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

2013-04-09

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

A computational theory of the hippocampal cognitive map.

Science.gov (United States)

O'Keefe, J

1990-01-01

Evidence from single unit and lesion studies suggests that the hippocampal formation acts as a spatial or cognitive map (O'Keefe and Nadel, 1978). In this chapter, I summarise some of the unit recording data and then outline the most recent computational version of the cognitive map theory. The novel aspects of the present version of the theory are that it identifies two allocentric parameters, the centroid and the eccentricity, which can be calculated from the array of cues in an environment and which can serve as the bases for an allocentric polar co-ordinate system. Computations within this framework enable the animal to identify its location within an environment, to predict the location which will be reached as a result of any specific movement from that location, and conversely, to calculate the spatial transformation necessary to go from the current location to a desired location. Aspects of the model are identified with the information provided by cells in the hippocampus and dorsal presubiculum. The hippocampal place cells are involved in the calculation of the centroid and the presubicular direction cells in the calculation of the eccentricity.

Enhancing the beamforming map of spherical arrays at low frequencies using acoustic holography

DEFF Research Database (Denmark)

Tiana Roig, Elisabet; Torras Rosell, Antoni; Fernandez Grande, Efren

2014-01-01

Recent studies have shown that the localization of acoustic sources based on circular arrays can be improved at low frequencies by combining beamforming with acoustic holography. This paper extends this technique to the three dimensional case by making use of spherical arrays. The pressure captur...

Commercial/industrial photovoltaic module and array requirement study. Low-cost solar array project engineering area

Science.gov (United States)

1981-01-01

Design requirements for photovoltaic modules and arrays used in commercial and industrial applications were identified. Building codes and referenced standards were reviewed for their applicability to commercial and industrial photovoltaic array installation. Four general installation types were identified - integral (replaces roofing), direct (mounted on top of roofing), stand-off (mounted away from roofing), and rack (for flat or low slope roofs, or ground mounted). Each of the generic mounting types can be used in vertical wall mounting systems. This implies eight mounting types exist in the commercial/industrial sector. Installation costs were developed for these mounting types as a function of panel/module size. Cost drivers were identified. Studies were performed to identify optimum module shapes and sizes and operating voltage cost drivers. The general conclusion is that there are no perceived major obstacles to the use of photovoltaic modules in commercial/industrial arrays.

Identifying regions of interest in medical images using self-organizing maps.

Science.gov (United States)

Teng, Wei-Guang; Chang, Ping-Lin

2012-10-01

Advances in data acquisition, processing and visualization techniques have had a tremendous impact on medical imaging in recent years. However, the interpretation of medical images is still almost always performed by radiologists. Developments in artificial intelligence and image processing have shown the increasingly great potential of computer-aided diagnosis (CAD). Nevertheless, it has remained challenging to develop a general approach to process various commonly used types of medical images (e.g., X-ray, MRI, and ultrasound images). To facilitate diagnosis, we recommend the use of image segmentation to discover regions of interest (ROI) using self-organizing maps (SOM). We devise a two-stage SOM approach that can be used to precisely identify the dominant colors of a medical image and then segment it into several small regions. In addition, by appropriately conducting the recursive merging steps to merge smaller regions into larger ones, radiologists can usually identify one or more ROIs within a medical image.

Genome-wide mapping of virulence in brown planthopper identifies loci that break down host plant resistance.

Science.gov (United States)

Jing, Shengli; Zhang, Lei; Ma, Yinhua; Liu, Bingfang; Zhao, Yan; Yu, Hangjin; Zhou, Xi; Qin, Rui; Zhu, Lili; He, Guangcun

2014-01-01

Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens) is the most destructive rice (Oryza sativa) pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5) and 14 (Qgr14). This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for controlling this most

Genome-wide mapping of virulence in brown planthopper identifies loci that break down host plant resistance.

Directory of Open Access Journals (Sweden)

Shengli Jing

Full Text Available Insects and plants have coexisted for over 350 million years and their interactions have affected ecosystems and agricultural practices worldwide. Variation in herbivorous insects' virulence to circumvent host resistance has been extensively documented. However, despite decades of investigation, the genetic foundations of virulence are currently unknown. The brown planthopper (Nilaparvata lugens is the most destructive rice (Oryza sativa pest in the world. The identification of the resistance gene Bph1 and its introduction in commercial rice varieties prompted the emergence of a new virulent brown planthopper biotype that was able to break the resistance conferred by Bph1. In this study, we aimed to construct a high density linkage map for the brown planthopper and identify the loci responsible for its virulence in order to determine their genetic architecture. Based on genotyping data for hundreds of molecular markers in three mapping populations, we constructed the most comprehensive linkage map available for this species, covering 96.6% of its genome. Fifteen chromosomes were anchored with 124 gene-specific markers. Using genome-wide scanning and interval mapping, the Qhp7 locus that governs preference for Bph1 plants was mapped to a 0.1 cM region of chromosome 7. In addition, two major QTLs that govern the rate of insect growth on resistant rice plants were identified on chromosomes 5 (Qgr5 and 14 (Qgr14. This is the first study to successfully locate virulence in the genome of this important agricultural insect by marker-based genetic mapping. Our results show that the virulence which overcomes the resistance conferred by Bph1 is controlled by a few major genes and that the components of virulence originate from independent genetic characters. The isolation of these loci will enable the elucidation of the molecular mechanisms underpinning the rice-brown planthopper interaction and facilitate the development of durable approaches for

Concept mapping-An effective method for identifying diversity and congruity in cognitive style.

Science.gov (United States)

Stoyanov, Slavi; Jablokow, Kathryn; Rosas, Scott R; Wopereis, Iwan G J H; Kirschner, Paul A

2017-02-01

This paper investigates the effects of cognitive style for decision making on the behaviour of participants in different phases of the group concept mapping process (GCM). It is argued that cognitive style should be included directly in the coordination of the GCM process and not simply considered as yet another demographic variable. The cognitive styles were identified using the Kirton Adaption-Innovation Inventory, which locates each person's style on a continuum ranging from very adaptive to very innovative. Cognitive style could explain diversity in the participants' behaviour in different phases of the GCM process. At the same time, the concept map as a group's common cognitive construct can consolidate individual differences and serves as a tool for managing diversity in groups of participants. Some of the results were that: (a) the more adaptive participants generated ideas that fit to a particular, well-established and consensually agreed paradigm, frame of reference, theory or practice; (b) the more innovative participants produced ideas that were more general in scope and required changing a settled structure (paradigm, frame of reference, theory or practice); and (c) the empirical comparison of the map configurations through Procrustes analysis indicated a strong dissimilarity between cognitive styles. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

NARCIS (Netherlands)

J. Shi (Jiajun); Zhang, Y. (Yanfeng); W. Zheng (Wei); K. Michailidou (Kyriaki); M. Ghoussaini (Maya); M.K. Bolla (Manjeet K.); Wang, Q. (Qin); J. Dennis (Joe); Lush, M. (Michael); R.L. Milne (Roger); X.-O. Shu (Xiao-Ou); J. Beesley (Jonathan); S. Kar (Siddhartha); I.L. Andrulis (Irene); H. Anton-Culver (Hoda); Arndt, V. (Volker); M.W. Beckmann (Matthias); Z. Zhao (Zhiguo); Guo, X. (Xingyi); J. Benítez (Javier); A. Beeghly-Fadiel (Alicia); W.J. Blot (William); N.V. Bogdanova (Natalia); S.E. Bojesen (Stig); H. Brauch (Hiltrud); H. Brenner (Hermann); L.A. Brinton (Louise); A. Broeks (Annegien); T. Brüning (Thomas); B. Burwinkel (Barbara); H. Cai (Hui); S. Canisius (Sander); J. Chang-Claude (Jenny); Choi, J.-Y. (Ji-Yeob); F.J. Couch (Fergus); A. Cox (Angela); S.S. Cross (Simon); K. Czene (Kamila); H. Darabi (Hatef); P. Devilee (Peter); A. Droit (Arnaud); T. Dörk (Thilo); P.A. Fasching (Peter); O. Fletcher (Olivia); H. Flyger (Henrik); F. Fostira (Florentia); Gaborieau, V. (Valerie); M. García-Closas (Montserrat); G.G. Giles (Graham); Grip, M. (Mervi); P. Guénel (Pascal); C.A. Haiman (Christopher A.); U. Hamann (Ute); J.M. Hartman (Joost); X. Miao; A. Hollestelle (Antoinette); J.L. Hopper (John); Hsiung, C.-N. (Chia-Ni); H. Ito (Hidemi); A. Jakubowska (Anna); Johnson, N. (Nichola); D. Torres (Diana); M. Kabisch (Maria); D. Kang (Daehee); S. Khan (Sofia); J.A. Knight (Julia); V-M. Kosma (Veli-Matti); Lambrechts, D. (Diether); J. Li (Jingmei); A. Lindblom (Annika); A. Lophatananon (Artitaya); J. Lubinski (Jan); A. Mannermaa (Arto); S. Manoukian (Siranoush); L. Le Marchand (Loic); S. Margolin (Sara); Marme, F. (Frederik); K. Matsuo (Keitaro); C.A. McLean (Catriona Ann); A. Meindl (Alfons); K.R. Muir (K.); S.L. Neuhausen (Susan); H. Nevanlinna (Heli); S. Nord (Silje); A.-L. Borresen-Dale (Anne-Lise); J.E. Olson (Janet); N. Orr (Nick); A.M.W. van den Ouweland (Ans); P. Peterlongo (Paolo); T.C. Putti (Thomas Choudary); Rudolph, A. (Anja); Sangrajrang, S. (Suleeporn); E.J. Sawyer (Elinor); M.K. Schmidt (Marjanka); R.K. Schmutzler (Rita); C.-Y. Shen (Chen-Yang); M.-F. Hou (Ming-Feng); M. Shrubsole (Martha); M.C. Southey (Melissa); A.J. Swerdlow (Anthony ); Hwang Teo, S. (Soo); B. Thienpont (Bernard); A.E. Toland (Amanda); R.A.E.M. Tollenaar (Rob); I.P. Tomlinson (Ian); T. Truong (Thérèse); C.-C. Tseng (Chiu-Chen); W. Wen (Wanqing); R. Winqvist (Robert); A.H. Wu (Anna); C. Har Yip (Cheng); P.M. Zamora (Pilar M.); Zheng, Y. (Ying); O.A.M. Floris; Cheng, C.-Y. (Ching-Yu); M.J. Hooning (Maartje); J.W.M. Martens (John); C.M. Seynaeve (Caroline); V. Kristensen (Vessela); P. Hall (Per); P.D.P. Pharoah (Paul); J. Simard (Jacques); G. Chenevix-Trench (Georgia); A.M. Dunning (Alison); A.C. Antoniou (Antonis C.); D.F. Easton (Douglas F.); Q. Cai (Qiuyin); J. Long (Jirong)

2016-01-01

textabstractPrevious genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb

Detecting Outlier Microarray Arrays by Correlation and Percentage of Outliers Spots

Directory of Open Access Journals (Sweden)

Song Yang

2006-01-01

Full Text Available We developed a quality assurance (QA tool, namely microarray outlier filter (MOF, and have applied it to our microarray datasets for the identification of problematic arrays. Our approach is based on the comparison of the arrays using the correlation coefficient and the number of outlier spots generated on each array to reveal outlier arrays. For a human universal reference (HUR dataset, which is used as a technical control in our standard hybridization procedure, 3 outlier arrays were identified out of 35 experiments. For a human blood dataset, 12 outlier arrays were identified from 185 experiments. In general, arrays from human blood samples displayed greater variation in their gene expression profiles than arrays from HUR samples. As a result, MOF identified two distinct patterns in the occurrence of outlier arrays. These results demonstrate that this methodology is a valuable QA practice to identify questionable microarray data prior to downstream analysis.

Fast and Lean Immutable Multi-Maps on the JVM based on Heterogeneous Hash-Array Mapped Tries

NARCIS (Netherlands)

M.J. Steindorfer (Michael); J.J. Vinju (Jurgen)

2016-01-01

textabstractAn immutable multi-map is a many-to-many thread-friendly map data structure with expected fast insert and lookup operations. This data structure is used for applications processing graphs or many-to-many relations as applied in static analysis of object-oriented systems. When

Generalized N-coupled maps with invariant measure in Bose ...

Indian Academy of Sciences (India)

chronization problem of an array of the linearly coupled map lattices of ... groups and graphs and also in the design of experiments, coding theory, partition ... coupled map lattice which covers internal and external couplings in a form of asso-.

Development of an Infrared Lamp Array for the Smap Spacecraft Thermal Balance Test

Science.gov (United States)

Miller, Jennifer R.; Emis, Nickolas; Forgette, Daniel

2015-01-01

NASA launched the SMAP observatory in January 2015 aboard a Delta II into a sun-synchronous orbit around Earth. The science payload of a radar and a radiometer utilizes a shared rotating six-meter antenna to provide a global map of the Earth's soil moisture content and its freeze/thaw state on a global, high-resolution scale in this three-year mission. An observatory-level thermal balance test conducted in May/June 2014 validated the thermal design and demonstrated launch readiness as part of the planned environmental test campaign. An infrared lamp array was designed and used in the thermal balance test to replicate solar heating on the solar array and sunlit side of the spacecraft that would normally be seen in orbit. The design, implementation, and operation of an infrared lamp array used for this nineteen-day system thermal test are described in this paper. Instrumental to the smooth operation of this lamp array was a characterization test performed in the same chamber two months prior to the observatory test to provide insight into its array operation and flux uniformity. This knowledge was used to identify the lamp array power settings that would provide the worst case predicted on-orbit fluxes during eclipse, cold, and hot cases. It also showed the lamp array variation when adjustments in flux were needed. Calorimeters calibrated prior to testing determined a relationship between calorimeter temperature and lamp array flux. This allowed the team to adjust the lamp output for the desired absorbed flux on the solar array. Flux levels were within 10% of the desired value at the center of the solar array with an ability to maintain these levels within 5% during steady state cases. All tests demonstrated the infrared lamp array functionality and furthered lamp array understanding for modeling purposes. This method contributed to a high-fidelity environmental simulation, which was required to replicate the extreme on-orbit thermal environments.

An Ultrasonic Wheel-Array Probe

Science.gov (United States)

Drinkwater, B. W.; Brotherhood, C. J.; Freemantle, R. J.

2004-02-01

This paper describes the development and modeling of an ultrasonic array wheel probe scanning system. The system operates at 10 MHz using a 64 element array transducer which is 50 mm in length and located in a fluid filled wheel. The wheel is coupled to the test structure dry, or with a small amount of liquid couplant. When the wheel is rolled over the surface of the test structure a defect map (C-Scan) is generated in real-time. The tyre is made from a soft, durable polymer which has very little acoustic loss. Two application studies are presented; the inspection of sealant layers in an aluminum aircraft wing structure and the detection of embedded defects in a thick section carbon composite sample.

A system and method for online high-resolution mapping of gastric slow-wave activity.

Science.gov (United States)

Bull, Simon H; O'Grady, Gregory; Du, Peng; Cheng, Leo K

2014-11-01

High-resolution (HR) mapping employs multielectrode arrays to achieve spatially detailed analyses of propagating bioelectrical events. A major current limitation is that spatial analyses must currently be performed "off-line" (after experiments), compromising timely recording feedback and restricting experimental interventions. These problems motivated development of a system and method for "online" HR mapping. HR gastric recordings were acquired and streamed to a novel software client. Algorithms were devised to filter data, identify slow-wave events, eliminate corrupt channels, and cluster activation events. A graphical user interface animated data and plotted electrograms and maps. Results were compared against off-line methods. The online system analyzed 256-channel serosal recordings with no unexpected system terminations with a mean delay 18 s. Activation time marking sensitivity was 0.92; positive predictive value was 0.93. Abnormal slow-wave patterns including conduction blocks, ectopic pacemaking, and colliding wave fronts were reliably identified. Compared to traditional analysis methods, online mapping had comparable results with equivalent coverage of 90% of electrodes, average RMS errors of less than 1 s, and CC of activation maps of 0.99. Accurate slow-wave mapping was achieved in near real-time, enabling monitoring of recording quality and experimental interventions targeted to dysrhythmic onset. This work also advances the translation of HR mapping toward real-time clinical application.

Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

Science.gov (United States)

Kumari, Amrita; Dorai, Kavita

2013-06-01

NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

Modifiers of notch transcriptional activity identified by genome-wide RNAi

Directory of Open Access Journals (Sweden)

Firnhaber Christopher B

2010-10-01

Full Text Available Abstract Background The Notch signaling pathway regulates a diverse array of developmental processes, and aberrant Notch signaling can lead to diseases, including cancer. To obtain a more comprehensive understanding of the genetic network that integrates into Notch signaling, we performed a genome-wide RNAi screen in Drosophila cell culture to identify genes that modify Notch-dependent transcription. Results Employing complementary data analyses, we found 399 putative modifiers: 189 promoting and 210 antagonizing Notch activated transcription. These modifiers included several known Notch interactors, validating the robustness of the assay. Many novel modifiers were also identified, covering a range of cellular localizations from the extracellular matrix to the nucleus, as well as a large number of proteins with unknown function. Chromatin-modifying proteins represent a major class of genes identified, including histone deacetylase and demethylase complex components and other chromatin modifying, remodeling and replacement factors. A protein-protein interaction map of the Notch-dependent transcription modifiers revealed that a large number of the identified proteins interact physically with these core chromatin components. Conclusions The genome-wide RNAi screen identified many genes that can modulate Notch transcriptional output. A protein interaction map of the identified genes highlighted a network of chromatin-modifying enzymes and remodelers that regulate Notch transcription. Our results open new avenues to explore the mechanisms of Notch signal regulation and the integration of this pathway into diverse cellular processes.

LOFAR lightning imaging : mapping lightning with nanosecond precision

NARCIS (Netherlands)

Hare, B.M.; Scholten, O.; Bonardi, A.; Buitink, S.; Corstanje, A.; Ebert, U.; Falcke, H.; Hörandel, J.R.; Leijnse, H.; Mitra, P.; Mulrey, K.; Nelles, A.; Rachen, J. P.; Rossetto, L.; Rutjes, C.; Schellart, P.; Thoudam, S.; Trinh, T.N.G.; ter Veen, S.; Winchen, T.

2018-01-01

Lightning mapping technology has proven instrumental in understanding lightning. In this work we present a pipeline that can use lightning observed by the LOw-Frequency ARray (LOFAR) radio telescope to construct a 3-D map of the flash. We show that LOFAR has unparalleled precision, on the order of

Combinatorial aspects of covering arrays

Directory of Open Access Journals (Sweden)

Charles J. Colbourn

2004-11-01

Full Text Available Covering arrays generalize orthogonal arrays by requiring that t -tuples be covered, but not requiring that the appearance of t -tuples be balanced.Their uses in screening experiments has found application in software testing, hardware testing, and a variety of fields in which interactions among factors are to be identified. Here a combinatorial view of covering arrays is adopted, encompassing basic bounds, direct constructions, recursive constructions, algorithmic methods, and applications.

Advanced Data Mining of Leukemia Cells Micro-Arrays

Directory of Open Access Journals (Sweden)

Richard S. Segall

2009-12-01

Full Text Available This paper provides continuation and extensions of previous research by Segall and Pierce (2009a that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM. As Segall and Pierce (2009a and Segall and Pierce (2009b the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is provided on the work of others pertaining to the applications of data mining to micro-array databases of Leukemia cells and micro-array databases in general. As noted in predecessor article by Segall and Pierce (2009a, micro-array databases are one of the most popular functional genomics tools in use today. This research in this paper is intended to use advanced data mining technologies for better interpretations and knowledge discovery as generated by the patterns of gene expressions of HL60, Jurkat, NB4 and U937 Leukemia cells. The advanced data mining performed entailed using other data mining tools such as cubic clustering criterion, variable importance rankings, decision trees, and more detailed examinations of data mining statistics and study of other self-organized maps (SOM clustering regions of workspace as generated by SAS Enterprise Miner version 4. Conclusions and future directions of the research are also presented.

Identifying ozone-sensitive communities of (semi-)natural vegetation suitable for mapping exceedance of critical levels

International Nuclear Information System (INIS)

Mills, G.; Hayes, F.; Jones, M.L.M.; Cinderby, S.

2007-01-01

Using published data on the responses of individual species to ozone, 54 EUNIS (European Nature Information System) level 4 communities with six or more ozone-sensitive species (%OS) and c. 20% or more species tested for ozone sensitivity, were identified as potentially ozone-sensitive. The largest number of these communities (23) was associated with Grasslands, with Heathland, scrub and tundra, and Mires, bogs and fens having the next highest representation at 11 and 8 level 4 communities each respectively. Within the grasslands classification, E4 (Alpine and sub-alpine grasslands), E5 (Woodland fringes and clearings) and E1 (Dry grasslands) were the most sensitive with 68.1, 51.6 and 48.6%OS respectively. It is feasible to map the land-cover for these and other communities at level 2, but it may not be currently possible to map the land-cover for all communities identified to be ozone-sensitive at levels 3 and 4. - Grassland communities such as alpine and sub-alpine grasslands have the highest potential sensitivity ozone, based on the responses of their component species

Identifying Multi-Level Culturally Appropriate Smoking Cessation Strategies for Aboriginal Health Staff: A Concept Mapping Approach

Science.gov (United States)

Dawson, Anna P.; Cargo, Margaret; Stewart, Harold; Chong, Alwin; Daniel, Mark

2013-01-01

Aboriginal Australians, including Aboriginal Health Workers (AHWs), smoke at rates double the non-Aboriginal population. This study utilized concept mapping methodology to identify and prioritize culturally relevant strategies to promote smoking cessation in AHWs. Stakeholder participants included AHWs, other health service employees and tobacco…

A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations.

Science.gov (United States)

Comeron, Josep M; Reed, Jordan; Christie, Matthew; Jacobs, Julia S; Dierdorff, Jason; Eberl, Daniel F; Manak, J Robert

2016-04-05

Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1) genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2) identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3) screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv) gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.

Visualizing the Logistic Map with a Microcontroller

Science.gov (United States)

Serna, Juan D.; Joshi, Amitabh

2012-01-01

The logistic map is one of the simplest nonlinear dynamical systems that clearly exhibits the route to chaos. In this paper, we explore the evolution of the logistic map using an open-source microcontroller connected to an array of light-emitting diodes (LEDs). We divide the one-dimensional domain interval [0,1] into ten equal parts, an associate…

A Novel Imaging Technique (X-Map) to Identify Acute Ischemic Lesions Using Noncontrast Dual-Energy Computed Tomography.

Science.gov (United States)

Noguchi, Kyo; Itoh, Toshihide; Naruto, Norihito; Takashima, Shutaro; Tanaka, Kortaro; Kuroda, Satoshi

2017-01-01

We evaluated whether X-map, a novel imaging technique, can visualize ischemic lesions within 20 hours after the onset in patients with acute ischemic stroke, using noncontrast dual-energy computed tomography (DECT). Six patients with acute ischemic stroke were included in this study. Noncontrast head DECT scans were acquired with 2 X-ray tubes operated at 80 kV and Sn150 kV between 32 minutes and 20 hours after the onset. Using these DECT scans, the X-map was reconstructed based on 3-material decomposition and compared with a simulated standard (120 kV) computed tomography (CT) and diffusion-weighted imaging (DWI). The X-map showed more sensitivity to identify the lesions as an area of lower attenuation value than a simulated standard CT in all 6 patients. The lesions on the X-map correlated well with those on DWI. In 3 of 6 patients, the X-map detected a transient decrease in the attenuation value in the peri-infarct area within 1 day after the onset. The X-map is a powerful tool to supplement a simulated standard CT and characterize acute ischemic lesions. However, the X-map cannot replace a simulated standard CT to diagnose acute cerebral infarction. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

The data array, a tool to interface the user to a large data base

Science.gov (United States)

Foster, G. H.

1974-01-01

Aspects of the processing of spacecraft data is considered. Use of the data array in a large address space as an intermediate form in data processing for a large scientific data base is advocated. Techniques for efficient indexing in data arrays are reviewed and the data array method for mapping an arbitrary structure onto linear address space is shown. A compromise between the two forms is given. The impact of the data array on the user interface are considered along with implementation.

The Use of AIS Data for Identifying and Mapping Calcareous Soils in Western Nebraska

Science.gov (United States)

Samson, S. A.

1985-01-01

The identification of calcareous soils, through unique spectral responses of the vegetation to the chemical nature of calcareous soils, can improve the accuracy of delineating the boundaries of soil mapping units over conventional field techniques. The objective of this experiment is to evaluate the use of the Airborne Imaging Spectrometer (AIS) in the identification and delineation of calcareous soils in the western Sandhills of Nebraska. Based upon statistical differences found in separating the spectral curves below 1.3 microns, calcareous and non-calcareous soils may be identified by differences in species of vegetation. Additional work is needed to identify biogeochemical differences between the two soils.

Estimates of the Lightning NOx Profile in the Vicinity of the North Alabama Lightning Mapping Array

Science.gov (United States)

Koshak, William J.; Peterson, Harold S.; McCaul, Eugene W.; Blazar, Arastoo

2010-01-01

The NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) is applied to August 2006 North Alabama Lightning Mapping Array (NALMA) data to estimate the (unmixed and otherwise environmentally unmodified) vertical source profile of lightning nitrogen oxides, NOx = NO + NO2. Data from the National Lightning Detection Network (Trademark) (NLDN) is also employed. This is part of a larger effort aimed at building a more realistic lightning NOx emissions inventory for use by the U.S. Environmental Protection Agency (EPA) Community Multiscale Air Quality (CMAQ) modeling system. Overall, special attention is given to several important lightning variables including: the frequency and geographical distribution of lightning in the vicinity of the NALMA network, lightning type (ground or cloud flash), lightning channel length, channel altitude, channel peak current, and the number of strokes per flash. Laboratory spark chamber results from the literature are used to convert 1-meter channel segments (that are located at a particular known altitude; i.e., air density) to NOx concentration. The resulting lightning NOx source profiles are discussed.

Phenotype and 244k array-CGH characterization of chromosome 13q deletions: an update of the phenotypic map of 13q21.1-qter

DEFF Research Database (Denmark)

Kirchhoff, Maria; Bisgaard, Anne-Marie; Stoeva, Radka

2009-01-01

Partial deletions of the long arm of chromosome 13 lead to variable phenotypes dependant on the size and position of the deleted region. In order to update the phenotypic map of chromosome 13q21.1-qter deletions, we applied 244k Agilent oligonucleotide-based array-CGH to determine the exact break......-genotype correlation on chromosome 13. In contrast to previous reports of carriers of 13q32 band deletions as the most seriously affected patients, we present two such individuals with long-term survival, 28 and 2.5 years....

Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao.

Science.gov (United States)

Livingstone, Donald; Royaert, Stefan; Stack, Conrad; Mockaitis, Keithanne; May, Greg; Farmer, Andrew; Saski, Christopher; Schnell, Ray; Kuhn, David; Motamayor, Juan Carlos

2015-08-01

Theobroma cacao, the key ingredient in chocolate production, is one of the world's most important tree fruit crops, with ∼4,000,000 metric tons produced across 50 countries. To move towards gene discovery and marker-assisted breeding in cacao, a single-nucleotide polymorphism (SNP) identification project was undertaken using RNAseq data from 16 diverse cacao cultivars. RNA sequences were aligned to the assembled transcriptome of the cultivar Matina 1-6, and 330,000 SNPs within coding regions were identified. From these SNPs, a subset of 6,000 high-quality SNPs were selected for inclusion on an Illumina Infinium SNP array: the Cacao6kSNP array. Using Cacao6KSNP array data from over 1,000 cacao samples, we demonstrate that our custom array produces a saturated genetic map and can be used to distinguish among even closely related genotypes. Our study enhances and expands the genetic resources available to the cacao research community, and provides the genome-scale set of tools that are critical for advancing breeding with molecular markers in an agricultural species with high genetic diversity. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.).

Science.gov (United States)

Zhang, Guoyu; Ren, Yi; Sun, Honghe; Guo, Shaogui; Zhang, Fan; Zhang, Jie; Zhang, Haiying; Jia, Zhangcai; Fei, Zhangjun; Xu, Yong; Li, Haizhen

2015-12-24

Pumpkin (Cucurbita maxima Duch.) is an economically important crop belonging to the Cucurbitaceae family. However, very few genomic and genetic resources are available for this species. As part of our ongoing efforts to sequence the pumpkin genome, high-density genetic map is essential for anchoring and orienting the assembled scaffolds. In addition, a saturated genetic map can facilitate quantitative trait locus (QTL) mapping. A set of 186 F2 plants derived from the cross of pumpkin inbred lines Rimu and SQ026 were genotyped using the genotyping-by-sequencing approach. Using the SNPs we identified, a high-density genetic map containing 458 bin-markers was constructed, spanning a total genetic distance of 2,566.8 cM across the 20 linkage groups of C. maxima with a mean marker density of 5.60 cM. Using this map we were able to anchor 58 assembled scaffolds that covered about 194.5 Mb (71.7%) of the 271.4 Mb assembled pumpkin genome, of which 44 (183.0 Mb; 67.4%) were oriented. Furthermore, the high-density genetic map was used to identify genomic regions highly associated with an important agronomic trait, dwarf vine. Three QTLs on linkage groups (LGs) 1, 3 and 4, respectively, were recovered. One QTL, qCmB2, which was located in an interval of 0.42 Mb on LG 3, explained 21.4% phenotypic variations. Within qCmB2, one gene, Cma_004516, encoding the gibberellin (GA) 20-oxidase in the GA biosynthesis pathway, had a 1249-bp deletion in its promoter in bush type lines, and its expression level was significantly increased during the vine growth and higher in vine type lines than bush type lines, supporting Cma_004516 as a possible candidate gene controlling vine growth in pumpkin. A high-density pumpkin genetic map was constructed, which was used to successfully anchor and orient the assembled genome scaffolds, and to identify QTLs highly associated with pumpkin vine length. The map provided a valuable resource for gene cloning and marker assisted breeding in pumpkin and

Manycore Performance-Portability: Kokkos Multidimensional Array Library

Directory of Open Access Journals (Sweden)

H. Carter Edwards

2012-01-01

Full Text Available Large, complex scientific and engineering application code have a significant investment in computational kernels to implement their mathematical models. Porting these computational kernels to the collection of modern manycore accelerator devices is a major challenge in that these devices have diverse programming models, application programming interfaces (APIs, and performance requirements. The Kokkos Array programming model provides library-based approach to implement computational kernels that are performance-portable to CPU-multicore and GPGPU accelerator devices. This programming model is based upon three fundamental concepts: (1 manycore compute devices each with its own memory space, (2 data parallel kernels and (3 multidimensional arrays. Kernel execution performance is, especially for NVIDIA® devices, extremely dependent on data access patterns. Optimal data access pattern can be different for different manycore devices – potentially leading to different implementations of computational kernels specialized for different devices. The Kokkos Array programming model supports performance-portable kernels by (1 separating data access patterns from computational kernels through a multidimensional array API and (2 introduce device-specific data access mappings when a kernel is compiled. An implementation of Kokkos Array is available through Trilinos [Trilinos website, http://trilinos.sandia.gov/, August 2011].

A hidden Markov model approach for determining expression from genomic tiling micro arrays

Directory of Open Access Journals (Sweden)

Krogh Anders

2006-05-01

Full Text Available Abstract Background Genomic tiling micro arrays have great potential for identifying previously undiscovered coding as well as non-coding transcription. To-date, however, analyses of these data have been performed in an ad hoc fashion. Results We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genomic sequence. A hidden Markov model (HMM is used to model the distributions of tiling array probe scores in expressed and non-expressed regions. The HMM is trained on sets of probes mapped to regions of annotated expression and non-expression. Subsequently, prediction of transcribed fragments is made on tiled genomic sequence. The prediction is accompanied by an expression probability curve for visual inspection of the supporting evidence. We test ExpressHMM on data from the Cheng et al. (2005 tiling array experiments on ten Human chromosomes 1. Results can be downloaded and viewed from our web site 2. Conclusion The value of adaptive modelling of fluorescence scores prior to categorisation into expressed and non-expressed probes is demonstrated. Our results indicate that our adaptive approach is superior to the previous analysis in terms of nucleotide sensitivity and transfrag specificity.

INTEGRATION OF PALSAR AND ASTER SATELLITE DATA FOR GEOLOGICAL MAPPING IN TROPICS

Directory of Open Access Journals (Sweden)

A. Beiranvand Pour

2015-10-01

Full Text Available This research investigates the integration of the Phased Array type L-band Synthetic Aperture Radar (PALSAR and the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER satellite data for geological mapping applications in tropical environments. The eastern part of the central belt of peninsular Malaysia has been investigated to identify structural features and mineral mapping using PALSAR and ASTER data. Adaptive local sigma and directional filters were applied to PALSAR data for detecting geological structure elements in the study area. The vegetation, mineralogic and lithologic indices for ASTER bands were tested in tropical climate. Lineaments (fault and fractures and curvilinear (anticline or syncline were detected using PALSAR fused image of directional filters (N-S, NE-SW, and NW-SE.Vegetation index image map show vegetation cover by fusing ASTER VNIR bands. High concentration of clay minerals zone was detected using fused image map derived from ASTER SWIR bands. Fusion of ASTER TIR bands produced image map of the lithological units. Results indicate that data integration and data fusion from PALSAR and ASTER sources enhanced information extraction for geological mapping in tropical environments.

A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L.

Directory of Open Access Journals (Sweden)

Liezhao Liu

Full Text Available A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape was constructed in a late-generation recombinant inbred line (RIL population, using genome-wide single nucleotide polymorphism (SNP markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL, cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.

Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

DEFF Research Database (Denmark)

Li, Yun R.; van Setten, Jessica; Verma, Shefali S.

2015-01-01

genome-wide genotyping array, the 'TxArray', comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples...

The first genetic map of pigeon pea based on diversity arrays ...

Indian Academy of Sciences (India)

2016-08-26

Aug 26, 2016 ... a total of 554 diversity arrays technology (DArT) markers showed ... EH Graham Centre for Agricultural Innovation (NSW Department of Industry and ... India; Theme-Comparative and Applied Genomics, Generation Challenge ...

Multistudy fine mapping of chromosome 2q identifies XRCC5 as a chronic obstructive pulmonary disease susceptibility gene

DEFF Research Database (Denmark)

Hersh, Craig P; Pillai, Sreekumar G; Zhu, Guohua

2010-01-01

RATIONALE: Several family-based studies have identified genetic linkage for lung function and airflow obstruction to chromosome 2q. OBJECTIVES: We hypothesized that merging results of high-resolution single nucleotide polymorphism (SNP) mapping in four separate populations would lead to the ident......RATIONALE: Several family-based studies have identified genetic linkage for lung function and airflow obstruction to chromosome 2q. OBJECTIVES: We hypothesized that merging results of high-resolution single nucleotide polymorphism (SNP) mapping in four separate populations would lead...... the National Emphysema Treatment Trial and 330 community control subjects. Significant associations from the combined results across the two case-control studies were followed up in 1,839 individuals from 603 families from the International COPD Genetics Network (ICGN) and in 949 individuals from 127 families...

Stretchable Active Matrix Temperature Sensor Array of Polyaniline Nanofibers for Electronic Skin.

Science.gov (United States)

Hong, Soo Yeong; Lee, Yong Hui; Park, Heun; Jin, Sang Woo; Jeong, Yu Ra; Yun, Junyeong; You, Ilhwan; Zi, Goangseup; Ha, Jeong Sook

2016-02-03

A stretchable polyaniline nanofiber temperature sensor array with an active matrix consisting of single-walled carbon nanotube thin-film transistors is demonstrated. The integrated temperature sensor array gives mechanical stability under biaxial stretching of 30%, and the resultant spatial temperature mapping does not show any mechanical or electrical degradation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recent achievements on the development of the HERSCHEL/PACS bolometer arrays

International Nuclear Information System (INIS)

Billot, N.; Agnese, P.; Boulade, O.; Cigna, C.; Doumayrou, E.; Horeau, B.; Lepennec, J.; Martignac, J.; Pornin, J.-L.; Reveret, V.; Rodriguez, L.; Sauvage, M.; Simoens, F.; Vigroux, L.

2006-01-01

A new type of bolometer arrays sensitive in the far Infrared and Submillimeter range has been developed and manufactured by CEA/LETI/SLIR since 1997. These arrays will be integrated in the PACS instrument (Photodetector Array Camera and Spectrometer) of ESA's Herschel Space Observatory (launch date 2007). The main innovations of CEA bolometers are their collective manufacturing technique (production of 3-side buttable 16x16 arrays) and their high mapping efficiency (large format detector and instantaneous Nyquist sampling). The measured NEP is 2.10 -16 W/Hz and the thermometric passband about 4-5Hz. In this article we describe CEA bolometers and present the results obtained during the last test campaign

Recent achievements on the development of the HERSCHEL/PACS bolometer arrays

Energy Technology Data Exchange (ETDEWEB)

Billot, N. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France)]. E-mail: nbillot@cea.fr; Agnese, P. [CEA/LETI Grenoble, 17 Avenue des Martyrs, 38054 Grenoble (France); Boulade, O. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Cigna, C. [CEA/LETI Grenoble, 17 Avenue des Martyrs, 38054 Grenoble (France); Doumayrou, E. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Horeau, B. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Lepennec, J. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Martignac, J. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Pornin, J.-L. [CEA/LETI Grenoble, 17 Avenue des Martyrs, 38054 Grenoble (France); Reveret, V. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Rodriguez, L. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Sauvage, M. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Simoens, F. [CEA/LETI Grenoble, 17 Avenue des Martyrs, 38054 Grenoble (France); Vigroux, L. [CEA/Saclay/SAp, UMR CEA/CNRS/UP7 Laboratoire AIM, Bat. 709, l' Orme des merisiers, 91191 Gif-sur-Yvette (France); Institut d' Astrophysique de Paris, 75014 Paris (France)

2006-11-01

A new type of bolometer arrays sensitive in the far Infrared and Submillimeter range has been developed and manufactured by CEA/LETI/SLIR since 1997. These arrays will be integrated in the PACS instrument (Photodetector Array Camera and Spectrometer) of ESA's Herschel Space Observatory (launch date 2007). The main innovations of CEA bolometers are their collective manufacturing technique (production of 3-side buttable 16x16 arrays) and their high mapping efficiency (large format detector and instantaneous Nyquist sampling). The measured NEP is 2.10{sup -16}W/Hz and the thermometric passband about 4-5Hz. In this article we describe CEA bolometers and present the results obtained during the last test campaign.

A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

Science.gov (United States)

2011-01-01

Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in

A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.

Directory of Open Access Journals (Sweden)

Schaffer Arthur

2011-07-01

Full Text Available Abstract Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L. over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS. Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org, an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability

Nanoelectrode array for electrochemical analysis

Energy Technology Data Exchange (ETDEWEB)

Yelton, William G [Sandia Park, NM; Siegal, Michael P [Albuquerque, NM

2009-12-01

A nanoelectrode array comprises a plurality of nanoelectrodes wherein the geometric dimensions of the electrode controls the electrochemical response, and the current density is independent of time. By combining a massive array of nanoelectrodes in parallel, the current signal can be amplified while still retaining the beneficial geometric advantages of nanoelectrodes. Such nanoelectrode arrays can be used in a sensor system for rapid, non-contaminating field analysis. For example, an array of suitably functionalized nanoelectrodes can be incorporated into a small, integrated sensor system that can identify many species rapidly and simultaneously under field conditions in high-resistivity water, without the need for chemical addition to increase conductivity.

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

Science.gov (United States)

Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2016-07-01

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

A SNP Genotyping Array for Hexaploid Oat

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Nicholas A. Tinker

2014-11-01

Full Text Available Recognizing a need in cultivated hexaploid oat ( L. for a reliable set of reference single nucleotide polymorphisms (SNPs, we have developed a 6000 (6K BeadChip design containing 257 Infinium I and 5486 Infinium II designs corresponding to 5743 SNPs. Of those, 4975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in complementary DNA (cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six recombinant inbred line (RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernible Mendelian polymorphisms. Here, we present an annotation of these SNPs, including methods of discovery, gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.

Multiplatform serum metabolic phenotyping combined with pathway mapping to identify biochemical differences in smokers.

Science.gov (United States)

Kaluarachchi, Manuja R; Boulangé, Claire L; Garcia-Perez, Isabel; Lindon, John C; Minet, Emmanuel F

2016-10-01

Determining perturbed biochemical functions associated with tobacco smoking should be helpful for establishing causal relationships between exposure and adverse events. A multiplatform comparison of serum of smokers (n = 55) and never-smokers (n = 57) using nuclear magnetic resonance spectroscopy, UPLC-MS and statistical modeling revealed clustering of the classes, distinguished by metabolic biomarkers. The identified metabolites were subjected to metabolic pathway enrichment, modeling adverse biological events using available databases. Perturbation of metabolites involved in chronic obstructive pulmonary disease, cardiovascular diseases and cancer were identified and discussed. Combining multiplatform metabolic phenotyping with knowledge-based mapping gives mechanistic insights into disease development, which can be applied to next-generation tobacco and nicotine products for comparative risk assessment.

MISSION-ORIENTED SENSOR ARRAYS AND UAVs – A CASE STUDY ON ENVIRONMENTAL MONITORING

Directory of Open Access Journals (Sweden)

N. M. Figueira

2015-08-01

Full Text Available This paper presents a new concept of UAV mission design in geomatics, applied to the generation of thematic maps for a multitude of civilian and military applications. We discuss the architecture of Mission-Oriented Sensors Arrays (MOSA, proposed in Figueira et Al. (2013, aimed at splitting and decoupling the mission-oriented part of the system (non safety-critical hardware and software from the aircraft control systems (safety-critical. As a case study, we present an environmental monitoring application for the automatic generation of thematic maps to track gunshot activity in conservation areas. The MOSA modeled for this application integrates information from a thermal camera and an on-the-ground microphone array. The use of microphone arrays technology is of particular interest in this paper. These arrays allow estimation of the direction-of-arrival (DOA of the incoming sound waves. Information about events of interest is obtained by the fusion of the data provided by the microphone array, captured by the UAV, fused with information from the termal image processing. Preliminary results show the feasibility of the on-the-ground sound processing array and the simulation of the main processing module, to be embedded into an UAV in a future work. The main contributions of this paper are the proposed MOSA system, including concepts, models and architecture.

Mapping the Landscape of Future Research Themes in Supply Chain Management

DEFF Research Database (Denmark)

Wieland, Andreas; Handfield, Robert; Durach, Christian F.

2016-01-01

Supply chain researchers are confronted with a dizzying array of research questions, many of which are not mutually independent. This research was motivated by the need to map the landscape of research themes, identify potential overlapping areas and interactions, and provide guidelines on areas...... of focus for researchers to pursue. We conducted a three-phase research study, beginning with an open-ended collection of opinions on research themes collected from 102 supply chain management (SCM) researchers, followed by an evaluation of a consolidated list of themes by 141 SCM researchers...

Microbial genome sequencing using optical mapping and Illumina sequencing

Science.gov (United States)

Introduction Optical mapping is a technique in which strands of genomic DNA are digested with one or more restriction enzymes, and a physical map of the genome constructed from the resulting image. In outline, genomic DNA is extracted from a pure culture, linearly arrayed on a specialized glass sli...

Supercritical fluid chromatography-photodiode array detection-electrospray ionization mass spectrometry as a framework for impurity fate mapping in the development and manufacture of drug substances.

Science.gov (United States)

Pirrone, Gregory F; Mathew, Rose M; Makarov, Alexey A; Bernardoni, Frank; Klapars, Artis; Hartman, Robert; Limanto, John; Regalado, Erik L

2018-03-30

Impurity fate and purge studies are critical in order to establish an effective impurity control strategy for approval of the commercial filing application of new medicines. Reversed phase liquid chromatography-diode array-mass spectrometry (RPLC-DAD-MS) has traditionally been the preferred tool for impurity fate mapping. However, separation of some reaction mixtures by LC can be very problematic requiring combination LC-UV for area % analysis and a different LC-MS method for peak identification. In addition, some synthetic intermediates might be chemically susceptible to the aqueous conditions used in RPLC separations. In this study, the use of supercritical fluid chromatography-photodiode array-electrospray ionization mass spectrometry (SFC-PDA-ESIMS) for fate and purge of two specified impurities in the 1-uridine starting material from the synthesis of a bis-piv 2'keto-uridine, an intermediate in the synthesis of uprifosbuvir, a treatment under investigation for chronic hepatitis C infection. Readily available SFC instrumentation with a Chiralpak IC column (4.6 × 150 mm, 3 μm) and ethanol: carbon dioxide based mobile phase eluent enabled the separation of closely related components from complex reaction mixtures where RLPC failed to deliver optimal chromatographic performance. These results illustrate how SFC combined with PDA and ESI-MS detection can become a powerful tool for direct impurity fate mapping across multiple reaction steps. Copyright © 2018 Elsevier B.V. All rights reserved.

Road map for photovoltaic electricity

International Nuclear Information System (INIS)

2011-02-01

This road map aims at highlighting industrial, technological and social challenges, at elaborating comprehensive visions, at highlighting technological locks, and at outlining research needs for the photovoltaic sector. It considers the following sector components: preparation of photo-sensitive materials, manufacturing of photovoltaic cells, manufacturing of photovoltaic arrays, design and manufacturing of electric equipment to control photovoltaic arrays and to connect them to the grid. It highlights the demand for photovoltaic installations, analyzes the value chain, proposes a vision of the sector by 2050 and defines target for 2020, discusses needs for demonstration and experimentation

Where to Go Next? Identifying Target Areas in the North Atlantic for Future Seafloor Mapping Initiatives

Science.gov (United States)

Woelfl, A. C.; Jencks, J.; Johnston, G.; Varner, J. D.; Devey, C. W.

2017-12-01

Human activities are rapidly expanding into the oceans, yet detailed bathymetric maps do not exist for most of the seafloor that would permit governments to formulate sensible usage rules. Changing this situation will require an enormous international mapping effort. To ensure that this effort is directed towards the regions most in need of mapping, we need to know which areas have already been mapped and which areas are potentially most interesting. Despite various mapping efforts in recent years, large parts of the Atlantic still lack detailed bathymetric information. To successfully plan for future mapping efforts to fill these gaps, knowledge of current data coverage is imperative to avoid duplication of effort. While certain datasets are publically available online (e.g. NOAA's NCEI, EMODnet, IHO-DCDB, LDEO's GMRT), many are not. However, with the limited information we do have at hand, the question remains, where should we map next? And what criteria should we take into account? In 2016, a study was taken on as part of the efforts of the International Atlantic Seabed Mapping Working Group (ASMIWG). The ASMIWG, established by the Tri-Partite Galway Statement Implementation Committee, was tasked to develop a cohesive seabed mapping strategy for the Atlantic Ocean. The aim of our study was to develop a reproducible process for identifying and evaluating potential target areas within the North Atlantic that represent suitable sites for future bathymetric surveys. The sites were selected by applying a GIS-based suitability analysis that included specific user group-based parameters of the marine environment. Furthermore, information regarding current data coverage were gathered to take into account in the selection process. The results reveal the suitability of sites within the North Atlantic based on the selected criteria. Three potential target sites should be seen as flexible suggestions for future mapping initiatives rather than a rigid, defined set of areas

Micromirror array nanostructures for anticounterfeiting applications

Science.gov (United States)

Lee, Robert A.

2004-06-01

The optical characteristics of pixellated passive micro mirror arrays are derived and applied in the context of their use as reflective optically variable device (OVD) nanostructures for the protection of documents from counterfeiting. The traditional design variables of foil based diffractive OVDs are shown to be able to be mapped to a corresponding set of design parameters for reflective optical micro mirror array (OMMA) devices. The greatly increased depth characteristics of micro mirror array OVDs provides an opportunity for directly printing the OVD microstructure onto the security document in-line with the normal printing process. The micro mirror array OVD architecture therefore eliminates the need for hot stamping foil as the carrier of the OVD information, thereby reducing costs. The origination of micro mirror array devices via a palette based data format and a combination electron beam lithography and photolithography techniques is discussed via an artwork example and experimental tests. Finally the application of the technology to the design of a generic class of devices which have the interesting property of allowing for both application and customer specific OVD image encoding and data encoding at the end user stage of production is described. Because of the end user nature of the image and data encoding process these devices are particularly well suited to ID document applications and for this reason we refer this new OVD concept as biometric OVD technology.

rasdaman Array Database: current status

Science.gov (United States)

Merticariu, George; Toader, Alexandru

2015-04-01

rasdaman (Raster Data Manager) is a Free Open Source Array Database Management System which provides functionality for storing and processing massive amounts of raster data in the form of multidimensional arrays. The user can access, process and delete the data using SQL. The key features of rasdaman are: flexibility (datasets of any dimensionality can be processed with the help of SQL queries), scalability (rasdaman's distributed architecture enables it to seamlessly run on cloud infrastructures while offering an increase in performance with the increase of computation resources), performance (real-time access, processing, mixing and filtering of arrays of any dimensionality) and reliability (legacy communication protocol replaced with a new one based on cutting edge technology - Google Protocol Buffers and ZeroMQ). Among the data with which the system works, we can count 1D time series, 2D remote sensing imagery, 3D image time series, 3D geophysical data, and 4D atmospheric and climate data. Most of these representations cannot be stored only in the form of raw arrays, as the location information of the contents is also important for having a correct geoposition on Earth. This is defined by ISO 19123 as coverage data. rasdaman provides coverage data support through the Petascope service. Extensions were added on top of rasdaman in order to provide support for the Geoscience community. The following OGC standards are currently supported: Web Map Service (WMS), Web Coverage Service (WCS), and Web Coverage Processing Service (WCPS). The Web Map Service is an extension which provides zoom and pan navigation over images provided by a map server. Starting with version 9.1, rasdaman supports WMS version 1.3. The Web Coverage Service provides capabilities for downloading multi-dimensional coverage data. Support is also provided for several extensions of this service: Subsetting Extension, Scaling Extension, and, starting with version 9.1, Transaction Extension, which

Fast and Lean Immutable Multi-Maps on the JVM based on Heterogeneous Hash-Array Mapped Tries

OpenAIRE

Steindorfer, Michael J.; Vinju, Jurgen J.

2016-01-01

textabstractAn immutable multi-map is a many-to-many thread-friendly map data structure with expected fast insert and lookup operations. This data structure is used for applications processing graphs or many-to-many relations as applied in static analysis of object-oriented systems. When processing such big data sets the memory overhead of the data structure encoding itself is a memory usage bottleneck. Motivated by reuse and type-safety, libraries for Java, Scala and Clojure typically implem...

Gender Fair Efficacy of Concept Mapping Tests in Identifying Students' Difficulties in High School Organic Chemistry

Science.gov (United States)

Gafoor, Kunnathodi Abdul; Shilna, V.

2014-01-01

In view of the perceived difficulty of organic chemistry unit for high schools students, this study examined the usefulness of concept mapping as a testing device to assess students' difficulty in the select areas. Since many tests used for identifying students misconceptions and difficulties in school subjects are observed to favour one or the…

Development and Evaluation of a Barley 50k iSelect SNP Array

Directory of Open Access Journals (Sweden)

Micha M. Bayer

2017-10-01

Full Text Available High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012 and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise × Morex cross (Liu et al., 2014 and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at https://ics.hutton.ac.uk/50k.

Analysis of the Mitogen-activated protein kinase kinase 4 (MAP2K4) tumor suppressor gene in ovarian cancer

International Nuclear Information System (INIS)

Davis, Sally J; Choong, David YH; Ramakrishna, Manasa; Ryland, Georgina L; Campbell, Ian G; Gorringe, Kylie L

2011-01-01

MAP2K4 is a putative tumor and metastasis suppressor gene frequently found to be deleted in various cancer types. We aimed to conduct a comprehensive analysis of this gene to assess its involvement in ovarian cancer. We screened for mutations in MAP2K4 using High Resolution Melt analysis of 149 primary ovarian tumors and methylation at the promoter using Methylation-Specific Single-Stranded Conformation Polymorphism analysis of 39 tumors. We also considered the clinical impact of changes in MAP2K4 using publicly available expression and copy number array data. Finally, we used siRNA to measure the effect of reducing MAP2K4 expression in cell lines. In addition to 4 previously detected homozygous deletions, we identified a homozygous 16 bp truncating deletion and a heterozygous 4 bp deletion, each in one ovarian tumor. No promoter methylation was detected. The frequency of MAP2K4 homozygous inactivation was 5.6% overall, and 9.8% in high-grade serous cases. Hemizygous deletion of MAP2K4 was observed in 38% of samples. There were significant correlations of copy number and expression in three microarray data sets. There was a significant correlation between MAP2K4 expression and overall survival in one expression array data set, but this was not confirmed in an independent set. Treatment of JAM and HOSE6.3 cell lines with MAP2K4 siRNA showed some reduction in proliferation. MAP2K4 is targeted by genetic inactivation in ovarian cancer and restricted to high grade serous and endometrioid carcinomas in our cohort

Spatio-temporal chaos and thermal noise in Josephson junction series arrays

International Nuclear Information System (INIS)

Dominguez, D.; Cerdeira, H.A.

1995-01-01

We study underdamped Josephson junction series arrays that are globally coupled through a resistive shunting load and driven by an rf bias current. We find that they can be an experimental realization of many phenomena currently studied in globally coupled logistic map. Depending on the bias current the array can show Shapiro steps but also spatio-temporal chaos or ''turbulence'' in the IV characteristics. In the turbulent phase there is a saturation of the broad band noise for a large number of junctions. This corresponds to a break down of the law of large numbers as seen in globally coupled maps. We study this phenomenon as a function of thermal noise. We find that when increasing the temperature the broad band noise decreases. (author). 8 refs, 1 fig

The structure of mode-locking regions of piecewise-linear continuous maps: II. Skew sawtooth maps

Science.gov (United States)

Simpson, D. J. W.

2018-05-01

In two-parameter bifurcation diagrams of piecewise-linear continuous maps on , mode-locking regions typically have points of zero width known as shrinking points. Near any shrinking point, but outside the associated mode-locking region, a significant proportion of parameter space can be usefully partitioned into a two-dimensional array of annular sectors. The purpose of this paper is to show that in these sectors the dynamics is well-approximated by a three-parameter family of skew sawtooth circle maps, where the relationship between the skew sawtooth maps and the N-dimensional map is fixed within each sector. The skew sawtooth maps are continuous, degree-one, and piecewise-linear, with two different slopes. They approximate the stable dynamics of the N-dimensional map with an error that goes to zero with the distance from the shrinking point. The results explain the complicated radial pattern of periodic, quasi-periodic, and chaotic dynamics that occurs near shrinking points.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

Directory of Open Access Journals (Sweden)

Moreau Yves

2005-05-01

Full Text Available Abstract Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH. One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

Characterization of switching field distributions in Ising-like magnetic arrays

Science.gov (United States)

Fraleigh, Robert D.; Kempinger, Susan; Lammert, Paul E.; Zhang, Sheng; Crespi, Vincent H.; Schiffer, Peter; Samarth, Nitin

2017-04-01

The switching field distribution within arrays of single-domain ferromagnetic islands incorporates both island-island interactions and quenched disorder in island geometry. Separating these two contributions is important for disentangling the effects of disorder and interactions in the magnetization dynamics of island arrays. Using submicron, spatially resolved Kerr imaging in an external magnetic field for islands with perpendicular magnetic anisotropy, we map out the evolution of island arrays during hysteresis loops. Resolving and tracking individual islands across four different lattice types and a range of interisland spacings, we can extract the individual switching fields of every island and thereby quantitatively determine the contributions of interactions and quenched disorder in the arrays. The width of the switching field distribution is found to be well fitted by a simple model comprising the sum of an array-independent contribution (interpreted as disorder induced) and a term proportional to the maximum field the entire rest of the array could exert on a single island, i.e., in a fully polarized state. This supports the claim that disorder in these arrays is primarily a single-island property and provides a methodology by which to quantify such disorder.

A 7T spine array based on electric dipole transmitters.

Science.gov (United States)

Duan, Qi; Nair, Govind; Gudino, Natalia; de Zwart, Jacco A; van Gelderen, Peter; Murphy-Boesch, Joe; Reich, Daniel S; Duyn, Jeff H; Merkle, Hellmut

2015-10-01

The goal of this study was to explore the feasibility of using an array of electric dipole antennas for RF transmission in spine MRI at high fields. A two-channel transmit array based on an electric dipole design was quantitatively optimized for 7T spine imaging and integrated with a receive array combining eight loop coils. Using B1+ mapping, the transmit efficiency of the dipole array was compared with a design using quadrature loop pairs. The radiofrequency energy deposition for each array was measured using a home-built dielectric phantom and MR thermometry. The performance of the proposed array was qualitatively demonstrated in human studies. The results indicate dramatically improved transmit efficiency for the dipole design compared with the loop excitation. A gain of up to 76% was achieved within the spinal region. For imaging of the spine, electric dipole-based transmitters provide an attractive alternative to the traditional loop-based design. Easy integration with existing receive array technology facilitates practical use at high fields. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Observations of basin ground motions from a dense seismic array in San Jose, California

Science.gov (United States)

Frankel, A.; Carver, D.; Cranswick, E.; Bice, T.; Sell, R.; Hanson, S.

2001-01-01

We installed a dense array of 41 digital seismographs in San Jose, California, to evaluate in detail the effects of a deep sedimentary basin and shallow sedimentary deposits on earthquake ground motions. This urban array is located near the eastern edge of the Santa Clara Valley and spans the Evergreen sedimentary basin identified by gravity data. Average station spacing is 1 km, with three stations initially spaced 110 m apart. Despite the high-noise urban environment, the stations of the array successfully triggered on and recorded small local earthquakes (M 2.5-2.8 at 10-25 km distance) and larger regional events such as the M 5.0 Bolinas earthquake (90 km distance), M 4.6-5.6 earthquakes near Mammoth Lakes (270 km distance), M 4.9-5.6 events in western Nevada (420 km distance) and the M 7.1 Hector Mine earthquake (590 km distance). Maps of spectral ratios across the array show that the highest amplitudes in all frequency bands studied (0.125-8 Hz) are generally observed at stations farther from the eastern edge of the Santa Clara Valley. Larger spectral amplitudes are often observed above the western edge of the Evergreen Basin. Snapshots of the recorded wavefield crossing the array for regional events to the east reveal that large, low-frequency (0.125-0.5 Hz) arrivals after the S-wave travel from south to north across the array. A moving-window, cross-correlation analysis finds that these later arrivals are surface waves traveling from the south. The timing and propagation direction of these arrivals indicates that they were likely produced by scattering of incident S waves at the border of the Santa Clara Valley to the south of the array. It is remarkable that the largest low-frequency phases at many of the valley sites for regional events to the east are basin surface waves coming from a direction about 70 degrees different from that of the epicenters. Basin surface waves emanating from the eastern edge of the valley are also identified by the cross

A Map of Copy Number Variations in Chinese Populations

Science.gov (United States)

Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in

A map of copy number variations in Chinese populations.

Directory of Open Access Journals (Sweden)

Haiyi Lou

Full Text Available It has been shown that the human genome contains extensive copy number variations (CNVs. Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%, which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a

Nonlinear dynamics of solitary and optically injected two-element laser arrays with four different waveguide structures: a numerical study.

Science.gov (United States)

Li, Nianqiang; Susanto, H; Cemlyn, B R; Henning, I D; Adams, M J

2018-02-19

We study the nonlinear dynamics of solitary and optically injected two-element laser arrays with a range of waveguide structures. The analysis is performed with a detailed direct numerical simulation, where high-resolution dynamic maps are generated to identify regions of dynamic instability in the parameter space of interest. Our combined one- and two-parameter bifurcation analysis uncovers globally diverse dynamical regimes (steady-state, oscillation, and chaos) in the solitary laser arrays, which are greatly influenced by static design waveguiding structures, the amplitude-phase coupling factor of the electric field, i.e. the linewidth-enhancement factor, as well as the control parameter, e.g. the pump rate. When external optical injection is introduced to one element of the arrays, we show that the whole system can be either injection-locked simultaneously or display rich, different dynamics outside the locking region. The effect of optical injection is to significantly modify the nature and the regions of nonlinear dynamics from those found in the solitary case. We also show similarities and differences (asymmetry) between the oscillation amplitude of the two elements of the array in specific well-defined regions, which hold for all the waveguiding structures considered. Our findings pave the way to a better understanding of dynamic instability in large arrays of lasers.

A genetic linkage map for the saltwater crocodile (Crocodylus porosus

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Lance Stacey L

2009-07-01

Full Text Available Abstract Background Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL, and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary. Results A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1. Conclusion We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD. However, at this point the reason for this disparity in saltwater crocodiles remains unclear. This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition

Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

Science.gov (United States)

Memon, Farhat N; Owen, Anne M; Sanchez-Graillet, Olivia; Upton, Graham J G; Harrison, Andrew P

2010-01-15

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays.

Evolution of an array of elements with logistic transition probability

International Nuclear Information System (INIS)

Majernik, Vladimir; Surda, Anton

1996-01-01

The paper addresses the problem how the state of an array of elements changes if the transition probabilities of its elements is chosen in the form of a logistic map. This problem leads to a special type of a discrete-time Markov which we simulated numerically for the different transition probabilities and the number of elements in the array. We show that the time evolution of the array exhibits a wide scale of behavior depending on the value of the total number of its elements and on the logistic constant a. We point out that this problem can be applied for description of a spin system with a certain type of mean field and of the multispecies ecosystems with an internal noise. (authors)

Identifying environmental risk factors and mapping the risk of human West Nile virus in South Dakota.

Science.gov (United States)

Hess, A.; Davis, J. K.; Wimberly, M. C.

2017-12-01

Human West Nile virus (WNV) first arrived in the USA in 1999 and has since then spread across the country. Today, the highest incidence rates are found in the state of South Dakota. The disease occurrence depends on the complex interaction between the mosquito vector, the bird host and the dead-end human host. Understanding the spatial domain of this interaction and being able to identify disease transmission hotspots is crucial for effective disease prevention and mosquito control. In this study we use geospatial environmental information to understand what drives the spatial distribution of cases of human West Nile virus in South Dakota and to map relative infection risk across the state. To map the risk of human West Nile virus in South Dakota, we used geocoded human case data from the years 2004-2016. Satellite data from the Landsat ETM+ and MODIS for the years 2003 to 2016 were used to characterize environmental patterns. From these datasets we calculated indices, such as the normalized differenced vegetation index (NDVI) and the normalized differenced water index (NDWI). In addition, datasets such as the National Land Data Assimilation System (NLDAS), National Land Cover Dataset (NLCD), National Wetland inventory (NWI), National Elevation Dataset (NED) and Soil Survey Geographic Database (SSURGO) were utilized. Environmental variables were summarized for a buffer zone around the case and control points. We used a boosted regression tree model to identify the most important variables describing the risk of WNV infection. We generated a risk map by applying this model across the entire state. We found that the highest relative risk is present in the James River valley in northeastern South Dakota. Factors that were identified as influencing the transmission risk include inter-annual variability of vegetation cover, water availability and temperature. Land covers such as grasslands, low developed areas and wetlands were also found to be good predictors for human

An Optimal DEM Reconstruction Method for Linear Array Synthetic Aperture Radar Based on Variational Model

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Shi Jun

2015-02-01

Full Text Available Downward-looking Linear Array Synthetic Aperture Radar (LASAR has many potential applications in the topographic mapping, disaster monitoring and reconnaissance applications, especially in the mountainous area. However, limited by the sizes of platforms, its resolution in the linear array direction is always far lower than those in the range and azimuth directions. This disadvantage leads to the blurring of Three-Dimensional (3D images in the linear array direction, and restricts the application of LASAR. To date, the research on 3D SAR image enhancement has focused on the sparse recovery technique. In this case, the one-to-one mapping of Digital Elevation Model (DEM brakes down. To overcome this, an optimal DEM reconstruction method for LASAR based on the variational model is discussed in an effort to optimize the DEM and the associated scattering coefficient map, and to minimize the Mean Square Error (MSE. Using simulation experiments, it is found that the variational model is more suitable for DEM enhancement applications to all kinds of terrains compared with the Orthogonal Matching Pursuit (OMPand Least Absolute Shrinkage and Selection Operator (LASSO methods.

Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations.

Science.gov (United States)

Yoneyama, S; Yao, J; Guo, X; Fernandez-Rhodes, L; Lim, U; Boston, J; Buzková, P; Carlson, C S; Cheng, I; Cochran, B; Cooper, R; Ehret, G; Fornage, M; Gong, J; Gross, M; Gu, C C; Haessler, J; Haiman, C A; Henderson, B; Hindorff, L A; Houston, D; Irvin, M R; Jackson, R; Kuller, L; Leppert, M; Lewis, C E; Li, R; Le Marchand, L; Matise, T C; Nguyen, K-Dh; Chakravarti, A; Pankow, J S; Pankratz, N; Pooler, L; Ritchie, M D; Bien, S A; Wassel, C L; Chen, Y-D I; Taylor, K D; Allison, M; Rotter, J I; Schreiner, P J; Schumacher, F; Wilkens, L; Boerwinkle, E; Kooperberg, C; Peters, U; Buyske, S; Graff, M; North, K E

2017-02-01

Central adiposity measures such as waist circumference (WC) and waist-to-hip ratio (WHR) are associated with cardiometabolic disorders independently of body mass index (BMI) and are gaining clinically utility. Several studies report genetic variants associated with central adiposity, but most utilize only European ancestry populations. Understanding whether the genetic associations discovered among mainly European descendants are shared with African ancestry populations will help elucidate the biological underpinnings of abdominal fat deposition. To identify the underlying functional genetic determinants of body fat distribution, we conducted an array-wide association meta-analysis among persons of African ancestry across seven studies/consortia participating in the Population Architecture using Genomics and Epidemiology (PAGE) consortium. We used the Metabochip array, designed for fine-mapping cardiovascular-associated loci, to explore novel array-wide associations with WC and WHR among 15 945 African descendants using all and sex-stratified groups. We further interrogated 17 known WHR regions for African ancestry-specific variants. Of the 17 WHR loci, eight single-nucleotide polymorphisms (SNPs) located in four loci were replicated in the sex-combined or sex-stratified meta-analyses. Two of these eight independently associated with WHR after conditioning on the known variant in European descendants (rs12096179 in TBX15-WARS2 and rs2059092 in ADAMTS9). In the fine-mapping assessment, the putative functional region was reduced across all four loci but to varying degrees (average 40% drop in number of putative SNPs and 20% drop in genomic region). Similar to previous studies, the significant SNPs in the female-stratified analysis were stronger than the significant SNPs from the sex-combined analysis. No novel associations were detected in the array-wide analyses. Of 17 previously identified loci, four loci replicated in the African ancestry populations of this

Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations

Science.gov (United States)

Yoneyama, Sachiko; Yao, Jie; Guo, Xiuqing; Fernandez-Rhodes, Lindsay; Lim, Unhee; Boston, Jonathan; Buzková, Petra; Carlson, Christopher S.; Cheng, Iona; Cochran, Barbara; Cooper, Richard; Ehret, Georg; Fornage, Myriam; Gong, Jian; Gross, Myron; Gu, C. Charles; Haessler, Jeff; Haiman, Christopher A.; Henderson, Brian; Hindorff, Lucia A.; Houston, Denise; Irvin, Marguerite R.; Jackson, Rebecca; Kuller, Lew; Leppert, Mark; Lewis, Cora E.; Li, Rongling; Le Marchand, Loic; Matise, Tara C.; Nguyen, Khanh-Dung H.; Chakravarti, Aravinda; Pankow, James S.; Pankratz, Nathan; Pooler, Loreall; Ritchie, Marylyn D.; Bien, Stephanie A.; Wassel, Christina L.; Chen, Yii-Der I.; Taylor, Kent D.; Allison, Matthew; Rotter, Jerome I.; Schreiner, Pamela J.; Schumacher, Fredrick; Wilkens, Lynne; Boerwinkle, Eric; Kooperberg, Charles; Peters, Ulrike; Buyske, Steven; Graff, Mariaelisa; North, Kari E.

2016-01-01

Background/Objectives Central adiposity measures such as waist circumference (WC) and waist-to-hip ratio (WHR) are associated with cardiometabolic disorders independently of BMI and are gaining clinically utility. Several studies report genetic variants associated with central adiposity, but most utilize only European ancestry populations. Understanding whether the genetic associations discovered among mainly European descendants are shared with African ancestry populations will help elucidate the biological underpinnings of abdominal fat deposition. Subjects/Methods To identify the underlying functional genetic determinants of body fat distribution, we conducted an array-wide association meta-analysis among persons of African ancestry across seven studies/consortia participating in the Population Architecture using Genomics and Epidemiology (PAGE) consortium. We used the Metabochip array, designed for fine mapping cardiovascular associated loci, to explore novel array-wide associations with WC and WHR among 15 945 African descendants using all and sex-stratified groups. We further interrogated 17 known WHR regions for African ancestry-specific variants. Results Of the 17 WHR loci, eight SNPs located in four loci were replicated in the sex-combined or sex-stratified meta-analyses. Two of these eight independently associated with WHR after conditioning on the known variant in European descendants (rs12096179 in TBX15-WARS2 and rs2059092 in ADAMTS9). In the fine mapping assessment, the putative functional region was reduced across all four loci but to varying degrees (average 40% drop in number of putative SNPs and 20% drop in genomic region). Similar to previous studies, the significant SNPs in the female stratified analysis were stronger than the significant SNPs from the sex-combined analysis. No novel associations were detected in the array-wide analyses. Conclusions Of 17 previously identified loci, four loci replicated in the African ancestry populations of

CRISPRDetect: A flexible algorithm to define CRISPR arrays.

Science.gov (United States)

Biswas, Ambarish; Staals, Raymond H J; Morales, Sergio E; Fineran, Peter C; Brown, Chris M

2016-05-17

CRISPR (clustered regularly interspaced short palindromic repeats) RNAs provide the specificity for noncoding RNA-guided adaptive immune defence systems in prokaryotes. CRISPR arrays consist of repeat sequences separated by specific spacer sequences. CRISPR arrays have previously been identified in a large proportion of prokaryotic genomes. However, currently available detection algorithms do not utilise recently discovered features regarding CRISPR loci. We have developed a new approach to automatically detect, predict and interactively refine CRISPR arrays. It is available as a web program and command line from bioanalysis.otago.ac.nz/CRISPRDetect. CRISPRDetect discovers putative arrays, extends the array by detecting additional variant repeats, corrects the direction of arrays, refines the repeat/spacer boundaries, and annotates different types of sequence variations (e.g. insertion/deletion) in near identical repeats. Due to these features, CRISPRDetect has significant advantages when compared to existing identification tools. As well as further support for small medium and large repeats, CRISPRDetect identified a class of arrays with 'extra-large' repeats in bacteria (repeats 44-50 nt). The CRISPRDetect output is integrated with other analysis tools. Notably, the predicted spacers can be directly utilised by CRISPRTarget to predict targets. CRISPRDetect enables more accurate detection of arrays and spacers and its gff output is suitable for inclusion in genome annotation pipelines and visualisation. It has been used to analyse all complete bacterial and archaeal reference genomes.

Admixture mapping of 15,280 African Americans identifies obesity susceptibility loci on chromosomes 5 and X.

Directory of Open Access Journals (Sweden)

Ching-Yu Cheng

2009-05-01

Full Text Available The prevalence of obesity (body mass index (BMI > or =30 kg/m(2 is higher in African Americans than in European Americans, even after adjustment for socioeconomic factors, suggesting that genetic factors may explain some of the difference. To identify genetic loci influencing BMI, we carried out a pooled analysis of genome-wide admixture mapping scans in 15,280 African Americans from 14 epidemiologic studies. Samples were genotyped at a median of 1,411 ancestry-informative markers. After adjusting for age, sex, and study, BMI was analyzed both as a dichotomized (top 20% versus bottom 20% and a continuous trait. We found that a higher percentage of European ancestry was significantly correlated with lower BMI (rho = -0.042, P = 1.6x10(-7. In the dichotomized analysis, we detected two loci on chromosome X as associated with increased African ancestry: the first at Xq25 (locus-specific LOD = 5.94; genome-wide score = 3.22; case-control Z = -3.94; and the second at Xq13.1 (locus-specific LOD = 2.22; case-control Z = -4.62. Quantitative analysis identified a third locus at 5q13.3 where higher BMI was highly significantly associated with greater European ancestry (locus-specific LOD = 6.27; genome-wide score = 3.46. Further mapping studies with dense sets of markers will be necessary to identify the alleles in these regions of chromosomes X and 5 that may be associated with variation in BMI.

Joint Analysis of BICEP2/Keck Array and Planck Data

DEFF Research Database (Denmark)

Ade, P. A. R.; Aghanim, N.; Ahmed, Z.

2015-01-01

We report the results of a joint analysis of data from BICEP2/Keck Array and Planck. BICEP2 and Keck Array have observed the same approximately 400 deg2 patch of sky centered on RA 0 h, Dec. -57.5°. The combined maps reach a depth of 57 nK deg in Stokes Q and U in a band centered at 150 GHz. Planck...... GHz to a lensed-ΛCDM model that includes dust and a possible contribution from inflationary gravitational waves (as parametrized by the tensor-to-scalar ratio r), using a prior on the frequency spectral behavior of polarized dust emission from previous Planck analysis of other regions of the sky. We...... present an alternative analysis which is similar to a map-based cleaning of the dust contribution, and show that this gives similar constraints. The final result is expressed as a likelihood curve for r, and yields an upper limit r 0.05

Don't throw the baby out with the bathwater: identifying and mapping paralogs in salmonids.

Science.gov (United States)

Dufresne, France

2016-01-01

Many eukaryotic genomes contain a large fraction of gene duplicates (or paralogs) as a result of ancient or recent whole-genome duplications (Ohno 1970; Jaillon et al. 2004; Kellis et al. 2004). Identifying paralogs with NGS data is a pervasive problem in both ancient polyploids and neopolyploids. Likewise, paralogs are often treated as a nuisance that has to be detected and removed (Everett et al. 2012). In this issue of Molecular Ecology Resources, Waples et al. (2015) show that exclusion might not be necessary and how we may miss out on important genomic information in doing so. They present a novel statistical approach to detect paralogs based on the segregation of RAD loci in haploid offspring and test their method by constructing linkage maps with and without these duplicated loci in chum salmon, Oncorhynchus keta (Fig.1). Their linkage map including the resolved paralogs shows that these are mostly located in the distal regions of several linkage groups. Particularly intriguing is their finding that these homoeologous regions appear impoverished in transposable elements (TE). Given the role that TE play in genome remodelling, it is noteworthy that these elements are of low abundance in regions showing residual tetrasomic inheritance. This raises the question whether re-diploidization is constrained in these regions and whether they might have a role to play in salmonid speciation. This study provides an original approach to identifying duplicated loci in species with a pedigree, as well as providing a dense linkage map for chum salmon, and interesting insights into the retention of gene duplicates in an ancient polyploid. © 2015 John Wiley & Sons Ltd.

Array capabilities and future arrays

International Nuclear Information System (INIS)

Radford, D.

1993-01-01

Early results from the new third-generation instruments GAMMASPHERE and EUROGAM are confirming the expectation that such arrays will have a revolutionary effect on the field of high-spin nuclear structure. When completed, GAMMASHPERE will have a resolving power am order of magnitude greater that of the best second-generation arrays. When combined with other instruments such as particle-detector arrays and fragment mass analysers, the capabilites of the arrays for the study of more exotic nuclei will be further enhanced. In order to better understand the limitations of these instruments, and to design improved future detector systems, it is important to have some intelligible and reliable calculation for the relative resolving power of different instrument designs. The derivation of such a figure of merit will be briefly presented, and the relative sensitivities of arrays currently proposed or under construction presented. The design of TRIGAM, a new third-generation array proposed for Chalk River, will also be discussed. It is instructive to consider how far arrays of Compton-suppressed Ge detectors could be taken. For example, it will be shown that an idealised open-quote perfectclose quotes third-generation array of 1000 detectors has a sensitivity an order of magnitude higher again than that of GAMMASPHERE. Less conventional options for new arrays will also be explored

Performance Analysis of Compact FD-MIMO Antenna Arrays in a Correlated Environment

KAUST Repository

Nadeem, Qurrat-Ul-Ain

2017-03-06

Full dimension multiple-input-multiple-output (FDMIMO) is one of the key technologies proposed in the 3rd Generation Partnership Project (3GPP) for the fifth generation (5G) communication systems. The reason can be attributed to its ability to yield significant performance gains through the deployment of active antenna elements at the base station in the vertical as well as the conventional horizontal directions, enabling several elevation beamforming strategies. The resulting improvement in spectral efficiency largely depends on the orthogonality of the sub-channels constituting the FD-MIMO system. Accommodating a large number of antenna elements with sufficient spacing poses several constraints for practical implementation, making it imperative to consider compact antenna arrangements that minimize the overall channel correlation. Two such configurations considered in this work are the uniform linear array (ULA) and the uniform circular array (UCA) of antenna ports, where each port is mapped to a group of physical antenna elements arranged in the vertical direction. The generalized analytical expression for the spatial correlation function (SCF) for the UCA is derived, exploiting results on spherical harmonics and Legendre polynomials. The mutual coupling between antenna dipoles is accounted for and the resulting SCF is also presented. The second part of this work compares the spatial correlation and mutual information (MI) performance of the ULA and UCA configurations in the 3GPP 3D urban-macro and urban-micro cell scenarios, utilizing results from Random Matrix Theory (RMT) on the deterministic equivalent of the MI for the Kronecker channel model. Simulation results study the performance patterns of the two arrays as a function of several channel and array parameters and identify applications and environments suitable for the deployment of each array.

Urinary Colorimetric Sensor Array and Algorithm to Distinguish Kawasaki Disease from Other Febrile Illnesses.

Directory of Open Access Journals (Sweden)

Zhen Li

Full Text Available Kawasaki disease (KD is an acute pediatric vasculitis of infants and young children with unknown etiology and no specific laboratory-based test to identify. A specific molecular diagnostic test is urgently needed to support the clinical decision of proper medical intervention, preventing subsequent complications of coronary artery aneurysms. We used a simple and low-cost colorimetric sensor array to address the lack of a specific diagnostic test to differentiate KD from febrile control (FC patients with similar rash/fever illnesses.Demographic and clinical data were prospectively collected for subjects with KD and FCs under standard protocol. After screening using a genetic algorithm, eleven compounds including metalloporphyrins, pH indicators, redox indicators and solvatochromic dye categories, were selected from our chromatic compound library (n = 190 to construct a colorimetric sensor array for diagnosing KD. Quantitative color difference analysis led to a decision-tree-based KD diagnostic algorithm.This KD sensing array allowed the identification of 94% of KD subjects (receiver operating characteristic [ROC] area under the curve [AUC] 0.981 in the training set (33 KD, 33 FC and 94% of KD subjects (ROC AUC: 0.873 in the testing set (16 KD, 17 FC. Color difference maps reconstructed from the digital images of the sensing compounds demonstrated distinctive patterns differentiating KD from FC patients.The colorimetric sensor array, composed of common used chemical compounds, is an easily accessible, low-cost method to realize the discrimination of subjects with KD from other febrile illness.

Galaxy evolution, cosmology and dark energy with the Square Kilometer Array

NARCIS (Netherlands)

Rawlings, S; Abdalla, FB; Bridle, SL; Blake, CA; Baugh, CM; Greenhill, LJ; van der Hulst, JM

2004-01-01

The present-day Universe is seemingly dominated by dark energy and dark matter, but mapping the normal (baryonic) content remains vital for both astrophysics - understanding how galaxies form - and astro-particle physics inferring properties of the dark components. The Square Kilometer Array (SKA)

Evaluation of realistic layouts for next generation on-scalp MEG: spatial information density maps.

Science.gov (United States)

Riaz, Bushra; Pfeiffer, Christoph; Schneiderman, Justin F

2017-08-01

While commercial magnetoencephalography (MEG) systems are the functional neuroimaging state-of-the-art in terms of spatio-temporal resolution, MEG sensors have not changed significantly since the 1990s. Interest in newer sensors that operate at less extreme temperatures, e.g., high critical temperature (high-T c ) SQUIDs, optically-pumped magnetometers, etc., is growing because they enable significant reductions in head-to-sensor standoff (on-scalp MEG). Various metrics quantify the advantages of on-scalp MEG, but a single straightforward one is lacking. Previous works have furthermore been limited to arbitrary and/or unrealistic sensor layouts. We introduce spatial information density (SID) maps for quantitative and qualitative evaluations of sensor arrays. SID-maps present the spatial distribution of information a sensor array extracts from a source space while accounting for relevant source and sensor parameters. We use it in a systematic comparison of three practical on-scalp MEG sensor array layouts (based on high-T c SQUIDs) and the standard Elekta Neuromag TRIUX magnetometer array. Results strengthen the case for on-scalp and specifically high-T c SQUID-based MEG while providing a path for the practical design of future MEG systems. SID-maps are furthermore general to arbitrary magnetic sensor technologies and source spaces and can thus be used for design and evaluation of sensor arrays for magnetocardiography, magnetic particle imaging, etc.

Maximum power point tracking of partially shaded solar photovoltaic arrays

Energy Technology Data Exchange (ETDEWEB)

Roy Chowdhury, Shubhajit; Saha, Hiranmay [IC Design and Fabrication Centre, Department of Electronics and Telecommunication Engineering, Jadavpur University (India)

2010-09-15

The paper presents the simulation and hardware implementation of maximum power point (MPP) tracking of a partially shaded solar photovoltaic (PV) array using a variant of Particle Swarm Optimization known as Adaptive Perceptive Particle Swarm Optimization (APPSO). Under partially shaded conditions, the photovoltaic (PV) array characteristics get more complex with multiple maxima in the power-voltage characteristic. The paper presents an algorithmic technique to accurately track the maximum power point (MPP) of a PV array using an APPSO. The APPSO algorithm has also been validated in the current work. The proposed technique uses only one pair of sensors to control multiple PV arrays. This result in lower cost and higher accuracy of 97.7% compared to earlier obtained accuracy of 96.41% using Particle Swarm Optimization. The proposed tracking technique has been mapped onto a MSP430FG4618 microcontroller for tracking and control purposes. The whole system based on the proposed has been realized on a standard two stage power electronic system configuration. (author)

A high-density Diversity Arrays Technology (DArT microarray for genome-wide genotyping in Eucalyptus

Directory of Open Access Journals (Sweden)

Myburg Alexander A

2010-06-01

Full Text Available Abstract Background A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. Findings After testing several genome complexity reduction methods we identified the PstI/TaqI method as the most effective for Eucalyptus and developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56% were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. Conclusions This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees

Passive cavitation imaging with ultrasound arrays.

Science.gov (United States)

Salgaonkar, Vasant A; Datta, Saurabh; Holland, Christy K; Mast, T Douglas

2009-12-01

A method is presented for passive imaging of cavitational acoustic emissions using an ultrasound array, with potential application in real-time monitoring of ultrasound ablation. To create such images, microbubble emissions were passively sensed by an imaging array and dynamically focused at multiple depths. In this paper, an analytic expression for a passive image is obtained by solving the Rayleigh-Sommerfield integral, under the Fresnel approximation, and passive images were simulated. A 192-element array was used to create passive images, in real time, from 520-kHz ultrasound scattered by a 1-mm steel wire. Azimuthal positions of this target were accurately estimated from the passive images. Next, stable and inertial cavitation was passively imaged in saline solution sonicated at 520 kHz. Bubble clusters formed in the saline samples were consistently located on both passive images and B-scans. Passive images were also created using broadband emissions from bovine liver sonicated at 2.2 MHz. Agreement was found between the images and source beam shape, indicating an ability to map therapeutic ultrasound beams in situ. The relation between these broadband emissions, sonication amplitude, and exposure conditions are discussed.

Tunoe Knob wind turbine array. Visualization and aesthetic evaluation

International Nuclear Information System (INIS)

1994-09-01

The aesthetic affects of locating a wind turbine array in the Danish coastal waters at Tunoe Knob between Tunoe and the Juttish east coast are discussed. The visualization project made use of a video film which analyzed the effect of the configurations of the wind turbine array on the coastal landscape as seen from a number viewpoints. A computer model illustrated the aesthetic effects of viewing the windmills as the viewer moves along the east coast of Jutland and across the sea towards the islands of Tunoe and Samsoe. The results should form the basis of the authorities' decision-making regarding the configuration of the wind turbine array. An account of the methods of visualization and a description of the visualization methods, in addition to the criteria on which the choice of the configuration was based are given. The chosen configuration is visualized, from points that are near and far from the wind turbine array, in the form of maps, diagrams and photographs of the sea and landscape. (AB)

A Wearable Transcranial Doppler Ultrasound Phased Array System.

Science.gov (United States)

Pietrangelo, Sabino J; Lee, Hae-Seung; Sodini, Charles G

2018-01-01

 Practical deficiencies related to conventional transcranial Doppler (TCD) sonography have restricted its use and applicability. This work seeks to mitigate several such constraints through the development of a wearable, electronically steered TCD velocimetry system, which enables noninvasive measurement of cerebral blood flow velocity (CBFV) for monitoring applications with limited operator interaction. A highly-compact, discrete prototype system was designed and experimentally validated through flow phantom and preliminary human subject testing. The prototype system incorporates a custom two-dimensional transducer array and multi-channel transceiver electronics, thereby facilitating acoustic beamformation via phased array operation. Electronic steering of acoustic energy enables algorithmic system controls to map Doppler power throughout the tissue volume of interest and localize regions of maximal flow. Multi-focal reception permits dynamic vessel position tracking and simultaneous flow velocimetry over the time-course of monitoring. Experimental flow phantom testing yielded high correlation with concurrent flowmeter recordings across the expected range of physiological flow velocities. Doppler power mapping has been validated in both flow phantom and preliminary human subject testing, resulting in average vessel location mapping times testing. A wearable prototype CBFV measurement system capable of autonomous vessel search and tracking has been presented. Although flow phantom and preliminary human validation show promise, further human subject testing is necessary to compare velocimetry data against existing commercial TCD systems. Additional human subject testing must also verify acceptable vessel search and tracking performance under a variety of subject populations and motion dynamics-such as head movement and ambulation.

The optimal configuration of photovoltaic module arrays based on adaptive switching controls

International Nuclear Information System (INIS)

Chao, Kuei-Hsiang; Lai, Pei-Lun; Liao, Bo-Jyun

2015-01-01

Highlights: • We propose a strategy for determining the optimal configuration of a PV array. • The proposed strategy was based on particle swarm optimization (PSO) method. • It can identify the optimal module array connection scheme in the event of shading. • It can also find the optimal connection of a PV array even in module malfunctions. - Abstract: This study proposes a strategy for determining the optimal configuration of photovoltaic (PV) module arrays in shading or malfunction conditions. This strategy was based on particle swarm optimization (PSO). If shading or malfunctions of the photovoltaic module array occur, the module array immediately undergoes adaptive reconfiguration to increase the power output of the PV power generation system. First, the maximal power generated at various irradiation levels and temperatures was recorded during normal array operation. Subsequently, the irradiation level and module temperature, regardless of operating conditions, were used to recall the maximal power previously recorded. This previous maximum was compared with the maximal power value obtained using the maximum power point tracker to assess whether the PV module array was experiencing shading or malfunctions. After determining that the array was experiencing shading or malfunctions, PSO was used to identify the optimal module array connection scheme in abnormal conditions, and connection switches were used to implement optimal array reconfiguration. Finally, experiments were conducted to assess the strategy for identifying the optimal reconfiguration of a PV module array in the event of shading or malfunctions

Breakdown of the law of large numbers in Josephson junction series arrays

International Nuclear Information System (INIS)

Dominguez, D.; Cerdeira, H.A.

1994-01-01

We study underdamped Josephson junction series arrays that are globally coupled through a resistive shunting load and driven by an rf bias current. We find that they can be an experimental realization of many phenomena currently studied in globally coupled logistic maps. We find coherent, ordered, partially ordered and turbulent phases in the IV characteristics of the array. The ordered phase corresponds to giant Shapiro steps. In the turbulent phase there is a saturation of the broad band noise for a large number of junctions. This corresponds to a break down of the law of large numbers as seen in the globally coupled maps. Coexisting with this, we find an emergence of novel pseudo-steps in the IV characteristics. This effect can be experimentally distinguished from the Shapiro steps, which do not have broad band noise emission. (author). 21 refs, 5 figs

Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs)

OpenAIRE

Darabi, Hatef; Beesley, Jonathan; Droit, Arnaud; Kar, Siddhartha; Nord, Silje; Moradi Marjaneh, Mahdi; Soucy, Penny; Michailidou, Kyriaki; Ghoussaini, Maya; Fues Wahl, Hanna; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Alonso, M Rosario; Andrulis, Irene L.

2016-01-01

Genome-wide association studies have found SNPs at 17q22 to be associated with breast cancer risk. To identify potential causal variants related to breast cancer risk, we performed a high resolution fine-mapping analysis that involved genotyping 517 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of genotypes for 3,134 SNPs in more than 89,000 participants of European ancestry from the Breast Cancer Association Consortium (BCAC). We identified 28 highly correlated co...

Physical mapping of QTL for tuber yield, starch content and starch yield in tetraploid potato (Solanum tuberosum L.) by means of genome wide genotyping by sequencing and the 8.3 K SolCAP SNP array.

Science.gov (United States)

Schönhals, Elske Maria; Ding, Jia; Ritter, Enrique; Paulo, Maria João; Cara, Nicolás; Tacke, Ekhard; Hofferbert, Hans-Reinhard; Lübeck, Jens; Strahwald, Josef; Gebhardt, Christiane

2017-08-22

Tuber yield and starch content of the cultivated potato are complex traits of decisive importance for breeding improved varieties. Natural variation of tuber yield and starch content depends on the environment and on multiple, mostly unknown genetic factors. Dissection and molecular identification of the genes and their natural allelic variants controlling these complex traits will lead to the development of diagnostic DNA-based markers, by which precision and efficiency of selection can be increased (precision breeding). Three case-control populations were assembled from tetraploid potato cultivars based on maximizing the differences between high and low tuber yield (TY), starch content (TSC) and starch yield (TSY, arithmetic product of TY and TSC). The case-control populations were genotyped by restriction-site associated DNA sequencing (RADseq) and the 8.3 k SolCAP SNP genotyping array. The allele frequencies of single nucleotide polymorphisms (SNPs) were compared between cases and controls. RADseq identified, depending on data filtering criteria, between 6664 and 450 genes with one or more differential SNPs for one, two or all three traits. Differential SNPs in 275 genes were detected using the SolCAP array. A genome wide association study using the SolCAP array on an independent, unselected population identified SNPs associated with tuber starch content in 117 genes. Physical mapping of the genes containing differential or associated SNPs, and comparisons between the two genome wide genotyping methods and two different populations identified genome segments on all twelve potato chromosomes harboring one or more quantitative trait loci (QTL) for TY, TSC and TSY. Several hundred genes control tuber yield and starch content in potato. They are unequally distributed on all potato chromosomes, forming clusters between 0.5-4 Mbp width. The largest fraction of these genes had unknown function, followed by genes with putative signalling and regulatory functions. The

Optimization of a large-area detector-block based on SiPM and pixelated LYSO crystal arrays.

Science.gov (United States)

Calva-Coraza, E; Alva-Sánchez, H; Murrieta-Rodríguez, T; Martínez-Dávalos, A; Rodríguez-Villafuerte, M

2017-10-01

We present the performance evaluation of a large-area detector module based on the ArrayC-60035-64P, an 8×8 array of tileable, 7.2mm pitch, silicon photomultipliers (SiPM) by SensL, covering a total area of 57.4mm×57.4mm. We characterized the ArrayC-60035-64P, operating at room temperature, using LYSO pixelated crystal arrays of different pitch sizes (1.075, 1.430, 1.683, 2.080 and 2.280mm) to determine the resolvable crystal size. After an optimization process, a 7mm thick coupling light guide was used for all crystal pitches. To identify the interaction position a 16-channel (8 columns, 8 rows) symmetric charge division (SCD) readout board together with a center-of-gravity algorithm was used. Based on this, we assembled the detector modules using a 40×40 LYSO, 1.43mm pitch array, covering the total detector area. Calibration was performed using a 137 Cs source resulting in excellent crystal maps with minor geometric distortion, a mean 4.1 peak-to-valley ratio and 9.6% mean energy resolution for 662keV photons in the central region. The resolvability index was calculated in the x and y directions with values under 0.42 in all cases. We show that these large area SiPM arrays, combined with a 16-channel SCD readout board, can offer high spatial resolution, without processing a big number of signals, attaining excellent energy resolution and detector uniformity. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Observing the Sun with the Atacama Large Millimeter/submillimeter Array (ALMA): Fast-Scan Single-Dish Mapping

Science.gov (United States)

White, S. M.; Iwai, K.; Phillips, N. M.; Hills, R. E.; Hirota, A.; Yagoubov, P.; Siringo, G.; Shimojo, M.; Bastian, T. S.; Hales, A. S.; Sawada, T.; Asayama, S.; Sugimoto, M.; Marson, R. G.; Kawasaki, W.; Muller, E.; Nakazato, T.; Sugimoto, K.; Brajša, R.; Skokić, I.; Bárta, M.; Kim, S.; Remijan, A. J.; de Gregorio, I.; Corder, S. A.; Hudson, H. S.; Loukitcheva, M.; Chen, B.; De Pontieu, B.; Fleishmann, G. D.; Gary, D. E.; Kobelski, A.; Wedemeyer, S.; Yan, Y.

2017-07-01

The Atacama Large Millimeter/submillimeter Array (ALMA) radio telescope has commenced science observations of the Sun starting in late 2016. Since the Sun is much larger than the field of view of individual ALMA dishes, the ALMA interferometer is unable to measure the background level of solar emission when observing the solar disk. The absolute temperature scale is a critical measurement for much of ALMA solar science, including the understanding of energy transfer through the solar atmosphere, the properties of prominences, and the study of shock heating in the chromosphere. In order to provide an absolute temperature scale, ALMA solar observing will take advantage of the remarkable fast-scanning capabilities of the ALMA 12 m dishes to make single-dish maps of the full Sun. This article reports on the results of an extensive commissioning effort to optimize the mapping procedure, and it describes the nature of the resulting data. Amplitude calibration is discussed in detail: a path that uses the two loads in the ALMA calibration system as well as sky measurements is described and applied to commissioning data. Inspection of a large number of single-dish datasets shows significant variation in the resulting temperatures, and based on the temperature distributions, we derive quiet-Sun values at disk center of 7300 K at λ = 3 mm and 5900 K at λ = 1.3 mm. These values have statistical uncertainties of about 100 K, but systematic uncertainties in the temperature scale that may be significantly larger. Example images are presented from two periods with very different levels of solar activity. At a resolution of about 25'', the 1.3 mm wavelength images show temperatures on the disk that vary over about a 2000 K range. Active regions and plages are among the hotter features, while a large sunspot umbra shows up as a depression, and filament channels are relatively cool. Prominences above the solar limb are a common feature of the single-dish images.

An initial comparative map of copy number variations in the goat (Capra hircus genome

Directory of Open Access Journals (Sweden)

Casadio Rita

2010-11-01

Full Text Available Abstract Background The goat (Capra hircus represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH experiment in order to identify copy number variations (CNVs in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. Results We identified a total of 161 CNVs (an average of 17.9 CNVs per goat, with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs: on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome. These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P Conclusions We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the

Identifying and Mapping Linkages between Actors in the Climate ...

African Journals Online (AJOL)

Promoting innovations in climate change requires innovation partnerships and linkages and also creating an enabling environment for actors. The paper reviewed available information on the identification and mapping of linkages between actors in the climate change innovation system. The findings showed different ...

Array-based techniques for fingerprinting medicinal herbs

Directory of Open Access Journals (Sweden)

Xue Charlie

2011-05-01

Full Text Available Abstract Poor quality control of medicinal herbs has led to instances of toxicity, poisoning and even deaths. The fundamental step in quality control of herbal medicine is accurate identification of herbs. Array-based techniques have recently been adapted to authenticate or identify herbal plants. This article reviews the current array-based techniques, eg oligonucleotides microarrays, gene-based probe microarrays, Suppression Subtractive Hybridization (SSH-based arrays, Diversity Array Technology (DArT and Subtracted Diversity Array (SDA. We further compare these techniques according to important parameters such as markers, polymorphism rates, restriction enzymes and sample type. The applicability of the array-based methods for fingerprinting depends on the availability of genomics and genetics of the species to be fingerprinted. For the species with few genome sequence information but high polymorphism rates, SDA techniques are particularly recommended because they require less labour and lower material cost.

WAMI: a web server for the analysis of minisatellite maps

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El-Kalioby Mohamed

2010-06-01

Full Text Available Abstract Background Minisatellites are genomic loci composed of tandem arrays of short repetitive DNA segments. A minisatellite map is a sequence of symbols that represents the tandem repeat array such that the set of symbols is in one-to-one correspondence with the set of distinct repeats. Due to variations in repeat type and organization as well as copy number, the minisatellite maps have been widely used in forensic and population studies. In either domain, researchers need to compare the set of maps to each other, to build phylogenetic trees, to spot structural variations, and to study duplication dynamics. Efficient algorithms for these tasks are required to carry them out reliably and in reasonable time. Results In this paper we present WAMI, a web-server for the analysis of minisatellite maps. It performs the above mentioned computational tasks using efficient algorithms that take the model of map evolution into account. The WAMI interface is easy to use and the results of each analysis task are visualized. Conclusions To the best of our knowledge, WAMI is the first server providing all these computational facilities to the minisatellite community. The WAMI web-interface and the source code of the underlying programs are available at http://www.nubios.nileu.edu.eg/tools/wami.

Systems and methods that generate height map models for efficient three dimensional reconstruction from depth information

Science.gov (United States)

Frahm, Jan-Michael; Pollefeys, Marc Andre Leon; Gallup, David Robert

2015-12-08

Methods of generating a three dimensional representation of an object in a reference plane from a depth map including distances from a reference point to pixels in an image of the object taken from a reference point. Weights are assigned to respective voxels in a three dimensional grid along rays extending from the reference point through the pixels in the image based on the distances in the depth map from the reference point to the respective pixels, and a height map including an array of height values in the reference plane is formed based on the assigned weights. An n-layer height map may be constructed by generating a probabilistic occupancy grid for the voxels and forming an n-dimensional height map comprising an array of layer height values in the reference plane based on the probabilistic occupancy grid.

Fine mapping of a linkage peak with integration of lipid traits identifies novel coronary artery disease genes on chromosome 5

Directory of Open Access Journals (Sweden)

Nolan Daniel K

2012-02-01

Full Text Available Abstract Background Coronary artery disease (CAD, and one of its intermediate risk factors, dyslipidemia, possess a demonstrable genetic component, although the genetic architecture is incompletely defined. We previously reported a linkage peak on chromosome 5q31-33 for early-onset CAD where the strength of evidence for linkage was increased in families with higher mean low density lipoprotein-cholesterol (LDL-C. Therefore, we sought to fine-map the peak using association mapping of LDL-C as an intermediate disease-related trait to further define the etiology of this linkage peak. The study populations consisted of 1908 individuals from the CATHGEN biorepository of patients undergoing cardiac catheterization; 254 families (N = 827 individuals from the GENECARD familial study of early-onset CAD; and 162 aorta samples harvested from deceased donors. Linkage disequilibrium-tagged SNPs were selected with an average of one SNP per 20 kb for 126.6-160.2 MB (region of highest linkage and less dense spacing (one SNP per 50 kb for the flanking regions (117.7-126.6 and 160.2-167.5 MB and genotyped on all samples using a custom Illumina array. Association analysis of each SNP with LDL-C was performed using multivariable linear regression (CATHGEN and the quantitative trait transmission disequilibrium test (QTDT; GENECARD. SNPs associated with the intermediate quantitative trait, LDL-C, were then assessed for association with CAD (i.e., a qualitative phenotype using linkage and association in the presence of linkage (APL; GENECARD and logistic regression (CATHGEN and aortas. Results We identified four genes with SNPs that showed the strongest and most consistent associations with LDL-C and CAD: EBF1, PPP2R2B, SPOCK1, and PRELID2. The most significant results for association of SNPs with LDL-C were: EBF1, rs6865969, p = 0.01; PPP2R2B, rs2125443, p = 0.005; SPOCK1, rs17600115, p = 0.003; and PRELID2, rs10074645, p = 0.0002. The most significant results for

Damage detection on mesosurfaces using distributed sensor network and spectral diffusion maps

International Nuclear Information System (INIS)

Chinde, V; Vaidya, U; Laflamme, S; Cao, L

2016-01-01

In this work, we develop a data-driven method for the diagnosis of damage in mesoscale mechanical structures using an array of distributed sensor networks. The proposed approach relies on comparing intrinsic geometries of data sets corresponding to the undamaged and damaged states of the system. We use a spectral diffusion map approach to identify the intrinsic geometry of the data set. In particular, time series data from distributed sensors is used for the construction of diffusion maps. The low dimensional embedding of the data set corresponding to different damage levels is obtained using a singular value decomposition of the diffusion map. We construct appropriate metrics in the diffusion space to compare the different data sets corresponding to different damage cases. The developed algorithm is applied for damage diagnosis of wind turbine blades. To achieve this goal, we developed a detailed finite element-based model of CX-100 blade in ANSYS using shell elements. Typical damage, such as crack or delamination, will lead to a loss of stiffness, is modeled by altering the stiffness of the laminate layer. One of the main challenges in the development of health monitoring algorithms is the ability to use sensor data with a relatively small signal-to-noise ratio. Our developed diffusion map-based algorithm is shown to be robust to the presence of sensor noise. The proposed diffusion map-based algorithm is advantageous by enabling the comparison of data from numerous sensors of similar or different types of data through data fusion, hereby making it attractive to exploit the distributed nature of sensor arrays. This distributed nature is further exploited for the purpose of damage localization. We perform extensive numerical simulations to demonstrate that the proposed method can successfully determine the extent of damage on the wind turbine blade and also localize the damage. We also present preliminary results for the application of the developed algorithm on

Advanced Geophysical Classification with the Marine Towed Array

Science.gov (United States)

Steinhurst, D.; Harbaugh, G.; Keiswetter, D.; Bell, T. W.; Massey, G.; Wright, D.

2017-12-01

The Marine Towed Array, or MTA, is an underwater dual-mode sensor array that has been successfully deployed at multiple marine venues in support of Strategic Environmental Research and Development Program (SERDP) and Environmental Security Technology Certification Program (ESTCP) demonstrations beginning in 2004. It provided both marine electromagnetic and marine magnetic sensors for detection and mapping of underwater UXO. The EMI sensor array was based on older technology, which in several ESTCP demonstrations has not been able to support advanced geophysical classification (AGC). Under ESTCP funding, the U.S. Naval Research Laboratory is in the process of upgrading the MTA with modern, advanced electromagnetic (EMI) electronics and replacing the sensor array with a modern, multistatic array design. A half-scale version of the proposed array has been built and tested on land. Six tri-axial receiver cubes were placed inside two- and three- transmit coil configurations in equivalent positions to design locations for the MTA wing. The responses of a variety of munitions items and test spheres were measured over a range of target-to-array geometries and in both static and simulated dynamic data collection modes. The multi-transmit coil configuration was shown to provide enhanced single-pass classification performance over the original single coil design, particularly as a function of target location relative to the centerline. The ability to go beyond anomaly detection and additionally classify detected anomalies from survey data would dramatically improve the state of the art for underwater UXO remediation by reducing costs and improving the efficiency of these efforts. The results of our efforts to return the MTA to service and validating the new EMI array's design for UXO detection and classification in the underwater environment will be the focus of this presentation.

Electrocorticographic Frequency Alteration Mapping of Speech Cortex during an Awake Craniotomy: Case Report

Science.gov (United States)

Breshears, J.; Sharma, M.; Anderson, N.R.; Rashid, S.; Leuthardt, E.C.

2010-01-01

Objective Traditional electrocortical stimulation (ECS) mapping is limited by the lengthy serial investigation (one location at a time) and the risk of afterdischarges in localizing eloquent cortex. Electrocorticographic frequency alteration mapping (EFAM) allows the parallel investigation of many cortical sites in much less time and with no risk of afterdischarges because of its passive nature. We examined its use with ECS in the context of language mapping during an awake craniotomy for a tumor resection. Clinical Presentation The patient was a 61-year-old right-handed Caucasian male who presented with headache and mild aphasia. Imaging demonstrated a 3-cm cystic mass in the posterior temporal-parietal lobe. The patient underwent an awake craniotomy for the mapping of his speech cortex and resection of the mass. Intervention Using a 32-contact electrode array, electrocorticographic signals were recorded from the exposed cortex as the patient participated in a 3-min screening task involving active (patient naming visually presented words) and rest (patient silent) conditions. A spectral comparison of the 2 conditions revealed specific cortical locations associated with activation during speech. The patient was then widely mapped using ECS. Three of 4 sites identified by ECS were also identified passively and in parallel by EFAM, 2 with statistical significance and the third by qualitative inspection. Conclusion EFAM was technically achieved in an awake craniotomy patient and had good concordance with ECS mapping. Because it poses no risk of afterdischarges and offers substantial time savings, EFAM holds promise for future development as an adjunct intraoperative mapping tool. Additionally, the cortical signals obtained by this modality can be utilized for localization in the presence of a tumor adjacent to the eloquent regions. PMID:19940544

Using hazard maps to identify and eliminate workplace hazards: a union-led health and safety training program.

Science.gov (United States)

Anderson, Joe; Collins, Michele; Devlin, John; Renner, Paul

2012-01-01

The Institute for Sustainable Work and Environment and the Utility Workers Union of America worked with a professional evaluator to design, implement, and evaluate the results of a union-led system of safety-based hazard identification program that trained workers to use hazard maps to identify workplace hazards and target them for elimination. The evaluation documented program implementation and impact using data collected from both qualitative interviews and an on-line survey from worker trainers, plant managers, and health and safety staff. Managers and workers reported that not only were many dangerous hazards eliminated as a result of hazard mapping, some of which were long-standing, difficult-to-resolve issues, but the evaluation also documented improved communication between union members and management that both workers and managers agreed resulted in better, more sustainable hazard elimination.

SAQC: SNP Array Quality Control

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Li Ling-Hui

2011-04-01

Full Text Available Abstract Background Genome-wide single-nucleotide polymorphism (SNP arrays containing hundreds of thousands of SNPs from the human genome have proven useful for studying important human genome questions. Data quality of SNP arrays plays a key role in the accuracy and precision of downstream data analyses. However, good indices for assessing data quality of SNP arrays have not yet been developed. Results We developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples. Conclusions This study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC. SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm.

Challenging aspects of contemporary cochlear implant electrode array design.

Science.gov (United States)

Mistrík, Pavel; Jolly, Claude; Sieber, Daniel; Hochmair, Ingeborg

2017-12-01

A design comparison of current perimodiolar and lateral wall electrode arrays of the cochlear implant (CI) is provided. The focus is on functional features such as acoustic frequency coverage and tonotopic mapping, battery consumption and dynamic range. A traumacity of their insertion is also evaluated. Review of up-to-date literature. Perimodiolar electrode arrays are positioned in the basal turn of the cochlea near the modiolus. They are designed to initiate the action potential in the proximity to the neural soma located in spiral ganglion. On the other hand, lateral wall electrode arrays can be inserted deeper inside the cochlea, as they are located along the lateral wall and such insertion trajectory is less traumatic. This class of arrays targets primarily surviving neural peripheral processes. Due to their larger insertion depth, lateral wall arrays can deliver lower acoustic frequencies in manner better corresponding to cochlear tonotopicity. In fact, spiral ganglion sections containing auditory nerve fibres tuned to low acoustic frequencies are located deeper than 1 and half turn inside the cochlea. For this reason, a significant frequency mismatch might be occurring for apical electrodes in perimodiolar arrays, detrimental to speech perception. Tonal languages such as Mandarin might be therefore better treated with lateral wall arrays. On the other hand, closer proximity to target tissue results in lower psychophysical threshold levels for perimodiolar arrays. However, the maximal comfort level is also lower, paradoxically resulting in narrower dynamic range than that of lateral wall arrays. Battery consumption is comparable for both types of arrays. Lateral wall arrays are less likely to cause trauma to cochlear structures. As the current trend in cochlear implantation is the maximal protection of residual acoustic hearing, the lateral wall arrays seem more suitable for hearing preservation CI surgeries. Future development could focus on combining the

Automated installation methods for photovoltaic arrays

Science.gov (United States)

Briggs, R.; Daniels, A.; Greenaway, R.; Oster, J., Jr.; Racki, D.; Stoeltzing, R.

1982-11-01

Since installation expenses constitute a substantial portion of the cost of a large photovoltaic power system, methods for reduction of these costs were investigated. The installation of the photovoltaic arrays includes all areas, starting with site preparation (i.e., trenching, wiring, drainage, foundation installation, lightning protection, grounding and installation of the panel) and concluding with the termination of the bus at the power conditioner building. To identify the optimum combination of standard installation procedures and automated/mechanized techniques, the installation process was investigated including the equipment and hardware available, the photovoltaic array structure systems and interfaces, and the array field and site characteristics. Preliminary designs of hardware for both the standard installation method, the automated/mechanized method, and a mix of standard installation procedures and mechanized procedures were identified to determine which process effectively reduced installation costs. In addition, costs associated with each type of installation method and with the design, development and fabrication of new installation hardware were generated.

Identifying Generalizable Image Segmentation Parameters for Urban Land Cover Mapping through Meta-Analysis and Regression Tree Modeling

Directory of Open Access Journals (Sweden)

Brian A. Johnson

2018-01-01

Full Text Available The advent of very high resolution (VHR satellite imagery and the development of Geographic Object-Based Image Analysis (GEOBIA have led to many new opportunities for fine-scale land cover mapping, especially in urban areas. Image segmentation is an important step in the GEOBIA framework, so great time/effort is often spent to ensure that computer-generated image segments closely match real-world objects of interest. In the remote sensing community, segmentation is frequently performed using the multiresolution segmentation (MRS algorithm, which is tuned through three user-defined parameters (the scale, shape/color, and compactness/smoothness parameters. The scale parameter (SP is the most important parameter and governs the average size of generated image segments. Existing automatic methods to determine suitable SPs for segmentation are scene-specific and often computationally intensive, so an approach to estimating appropriate SPs that is generalizable (i.e., not scene-specific could speed up the GEOBIA workflow considerably. In this study, we attempted to identify generalizable SPs for five common urban land cover types (buildings, vegetation, roads, bare soil, and water through meta-analysis and nonlinear regression tree (RT modeling. First, we performed a literature search of recent studies that employed GEOBIA for urban land cover mapping and extracted the MRS parameters used, the image properties (i.e., spatial and radiometric resolutions, and the land cover classes mapped. Using this data extracted from the literature, we constructed RT models for each land cover class to predict suitable SP values based on the: image spatial resolution, image radiometric resolution, shape/color parameter, and compactness/smoothness parameter. Based on a visual and quantitative analysis of results, we found that for all land cover classes except water, relatively accurate SPs could be identified using our RT modeling results. The main advantage of our

Novel Abscisic Acid Antagonists Identified with Chemical Array Screening.

Science.gov (United States)

Ito, Takuya; Kondoh, Yasumitsu; Yoshida, Kazuko; Umezawa, Taishi; Shimizu, Takeshi; Shinozaki, Kazuo; Osada, Hiroyuki

2015-11-01

Abscisic acid (ABA) signaling is involved in multiple processes in plants, such as water stress control and seed dormancy. Major regulators of ABA signaling are the PYR/PYL/RCAR family receptor proteins, group A protein phosphatases 2C (PP2Cs), and subclass III of SNF1-related protein kinase 2 (SnRK2). Novel ABA agonists and antagonists to modulate the functions of these proteins would not only contribute to clarification of the signaling mechanisms but might also be used to improve crop yields. To obtain small molecules that interact with Arabidopsis ABA receptor PYR1, we screened 24 275 compounds from a chemical library at the RIKEN Natural Products Depository by using a chemical array platform. Subsequent SnRK2 and PP2C assays narrowed down the candidates to two molecules. One antagonized ABA in a competitive manner and inhibited the formation of the PYR1-ABA-PP2C ternary complex. These compounds might have potential as bioprobes to analyze ABA signaling. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Admixture mapping of African-American women in the AMBER Consortium identifies new loci for breast cancer and estrogen-receptor subtypes

Directory of Open Access Journals (Sweden)

Edward Antonio Ruiz-Narvaez

2016-09-01

Full Text Available Recent genetic admixture coupled with striking differences in incidence of estrogen receptor (ER breast cancer subtypes, as well as severity, between women of African and European ancestry, provides an excellent rationale for performing admixture mapping in African American women with breast cancer risk. We performed the largest breast cancer admixture mapping study with in African American women to identify novel genomic regions associated with the disease. We conducted a genome-wide admixture scan using 2,624 autosomal ancestry informative markers (AIMs in 3,629 breast cancer cases (including 1,968 ER-positive, 1093 ER-negative and 601 triple-negative and 4,658 controls from the African American Breast Cancer Epidemiology and Risk (AMBER Consortium, a collaborative study of four large geographically different epidemiological studies of breast cancer in African American women. We used an independent case-control study to test for SNP association in regions with genome-wide significant admixture signals. We found two novel genome-wide significant regions of excess African ancestry, 4p16.1 and 17q25.1, associated with ER-positive breast cancer. Two regions known to harbor breast cancer variants, 10q26 and 11q13, were also identified with excess of African ancestry. Fine-mapping of the identified genome-wide significant regions suggests the presence of significant genetic associations with ER-positive breast cancer in 4p16.1 and 11q13. In summary, we identified three novel genomic regions associated with breast cancer risk by ER status, suggesting that additional previously unidentified variants may contribute to the racial differences in breast cancer risk in the African American population.

Fine-scale mapping of the 4q24 locus identifies & pr two Independent loci associated with breast cancer risk

NARCIS (Netherlands)

X. Guo (Xingyi); J. Long (Jirong); C. Zeng (Chenjie); K. Michailidou (Kyriaki); M. Ghoussaini (Maya); M.K. Bolla (Manjeet); Q. Wang (Qing); R.L. Milne (Roger L.); X.-O. Shu (Xiao-Ou); Q. Cai (Qiuyin); J. Beesley (Jonathan); S. Kar (Siddhartha); I.L. Andrulis (Irene); H. Anton-Culver (Hoda); V. Arndt (Volker); M.W. Beckmann (Matthias); A. Beeghly-Fadiel (Alicia); J. Benítez (Javier); W.J. Blot (William); N.V. Bogdanova (Natalia); S.E. Bojesen (Stig); H. Brauch (Hiltrud); H. Brenner (Hermann); L.A. Brinton (Louise); A. Broekss (Annegien); T. Brüning (Thomas); B. Burwinkel (Barbara); H. Cai (Hui); S. Canisius (Sander); J. Chang-Claude (Jenny); J.-Y. Choi (J.); F.J. Couch (Fergus); A. Cox (Angela); S.S. Cross (Simon); K. Czene (Kamila); H. Darabi (Hatef); P. Devilee (Peter); A. Droit (Arnaud); T. Dörk (Thilo); P.A. Fasching (Peter); O. Fletcher (Olivia); H. Flyger (Henrik); F. Fostira (Florentia); V. Gaborieau (Valerie); M. García-Closas (Montserrat); G.G. Giles (Graham G.); M. Grip (Mervi); P. Guénel (Pascal); C.A. Haiman (Christopher A.); U. Hamann (Ute); J.M. Hartman (Joost); A. Hollestelle (Antoinette); J.L. Hopper (John L.); C.-N. Hsiung (Chia-Ni); H. Ito (Hidemi); A. Jakubowska (Anna); N. Johnson (Nichola); M. Kabisch (Maria); D. Kang (Daehee); S. Khan (Sofia); J.A. Knight (Julia); V-M. Kosma (Veli-Matti); D. Lambrechts (Diether); L. Le Marchand (Loic); J. Li (Jingmei); A. Lindblom (Annika); A. Lophatananon (Artitaya); J. Lubinski (Jan); A. Mannermaa (Arto); S. Manoukian (Siranoush); S. Margolin (Sara); F. Marme (Federick); K. Matsuo (Keitaro); C.A. McLean (Catriona Ann); A. Meindl (Alfons); K. Muir (Kenneth); S.L. Neuhausen (Susan); H. Nevanlinna (Heli); S. Nord (Silje); J.E. Olson (Janet); N. Orr (Nick); P. Peterlongo (Paolo); T.C. Putti (Thomas Choudary); A. Rudolph (Anja); S. Sangrajrang (Suleeporn); E.J. Sawyer (Elinor); M.K. Schmidt (Marjanka); R.K. Schmutzler (Rita); C-Y. Shen (Chen-Yang); J. Shi (Jiajun); M. Shrubsole (Martha); M.C. Southey (Melissa); A.J. Swerdlow (Anthony ); S.H. Teo (Soo Hwang); B. Thienpont (Bernard); A.E. Toland (Amanda); R.A.E.M. Tollenaar (Rob); I. Tomlinson (Ian); T. Truong (Thérèse); C.-C. Tseng (Chiu-chen); A.M.W. van den Ouweland (Ans); W. Wen (Wanqing); R. Winqvist (Robert); A. Wu (Anna); C.H. Yip (Cheng Har); M.P. Zamora (Pilar); Y. Zheng (Ying); P. Hall (Per); P.D.P. Pharoah (Paul); J. Simard (Jacques); G. Chenevix-Trench (Georgia); A.M. Dunning (Alison); D.F. Easton (Douglas F.); W. Zheng (Wei); R. Eeles (Rosalind); A.A. Al Olama (Ali Amin); Z. Kote-Jarai; S. Benlloch (Sara); A.C. Antoniou (Antonis C.); L. McGuffog (Lesley); K. Offit (Kenneth); A. Lee (Andrew); E. Dicks (Ed); C. Luccarini (Craig); D.C. Tessier (Daniel C.); F. Bacot (Francois); D. Vincent (Daniel); S. La Boissière (Sylvie); F. Robidoux (Frederic); S.F. Nielsen (Sune); J.M. Cunningham (Julie); S.A. Windebank (Sharon A.); C.A. Hilker (Christopher A.); J. Meyer (Jeffrey); M. Angelakos (Maggie); J. Maskiell (Judi); E.J. Rutgers (Emiel J.); S. Verhoef; F.B.L. Hogervorst (Frans); P. Boonyawongviroj (Prat); P. Siriwanarungsan (Pornthep); A. Schrauder (André); M. Rübner (Matthias); S. Oeser (Sonja); S. Landrith (Silke); E. Williams (Eileen); E. Ryder-Mills (Elaine); K. Sargus (Kara); N. McInerney (Niall); G. Colleran (Gabrielle); A. Rowan (Andrew); A. Jones (Angela); C. Sohn (Christof); A. Schneeweiß (Andeas); P. Bugert (Peter); N. Álvarez (Nuria); L. Bernstein (Leslie); J. Lacey (James); S. Wang (Sophia); H. Ma (Huiyan); Y. Lu (Yani); J. Clague De Hart (Jessica); D. Deapen (Dennis); R. Pinder (Rich); E. Lee (Eunjung); F.R. Schumacher (Fredrick); P. Horn-Ross (Pam); P. Reynolds (Peggy); D. Nelson (David); H. Park (Hannah); H. Ziegler (Hartwig); S. Wolf (Sonja); V. Hermann (Volker); W.-Y. Lo (Wing-Yee); C. Justenhoven (Christina); Y.-D. Ko (Yon-Dschun); C. Baisch (Christian); H.-P. Fischer (Hans-Peter); B. Pesch (Beate); S. Rabstein (Sylvia); A. Lotz (Anne); V. Harth (Volker); T. Heikkinen (Tuomas); I. Erkkilä (Irja); K. Aaltonen (Kirsimari); K. von Smitten (Karl); N.N. Antonenkova (Natalia); P. Hillemanns (Peter); H. Christiansen (Hans); E. Myöhänen (Eija); H. Kemiläinen (Helena); H. Thorne (Heather); E. Niedermayr (Eveline); D. Bowtell; G. Chenevix-Trench (Georgia); A. De Fazio (Anna); D. Gertig; A. Green; P. Webb (Penny); A. Green; P. Parsons; N. Hayward; P.M. Webb (P.); D. Whiteman; A. Fung (Annie); J. Yashiki (June); G. Peuteman (Gilian); D. Smeets (Dominiek); T. Van Brussel (Thomas); K. Corthouts (Kathleen); N. Obi (Nadia); J. Heinz (Judith); T.W. Behrens (Timothy); U. Eilber (Ursula); M. Celik (Muhabbet); T. Olchers (Til); B. Peissel (Bernard); G. Scuvera (Giulietta); D. Zaffaroni (Daniela); B. Bonnani (Bernardo); I. Feroce (Irene); A. Maniscalco (Angela); A. Rossi (Alessandra); L. Bernard (Loris); M. Tranchant (Martine); M.-F. Valois (Marie-France); A. Turgeon (Annie); L. Heguy (Lea); P.S. Yee (Phuah Sze); P. Kang (Peter); K.I. Nee (Kang In); S. Mariapun (Shivaani); Y. Sook-Yee (Yoon); D.S.C. Lee (Daphne S.C.); T.Y. Ching (Teh Yew); N.A.M. Taib (Nur Aishah Mohd); M. Otsukka (Meeri); K. Mononen (Kari); T. Selander (Teresa); N. Weerasooriya (Nayana); E.M.M. Krol-Warmerdam (Elly); J. Molenaar; J. Blom; N. Szeszenia-Dabrowska (Neonilia); B. Peplonska (Beata); W. Zatonski (Witold); P. Chao (Pei); M. Stagner (Michael); P. Bos (Petra); J. Blom (Jannet); E. Crepin (Ellen); A. Nieuwlaat (Anja); A. Heemskerk (Annette); S. Higham (Sue); H.E. Cramp (Helen); D. Connley (Daniel); S. Balasubramanian (Sabapathy); I.W. Brock (Ian); M. Kerin (Michael); N. Miller (Nicola); P. Kerbrat (Pierre); P. Arveux (Patrick); R. Le Scodan (Romuald); Y. Raoul (Yves); P. Laurent-Puig (Pierre); C. Mulot (Claire); C. Stegmaier (Christa); K. Butterbach (Katja); J.H. Karstens (Johann); D. Flesch-Janys (Dieter); P. Seibold (Petra); A. Vrieling (Alina); S. Nickels (Stefan); P. Radice (Paolo); K. Pykäs (Katri); A. Jukkola-Vuorinen (Arja); S. Kauppila (Saila); D. Conroy (Don); C. Baynes (Caroline); K. Chua (Kimberley); R. Pilarski (Robert)

2015-01-01

textabstractBackground: A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. Methods: We conducted a fine-mapping analysis in 55,540

Interferometric Mapping of Perseus Outflows with MASSES

Science.gov (United States)

Stephens, Ian; Dunham, Michael; Myers, Philip C.; MASSES Team

2017-01-01

The MASSES (Mass Assembly of Stellar Systems and their Evolution with the SMA) survey, a Submillimeter Array (SMA) large-scale program, is mapping molecular lines and continuum emission about the 75 known Class 0/I sources in the Perseus Molecular Cloud. In this talk, I present some of the key results of this project, with a focus on the CO(2-1) maps of the molecular outflows. In particular, I investigate how protostars inherit their rotation axes from large-scale magnetic fields and filamentary structure.

Implementation of digital equality comparator circuit on memristive memory crossbar array using material implication logic

Science.gov (United States)

Haron, Adib; Mahdzair, Fazren; Luqman, Anas; Osman, Nazmie; Junid, Syed Abdul Mutalib Al

2018-03-01

One of the most significant constraints of Von Neumann architecture is the limited bandwidth between memory and processor. The cost to move data back and forth between memory and processor is considerably higher than the computation in the processor itself. This architecture significantly impacts the Big Data and data-intensive application such as DNA analysis comparison which spend most of the processing time to move data. Recently, the in-memory processing concept was proposed, which is based on the capability to perform the logic operation on the physical memory structure using a crossbar topology and non-volatile resistive-switching memristor technology. This paper proposes a scheme to map digital equality comparator circuit on memristive memory crossbar array. The 2-bit, 4-bit, 8-bit, 16-bit, 32-bit, and 64-bit of equality comparator circuit are mapped on memristive memory crossbar array by using material implication logic in a sequential and parallel method. The simulation results show that, for the 64-bit word size, the parallel mapping exhibits 2.8× better performance in total execution time than sequential mapping but has a trade-off in terms of energy consumption and area utilization. Meanwhile, the total crossbar area can be reduced by 1.2× for sequential mapping and 1.5× for parallel mapping both by using the overlapping technique.

Development of Gene Expression Fingerprints for Identification of Environmental Contaminants Using cDNA Arrays

National Research Council Canada - National Science Library

Inouye, L

2004-01-01

...) to develop cDNA array-based assays that map gene expression from contaminant exposures. Results substantiate that distinct gene expression profiles exist for major contaminant classes such as PARs, PCBs, and PCDD/Fs...

Friction Stir Weld Inspection Through Conductivity Imaging Using Shaped Field MWM(Registered Trademark) - Arrays

Science.gov (United States)

Goldfine, Neil; Grundy, David; Zilberstein, Vladimir; Kinchen, David G.; McCool, Alex (Technical Monitor)

2002-01-01

Friction Stir Welds (FSW) of Al 2195-T8 and Al 2219-T8, provided by Lockheed Martin Michoud Operations, were inspected for lack-of-penetration (LOP) defects using a custom designed MWM-Array, a multi-element eddy-current sensor. MWM (registered trademark) electrical conductivity mapping demonstrated high sensitivity to LOP as small as 0.75 mm (0.03 in.), as confirmed by metallographic data that characterized the extent of LOP defects. High sensitivity and high spatial resolution was achieved via a 37-element custom designed MWM-Array allowing LOP detection using the normalized longitudinal component of the MWM measured conductivity. This permitted both LOP detection and correlation of MWM conductivity features with the LOP defect size, as changes in conductivity were apparently associated with metallurgical features within the near-surface layer of the LOP defect zone. MWM conductivity mapping reveals information similar to macro-etching as the MWM-Array is sensitive to small changes in conductivity due to changes in microstructure associated with material thermal processing, in this case welding. The electrical conductivity measured on the root side of FSWs varies across the weld due to microstructural differences introduced by the FSW process, as well as those caused by planar flaws. Weld metal, i.e., dynamically recrystallized zone (DXZ), thermomechanically affected zone (TMZ), heat-affected zone (HAZ), and parent metal (PM) are all evident in the conductivity maps. While prior efforts had met with limited success for NDE (Nondestructive Evaluation) of dissimilar alloy, Al2219 to Al2195 FSW, the new custom designed multi-element MWM-Array achieved detection of all LOP defects even in dissimilar metal welds.

The Status of the Telescope Array experiment

Energy Technology Data Exchange (ETDEWEB)

Tokuno, H; Azuma, R [Tokyo Institute of Technology, Meguro, Tokyo (Japan); Abu-Zayyad, T; Allen, M; Barcikowski, E; Belz, J W; Blake, S A; Brusova, O; Cady, R [University of Utah, High Energy Astrophysics Institute, Salt Lake City, Utah (United States); Aida, R [University of Yamanashi, Interdisciplinary Graduate School of Medicine and Engineering, Kofu, Yamanashi (Japan); Benno, T; Chikawa, M; Doura, K [Kinki University, Higashi Osaka, Osaka (Japan); Bergman, D R [Rutgers University, Piscataway (United States); Cheon, B G; Cho, E J [Hanyang University, Seongdong-gu, Seoul (Korea, Republic of); Chiba, J [Tokyo University of Science, Noda, Chiba (Japan); Cho, L S; Cho, W R [Yonsei University, Seodaemun-gu, Seoul (Korea, Republic of); Cohen, F, E-mail: htokuno@cr.phys.titech.ac.jp [Institute for Cosmic Ray Research, University of Tokyo, Kashiwa, Chiba (Japan)

2011-04-01

The purpose of The Telescope Array experiment is to identify origin of the ultra high energy cosmic rays. The Telescope Array is a hybrid detector consists of a surface detector array and air fluorescence detectors. This hybrid detector is observing extensive air showers to measure the energy spectrum, anisotropy and composition of Ultra High Energy Cosmic Rays. The detector construction has been completed in March 2008, and the hybrid observation with the full configuration has been running since that time. In this talk, the status of observation and our prospects are described.

Break down of the law of large numbers in Josephson junction series arrays

International Nuclear Information System (INIS)

Dominguez, D.; Cerdeira, H.A.

1995-01-01

We study underdamped Josephson junction series arrays that are globally coupled through a resistive shunting load and driven by an rf bias current. We find that they can be an experimental realization of many phenomena currently studied in globally coupled logistic maps. We find coherent, ordered, partially ordered and turbulent phases in the IV characteristics of the array. The ordered phase corresponds to giant Shapiro steps. In the turbulent phase there is a saturation of the broad band noise for a large number of junctions. This corresponds to a break down of the law of large numbers as seen in globally coupled maps. Coexisting with this, we find an emergence of novel pseudo-steps in the IV characteristics. This effect can be experimentally distinguished from the true Shapiro steps, which do not have broad band noise emission. (author). 21 refs, 5 figs

A novel intra-operative, high-resolution atrial mapping approach.

Science.gov (United States)

Yaksh, Ameeta; van der Does, Lisette J M E; Kik, Charles; Knops, Paul; Oei, Frans B S; van de Woestijne, Pieter C; Bekkers, Jos A; Bogers, Ad J J C; Allessie, Maurits A; de Groot, Natasja M S

2015-12-01

A new technique is demonstrated for extensive high-resolution intra-operative atrial mapping that will facilitate the localization of atrial fibrillation (AF) sources and identification of the substrate perpetuating AF. Prior to the start of extra-corporal circulation, a 8 × 24-electrode array (2-mm inter-electrode distance) is placed subsequently on all the right and left epicardial atrial sites, including Bachmann's bundle, for recording of unipolar electrograms during sinus rhythm and (induced) AF. AF is induced by high-frequency pacing at the right atrial free wall. A pacemaker wire stitched to the right atrium serves as a reference signal. The indifferent pole is connected to a steal wire fixed to subcutaneous tissue. Electrograms are recorded by a computerized mapping system and, after amplification (gain 1000), filtering (bandwidth 0.5-400 Hz), sampling (1 kHz) and analogue to digital conversion (16 bits), automatically stored on hard disk. During the mapping procedure, real-time visualization secures electrogram quality. Analysis will be performed offline. This technique was performed in 168 patients of 18 years and older, with coronary and/or structural heart disease, with or without AF, electively scheduled for cardiac surgery and a ventricular ejection fraction above 40 %. The mean duration of the entire mapping procedure including preparation time was 9 ± 2 min. Complications related to the mapping procedure during or after cardiac surgery were not observed. We introduce the first epicardial atrial mapping approach with a high resolution of ≥1728 recording sites which can be performed in a procedure time of only 9±2 mins. This mapping technique can potentially identify areas responsible for initiation and persistence of AF and hopefully can individualize both diagnosis and therapy of AF.

Identifying Key Flavors in Strawberries Driving Liking via Internal and External Preference Mapping.

Science.gov (United States)

Oliver, Penelope; Cicerale, Sara; Pang, Edwin; Keast, Russell

2018-04-01

Australian consumers desire the development of a more flavorsome Australian strawberry cultivar. To aid in the development of well-liked strawberries, the attributes driving liking need to be identified. The objective of this research is to apply Preference Mapping (PM) techniques to the descriptive profile of commercial and newly bred strawberry cultivars, together with consumer preference data to determine the flavors contributing to liking. A trained sensory panel (n = 12) used Quantitative Descriptive Analysis (QDA®) methodology to evaluate two appearance, seven aroma, five texture, 10 flavor and 10 aftertaste attributes of three commercial strawberry cultivars and six elite breeding lines grown in Victoria, Australia. Strawberry consumers (n = 150) assessed their liking of the same strawberry cultivars. QDA® significantly discriminated strawberries on 28 of the 34 sensory attributes. There were significant differences in hedonic ratings of strawberries (F(8,714) = 11.5, P = 0.0001), with Hierarchical Cluster Analysis (HCA) identifying three consumer clusters each displaying differing patterns of preference. Internal and external PM techniques were applied to the data to identify the attributes driving consumer acceptability. Sweet, berry, caramel, fruity and floral attributes were identified as most contributing to liking. Sour, citrus, green, astringent, firm and gritty attributes were conversely associated with a reduction in consumer liking. Elite Lines 2 and 6 have been identified as having the broadest appeal, satisfying between 60% and 70% of consumers in the population assessed, thus the introduction of these cultivars should satisfy the largest group of consumers in the Australian market. The results of this research could be applied to breeding programs, to ensure newly bred cultivars express characteristics that were identified as well-liked amongst consumers. In addition, this research provides evidence for marketing strawberries by

Sprite-producing Convective Storms within the Colorado Lightning Mapping Array

Science.gov (United States)

Lyons, W. A.; Cummer, S. A.; Rison, W.; Krehbiel, P. R.; Lang, T. J.; Rutledge, S. A.; Lu, G.; Stanley, M. A.; Ashcraft, T.; Nelson, T. E.

2012-12-01

The multi-year, multi-institution effort entitled Physical Origins of Coupling to the Upper Atmosphere from Lightning (PhOCAL), has among its goals to qualitatively understand the meteorology and lightning flash characteristics that produce the unusual and/or very energetic lightning responsible for phenomena such as sprites, halos, elves, blue jets and gigantic jets, collectively known as Transient Luminous Events (TLEs). A key task is to obtain simultaneous video, ideally with a high-speed imager (HSI), of both a TLE and its parent lightning discharge, within the domain of a 3-D Lightning Mapping Array (LMA). While conceptually simple, this task is logistically quite complicated. In 2012, a new 15-station Colorado LMA (COLMA) became operational, covering northeastern Colorado, with the Yucca Ridge Field Station (YRFS) near its western edge. The National Charge Moment Change Network (CMCN), which since 2007 has been documenting sprite-class +CGs (those with impulse change moment changes >100 C km), indicates that a strong gradient of energetic +CGs exists west-to-east through the COLMA, with the most likely region for sprite-producing storms being in the COLMA eastern fringes (western Kansas and Nebraska). Yet, on 8 and 25 June, 2012, intense convective systems formed in the COLMA along and just east of the Front Range, producing severe weather and intense lightning. On the 8th, four sprite parent +CGs were captured at 3000 fps from YRFS with the sprites confirmed by dual (conventional speed) cameras in New Mexico. In a second storm on the 25th, viewing conditions prevented +CG video acquisition, but sprites were logged over the COLMA and detailed reconstructions of the discharges are being made. The parent discharges often began as upward negative leaders propagating into a mid-level positive charge layer at 8-10 km. They often originated within or near the convective core before expanding outward into a stratiform region and involving several hundred square

Visualisation of air–water bubbly column flow using array Ultrasonic Velocity Profiler

Directory of Open Access Journals (Sweden)

Munkhbat Batsaikhan

2017-11-01

Full Text Available In the present work, an experimental study of bubbly two-phase flow in a rectangular bubble column was performed using two ultrasonic array sensors, which can measure the instantaneous velocity of gas bubbles on multiple measurement lines. After the sound pressure distribution of sensors had been evaluated with a needle hydrophone technique, the array sensors were applied to two-phase bubble column. To assess the accuracy of the measurement system with array sensors for one and two-dimensional velocity, a simultaneous measurement was performed with an optical measurement technique called particle image velocimetry (PIV. Experimental results showed that accuracy of the measurement system with array sensors is under 10% for one-dimensional velocity profile measurement compared with PIV technique. The accuracy of the system was estimated to be under 20% along the mean flow direction in the case of two-dimensional vector mapping.

Mapping Meaningful Places on Washington's Olympic Peninsula: Toward a Deeper Understanding of Landscape Values.

Science.gov (United States)

Cerveny, Lee Karol; Biedenweg, Kelly; McLain, Rebecca

2017-10-01

Landscape values mapping has been widely employed as a form of public participation GIS (PPGIS) in natural resource planning and decision-making to capture the complex array of values, uses, and interactions between people and landscapes. A landscape values typology has been commonly employed in the mapping of social and environmental values in a variety of management settings and scales. We explore how people attribute meanings and assign values to special places on the Olympic Peninsula (Washington, USA) using both a landscape values typology and qualitative responses about residents' place-relationships. Using geographically referenced social values data collected in community meetings (n = 169), we identify high-frequency landscape values and examine how well the landscape values are reflected in open-ended descriptions of place-relations. We also explore the various interpretations of 14 landscape values used in the study. In particular, we investigate any overlapping meanings or blurriness among landscape values and reveal potentially emergent landscape values from the qualitative data. The results provide insights on the use of landscape values mapping typologies for practitioners and researchers engaged in the mapping of social values for PPGIS.

Mapping Meaningful Places on Washington's Olympic Peninsula: Toward a Deeper Understanding of Landscape Values

Science.gov (United States)

Cerveny, Lee Karol; Biedenweg, Kelly; McLain, Rebecca

2017-10-01

Landscape values mapping has been widely employed as a form of public participation GIS (PPGIS) in natural resource planning and decision-making to capture the complex array of values, uses, and interactions between people and landscapes. A landscape values typology has been commonly employed in the mapping of social and environmental values in a variety of management settings and scales. We explore how people attribute meanings and assign values to special places on the Olympic Peninsula (Washington, USA) using both a landscape values typology and qualitative responses about residents' place-relationships. Using geographically referenced social values data collected in community meetings ( n = 169), we identify high-frequency landscape values and examine how well the landscape values are reflected in open-ended descriptions of place-relations. We also explore the various interpretations of 14 landscape values used in the study. In particular, we investigate any overlapping meanings or blurriness among landscape values and reveal potentially emergent landscape values from the qualitative data. The results provide insights on the use of landscape values mapping typologies for practitioners and researchers engaged in the mapping of social values for PPGIS.

Regional Mapping of Plantation Extent Using Multisensor Imagery

Science.gov (United States)

Torbick, N.; Ledoux, L.; Hagen, S.; Salas, W.

2016-12-01

Industrial forest plantations are expanding rapidly across the tropics and monitoring extent is critical for understanding environmental and socioeconomic impacts. In this study, new, multisensor imagery were evaluated and integrated to extract the strengths of each sensor for mapping plantation extent at regional scales. Three distinctly different landscapes with multiple plantation types were chosen to consider scalability and transferability. These were Tanintharyi, Myanmar, West Kalimantan, Indonesia, and southern Ghana. Landsat-8 Operational Land Imager (OLI), Phased Array L-band Synthetic Aperture Radar-2 (PALSAR-2), and Sentinel-1A images were fused within a Classification and Regression Tree (CART) framework using random forest and high-resolution surveys. Multi-criteria evaluations showed both L-and C-band gamma nought γ° backscatter decibel (dB), Landsat reflectance ρλ, and texture indices were useful for distinguishing oil palm and rubber plantations from other land types. The classification approach identified 750,822 ha or 23% of the Taninathryi, Myanmar, and 216,086 ha or 25% of western West Kalimantan as plantation with very high cross validation accuracy. The mapping approach was scalable and transferred well across the different geographies and plantation types. As archives for Sentinel-1, Landsat-8, and PALSAR-2 continue to grow, mapping plantation extent and dynamics at moderate resolution over large regions should be feasible.

Transitive Relational Mappings in Three- and Four-Year-Olds: The Analogy of Goldilocks and the Three Bears.

Science.gov (United States)

Goswami, Usha

1995-01-01

In three experiments, three- and four-year olds were asked to map relative size from one array of objects to another, map relative size to relative proportion, and map relative size to a variety of perceptual dimensions. Children were able to make relational mappings based on size when spatial positions and concrete representations of size of…

LOFAR Lightning Imaging: Mapping Lightning With Nanosecond Precision

Science.gov (United States)

Hare, B. M.; Scholten, O.; Bonardi, A.; Buitink, S.; Corstanje, A.; Ebert, U.; Falcke, H.; Hörandel, J. R.; Leijnse, H.; Mitra, P.; Mulrey, K.; Nelles, A.; Rachen, J. P.; Rossetto, L.; Rutjes, C.; Schellart, P.; Thoudam, S.; Trinh, T. N. G.; ter Veen, S.; Winchen, T.

2018-03-01

Lightning mapping technology has proven instrumental in understanding lightning. In this work we present a pipeline that can use lightning observed by the LOw-Frequency ARray (LOFAR) radio telescope to construct a 3-D map of the flash. We show that LOFAR has unparalleled precision, on the order of meters, even for lightning flashes that are over 20 km outside the area enclosed by LOFAR antennas (˜3,200 km2), and can potentially locate over 10,000 sources per lightning flash. We also show that LOFAR is the first lightning mapping system that is sensitive to the spatial structure of the electrical current during individual lightning leader steps.

A Low-Complexity ESPRIT-Based DOA Estimation Method for Co-Prime Linear Arrays.

Science.gov (United States)

Sun, Fenggang; Gao, Bin; Chen, Lizhen; Lan, Peng

2016-08-25

The problem of direction-of-arrival (DOA) estimation is investigated for co-prime array, where the co-prime array consists of two uniform sparse linear subarrays with extended inter-element spacing. For each sparse subarray, true DOAs are mapped into several equivalent angles impinging on the traditional uniform linear array with half-wavelength spacing. Then, by applying the estimation of signal parameters via rotational invariance technique (ESPRIT), the equivalent DOAs are estimated, and the candidate DOAs are recovered according to the relationship among equivalent and true DOAs. Finally, the true DOAs are estimated by combining the results of the two subarrays. The proposed method achieves a better complexity-performance tradeoff as compared to other existing methods.

Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array.

Science.gov (United States)

Vathipadiekal, Vinod; Wang, Victoria; Wei, Wei; Waldron, Levi; Drapkin, Ronny; Gillette, Michael; Skates, Steven; Birrer, Michael

2015-11-01

To generate a comprehensive "Secretome" of proteins potentially found in the blood and derive a virtual Affymetrix array. To validate the utility of this database for the discovery of novel serum-based biomarkers using ovarian cancer transcriptomic data. The secretome was constructed by aggregating the data from databases of known secreted proteins, transmembrane or membrane proteins, signal peptides, G-protein coupled receptors, or proteins existing in the extracellular region, and the virtual array was generated by mapping them to Affymetrix probeset identifiers. Whole-genome microarray data from ovarian cancer, normal ovarian surface epithelium, and fallopian tube epithelium were used to identify transcripts upregulated in ovarian cancer. We established the secretome from eight public databases and a virtual array consisting of 16,521 Affymetrix U133 Plus 2.0 probesets. Using ovarian cancer transcriptomic data, we identified candidate blood-based biomarkers for ovarian cancer and performed bioinformatic validation by demonstrating rediscovery of known biomarkers including CA125 and HE4. Two novel top biomarkers (FGF18 and GPR172A) were validated in serum samples from an independent patient cohort. We present the secretome, comprising the most comprehensive resource available for protein products that are potentially found in the blood. The associated virtual array can be used to translate gene-expression data into cancer biomarker discovery. A list of blood-based biomarkers for ovarian cancer detection is reported and includes CA125 and HE4. FGF18 and GPR172A were identified and validated by ELISA as being differentially expressed in the serum of ovarian cancer patients compared with controls. ©2015 American Association for Cancer Research.

A VAX/VMS mapped section/virtual memory utility package: Yucca Mountain Project

International Nuclear Information System (INIS)

Yarrington, L.

1990-02-01

A VAX/VMS Mapped Section/Virtual Memory Utility Package is a collection of FORTRAN subprograms that allocate virtual memory and, optionally, map that memory to a file. The subprograms use VMS system services and run-time libraries for allocating and mapping memory; therefore, the utility package is system dependent and functional on that platform only. FORTRAN-77 is one of the most widely used languages for computer programming. Languages have been developed in the past few decades that provide more powerful tools than FORTRAN and overcome some of its limitations. Two limitations addressed by this paper which have been a source of frustration to many programmers are that (1) FORTRAN does not provide dynamic array allocation and (2) FORTRAN file input-output is very slow. The solutions presented here are for the VAX/VMS operating system and use system services that are not part of the standard FORTRAN language description. Also discussed in this paper are dynamic array allocation, mapped sections of the program memory, and support modules. 3 refs

The Applicability of Incoherent Array Processing to IMS Seismic Array Stations

Science.gov (United States)

Gibbons, S. J.

2012-04-01

The seismic arrays of the International Monitoring System for the CTBT differ greatly in size and geometry, with apertures ranging from below 1 km to over 60 km. Large and medium aperture arrays with large inter-site spacings complicate the detection and estimation of high frequency phases since signals are often incoherent between sensors. Many such phases, typically from events at regional distances, remain undetected since pipeline algorithms often consider only frequencies low enough to allow coherent array processing. High frequency phases that are detected are frequently attributed qualitatively incorrect backazimuth and slowness estimates and are consequently not associated with the correct event hypotheses. This can lead to missed events both due to a lack of contributing phase detections and by corruption of event hypotheses by spurious detections. Continuous spectral estimation can be used for phase detection and parameter estimation on the largest aperture arrays, with phase arrivals identified as local maxima on beams of transformed spectrograms. The estimation procedure in effect measures group velocity rather than phase velocity and the ability to estimate backazimuth and slowness requires that the spatial extent of the array is large enough to resolve time-delays between envelopes with a period of approximately 4 or 5 seconds. The NOA, AKASG, YKA, WRA, and KURK arrays have apertures in excess of 20 km and spectrogram beamforming on these stations provides high quality slowness estimates for regional phases without additional post-processing. Seven arrays with aperture between 10 and 20 km (MJAR, ESDC, ILAR, KSRS, CMAR, ASAR, and EKA) can provide robust parameter estimates subject to a smoothing of the resulting slowness grids, most effectively achieved by convolving the measured slowness grids with the array response function for a 4 or 5 second period signal. The MJAR array in Japan recorded high SNR Pn signals for both the 2006 and 2009 North Korea

Genetic linkage mapping in an F2 perennial ryegrass population using DArT markers

DEFF Research Database (Denmark)

Tomaszewski, Céline; Byrne, Stephen; Foito, Alexandra

2012-01-01

Perennial ryegrass is the principal forage grass species used in temperate agriculture. In recent years, significant efforts have been made to develop molecular marker strategies to allow cost-effective characterization of a large number of loci simultaneously. One such strategy involves using DAr......T markers, and a DArT array has recently been developed for the Lolium-Festuca complex. In this study, we report the first use of the DArTFest array to generate a genetic linkage map based on 326 markers in a Lolium perenne F2 population, consisting of 325 genotypes. For proof of concept, the map was used...

First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi

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Nguyen H. Nguyen

2018-04-01

Full Text Available The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK (Seriola lalandi are relative sparse. To overcome this, we aimed (1 to develop a linkage map for this species, and (2 to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight. Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseqTM in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs, with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS and identified six variants/SNPs associated with body weight (P < 5e-8 when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi.

First High-Density Linkage Map and Single Nucleotide Polymorphisms Significantly Associated With Traits of Economic Importance in Yellowtail Kingfish Seriola lalandi.

Science.gov (United States)

Nguyen, Nguyen H; Rastas, Pasi M A; Premachandra, H K A; Knibb, Wayne

2018-01-01

The genetic resources available for the commercially important fish species Yellowtail kingfish (YTK) ( Seriola lalandi) are relative sparse. To overcome this, we aimed (1) to develop a linkage map for this species, and (2) to identify markers/variants associated with economically important traits in kingfish (with an emphasis on body weight). Genetic and genomic analyses were conducted using 13,898 single nucleotide polymorphisms (SNPs) generated from a new high-throughput genotyping by sequencing platform, Diversity Arrays Technology (DArTseq TM ) in a pedigreed population comprising 752 animals. The linkage analysis enabled to map about 4,000 markers to 24 linkage groups (LGs), with an average density of 3.4 SNPs per cM. The linkage map was integrated into a genome-wide association study (GWAS) and identified six variants/SNPs associated with body weight ( P 5e -8 ) when a multi-locus mixed model was used. Two out of the six significant markers were mapped to LGs 17 and 23, and collectively they explained 5.8% of the total genetic variance. It is concluded that the newly developed linkage map and the significantly associated markers with body weight provide fundamental information to characterize genetic architecture of growth-related traits in this population of YTK S. lalandi .

Development and validation of the Axiom(®) Apple480K SNP genotyping array.

Science.gov (United States)

Bianco, Luca; Cestaro, Alessandro; Linsmith, Gareth; Muranty, Hélène; Denancé, Caroline; Théron, Anthony; Poncet, Charles; Micheletti, Diego; Kerschbamer, Emanuela; Di Pierro, Erica A; Larger, Simone; Pindo, Massimo; Van de Weg, Eric; Davassi, Alessandro; Laurens, François; Velasco, Riccardo; Durel, Charles-Eric; Troggio, Michela

2016-04-01

Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom(®) genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom(®) Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom(®) Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Ambient noise tomography across Mount St. Helens using a dense seismic array

KAUST Repository

Wang, Yadong

2017-05-08

We investigated upper crustal structure with data from a dense seismic array deployed around Mount St. Helens for 2 weeks in the summer of 2014. Interstation cross correlations of ambient seismic noise data from the array were obtained, and clear fundamental mode Rayleigh waves were observed between 2.5 and 5 s periods. In addition, higher-mode signals were observed around 2 s period. Frequency-time analysis was applied to measure fundamental mode Rayleigh wave phase velocities, which were used to invert for 2-D phase velocity maps. An azimuth-dependent traveltime correction was implemented to mitigate potential biases introduced due to an inhomogeneous noise source distribution. Reliable phase velocity maps were only obtained between 3 and 4 s periods due to limitations imposed by the array aperture and higher-mode contamination. The phase velocity tomography results, which are sensitive to structure shallower than 6 km depth, reveal an ~10–15% low-velocity anomaly centered beneath the volcanic edifice and peripheral high-velocity anomalies that likely correspond to cooled igneous intrusions. We suggest that the low-velocity anomaly reflects the high-porosity mixture of lava and ash deposits near the surface of the edifice, a highly fractured magmatic conduit and hydrothermal system beneath the volcano, and possibly a small contribution from silicate melt.

Linkage Maps of a Mediterranean × Continental Tall Fescue Population and their Comparative Analysis with Other Poaceae Species

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Ryan Dierking

2015-03-01

Full Text Available Temperate grasses belonging to the complex are important throughout the world in pasture and grassland agriculture. Tall fescue ( Schreb. is the predominant species in the United States, covering approximately 15 million ha. Tall fescue has distinctive morphotypes, two of which are Continental (summer active and Mediterranean (summer semidormant. This is the first report of a linkage map created for Mediterranean tall fescue, while updating the Continental map with additional simple sequence repeat and sequence-tagged site markers. Additionally, this is the first time that diversity arrays technology (DArT markers were used in the construction of a tall fescue map. The male parent (Continental, R43-64, map consisted of 594 markers arranged in 22 linkage groups (LGs and covered a total of 1577 cM. The female parent (Mediterranean, 103-2, map was shorter (1258 cM and consisted of only 208 markers arranged in 29 LGs. Marker densities for R43-64 and 103-2 were 2.65 and 6.08 cM per marker, respectively. When compared with the other Poaceae species, meadow fescue ( Huds., annual ryegrass ( Lam., perennial ryegrass ( L., (L. Beauv., and barley ( L., a total of 171 and 98 orthologous or homologous sequences, identified by DArT analysis, were identified in R43-64 and 103-2, respectively. By using genomic in situ hybridization, we aimed to identify potential progenitors of both morphotypes. However, no clear conclusion on genomic constitution was reached. These maps will aid in the search for quantitative trait loci of various traits as well as help define and distinguish genetic differences between the two morphotypes.

Correlation of Geophysical and Geotechnical Methods for Sediment Mapping in Sungai Batu, Kedah

Science.gov (United States)

Zakaria, M. T.; Taib, A.; Saidin, M. M.; Saad, R.; Muztaza, N. M.; Masnan, S. S. K.

2018-04-01

Exploration geophysics is widely used to map the subsurface characteristics of a region, to understand the underlying rock structures and spatial distribution of rock units. 2-D resistivity and seismic refraction methods were conducted in Sungai Batu locality with objective to identify and map the sediment deposit with correlation of borehole record. 2-D resistivity data was acquire using ABEM SAS4000 system with Pole-dipole array and 2.5 m minimum electrode spacing while for seismic refraction ABEM MK8 seismograph was used to record the seismic data and 5 kg sledgehammer used as a seismic source with geophones interval of 5 m spacing. The inversion model of 2-D resistivity result shows that, the resistivity values 500 Ωm as the hard layer for this study area. The seismic result indicates that the velocity values 3600 m/s interpreted as the hard layer in this locality.

Protein kinase substrate identification on functional protein arrays

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Zhou Fang

2008-02-01

Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

NovoTTF™-100A System (Tumor Treating Fields) transducer array layout planning for glioblastoma: a NovoTAL™ system user study.

Science.gov (United States)

Chaudhry, Aafia; Benson, Laura; Varshaver, Michael; Farber, Ori; Weinberg, Uri; Kirson, Eilon; Palti, Yoram

2015-11-11

Optune™, previously known as the NovoTTF-100A System™, generates Tumor Treating Fields (TTFields), an effective anti-mitotic therapy for glioblastoma. The system delivers intermediate frequency, alternating electric fields to the supratentorial brain. Patient therapy is personalized by configuring transducer array layout placement on the scalp to the tumor site using MRI measurements and the NovoTAL System. Transducer array layout mapping optimizes therapy by maximizing electric field intensity to the tumor site. This study evaluated physician performance in conducting transducer array layout mapping using the NovoTAL System compared with mapping performed by the Novocure in-house clinical team. Fourteen physicians (7 neuro-oncologists, 4 medical oncologists, and 3 neurosurgeons) evaluated five blinded cases of recurrent glioblastoma and performed head size and tumor location measurements using a standard Digital Imaging and Communications in Medicine reader. Concordance with Novocure measurement and intra- and inter-rater reliability were assessed using relevant correlation coefficients. The study criterion for success was a concordance correlation coefficient (CCC) >0.80. CCC for each physician versus Novocure on 20 MRI measurements was 0.96 (standard deviation, SD ± 0.03, range 0.90-1.00), indicating very high agreement between the two groups. Intra- and inter-rater reliability correlation coefficients were similarly high: 0.83 (SD ±0.15, range 0.54-1.00) and 0.80 (SD ±0.18, range 0.48-1.00), respectively. This user study demonstrated an excellent level of concordance between prescribing physicians and Novocure in-house clinical teams in performing transducer array layout planning. Intra-rater reliability was very high, indicating reproducible performance. Physicians prescribing TTFields, when trained on the NovoTAL System, can independently perform transducer array layout mapping required for the initiation and maintenance of patients on TTFields

Spatial normalization of array-CGH data

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Brennetot Caroline

2006-05-01

Full Text Available Abstract Background Array-based comparative genomic hybridization (array-CGH is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for experimental artifacts while preserving the true biological signal. We investigated various sources of systematic variation in array-CGH data and identified two distinct types of spatial effect of no biological relevance as the predominant experimental artifacts: continuous spatial gradients and local spatial bias. Local spatial bias affects a large proportion of arrays, and has not previously been considered in array-CGH experiments. Results We show that existing normalization techniques do not correct these spatial effects properly. We therefore developed an automatic method for the spatial normalization of array-CGH data. This method makes it possible to delineate and to eliminate and/or correct areas affected by spatial bias. It is based on the combination of a spatial segmentation algorithm called NEM (Neighborhood Expectation Maximization and spatial trend estimation. We defined quality criteria for array-CGH data, demonstrating significant improvements in data quality with our method for three data sets coming from two different platforms (198, 175 and 26 BAC-arrays. Conclusion We have designed an automatic algorithm for the spatial normalization of BAC CGH-array data, preventing the misinterpretation of experimental artifacts as biologically relevant outliers in the genomic profile. This algorithm is implemented in the R package MANOR (Micro-Array NORmalization, which is described at http://bioinfo.curie.fr/projects/manor and available from the Bioconductor site http://www.bioconductor.org. It can also be tested on the CAPweb bioinformatics platform at http://bioinfo.curie.fr/CAPweb.

Shallow velocity structure above the Socorro Magma Body from ambient noise tomography using the large-N Sevilleta array, central Rio Grande Rift, New Mexico

Science.gov (United States)

Worthington, L. L.; Ranasinghe, N. R.; Schmandt, B.; Jiang, C.; Finlay, T. S.; Bilek, S. L.; Aster, R. C.

2017-12-01

The Socorro Magma Body (SMB) is one of the largest recognized active mid-crustal magma intrusions globally. Inflation of the SMB drives sporadically seismogenic uplift at rates of up to of few millimeters per year. We examine the upper crustal structure of the northern section of the SMB region using ambient noise seismic data collected from the Sevilleta Array and New Mexico Tech (NMT) seismic network to constrain basin structure and identify possible upper crustal heterogeneities caused by heat flow and/or fluid or magma migration to shallower depths. The Sevilleta Array comprised 801 vertical-component Nodal seismic stations with 10-Hz seismometers deployed within the Sevilleta National Wildlife Refuge in the central Rio Grande rift north of Socorro, New Mexico, for a period of 12 days during February 2015. Five short period seismic stations from the NMT network located south of the Sevilleta array are also used to improve the raypath coverage outside the Sevilleta array. Inter-station ambient noise cross-correlations were computed from all available 20-minute time windows and stacked to obtain estimates of the vertical component Green's function. Clear fundamental mode Rayleigh wave energy is observed from 3 to 6 s period. Beamforming indicates prominent noise sources from the southwest, near Baja California, and the southeast, in the Gulf of Mexico. The frequency-time analysis method was implemented to measure fundamental mode Rayleigh wave phase velocities and the resulting inter-station travel times were inverted to obtain 2-D phase velocity maps. One-dimensional sensitivity kernels indicate that the Rayleigh wave phase velocity maps are sensitive to a depth interval of 1 to 8 km, depending on wave period. The maps show (up to 40%) variations in phase velocity within the Sevilleta Array, with the largest variations found for periods of 5-6 seconds. Holocene to upper Pleistocene, alluvial sediments found in the Socorro Basin consistently show lower phase

OpenADAM: an open source genome-wide association data management system for Affymetrix SNP arrays

Directory of Open Access Journals (Sweden)

Sham P C

2008-12-01

Full Text Available Abstract Background Large scale genome-wide association studies have become popular since the introduction of high throughput genotyping platforms. Efficient management of the vast array of data generated poses many challenges. Description We have developed an open source web-based data management system for the large amount of genotype data generated from the Affymetrix GeneChip® Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms. The database supports genotype calling using DM, BRLMM, BRLMM-P or Birdseed algorithms provided by the Affymetrix Power Tools. The genotype and corresponding pedigree data are stored in a relational database for efficient downstream data manipulation and analysis, such as calculation of allele and genotype frequencies, sample identity checking, and export of genotype data in various file formats for analysis using commonly-available software. A novel method for genotyping error estimation is implemented using linkage disequilibrium information from the HapMap project. All functionalities are accessible via a web-based user interface. Conclusion OpenADAM provides an open source database system for management of Affymetrix genome-wide association SNP data.

The Protein Identifier Cross-Referencing (PICR service: reconciling protein identifiers across multiple source databases

Directory of Open Access Journals (Sweden)

Leinonen Rasko

2007-10-01

Full Text Available Abstract Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR service, a web application that provides interactive and programmatic (SOAP and REST access to a mapping algorithm that uses the UniProt Archive (UniParc as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV or Microsoft Excel (XLS files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR

Specialization of Generic Array Accesses After Inlining

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Ryohei Tokuda

2017-02-01

Full Text Available We have implemented an optimization that specializes type-generic array accesses after inlining of polymorphic functions in the native-code OCaml compiler. Polymorphic array operations (read and write in OCaml require runtime type dispatch because of ad hoc memory representations of integer and float arrays. It cannot be removed even after being monomorphized by inlining because the intermediate language is mostly untyped. We therefore extended it with explicit type application like System F (while keeping implicit type abstraction by means of unique identifiers for type variables. Our optimization has achieved up to 21% speed-up of numerical programs.

Wafer-level radiometric performance testing of uncooled microbolometer arrays

Science.gov (United States)

Dufour, Denis G.; Topart, Patrice; Tremblay, Bruno; Julien, Christian; Martin, Louis; Vachon, Carl

2014-03-01

A turn-key semi-automated test system was constructed to perform on-wafer testing of microbolometer arrays. The system allows for testing of several performance characteristics of ROIC-fabricated microbolometer arrays including NETD, SiTF, ROIC functionality, noise and matrix operability, both before and after microbolometer fabrication. The system accepts wafers up to 8 inches in diameter and performs automated wafer die mapping using a microscope camera. Once wafer mapping is completed, a custom-designed quick insertion 8-12 μm AR-coated Germanium viewport is placed and the chamber is pumped down to below 10-5 Torr, allowing for the evaluation of package-level focal plane array (FPA) performance. The probe card is electrically connected to an INO IRXCAM camera core, a versatile system that can be adapted to many types of ROICs using custom-built interface printed circuit boards (PCBs). We currently have the capability for testing 384x288, 35 μm pixel size and 160x120, 52 μm pixel size FPAs. For accurate NETD measurements, the system is designed to provide an F/1 view of two rail-mounted blackbodies seen through the Germanium window by the die under test. A master control computer automates the alignment of the probe card to the dies, the positioning of the blackbodies, FPA image frame acquisition using IRXCAM, as well as data analysis and storage. Radiometric measurement precision has been validated by packaging dies measured by the automated probing system and re-measuring the SiTF and Noise using INO's pre-existing benchtop system.

The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

Directory of Open Access Journals (Sweden)

Oga Atsunori

2008-12-01

Full Text Available Abstract Background The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers. Methods Initially, the DNA copy number aberrations (DCNAs were analyzed by array-based comparative genomic hybridization (aCGH in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states. Results By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded – sample set. In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array. Conclusion These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma.

The development of a mini-array for estimating the disease state of gastric adenocarcinoma by array CGH

International Nuclear Information System (INIS)

Furuya, Tomoko; Uchiyama, Tetsuji; Adachi, Atsushi; Okada, Takae; Nakao, Motonao; Oga, Atsunori; Yang, Song-Ju; Kawauchi, Shigeto; Sasaki, Kohsuke

2008-01-01

The treatment strategy usually depends on the disease state in the individual patient. However, it is difficult to estimate the disease state before treatment in many patients. The purpose of this study was to develop a BAC (bacterial artificial chromosome) mini-array allowing for the estimation of node metastasis, liver metastasis, peritoneal dissemination and the depth of tumor invasion in gastric cancers. Initially, the DNA copy number aberrations (DCNAs) were analyzed by array-based comparative genomic hybridization (aCGH) in 83 gastric adenocarcinomas as a training-sample set. Next, two independent analytical methods were applied to the aCGH data to identify the BAC clones with DNA copy number aberrations that were linked with the disease states. One of the methods, a decision-tree model classifier, identified 6, 4, 4, 4, and 7 clones for estimating lymph node metastasis, liver metastasis, peritoneal dissemination, depth of tumor invasion, and histological type, respectively. In the other method, a clone-by-clone comparison of the frequency of the DNA copy number aberrations selected 26 clones to estimate the disease states. By spotting these 50 clones together with 26 frequently or rarely involved clones and 62 reference clones, a mini-array was made to estimate the above parameters, and the diagnostic performance of the mini-array was evaluated for an independent set of 30 gastric cancers (blinded – sample set). In comparison to the clinicopathological features, the overall accuracy was 66.7% for node metastasis, 86.7% for liver metastasis, 86.7% for peritoneal dissemination, and 96.7% for depth of tumor invasion. The intratumoral heterogeneity barely affected the diagnostic performance of the mini-array. These results suggest that the mini-array makes it possible to determine an optimal treatment for each of the patients with gastric adenocarcinoma

Experimental demonstration of conformal phased array antenna via transformation optics.

Science.gov (United States)

Lei, Juan; Yang, Juxing; Chen, Xi; Zhang, Zhiya; Fu, Guang; Hao, Yang

2018-02-28

Transformation Optics has been proven a versatile technique for designing novel electromagnetic devices and it has much wider applicability in many subject areas related to general wave equations. Among them, quasi-conformal transformation optics (QCTO) can be applied to minimize anisotropy of transformed media and has opened up the possibility to the design of broadband antennas with arbitrary geometries. In this work, a wide-angle scanning conformal phased array based on all-dielectric QCTO lens is designed and experimentally demonstrated. Excited by the same current distribution as such in a conventional planar array, the conformal system in presence of QCTO lens can preserve the same radiation characteristics of a planar array with wide-angle beam-scanning and low side lobe level (SLL). Laplace's equation subject to Dirichlet-Neumann boundary conditions is adopted to construct the mapping between the virtual and physical spaces. The isotropic lens with graded refractive index is realized by all-dielectric holey structure after an effective parameter approximation. The measurements of the fabricated system agree well with the simulated results, which demonstrate its excellent wide-angle beam scanning performance. Such demonstration paves the way to a robust but efficient array synthesis, as well as multi-beam and beam forming realization of conformal arrays via transformation optics.

Solar observations with the prototype of the Brazilian Decimetric Array

Science.gov (United States)

Sawant, H. S.; Ramesh, R.; Faria, C.; Cecatto, J. R.; Fernandes, F. C. R.; Madsen, F. H. R.; Subramanian, K. R.; Sundararajan, M. S.

The prototype of the Brazilian Decimetric Array BDA consists of 5 element alt-az mounted parabolic mesh type dishes of 4-meter diameter having base lines up to 220 meters in the E--W direction The array was put into regular operation at Cachoeira Paulista Brazil longitude 45 r 00 20 W and latitude 22 r 41 19 S This array operates in the frequency range of 1 2 -- 1 7 GHz Solar observations are carried at sim 1 4 GHz in transit and tracking modes Spatial fine structures superimposed on the one dimensional brightness map of the sun associated with active regions and or with solar activity and their time evolution will be presented In the second phase of the project the frequency range will be increased to 1 2 - 1 7 2 8 and 5 6 GHz Central part of the array will consist of 26 antennas with 4-meter diameter laid out randomically in the square of 256 by 256 meter with minimum and maximum base lines of 8 and 256 meters respectively Details of this array with imaging capabilities in snap shot mode for solar observations and procedure of the phase and amplitude calibrations will be presented The development of instrument will be completed by the beginning of 2008

SiO MASERS AROUND WX PSC MAPPED WITH THE KVN AND VERA ARRAY (KaVA)

Energy Technology Data Exchange (ETDEWEB)

Yun, Youngjoo; Cho, Se-Hyung; Kim, Jaeheon; Choi, Yoon Kyung; Kim, Dong-Jin; Yoon, Dong-Hwan; Byun, Do-Young; Chung, Hyunsoo; Chung, Moon-Hee; Han, Myoung-Hee [Korea Astronomy and Space Science Institute, 776 Daedeok-daero, Yuseong, Daejeon 305-348 (Korea, Republic of); Imai, Hiroshi; Oyadomari, Miyako [Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065 (Japan); Asaki, Yoshiharu [National Astronomical Observatory of Japan (NAOJ) Chile Observatory/Joint ALMA Observatory (JAO), Alonso de Cordova 3107, Vitacura 763 0355, Santiago (Chile); Chibueze, James O. [Department of Physics and Astronomy, Faculty of Physical Sciences, University of Nigeria, Carver Building, 1 University Road, Nsukka (Nigeria); Dodson, Richard; Rioja, María J. [International Centre for Radio Astronomy Research, M468, The University of Western Australia, 35 Stirling Hwy, Crawley, Western Australia 6009 (Australia); Kusuno, Kozue [Department of Space and Astronautical Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), 3-1-1 Yoshinodai, Chuou-Ku, Sagamihara, Kanagawa 252-5210 (Japan); Matsumoto, Naoko; Hagiwara, Yoshiaki [Mizusawa VLBI Observatory, National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Min, Cheulhong, E-mail: yjyun@kasi.re.kr, E-mail: cho@kasi.re.kr [Department of Astronomical Sciences, The Graduate University for Advanced Studies (SOKENDAI), 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); and others

2016-05-01

We present the first images of the v = 1 and v = 2 J = 1 → 0 SiO maser lines taken with KaVA, i.e., the combined array of the Korean Very Long Baseline Interferometry (VLBI) Network and the VLBI Exploration of Radio Astrometry (VERA), toward the OH/IR star WX Psc. The combination of long and short antenna baselines enabled us to detect a large number of maser spots, which exhibit a typical ring-like structure in both the v = 1 and v = 2 J = 1 → 0 SiO masers as those that have been found in previous VLBI observational results of WX Psc. The relative alignment of the v = 1 and v = 2 SiO maser spots are precisely derived from astrometric analysis, due to the absolute coordinates of the reference maser spot that were well determined in an independent astrometric observation with VERA. The superposition of the v = 1 and v = 2 maser spot maps shows a good spatial correlation between the v = 1 and v = 2 SiO maser features. Nevertheless, it is also shown that the v = 2 SiO maser spot is distributed in an inner region compared to the v = 1 SiO maser by about 0.5 mas on average. These results provide good support for the recent theoretical studies of the SiO maser pumping, in which both the collisional and the radiative pumping predict the strong spatial correlation and the small spatial discrepancy between the v = 1 and v = 2 SiO maser.

Fast photoacoustic imaging system based on 320-element linear transducer array

International Nuclear Information System (INIS)

Yin Bangzheng; Xing Da; Wang Yi; Zeng Yaguang; Tan Yi; Chen Qun

2004-01-01

A fast photoacoustic (PA) imaging system, based on a 320-transducer linear array, was developed and tested on a tissue phantom. To reconstruct a test tomographic image, 64 time-domain PA signals were acquired from a tissue phantom with embedded light-absorption targets. A signal acquisition was accomplished by utilizing 11 phase-controlled sub-arrays, each consisting of four transducers. The results show that the system can rapidly map the optical absorption of a tissue phantom and effectively detect the embedded light-absorbing target. By utilizing the multi-element linear transducer array and phase-controlled imaging algorithm, we thus can acquire PA tomography more efficiently, compared to other existing technology and algorithms. The methodology and equipment thus provide a rapid and reliable approach to PA imaging that may have potential applications in noninvasive imaging and clinic diagnosis

Energy Zones Study: A Comprehensive Web-Based Mapping Tool to Identify and Analyze Clean Energy Zones in the Eastern Interconnection

Energy Technology Data Exchange (ETDEWEB)

Koritarov, V.; Kuiper, J.; Hlava, K.; Orr, A.; Rollins, K.; Brunner, D.; Green, H.; Makar, J.; Ayers, A.; Holm, M.; Simunich, K.; Wang, J.; Augustine, C.; Heimiller, D.; Hurlbut, D. J.; Milbrandt, A.; Schneider, T. R.; et al.

2013-09-01

This report describes the work conducted in support of the Eastern Interconnection States’ Planning Council (EISPC) Energy Zones Study and the development of the Energy Zones Mapping Tool performed by a team of experts from three National Laboratories. The multi-laboratory effort was led by Argonne National Laboratory (Argonne), in collaboration with the National Renewable Energy Laboratory (NREL) and Oak Ridge National Laboratory (ORNL). In June 2009, the U.S. Department of Energy (DOE) and the National Energy Technology Laboratory published Funding Opportunity Announcement FOA-0000068, which invited applications for interconnection-level analysis and planning. In December 2009, the Eastern Interconnection Planning Collaborative (EIPC) and the EISPC were selected as two award recipients for the Eastern Interconnection. Subsequently, in 2010, DOE issued Research Call RC-BM-2010 to DOE’s Federal Laboratories to provide research support and assistance to FOA-0000068 awardees on a variety of key subjects. Argonne was selected as the lead laboratory to provide support to EISPC in developing a methodology and a mapping tool for identifying potential clean energy zones in the Eastern Interconnection. In developing the EISPC Energy Zones Mapping Tool (EZ Mapping Tool), Argonne, NREL, and ORNL closely collaborated with the EISPC Energy Zones Work Group which coordinated the work on the Energy Zones Study. The main product of the Energy Zones Study is the EZ Mapping Tool, which is a web-based decision support system that allows users to locate areas with high suitability for clean power generation in the U.S. portion of the Eastern Interconnection. The mapping tool includes 9 clean (low- or no-carbon) energy resource categories and 29 types of clean energy technologies. The EZ Mapping Tool contains an extensive geographic information system database and allows the user to apply a flexible modeling approach for the identification and analysis of potential energy zones

ASSESSING STUDENTS’ COMPETENCE IN DEVELOPING CHOROPLETH MAPS COMBINED WITH DIAGRAM MAPS

Directory of Open Access Journals (Sweden)

GABRIELA OSACI-COSTACHE

2015-01-01

Full Text Available Choropleth maps combined with diagram maps are frequently used in geography. For this reason, based on the maps developed by students, the study aims at the following: identifying and analyzing the errors made by the students; establishing and analyzing the competence level of the students; identifying the causes that led to these errors; and finding the best solutions to improve both the educational process aiming at the formation of this kind of competences and the students’ results. The map assessment was accomplished during two academic years (2013-2014 and 2014-2015, in the aftermath of the activities meant to train the competence. We assessed 105 maps prepared by the students in Cartography (Faculty of Geography, University of Bucharest based on an analytical evaluation grid, with dichotomous scale, comprising 15 criteria. This tool helped us identify the errors made by the students, as well as their competence level. By applying a questionnaire, we identified the source of the errors from the students’ perspective, while by comparing the errors and the competence levels at the end of the two academic years we were able to come up with potential solutions for the improvement of the teaching and learning process.

Aluminum tolerance association mapping in triticale

Directory of Open Access Journals (Sweden)

Niedziela Agnieszka

2012-02-01

Full Text Available Abstract Background Crop production practices and industrialization processes result in increasing acidification of arable soils. At lower pH levels (below 5.0, aluminum (Al remains in a cationic form that is toxic to plants, reducing growth and yield. The effect of aluminum on agronomic performance is particularly important in cereals like wheat, which has promoted the development of programs directed towards selection of tolerant forms. Even in intermediately tolerant cereals (i.e., triticale, the decrease in yield may be significant. In triticale, Al tolerance seems to be influenced by both wheat and rye genomes. However, little is known about the precise chromosomal location of tolerance-related genes, and whether wheat or rye genomes are crucial for the expression of that trait in the hybrid. Results A mapping population consisting of 232 advanced breeding triticale forms was developed and phenotyped for Al tolerance using physiological tests. AFLP, SSR and DArT marker platforms were applied to obtain a sufficiently large set of molecular markers (over 3000. Associations between the markers and the trait were tested using General (GLM and Multiple (MLM Linear Models, as well as the Statistical Machine Learning (SML approach. The chromosomal locations of candidate markers were verified based on known assignments of SSRs and DArTs or by using genetic maps of rye and triticale. Two candidate markers on chromosome 3R and 9, 15 and 11 on chromosomes 4R, 6R and 7R, respectively, were identified. The r2 values were between 0.066 and 0.220 in most cases, indicating a good fit of the data, with better results obtained with the GML than the MLM approach. Several QTLs on rye chromosomes appeared to be involved in the phenotypic expression of the trait, suggesting that rye genome factors are predominantly responsible for Al tolerance in triticale. Conclusions The Diversity Arrays Technology was applied successfully to association mapping studies

A 1.4-Billion Pixel Map of the Seafloor: BOEM's Mission to Visualize Dynamic Geology and Identify Natural Seep Sites in the Gulf of Mexico

Science.gov (United States)

Kramer, K.; Shedd, W. W.

2017-12-01

In May, 2017, the U.S. Department of the Interior's Bureau of Ocean Energy Management (BOEM) published a high-resolution seafloor map of the northern Gulf of Mexico region. The new map, derived from 3-D seismic surveys, provides the scientific community with enhanced resolution and reveals previously undiscovered and poorly resolved geologic features of the continental slope, salt minibasin province, abyssal plain, Mississippi Fan, and the Florida Shelf and Escarpment. It becomes an even more powerful scientific tool when paired with BOEM's public database of 35,000 seafloor features, identifying natural hydrocarbon seeps, hard grounds, mud volcanoes, sediment flows, pockmarks, slumps, and many others. BOEM has mapped the Gulf of Mexico seafloor since 1998 in a regulatory mission to identify natural oil and gas seeps and protect the coral and chemosynthetic communities growing at those sites. The nineteen-year mapping effort, still ongoing, resulted in the creation of the 1.4-billion pixel map and the seafloor features database. With these tools and continual collaboration with academia, professional scientific institutions, and the offshore energy industry, BOEM will continue to incorporate new data to update and expand these two resources on a regular basis. They can be downloaded for free from BOEM's website at https://www.boem.gov/Gulf-of-Mexico-Deepwater-Bathymetry/ and https://www.boem.gov/Seismic-Water-Bottom-Anomalies-Map-Gallery/.

An intron capture strategy used to identify and map a lysyl oxidase-like gene on chromosome 9 in the mouse

Energy Technology Data Exchange (ETDEWEB)

Wydner, K.S.; Passmore, H.C. [Rutgers Univ., Piscataway, NJ (United States); Kim, Houngho; Csiszar, K.; Boyd, C.D. [UMDNJ, New Brunswick, NJ (United States)

1997-03-01

An intron capture strategy involving use of polymerase chain reaction was used to identify and map the mouse homologue of a human lysyl oxidase-like gene (LOXL). Oligonucleotides complementary to conserved domains within exons 4 and 5 of the human lysyl oxidase-like gene were used to amplify the corresponding segment from mouse genomic DNA. Sequencing of the resulting mouse DNA fragment of approximately 1 kb revealed that the exon sequences at the ends of the amplified fragment are highly homologous (90% nucleotide identity) to exons 4 and 5 of the human lysyl oxidase-like gene. An AluI restriction site polymorphism within intron 4 was used to map the mouse lysyl oxidase-like gene (Loxl) to mouse Chromosome 9 in a region that shares linkage conservation with human chromosome 15q24, to which the LOXL was recently mapped. 22 refs., 3 figs.

High Frequency High Spectral Resolution Focal Plane Arrays for AtLAST

Science.gov (United States)

Baryshev, Andrey

2018-01-01

Large collecting area single dish telescope such as ATLAST will be especially effective for medium (R 1000) and high (R 50000) spectral resolution observations. Large focal plane array is a natural solution to increase mapping speed. For medium resolution direct detectors with filter banks (KIDs) and or heterodyne technology can be employed. We will analyze performance limits of comparable KID and SIS focal plane array taking into account quantum limit and high background condition of terrestrial observing site. For large heterodyne focal plane arrays, a high current density AlN junctions open possibility of large instantaneous bandwidth >40%. This and possible multi frequency band FPSs presents a practical challenge for spatial sampling and scanning strategies. We will discuss phase array feeds as a possible solution, including a modular back-end system, which can be shared between KID and SIS based FPA. Finally we will discuss achievable sensitivities and pixel co unts for a high frequency (>500 GHz) FPAs and address main technical challenges: LO distribution, wire counts, bias line multiplexing, and monolithic vs. discrete mixer component integration.

The use of the multiple-gradient array for geoelectrical resistivity and induced polarization imaging

Science.gov (United States)

Aizebeokhai, Ahzegbobor P.; Oyeyemi, Kehinde D.

2014-12-01

The use of most conventional electrode configurations in electrical resistivity survey is often time consuming and labour intensive, especially when using manual data acquisition systems. Often, data acquisition teams tend to reduce data density so as to speed up field operation thereby reducing the survey cost; but this could significantly degrade the quality and resolution of the inverse models. In the present work, the potential of using the multiple-gradient array, a non-conventional electrode configuration, for practical cost effective and rapid subsurface resistivity and induced polarization mapping was evaluated. The array was used to conduct 2D resistivity and time-domain induced polarization imaging along two traverses in a study site at Ota, southwestern Nigeria. The subsurface was characterised and the main aquifer delineated using the inverse resistivity and chargeability images obtained. The performance of the multiple-gradient array was evaluated by correlating the 2D resistivity and chargeability images with those of the conventional Wenner array as well as the result of some soundings conducted along the same traverses using Schlumberger array. The multiple-gradient array has been found to have the advantage of measurement logistics and improved image resolution over the Wenner array.

Identification of subsurface layer with Wenner-Schlumberger arrays configuration geoelectrical method

Science.gov (United States)

Jamaluddin; Prasetyawati Umar, Emi

2018-02-01

One of measurement methods to investigate the condition of the subsurface is by using geoelectric method. This research uses wenner-Schlumberger arrays configuration geoelectrical method which is mapping resistivity that is commonly known as profiling (2D) in order to identify the lateral and vertical anomaly of material resistivity. 2D resistivity cross section is obtained from the result of data- processing on software Res2Dinv. The data were obtained along 70 m using Wenner-Schlumberger configuration with 5 m spaced electrode. The approximated value of resistivity obtained from the data processing ranged from 1000-1548 Ωm and with the iteration error 87.9%. Based on the geological map of Ujung Pandang sheet, the location of the research is an alluvium and coastal precipitation area with grain in forms of gravel, sand, clay, mud, and coral limestone. Thus, by observing and analyzing the variety of the resistivity cross-section from the inversion data, there are areas (a) showing resistivity values ranged from 0.1-0.2 Ωm which is estimated to be salt water intrusion based on the resistivity table of Earth materials, and region (b) which is a mixture of sand and clay material with the range of resistivity values between 1-1000 μm.

High-Resolution Genome-Wide Linkage Mapping Identifies Susceptibility Loci for BMI in the Chinese Population

DEFF Research Database (Denmark)

Zhang, Dong Feng; Pang, Zengchang; Li, Shuxia

2012-01-01

The genetic loci affecting the commonly used BMI have been intensively investigated using linkage approaches in multiple populations. This study aims at performing the first genome-wide linkage scan on BMI in the Chinese population in mainland China with hypothesis that heterogeneity in genetic...... linkage could exist in different ethnic populations. BMI was measured from 126 dizygotic twins in Qingdao municipality who were genotyped using high-resolution Affymetrix Genome-Wide Human SNP arrays containing about 1 million single-nucleotide polymorphisms (SNPs). Nonparametric linkage analysis...... in western countries. Multiple loci showing suggestive linkage were found on chromosome 1 (lod score 2.38 at 242 cM), chromosome 8 (2.48 at 95 cM), and chromosome 14 (2.2 at 89.4 cM). The strong linkage identified in the Chinese subjects that is consistent with that found in populations of European origin...

The goya mouse mutant reveals distinct newly identified roles for MAP3K1 in the development and survival of cochlear sensory hair cells.

Science.gov (United States)

Parker, Andrew; Cross, Sally H; Jackson, Ian J; Hardisty-Hughes, Rachel; Morse, Susan; Nicholson, George; Coghill, Emma; Bowl, Michael R; Brown, Steve D M

2015-12-01

Mitogen-activated protein kinase, MAP3K1, plays an important role in a number of cellular processes, including epithelial migration during eye organogenesis. In addition, studies in keratinocytes indicate that MAP3K1 signalling through JNK is important for actin stress fibre formation and cell migration. However, MAP3K1 can also act independently of JNK in the regulation of cell proliferation and apoptosis. We have identified a mouse mutant, goya, which exhibits the eyes-open-at-birth and microphthalmia phenotypes. In addition, these mice also have hearing loss. The goya mice carry a splice site mutation in the Map3k1 gene. We show that goya and kinase-deficient Map3k1 homozygotes initially develop supernumerary cochlear outer hair cells (OHCs) that subsequently degenerate, and a progressive profound hearing loss is observed by 9 weeks of age. Heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. MAP3K1 is expressed in a number of inner-ear cell types, including outer and inner hair cells, stria vascularis and spiral ganglion. Investigation of targets downstream of MAP3K1 identified an increase in p38 phosphorylation (Thr180/Tyr182) in multiple cochlear tissues. We also show that the extra OHCs do not arise from aberrant control of proliferation via p27KIP1. The identification of the goya mutant reveals a signalling molecule involved with hair-cell development and survival. Mammalian hair cells do not have the ability to regenerate after damage, which can lead to irreversible sensorineural hearing loss. Given the observed goya phenotype, and the many diverse cellular processes that MAP3K1 is known to act upon, further investigation of this model might help to elaborate upon the mechanisms underlying sensory hair cell specification, and pathways important for their survival. In addition, MAP3K1 is revealed as a new candidate gene for human sensorineural hearing loss. © 2015. Published by The Company of

The goya mouse mutant reveals distinct newly identified roles for MAP3K1 in the development and survival of cochlear sensory hair cells

Directory of Open Access Journals (Sweden)

Andrew Parker

2015-12-01

Full Text Available Mitogen-activated protein kinase, MAP3K1, plays an important role in a number of cellular processes, including epithelial migration during eye organogenesis. In addition, studies in keratinocytes indicate that MAP3K1 signalling through JNK is important for actin stress fibre formation and cell migration. However, MAP3K1 can also act independently of JNK in the regulation of cell proliferation and apoptosis. We have identified a mouse mutant, goya, which exhibits the eyes-open-at-birth and microphthalmia phenotypes. In addition, these mice also have hearing loss. The goya mice carry a splice site mutation in the Map3k1 gene. We show that goya and kinase-deficient Map3k1 homozygotes initially develop supernumerary cochlear outer hair cells (OHCs that subsequently degenerate, and a progressive profound hearing loss is observed by 9 weeks of age. Heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. MAP3K1 is expressed in a number of inner-ear cell types, including outer and inner hair cells, stria vascularis and spiral ganglion. Investigation of targets downstream of MAP3K1 identified an increase in p38 phosphorylation (Thr180/Tyr182 in multiple cochlear tissues. We also show that the extra OHCs do not arise from aberrant control of proliferation via p27KIP1. The identification of the goya mutant reveals a signalling molecule involved with hair-cell development and survival. Mammalian hair cells do not have the ability to regenerate after damage, which can lead to irreversible sensorineural hearing loss. Given the observed goya phenotype, and the many diverse cellular processes that MAP3K1 is known to act upon, further investigation of this model might help to elaborate upon the mechanisms underlying sensory hair cell specification, and pathways important for their survival. In addition, MAP3K1 is revealed as a new candidate gene for human sensorineural hearing loss.

Marine Attack on Towed Hydrophone Arrays

National Research Council Canada - National Science Library

Kalmijn, Ad

2002-01-01

The original objective of the SIO Marine Attack project was to identify the electric and magnetic fields causing sharks to inflict serious damage upon the towed hydrophone arrays of US Navy submarines...

North America pipeline map

International Nuclear Information System (INIS)

Anon.

2005-01-01

This map presents details of pipelines currently in place throughout North America. Fifty-nine natural gas pipelines are presented, as well as 16 oil pipelines. The map also identifies six proposed natural gas pipelines. Major cities, roads and highways are included as well as state and provincial boundaries. The National Petroleum Reserve is identified, as well as the Arctic National Wildlife Refuge. The following companies placed advertisements on the map with details of the services they provide relating to pipeline management and construction: Ferus Gas Industries Trust; Proline; SulfaTreat Direct Oxidation; and TransGas. 1 map

Optical Whole-Genome Restriction Mapping as a Tool for Rapidly Distinguishing and Identifying Bacterial Contaminants in Clinical Samples

Science.gov (United States)

2015-08-01

Article 3. DATES COVERED (From – To) Oct 2011 – Aug 2012 4. TITLE AND SUBTITLE Optical Whole-Genome Restriction Mapping as a Tool for Rapidly...multiple bacteria could be uniquely identified within mixtures. In the first set of experiments, three unique organisms ( Bacillus subtilis subsp. globigii...be useful in monitoring nosocomial outbreaks in neonatal and intensive care wards, or even as an initial screen for antibiotic resistant strains

Mixed arrays - problems with current methods and rules

International Nuclear Information System (INIS)

Mennerdahl, D.

1987-01-01

Simplified methods are used to control the criticality safety of mixed arrays (non-identical units) in storage or in transport. The basis for these methods is that the analyses of arrays of identical units are sufficient for drawing proper conclusions on mixed arrays. In a recent study of the rules for transport, two general flaws in such methods have been identified. One flaw is caused by increased neutron return rate to the central part of the array. The other flaw is caused by increased neutron coupling between two or more fissile units in an array. In both cases, replacement of fissile units with other units, which appear to be less reactive, can lead to criticality. This paper shows that the two flaws are common in also in current methods used for storage of fissile materials. (author)

Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.).

Science.gov (United States)

Liu, Xueying; Teng, Zhonghua; Wang, Jinxia; Wu, Tiantian; Zhang, Zhiqin; Deng, Xianping; Fang, Xiaomei; Tan, Zhaoyun; Ali, Iftikhar; Liu, Dexin; Zhang, Jian; Liu, Dajun; Liu, Fang; Zhang, Zhengsheng

2017-12-01

Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29 cM with an average distance of 1.71 cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.

High speed vision processor with reconfigurable processing element array based on full-custom distributed memory

Science.gov (United States)

Chen, Zhe; Yang, Jie; Shi, Cong; Qin, Qi; Liu, Liyuan; Wu, Nanjian

2016-04-01

In this paper, a hybrid vision processor based on a compact full-custom distributed memory for near-sensor high-speed image processing is proposed. The proposed processor consists of a reconfigurable processing element (PE) array, a row processor (RP) array, and a dual-core microprocessor. The PE array includes two-dimensional processing elements with a compact full-custom distributed memory. It supports real-time reconfiguration between the PE array and the self-organized map (SOM) neural network. The vision processor is fabricated using a 0.18 µm CMOS technology. The circuit area of the distributed memory is reduced markedly into 1/3 of that of the conventional memory so that the circuit area of the vision processor is reduced by 44.2%. Experimental results demonstrate that the proposed design achieves correct functions.

A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A

Czech Academy of Sciences Publication Activity Database

Balcárková, Barbora; Frenkel, Z.; Škopová, Monika; Abrouk, Michael; Kumar, A.; Chao, S.; Kianian, S. F.; Akhunov, E.; Korol, A.; Doležel, Jaroslav; Valárik, Miroslav

2017-01-01

Roč. 7, JAN 10 (2017), č. článku 2063. ISSN 1664-462X R&D Projects: GA MŠk(CZ) LO1204; GA ČR(CZ) GA14-07164S Institutional support: RVO:61389030 Keywords : triticum-aestivum l. * bread wheat * high-density * agronomic traits * tetraploid wheat * hexaploid wheat * polyploid wheat * genetic maps * genomes * recombination * endosperm radiation hybrid panel * radiation hybrid map * wheat chromosome 4A * chromosome deletion bin map * Triticum aestivum * SNP iSelect array Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 4.298, year: 2016

Sao Paulo Lightning Mapping Array (SP-LMA): Network Assessment and Analyses for Intercomparison Studies and GOES-R Proxy Activities

Science.gov (United States)

Bailey, J. C.; Blakeslee, R. J.; Carey, L. D.; Goodman, S. J.; Rudlosky, S. D.; Albrecht, R.; Morales, C. A.; Anselmo, E. M.; Neves, J. R.; Buechler, D. E.

2014-01-01

A 12 station Lightning Mapping Array (LMA) network was deployed during October 2011 in the vicinity of Sao Paulo, Brazil (SP-LMA) to contribute total lightning measurements to an international field campaign [CHUVA - Cloud processes of tHe main precipitation systems in Brazil: A contribUtion to cloud resolVing modeling and to the GPM (GlobAl Precipitation Measurement)]. The SP-LMA was operational from November 2011 through March 2012 during the Vale do Paraiba campaign. Sensor spacing was on the order of 15-30 km, with a network diameter on the order of 40-50km. The SP-LMA provides good 3-D lightning mapping out to 150 km from the network center, with 2-D coverage considerably farther. In addition to supporting CHUVA science/mission objectives, the SP-LMA is supporting the generation of unique proxy data for the Geostationary Lightning Mapper (GLM) and Advanced Baseline Imager (ABI), on NOAA's Geostationary Operational Environmental Satellite-R (GOES-R: scheduled for a 2015 launch). These proxy data will be used to develop and validate operational algorithms so that they will be ready to use on "day1" following the GOES-R launch. As the CHUVA Vale do Paraiba campaign opportunity was formulated, a broad community-based interest developed for a comprehensive Lightning Location System (LLS) intercomparison and assessment study, leading to the participation and/or deployment of eight other ground-based networks and the space-based Lightning Imaging Sensor (LIS). The SP-LMA data is being intercompared with lightning observations from other deployed lightning networks to advance our understanding of the capabilities/contributions of each of these networks toward GLM proxy and validation activities. This paper addresses the network assessment including noise reduction criteria, detection efficiency estimates, and statistical and climatological (both temporal and spatially) analyses for intercomparison studies and GOES-R proxy activities.

Focal plane array with modular pixel array components for scalability

Science.gov (United States)

Kay, Randolph R; Campbell, David V; Shinde, Subhash L; Rienstra, Jeffrey L; Serkland, Darwin K; Holmes, Michael L

2014-12-09

A modular, scalable focal plane array is provided as an array of integrated circuit dice, wherein each die includes a given amount of modular pixel array circuitry. The array of dice effectively multiplies the amount of modular pixel array circuitry to produce a larger pixel array without increasing die size. Desired pixel pitch across the enlarged pixel array is preserved by forming die stacks with each pixel array circuitry die stacked on a separate die that contains the corresponding signal processing circuitry. Techniques for die stack interconnections and die stack placement are implemented to ensure that the desired pixel pitch is preserved across the enlarged pixel array.

High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays

DEFF Research Database (Denmark)

Buus, Søren; Rockberg, Johan; Forsström, Björn

2012-01-01

Antibodies empower numerous important scientific, clinical, diagnostic, and industrial applications. Ideally, the epitope(s) targeted by an antibody should be identified and characterized, thereby establishing antibody reactivity, highlighting possible cross-reactivities, and perhaps even warning...... against unwanted (e.g. autoimmune) reactivities. Antibodies target proteins as either conformational or linear epitopes. The latter are typically probed with peptides, but the cost of peptide screening programs tends to prohibit comprehensive specificity analysis. To perform high-throughput, high......-resolution mapping of linear antibody epitopes, we have used ultrahigh-density peptide microarrays generating several hundred thousand different peptides per array. Using exhaustive length and substitution analysis, we have successfully examined the specificity of a panel of polyclonal antibodies raised against...

Cymbal and BB underwater transducers and arrays

Energy Technology Data Exchange (ETDEWEB)

Newnham, R.E.; Zhang, J.; Alkoy, S.; Meyer, R.; Hughes, W.J.; Hladky-Hennion, A.C.; Cochran, J.; Markley, D. [Materials Research Laboratory, Penn State University, University Park, PA 16802 (United States)

2002-09-01

The cymbal is a miniaturized class V flextensional transducer that was developed for use as a shallow water sound projector and receiver. Single elements are characterized by high Q, low efficiency, and medium power output capability. Its low cost and thin profile allow the transducer to be assembled into large flexible arrays. Efforts were made to model both single elements and arrays using the ATILA code and the integral equation formulation (EQI).Millimeter size microprobe hydrophones (BBs) have been designed and fabricated from miniature piezoelectric hollow ceramic spheres for underwater applications such as mapping acoustic fields of projectors, and flow noise sensors for complex underwater structures. Green spheres are prepared from soft lead zirconate titanate powders using a coaxial nozzle slurry process. A compact hydrophone with a radially-poled sphere is investigated using inside and outside electrodes. Characterization of these hydrophones is done through measurement of hydrostatic piezoelectric charge coefficients, free field voltage sensitivities and directivity beam patterns. (orig.)

Timed arrays wideband and time varying antenna arrays

CERN Document Server

Haupt, Randy L

2015-01-01

Introduces timed arrays and design approaches to meet the new high performance standards The author concentrates on any aspect of an antenna array that must be viewed from a time perspective. The first chapters briefly introduce antenna arrays and explain the difference between phased and timed arrays. Since timed arrays are designed for realistic time-varying signals and scenarios, the book also reviews wideband signals, baseband and passband RF signals, polarization and signal bandwidth. Other topics covered include time domain, mutual coupling, wideband elements, and dispersion. The auth

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

Directory of Open Access Journals (Sweden)

Didion John P

2012-01-01

Full Text Available Abstract Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing

Identification of catecholamine neurotransmitters using fluorescence sensor array

Energy Technology Data Exchange (ETDEWEB)

Ghasemi, Forough [Department of Chemistry, Sharif University of Technology, Tehran 11155-9516 (Iran, Islamic Republic of); Hormozi-Nezhad, M. Reza, E-mail: hormozi@sharif.edu [Department of Chemistry, Sharif University of Technology, Tehran 11155-9516 (Iran, Islamic Republic of); Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran (Iran, Islamic Republic of); Mahmoudi, Morteza, E-mail: mahmoudi@stanford.edu [Department of Nanotechnology and Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 13169-43551 (Iran, Islamic Republic of); Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305-5101 (United States)

2016-04-21

A nano-based sensor array has been developed for identification and discrimination of catecholamine neurotransmitters based on optical properties of their oxidation products under alkaline conditions. To produce distinct fluorescence response patterns for individual catecholamine, quenching of thioglycolic acid functionalized cadmium telluride (CdTe) quantum dots, by oxidation products, were employed along with the variation of fluorescence spectra of oxidation products. The spectral changes were analyzed with hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify catecholamine patterns. The proposed sensor could efficiently discriminate the individual catecholamine (i.e., dopamine, norepinephrine, and L-DOPA) and their mixtures in the concentration range of 0.25–30 μmol L{sup −1}. Finally, we found that the sensor had capability to identify the various catecholamines in urine sample. - Highlights: • We have proposed a fluorescence sensor array to detect catecholamine neurotransmitters. • Visual differentiation of catecholamines is provided by fluorescence array fingerprints. • Discrimination of catecholamines from each other, and from their mixture is obtained on a PCA plot. • Proposed sensor array can be used for detection of catecholamines in urine samples.

ArrayBridge: Interweaving declarative array processing with high-performance computing

Energy Technology Data Exchange (ETDEWEB)

Xing, Haoyuan [The Ohio State Univ., Columbus, OH (United States); Floratos, Sofoklis [The Ohio State Univ., Columbus, OH (United States); Blanas, Spyros [The Ohio State Univ., Columbus, OH (United States); Byna, Suren [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Prabhat, Prabhat [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wu, Kesheng [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Brown, Paul [Paradigm4, Inc., Waltham, MA (United States)

2017-05-04

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.

Using SNP array to identify aneuploidy and segmental imbalance in translocation carriers

Directory of Open Access Journals (Sweden)

B. Xiong

2014-12-01

In addition to genetic testing techniques, the embryo biopsy stage (polar body, cleavage embryo or blastocyst and the mode of embryo transfer (fresh or frozen embryos can affect the outcome of PGD. It is now generally recommended that blastomere biopsy should be replaced by blastocyst biopsy to avoid a high mosaic rate and biopsy-related damage to cleavage-stage embryos, which might affect embryo development. However, more clinical data are required to confirm that the technique of SNP array-based PGD (SNP-PGD combined with trophectoderm (TE biopsy and frozen embryo transfer (FET is superior to traditional FISH-PGD combined with Day 3 (D3 blastomere biopsy and fresh embryo transfer.

The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.

Directory of Open Access Journals (Sweden)

Benjamin F Voight

Full Text Available Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the "Metabochip," a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation. The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.

Sentinel nodes are identifiable in formalin-fixed specimens after surgeon-performed ex vivo sentinel lymph node mapping in colorectal cancer.

LENUS (Irish Health Repository)

Smith, Fraser McLean

2012-02-03

BACKGROUND: In recent years, the technique of sentinel lymph node (SLN) mapping has been applied to colorectal cancer. One aim was to ultrastage patients who were deemed node negative by routine pathologic processing but who went on to develop systemic disease. Such a group may benefit from adjuvant chemotherapy. METHODS: With fully informed consent and ethical approval, 37 patients with primary colorectal cancer and 3 patients with large adenomas were prospectively mapped. Isosulfan blue dye (1 to 2 mL) was injected around tumors within 5 to 10 minutes of resection. After gentle massage to recreate in vivo lymph flow, specimens were placed directly into formalin. During routine pathologic analysis, all nodes were bivalved, and blue-staining nodes were noted. These later underwent multilevel step sectioning with hematoxylin and eosin and cytokeratin staining. RESULTS: SLNs were found in 39 of 40 patients (98% sensitivity), with an average of 4.1 SLNs per patient (range, 1-8). In 14 of 16 (88% specificity) patients with nodal metastases on routine reporting, SLN status was in accordance. Focused examination of SLNs identified occult tumor deposits in 6 (29%) of 21 node-negative patients. No metastatic cells were found in SLNs draining the three adenomas. CONCLUSIONS: The ability to identify SLNs after formalin fixation increases the ease and applicability of SLN mapping in colorectal cancer. Furthermore, the sensitivity and specificity of this simple ex vivo method for establishing regional lymph node status were directly comparable to those in previously published reports.

Fine mapping of breast cancer genome-wide association studies loci in women of African ancestry identifies novel susceptibility markers.

Science.gov (United States)

Zheng, Yonglan; Ogundiran, Temidayo O; Falusi, Adeyinka G; Nathanson, Katherine L; John, Esther M; Hennis, Anselm J M; Ambs, Stefan; Domchek, Susan M; Rebbeck, Timothy R; Simon, Michael S; Nemesure, Barbara; Wu, Suh-Yuh; Leske, Maria Cristina; Odetunde, Abayomi; Niu, Qun; Zhang, Jing; Afolabi, Chibuzor; Gamazon, Eric R; Cox, Nancy J; Olopade, Christopher O; Olopade, Olufunmilayo I; Huo, Dezheng

2013-07-01

Numerous single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility have been identified by genome-wide association studies (GWAS). However, these SNPs were primarily discovered and validated in women of European and Asian ancestry. Because linkage disequilibrium is ancestry-dependent and heterogeneous among racial/ethnic populations, we evaluated common genetic variants at 22 GWAS-identified breast cancer susceptibility loci in a pooled sample of 1502 breast cancer cases and 1378 controls of African ancestry. None of the 22 GWAS index SNPs could be validated, challenging the direct generalizability of breast cancer risk variants identified in Caucasians or Asians to other populations. Novel breast cancer risk variants for women of African ancestry were identified in regions including 5p12 (odds ratio [OR] = 1.40, 95% confidence interval [CI] = 1.11-1.76; P = 0.004), 5q11.2 (OR = 1.22, 95% CI = 1.09-1.36; P = 0.00053) and 10p15.1 (OR = 1.22, 95% CI = 1.08-1.38; P = 0.0015). We also found positive association signals in three regions (6q25.1, 10q26.13 and 16q12.1-q12.2) previously confirmed by fine mapping in women of African ancestry. In addition, polygenic model indicated that eight best markers in this study, compared with 22 GWAS-identified SNPs, could better predict breast cancer risk in women of African ancestry (per-allele OR = 1.21, 95% CI = 1.16-1.27; P = 9.7 × 10(-16)). Our results demonstrate that fine mapping is a powerful approach to better characterize the breast cancer risk alleles in diverse populations. Future studies and new GWAS in women of African ancestry hold promise to discover additional variants for breast cancer susceptibility with clinical implications throughout the African diaspora.

Software Development Initiatives to Identify and Mitigate Security Threats - Two Systematic Mapping Studies

Directory of Open Access Journals (Sweden)

Paulina Silva

2016-12-01

Full Text Available Software Security and development experts have addressed the problem of building secure software systems. There are several processes and initiatives to achieve secure software systems. However, most of these lack empirical evidence of its application and impact in building secure software systems. Two systematic mapping studies (SM have been conducted to cover the existent initiatives for identification and mitigation of security threats. The SMs created were executed in two steps, first in 2015 July, and complemented through a backward snowballing in 2016 July. Integrated results of these two SM studies show a total of 30 relevant sources were identified; 17 different initiatives covering threats identification and 14 covering the mitigation of threats were found. All the initiatives were associated to at least one activity of the Software Development Lifecycle (SDLC; while 6 showed signs of being applied in industrial settings, only 3 initiatives presented experimental evidence of its results through controlled experiments, some of the other selected studies presented case studies or proposals.

Identifying Genetic Hotspots by Mapping Molecular Diversity of Widespread Trees: When Commonness Matters.

Science.gov (United States)

Souto, Cintia P; Mathiasen, Paula; Acosta, María Cristina; Quiroga, María Paula; Vidal-Russell, Romina; Echeverría, Cristian; Premoli, Andrea C

2015-01-01

Conservation planning requires setting priorities at the same spatial scale at which decision-making processes are undertaken considering all levels of biodiversity, but current methods for identifying biodiversity hotspots ignore its genetic component. We developed a fine-scale approach based on the definition of genetic hotspots, which have high genetic diversity and unique variants that represent their evolutionary potential and evolutionary novelties. Our hypothesis is that wide-ranging taxa with similar ecological tolerances, yet of phylogenetically independent lineages, have been and currently are shaped by ecological and evolutionary forces that result in geographically concordant genetic patterns. We mapped previously published genetic diversity and unique variants of biparentally inherited markers and chloroplast sequences for 9 species from 188 and 275 populations, respectively, of the 4 woody dominant families of the austral temperate forest, an area considered a biodiversity hotspot. Spatial distribution patterns of genetic polymorphisms differed among taxa according to their ecological tolerances. Eight genetic hotspots were detected and we recommend conservation actions for some in the southern Coastal Range in Chile. Existing spatially explicit genetic data from multiple populations and species can help to identify biodiversity hotspots and guide conservation actions to establish science-based protected areas that will preserve the evolutionary potential of key habitats and species. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

From a meso- to micro-scale connectome: Array Tomography and mGRASP

Directory of Open Access Journals (Sweden)

Jinhyun eKim

2015-06-01

Full Text Available Mapping mammalian synaptic connectivity has long been an important goal of neuroscience because knowing how neurons and brain areas are connected underpins an understanding of brain function. Meeting this goal requires advanced techniques with single synapse resolution and large-scale capacity, especially at multiple scales tethering the meso- and micro-scale connectome. Among several advanced LM-based connectome technologies, Array Tomography (AT and mammalian GFP-Reconstitution Across Synaptic Partners (mGRASP can provide relatively high-throughput mapping synaptic connectivity at multiple scales. AT- and mGRASP-assisted circuit mapping (ATing and mGRASPing, combined with techniques such as retrograde virus, brain clearing techniques, and activity indicators will help unlock the secrets of complex neural circuits. Here, we discuss these useful new tools to enable mapping of brain circuits at multiple scales, some functional implications of spatial synaptic distribution, and future challenges and directions of these endeavors.

A Background Noise Reduction Technique Using Adaptive Noise Cancellation for Microphone Arrays

Science.gov (United States)

Spalt, Taylor B.; Fuller, Christopher R.; Brooks, Thomas F.; Humphreys, William M., Jr.; Brooks, Thomas F.

2011-01-01

Background noise in wind tunnel environments poses a challenge to acoustic measurements due to possible low or negative Signal to Noise Ratios (SNRs) present in the testing environment. This paper overviews the application of time domain Adaptive Noise Cancellation (ANC) to microphone array signals with an intended application of background noise reduction in wind tunnels. An experiment was conducted to simulate background noise from a wind tunnel circuit measured by an out-of-flow microphone array in the tunnel test section. A reference microphone was used to acquire a background noise signal which interfered with the desired primary noise source signal at the array. The technique s efficacy was investigated using frequency spectra from the array microphones, array beamforming of the point source region, and subsequent deconvolution using the Deconvolution Approach for the Mapping of Acoustic Sources (DAMAS) algorithm. Comparisons were made with the conventional techniques for improving SNR of spectral and Cross-Spectral Matrix subtraction. The method was seen to recover the primary signal level in SNRs as low as -29 dB and outperform the conventional methods. A second processing approach using the center array microphone as the noise reference was investigated for more general applicability of the ANC technique. It outperformed the conventional methods at the -29 dB SNR but yielded less accurate results when coherence over the array dropped. This approach could possibly improve conventional testing methodology but must be investigated further under more realistic testing conditions.

Alternative mapping of probes to genes for Affymetrix chips

DEFF Research Database (Denmark)

Gautier, Laurent; Møller, M.; Friis-Hansen, L.

2004-01-01

transcripts: the NCBI RefSeq database. We also built mappings and used them in place of the original probe to genes associations provided by the manufacturer of the arrays. Results: In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes...... by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data. Conclusions: While the probes on Affymetrix arrays remain the same for several years, the biological knowledge concerning the genomic sequences evolves rapidly. Using up...

Retina-like sensor based on a lens array with a large field of view.

Science.gov (United States)

Fan, Fan; Hao, Qun; Cheng, Xuemin

2015-12-20

This paper puts forward a retina-like sensor based on a lens array, which can be used in conventional optical systems. This sensor achieves log-polar mapping by dividing the imaging optical system's image plane using a lens array. In this paper the mathematical model has been set up with the relative structural parameters. Also, the simulation experiments and parameter analysis have been discussed to verify the reliability of this system. From the experiment results, it can be seen that this sensor realized the log-polar mapping with the transformed image output. Each lens corresponded to a circular region in the image plane with no crossover between different fields of view of adjacent lenses. When the number of rings changed, the relative error did not significantly change, and this error could be reduced to 1% when the number of lenses in each ring was increased. The work widely enlarged the application of this kind of sensor, which will lay a theoretical foundation for retina-like sensors.

Pattern Nulling of Linear Antenna Arrays Using Backtracking Search Optimization Algorithm

Directory of Open Access Journals (Sweden)

Kerim Guney

2015-01-01

Full Text Available An evolutionary method based on backtracking search optimization algorithm (BSA is proposed for linear antenna array pattern synthesis with prescribed nulls at interference directions. Pattern nulling is obtained by controlling only the amplitude, position, and phase of the antenna array elements. BSA is an innovative metaheuristic technique based on an iterative process. Various numerical examples of linear array patterns with the prescribed single, multiple, and wide nulls are given to illustrate the performance and flexibility of BSA. The results obtained by BSA are compared with the results of the following seventeen algorithms: particle swarm optimization (PSO, genetic algorithm (GA, modified touring ant colony algorithm (MTACO, quadratic programming method (QPM, bacterial foraging algorithm (BFA, bees algorithm (BA, clonal selection algorithm (CLONALG, plant growth simulation algorithm (PGSA, tabu search algorithm (TSA, memetic algorithm (MA, nondominated sorting GA-2 (NSGA-2, multiobjective differential evolution (MODE, decomposition with differential evolution (MOEA/D-DE, comprehensive learning PSO (CLPSO, harmony search algorithm (HSA, seeker optimization algorithm (SOA, and mean variance mapping optimization (MVMO. The simulation results show that the linear antenna array synthesis using BSA provides low side-lobe levels and deep null levels.

Omniscopes: Large area telescope arrays with only NlogN computational cost

International Nuclear Information System (INIS)

Tegmark, Max; Zaldarriaga, Matias

2010-01-01

We show that the class of antenna layouts for telescope arrays allowing cheap analysis hardware (with correlator cost scaling as NlogN rather than N 2 with the number of antennas N) is encouragingly large, including not only previously discussed rectangular grids but also arbitrary hierarchies of such grids, with arbitrary rotations and shears at each level. We show that all correlations for such a 2D array with an n-level hierarchy can be efficiently computed via a fast Fourier transform in not two but 2n dimensions. This can allow major correlator cost reductions for science applications requiring exquisite sensitivity at widely separated angular scales, for example, 21 cm tomography (where short baselines are needed to probe the cosmological signal and long baselines are needed for point source removal), helping enable future 21 cm experiments with thousands or millions of cheap dipolelike antennas. Such hierarchical grids combine the angular resolution advantage of traditional array layouts with the cost advantage of a rectangular fast Fourier transform telescope. We also describe an algorithm for how a subclass of hierarchical arrays can efficiently use rotation synthesis to produce global sky maps with minimal noise and a well-characterized synthesized beam.

Effect of interpolation on parameters extracted from seating interface pressure arrays.

Science.gov (United States)

Wininger, Michael; Crane, Barbara

2014-01-01

Interpolation is a common data processing step in the study of interface pressure data collected at the wheelchair seating interface. However, there has been no focused study on the effect of interpolation on features extracted from these pressure maps, nor on whether these parameters are sensitive to the manner in which the interpolation is implemented. Here, two different interpolation paradigms, bilinear versus bicubic spline, are tested for their influence on parameters extracted from pressure array data and compared against a conventional low-pass filtering operation. Additionally, analysis of the effect of tandem filtering and interpolation, as well as the interpolation degree (interpolating to 2, 4, and 8 times sampling density), was undertaken. The following recommendations are made regarding approaches that minimized distortion of features extracted from the pressure maps: (1) filter prior to interpolate (strong effect); (2) use of cubic interpolation versus linear (slight effect); and (3) nominal difference between interpolation orders of 2, 4, and 8 times (negligible effect). We invite other investigators to perform similar benchmark analyses on their own data in the interest of establishing a community consensus of best practices in pressure array data processing.

Advanced Data Mining of Leukemia Cells Micro-Arrays

OpenAIRE

Richard S. Segall; Ryan M. Pierce

2009-01-01

This paper provides continuation and extensions of previous research by Segall and Pierce (2009a) that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM). As Segall and Pierce (2009a) and Segall and Pierce (2009b) the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is pro...

Multiplex flow cytometry barcoding and antibody arrays identify surface antigen profiles of primary and metastatic colon cancer cell lines.

Directory of Open Access Journals (Sweden)

Kumar Sukhdeo

Full Text Available Colon cancer is a deadly disease affecting millions of people worldwide. Current treatment challenges include management of disease burden as well as improvements in detection and targeting of tumor cells. To identify disease state-specific surface antigen signatures, we combined fluorescent cell barcoding with high-throughput flow cytometric profiling of primary and metastatic colon cancer lines (SW480, SW620, and HCT116. Our multiplexed technique offers improvements over conventional methods by permitting the simultaneous and rapid screening of cancer cells with reduced effort and cost. The method uses a protein-level analysis with commercially available antibodies on live cells with intact epitopes to detect potential tumor-specific targets that can be further investigated for their clinical utility. Multiplexed antibody arrays can easily be applied to other tumor types or pathologies for discovery-based approaches to target identification.

Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

Science.gov (United States)

Petroli, César D.; Sansaloni, Carolina P.; Carling, Jason; Steane, Dorothy A.; Vaillancourt, René E.; Myburg, Alexander A.; da Silva, Orzenil Bonfim; Pappas, Georgios Joannis; Kilian, Andrzej; Grattapaglia, Dario

2012-01-01

Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference

Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.

Directory of Open Access Journals (Sweden)

César D Petroli

Full Text Available Diversity Arrays Technology (DArT provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for

The Simons Array: expanding POLARBEAR to three multi-chroic telescopes

Science.gov (United States)

Arnold, K.; Stebor, N.; Ade, P. A. R.; Akiba, Y.; Anthony, A. E.; Atlas, M.; Barron, D.; Bender, A.; Boettger, D.; Borrill, J.; Chapman, S.; Chinone, Y.; Cukierman, A.; Dobbs, M.; Elleflot, T.; Errard, J.; Fabbian, G.; Feng, C.; Gilbert, A.; Goeckner-Wald, N.; Halverson, N. W.; Hasegawa, M.; Hattori, K.; Hazumi, M.; Holzapfel, W. L.; Hori, Y.; Inoue, Y.; Jaehnig, G. C.; Jaffe, A. H.; Katayama, N.; Keating, B.; Kermish, Z.; Keskitalo, R.; Kisner, T.; Le Jeune, M.; Lee, A. T.; Leitch, E. M.; Linder, E.; Matsuda, F.; Matsumura, T.; Meng, X.; Miller, N. J.; Morii, H.; Myers, M. J.; Navaroli, M.; Nishino, H.; Okamura, T.; Paar, H.; Peloton, J.; Poletti, D.; Raum, C.; Rebeiz, G.; Reichardt, C. L.; Richards, P. L.; Ross, C.; Rotermund, K. M.; Schenck, D. E.; Sherwin, B. D.; Shirley, I.; Sholl, M.; Siritanasak, P.; Smecher, G.; Steinbach, B.; Stompor, R.; Suzuki, A.; Suzuki, J.; Takada, S.; Takakura, S.; Tomaru, T.; Wilson, B.; Yadav, A.; Zahn, O.

2014-08-01

The Simons Array is an expansion of the POLARBEAR cosmic microwave background (CMB) polarization experiment currently observing from the Atacama Desert in Northern Chile. This expansion will create an array of three 3.5m telescopes each coupled to a multichroic bolometric receiver. The Simons Array will have the sensitivity to produce a >= 5σ detection of inationary gravitational waves with a tensor-to-scalar ratio r >= 0:01, detect the known minimum 58 meV sum of the neutrino masses with 3σ confidence when combined with a next-generation baryon acoustic oscillation measurement, and make a lensing map of large-scale structure over the 80% of the sky available from its Chilean site. These goals require high sensitivity and the ability to extract the CMB signal from contaminating astrophysical foregrounds; these requirements are met by coupling the three high-throughput telescopes to novel multichroic lenslet-coupled pixels each measuring CMB photons in both linear polarization states over multiple spectral bands. We present the status of this instrument already under construction, and an analysis of its capabilities.

Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk.

Science.gov (United States)

Guo, Xingyi; Long, Jirong; Zeng, Chenjie; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K; Wang, Qin; Milne, Roger L; Shu, Xiao-Ou; Cai, Qiuyin; Beesley, Jonathan; Kar, Siddhartha P; Andrulis, Irene L; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W; Beeghly-Fadiel, Alicia; Benitez, Javier; Blot, William; Bogdanova, Natalia; Bojesen, Stig E; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J; Cox, Angela; Cross, Simon S; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dörk, Thilo; Fasching, Peter A; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G; Grip, Mervi; Guénel, Pascal; Haiman, Christopher A; Hamann, Ute; Hartman, Mikael; Hollestelle, Antoinette; Hopper, John L; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A; Kosma, Veli-Matti; Lambrechts, Diether; Le Marchand, Loic; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona A; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L; Nevanlinna, Heli; Nord, Silje; Olson, Janet E; Orr, Nick; Peterlongo, Paolo; Putti, Thomas Choudary; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J; Schmidt, Marjanka K; Schmutzler, Rita K; Shen, Chen-Yang; Shi, Jiajun; Shrubsole, Martha J; Southey, Melissa C; Swerdlow, Anthony; Teo, Soo Hwang; Thienpont, Bernard; Toland, Amanda Ewart; Tollenaar, Robert A E M; Tomlinson, Ian P M; Truong, Thérèse; Tseng, Chiu-Chen; van den Ouweland, Ans; Wen, Wanqing; Winqvist, Robert; Wu, Anna; Yip, Cheng Har; Zamora, M Pilar; Zheng, Ying; Hall, Per; Pharoah, Paul D P; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M; Easton, Douglas F; Zheng, Wei

2015-11-01

A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10(-4); OR, 1.04; 95% confidence interval (CI), 1.02-1.07] and rs77928427 (P = 1.86 × 10(-4); OR, 1.04; 95% CI, 1.02-1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r(2) ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor-binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk. ©2015 American Association for Cancer Research.

Advanced Antenna-Coupled Superconducting Detector Arrays for CMB Polarimetry

Science.gov (United States)

Bock, James

2014-01-01

We are developing high-sensitivity millimeter-wave detector arrays for measuring the polarization of the cosmic microwave background (CMB). This development is directed to advance the technology readiness of the Inflation Probe mission in NASA's Physics of the Cosmos program. The Inflation Probe is a fourth-generation CMB satellite that will measure the polarization of the CMB to astrophysical limits, characterizing the inflationary polarization signal, mapping large-scale structure based on polarization induced by gravitational lensing, and mapping Galactic magnetic fields through measurements of polarized dust emission. The inflationary polarization signal is produced by a background of gravitational waves from the epoch of inflation, an exponential expansion of space-time in the early universe, with an amplitude that depends on the physical mechanism producing inflation. The inflationary polarization signal may be distinguished by its unique 'B-mode' vector properties from polarization from the density variations that predominantly source CMB temperature anisotropy. Mission concepts for the Inflation Probe are being developed in the US, Europe and Japan. The arrays are based on planar antennas that provide integral beam collimation, polarization analysis, and spectral band definition in a compact lithographed format that eliminates discrete fore-optics such as lenses and feedhorns. The antennas are coupled to transition-edge superconducting bolometers, read out with multiplexed SQUID current amplifiers. The superconducting sensors and readouts developed in this program share common technologies with NASA X-ray and FIR detector applications. Our program targets developments required for space observations, and we discuss our technical progress over the past two years and plans for future development. We are incorporating arrays into active sub-orbital and ground-based experiments, which advance technology readiness while producing state of the art CMB

RADIO SOURCES FROM A 31 GHz SKY SURVEY WITH THE SUNYAEV-ZEL'DOVICH ARRAY

International Nuclear Information System (INIS)

Muchovej, Stephen; Hawkins, David; Lamb, James; Woody, David; Leitch, Erik; Carlstrom, John E.; Culverhouse, Thomas; Greer, Chris; Hennessy, Ryan; Loh, Michael; Marrone, Daniel P.; Pryke, Clem; Sharp, Matthew; Joy, Marshall; Miller, Amber; Mroczkowski, Tony

2010-01-01

We present the first sample of 31 GHz selected sources to flux levels of 1 mJy. From late 2005 to mid-2007, the Sunyaev-Zel'dovich Array observed 7.7 deg 2 of the sky at 31 GHz to a median rms of 0.18 mJy beam -1 . We identify 209 sources at greater than 5σ significance in the 31 GHz maps, ranging in flux from 0.7 mJy to ∼200 mJy. Archival NVSS data at 1.4 GHz and observations at 5 GHz with the Very Large Array are used to characterize the sources. We determine the maximum-likelihood integrated source count to be N(>S) = (27.2 ± 2.5)deg -2 x (S mJy ) -1.18±0.12 over the flux range 0.7-15 mJy. This result is significantly higher than predictions based on 1.4 GHz selected samples, a discrepancy which can be explained by a small shift in the spectral index distribution for faint 1.4 GHz sources. From comparison with previous measurements of sources within the central arcminute of massive clusters, we derive an overdensity of 6.8 ± 4.4, relative to field sources.

ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.

Science.gov (United States)

Lou, Shao-Ke; Ni, Bing; Lo, Leung-Yau; Tsui, Stephen Kwok-Wing; Chan, Ting-Fung; Leung, Kwong-Sak

2011-02-01

Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can be further analyzed. Current fast and memory-saving short-read mappers could give us a quick view of the transcriptome. However, they are neither designed for reads that span across splice junctions nor for repetitive reads, which can be mapped to multiple locations in the genome (multi-reads). Here, we describe a new software package: ABMapper, which is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature. The software is freely available at: http://abmapper.sourceforge.net/. The software is written in C++ and PERL. It runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.

A matrix-inversion method for gamma-source mapping from gamma-count data - 59082

International Nuclear Information System (INIS)

Bull, Richard K.; Adsley, Ian; Burgess, Claire

2012-01-01

Gamma ray counting is often used to survey the distribution of active waste material in various locations. Ideally the output from such surveys would be a map of the activity of the waste. In this paper a simple matrix-inversion method is presented. This allows an array of gamma-count data to be converted to an array of source activities. For each survey area the response matrix is computed using the gamma-shielding code Microshield [1]. This matrix links the activity array to the count array. The activity array is then obtained via matrix inversion. The method was tested on artificially-created arrays of count-data onto which statistical noise had been added. The method was able to reproduce, quite faithfully, the original activity distribution used to generate the dataset. The method has been applied to a number of practical cases, including the distribution of activated objects in a hot cell and to activated Nimonic springs amongst fuel-element debris in vaults at a nuclear plant. (authors)

The Telescope Array experiment: status and prospects

Energy Technology Data Exchange (ETDEWEB)

Tokuno, H; Cohen, F [Institute for Cosmic Ray Research, University of Tokyo, Kashiwa (Japan); Abbasi, R U; Abu-Zayyad, T; Belz, J W; Blake, S A; Brusova, O; Cady, R; Cao, Z [University of Utah, Salt Lake City (United States); Azuma, R [Tokyo Institute of Technology, Tokyo (Japan); Benno, T; Chikawa, M; Doura, K [Kinki University, Osaka (Japan); Bergman, D R [Rutgers University, Piscataway (United States); Cheon, B G [Hanyang University, Seoul (Korea, Republic of); Chiba, J [Tokyo University of Science, Noda (Japan); Cho, I S [Yonsei University, Seoul (Korea, Republic of); Chung, T [Ewha Womans University, Seoul (Korea, Republic of); Doyle, T [Utah State University, Logan (United States); Endo, A [Saitama University, Saitama (Japan)], E-mail: htokuno@icrr.u-tokyo.ac.jp (and others)

2008-07-15

Telescope Array (TA) is a hybrid detector of a surface detector array and fluorescence telescopes. This hybrid detector will measure the energy spectrum, anisotropy and composition of ultra-high energy cosmic rays (UHECRs) to identify their origin. The almost construction of the detector has been completed in May 2007, and the detector is running under test and adjustments. The first hybrid observation with the full configuration is planned in beginning of 2008. In this paper the status and prospects of TA detector is described.

Quantum Spin Lenses in Atomic Arrays

Directory of Open Access Journals (Sweden)

A. W. Glaetzle

2017-09-01

Full Text Available We propose and discuss quantum spin lenses, where quantum states of delocalized spin excitations in an atomic medium are focused in space in a coherent quantum process down to (essentially single atoms. These can be employed to create controlled interactions in a quantum light-matter interface, where photonic qubits stored in an atomic ensemble are mapped to a quantum register represented by single atoms. We propose Hamiltonians for quantum spin lenses as inhomogeneous spin models on lattices, which can be realized with Rydberg atoms in 1D, 2D, and 3D, and with strings of trapped ions. We discuss both linear and nonlinear quantum spin lenses: in a nonlinear lens, repulsive spin-spin interactions lead to focusing dynamics conditional to the number of spin excitations. This allows the mapping of quantum superpositions of delocalized spin excitations to superpositions of spatial spin patterns, which can be addressed by light fields and manipulated. Finally, we propose multifocal quantum spin lenses as a way to generate and distribute entanglement between distant atoms in an atomic lattice array.

Designing Flat-Plate Photovoltaic Arrays

Science.gov (United States)

Ross, R. G., Jr.

1984-01-01

Report presents overview of state of art in design techniques for flat-plate solar photovoltaic modules and arrays. Paper discusses design requirements, design analyses, and test methods identified and developed for this technology over past several years in effort to reduce cost and improve utility and reliability for broad spectrum of terrestrial applications.

Performance enhancement of photovoltaic array through string and central based MPPT system under non-uniform irradiance conditions

International Nuclear Information System (INIS)

Syafaruddin; Karatepe, Engin; Hiyama, Takashi

2012-01-01

Highlights: ► We propose MPPT method for tracking global MPP of PV arrays under non-uniform irradiance conditions. ► We compare the performance of string and central based MPPT. ► Intelligent control method is utilized to identify the global operating voltage in string and central based MPPT system. ► The performance of proposed method is tested on different size of PV. - Abstract: Mismatching losses reduction of photovoltaic (PV) array has been intensively discussed through the increasing penetration of residential and commercial PV systems. Many causes of mismatching losses have been identified and plenty of proposed methods to solve this problem have been recently proposed. This paper deals with reducing method of mismatching losses due to the non-uniform irradiance conditions. It is well-known that a certain number of multiple peaks occur on the power–voltage curve as the number of PV modules in one-string increases under non-uniform operating conditions. Since the conventional control method only drives the operating points of PV system to the local maxima close to open circuit voltage, only small portion of power can be extracted from the PV system. In this study, a radial basis function neural network (RBF-ANN) based intelligent control method is utilized to map the global operating voltage and non-irradiance operating condition in string and central based MPPT systems. The proposed method has been tested on 10 × 3 (2.2 kW), 15 × 3 (2.5 kW) and 20 × 3 (3.3 kW) of series–parallel PV array configuration under random-shaded and continuous-shaded patterns. The proposed method is compared with the ideal case and conventional method through a simple power–voltage curve of PV arrays. The simulation results show that there are significant increases of about 30–60% of the extracted power in one operating condition when the proposed method is able to shift the operating voltage of modules to their optimum voltages.

Mapping Medicare Disparities Tool

Data.gov (United States)

U.S. Department of Health & Human Services — The CMS Office of Minority Health has designed an interactive map, the Mapping Medicare Disparities Tool, to identify areas of disparities between subgroups of...

Autosomal dominant spastic paraplegia with peripheral neuropathy maps to chr12q23-24.

Science.gov (United States)

Schüle, R; Bonin, M; Dürr, A; Forlani, S; Sperfeld, A D; Klimpe, S; Mueller, J C; Seibel, A; van de Warrenburg, B P; Bauer, P; Schöls, L

2009-06-02

Hereditary spastic paraplegias (HSP) are genetically exceedingly heterogeneous. To date, 37 genetic loci for HSP have been described (SPG1-41), among them 16 loci for autosomal dominant disease. Notwithstanding, further genetic heterogeneity is to be expected in HSP, as various HSP families do not link to any of the known HSP loci. In this study, we aimed to map the disease locus in a German family segregating autosomal dominant complicated HSP. A genome-wide linkage analysis was performed using the GeneChip Mapping 10Kv2.0 Xba Array containing 10,204 SNP markers. Suggestive loci were further analyzed by mapping of microsatellite markers. One locus on chromosome 12q23-24, termed SPG36, was confirmed by high density microsatellite fine mapping with a significant LOD score of 3.2. SPG36 is flanked by markers D12S318 and D12S79. Linkage to SPG36 was excluded in >20 additional autosomal dominant HSP families. Candidate genes were selected and sequenced. No disease-causing mutations were identified in the coding regions of ATXN2, HSPB8, IFT81, Myo1H, UBE3B, and VPS29. SPG36 is complicated by a sensory and motor neuropathy; it is therefore the eighth autosomal dominant subtype of complicated HSP. We report mapping of a new locus for autosomal dominant hereditary spastic paraplegia (HSP) (SPG36) on chromosome 12q23-24 in a German family with autosomal dominant HSP complicated by peripheral neuropathy.

Authoring Tool for Identifying Learning Styles, Using Self-Organizing Maps on Mobile Devices

Directory of Open Access Journals (Sweden)

Ramón Zatarain Cabada

2011-05-01

Full Text Available This work explores a methodological proposal whose main objective is the identification of learning styles using a method of self-organizing maps designed to work, for the most part, on mobile devices. These maps can work in real time and without direct student interaction, which implies the absence of prior information. The results generated are an authoring tool for adaptive courses in Web 2.0 environments.

Marker-assisted introgression of drought tolerance from wild ancestors into popular Indian rice varieties using a 7K Infinium SNP array

Directory of Open Access Journals (Sweden)

Ravindra Donde

2017-10-01

Full Text Available Recent advances in the area of genomics have led to the development of high throughput genotyping platforms that have immensely contributed to molecular breeding programs. Custom-designed single nucleotide polymorphism (SNP arrays provide an efficient, cost effective, high throughput genotyping tool for QTL/gene mapping, variety identification, marker-assisted selection, etc. In the current study, two interspecific libraries of Chromosome Segment Substitution Lines (CSSLs were evaluated under both drought and control conditions to identify lines with superior yield under drought. The CSSL libraries consisted of 48 BC4F3 lines derived from O. sativa cv. Curinga (tropical japonica x O. rufipogon, and 32 BC4F3 lines derived from O. sativa cv. Curinga (tropical japonica x O. meridionalis. The phenotypic screening of these 80 CSSLs led to the identification of three lines, MER-20, RUF-16, and RUF-44, that yielded well under drought stress. This line was backcrossed with popular rice variety of India, Swarna-Sub1 to introgress wild chromosome segments responsible for reproductive stage drought tolerance. During backcrossing, tracking of wild introgressions and monitoring of recurrent parent genome recovery was facilitated by the use of the Cornell 6K and 7K Infinium rice SNP arrays. The 6K and 7K SNP arrays assayed 5275 SNPs and 7099 SNPs, respectively, distributed across the 12 chromosomes. In our populations of (MER-20X Swarna sub1 BC2F1 lines, 1775 SNPs were polymorphic using the 6K array. The percentage of recurrent parent genome in these backcrossed lines ranged from 33-92% and the percentage of wild donor genome ranged from 8-67%. Using genotypic selection, 5% of plants were identified for further marker assisted backcrossing, based on the presence of the target donor (wild segment and maximum recovery of recurrent parent background. In the next generation, BC3F1 lines were genotyped using the 7K SNP array, which identified 2521 polymorphic SNPs

Colorimetric Sensor Array for White Wine Tasting

Directory of Open Access Journals (Sweden)

Soo Chung

2015-07-01

Full Text Available A colorimetric sensor array was developed to characterize and quantify the taste of white wines. A charge-coupled device (CCD camera captured images of the sensor array from 23 different white wine samples, and the change in the R, G, B color components from the control were analyzed by principal component analysis. Additionally, high performance liquid chromatography (HPLC was used to analyze the chemical components of each wine sample responsible for its taste. A two-dimensional score plot was created with 23 data points. It revealed clusters created from the same type of grape, and trends of sweetness, sourness, and astringency were mapped. An artificial neural network model was developed to predict the degree of sweetness, sourness, and astringency of the white wines. The coefficients of determination (R2 for the HPLC results and the sweetness, sourness, and astringency were 0.96, 0.95, and 0.83, respectively. This research could provide a simple and low-cost but sensitive taste prediction system, and, by helping consumer selection, will be able to have a positive effect on the wine industry.

Colorimetric Sensor Array for White Wine Tasting.

Science.gov (United States)

Chung, Soo; Park, Tu San; Park, Soo Hyun; Kim, Joon Yong; Park, Seongmin; Son, Daesik; Bae, Young Min; Cho, Seong In

2015-07-24

A colorimetric sensor array was developed to characterize and quantify the taste of white wines. A charge-coupled device (CCD) camera captured images of the sensor array from 23 different white wine samples, and the change in the R, G, B color components from the control were analyzed by principal component analysis. Additionally, high performance liquid chromatography (HPLC) was used to analyze the chemical components of each wine sample responsible for its taste. A two-dimensional score plot was created with 23 data points. It revealed clusters created from the same type of grape, and trends of sweetness, sourness, and astringency were mapped. An artificial neural network model was developed to predict the degree of sweetness, sourness, and astringency of the white wines. The coefficients of determination (R2) for the HPLC results and the sweetness, sourness, and astringency were 0.96, 0.95, and 0.83, respectively. This research could provide a simple and low-cost but sensitive taste prediction system, and, by helping consumer selection, will be able to have a positive effect on the wine industry.

Customizable PCR-microplate array for differential identification of multiple pathogens.

Science.gov (United States)

Woubit, Abdela; Yehualaeshet, Teshome; Roberts, Sherrelle; Graham, Martha; Kim, Moonil; Samuel, Temesgen

2013-11-01

Customizable PCR-microplate arrays were developed for the rapid identification of Salmonella Typhimurium, Salmonella Saintpaul, Salmonella Typhi, Shigella dysenteriae, Escherichia coli O157:H7, Francisella tularensis subsp. tularensis, Francisella tularensis subsp. novicida, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis, and Yersinia pseudotuberculosis. Previously, we identified highly specific primers targeting each of these pathogens. Here, we report the development of customizable PCR-microplate arrays for simultaneous identification of the pathogens using the primers identified. A mixed aliquot of genomic DNA from 38 strains was used to validate three PCR-microplate array formats. Identical PCR conditions were used to run all the samples on the three formats. Specific amplifications were obtained on all three custom plates. In preliminary tests performed to evaluate the sensitivity of these assays in samples inoculated in the laboratory with Salmonella Typhimurium, amplifications were obtained from 1 g of beef hot dog inoculated at as low as 9 CFU/ml or from milk inoculated at as low as 78 CFU/ml. Such microplate arrays could be valuable tools for initial identification or secondary confirmation of contamination by these pathogens.

Deconvolution for the localization of sound sources using a circular microphone array

DEFF Research Database (Denmark)

Tiana Roig, Elisabet; Jacobsen, Finn

2013-01-01

During the last decade, the aeroacoustic community has examined various methods based on deconvolution to improve the visualization of acoustic fields scanned with planar sparse arrays of microphones. These methods assume that the beamforming map in an observation plane can be approximated by a c......-negative least squares, and the Richardson-Lucy. This investigation examines the matter with computer simulations and measurements....... that the beamformer's point-spread function is shift-invariant. This makes it possible to apply computationally efficient deconvolution algorithms that consist of spectral procedures in the entire region of interest, such as the deconvolution approach for the mapping of the acoustic sources 2, the Fourier-based non...

A molecular marker map for roses

NARCIS (Netherlands)

Debener, T.; Mattiesch, L.; Vosman, B.

2001-01-01

n addition to an existing core map for diploid roses which comprised 305 molecular markers 60 additional markers were mapped to extend the map. As a first application of the information contained in the map, the map position of a resistance gene from roses, Rdr1, was determined by identifying

The Argonne silicon strip-detector array

Energy Technology Data Exchange (ETDEWEB)

Wuosmaa, A H; Back, B B; Betts, R R; Freer, M; Gehring, J; Glagola, B G; Happ, Th; Henderson, D J; Wilt, P [Argonne National Lab., IL (United States); Bearden, I G [Purdue Univ., Lafayette, IN (United States). Dept. of Physics

1992-08-01

Many nuclear physics experiments require the ability to analyze events in which large numbers of charged particles are detected and identified simultaneously, with good resolution and high efficiency, either alone, or in coincidence with gamma rays. The authors have constructed a compact large-area detector array to measure these processes efficiently and with excellent energy resolution. The array consists of four double-sided silicon strip detectors, each 5x5 cm{sup 2} in area, with front and back sides divided into 16 strips. To exploit the capability of the device fully, a system to read each strip-detector segment has been designed and constructed, based around a custom-built multi-channel preamplifier. The remainder of the system consists of high-density CAMAC modules, including multi-channel discriminators, charge-sensing analog-to-digital converters, and time-to-digital converters. The array`s performance has been evaluated using alpha-particle sources, and in a number of experiments conducted at Argonne and elsewhere. Energy resolutions of {Delta}E {approx} 20-30 keV have been observed for 5 to 8 MeV alpha particles, as well as time resolutions {Delta}T {<=} 500 ps. 4 figs.

Genome-wide mapping of susceptibility to coronary artery disease identifies a novel replicated locus on chromosome 17.

Directory of Open Access Journals (Sweden)

Martin Farrall

2006-05-01

Full Text Available Coronary artery disease (CAD is a leading cause of death world-wide, and most cases have a complex, multifactorial aetiology that includes a substantial heritable component. Identification of new genes involved in CAD may inform pathogenesis and provide new therapeutic targets. The PROCARDIS study recruited 2,658 affected sibling pairs (ASPs with onset of CAD before age 66 y from four European countries to map susceptibility loci for CAD. ASPs were defined as having CAD phenotype if both had CAD, or myocardial infarction (MI phenotype if both had a MI. In a first study, involving a genome-wide linkage screen, tentative loci were mapped to Chromosomes 3 and 11 with the CAD phenotype (1,464 ASPs, and to Chromosome 17 with the MI phenotype (739 ASPs. In a second study, these loci were examined with a dense panel of grid-tightening markers in an independent set of families (1,194 CAD and 344 MI ASPs. This replication study showed a significant result on Chromosome 17 (MI phenotype; p = 0.009 after adjustment for three independent replication tests. An exclusion analysis suggests that further genes of effect size lambda(sib > 1.24 are unlikely to exist in these populations of European ancestry. To our knowledge, this is the first genome-wide linkage analysis to map, and replicate, a CAD locus. The region on Chromosome 17 provides a compelling target within which to identify novel genes underlying CAD. Understanding the genetic aetiology of CAD may lead to novel preventative and/or therapeutic strategies.

First results from the MAPS spectrometer at ISIS

International Nuclear Information System (INIS)

Frost, C.D.; Perring, T.G.

2001-01-01

The scientific commissioning of MAPS, the new state-of-the-art neutron scattering instrument at ISIS, has just begun. The design of MAPS has been optimised for studies of coherent excitations in single-crystals. The principal innovation is the use of position sensitive detectors that provide close to continuos coverage over a large solid angle detector array in the forward direction. The technical description of the spectrometer is presented, and examples from the first scientific experiments are used to illustrate how the position sensitive detectors coupled with easy-to-use visualisation software is already beginning to have an impact in the measurement of excitations in single crystals. (author)

First results from the MAPS spectrometer at ISIS

Energy Technology Data Exchange (ETDEWEB)

Frost, C.D.; Perring, T.G. [ISIS Facility, CLRC Rutherford Appleton Laboratory, Didcot, Oxon (United Kingdom)

2001-03-01

The scientific commissioning of MAPS, the new state-of-the-art neutron scattering instrument at ISIS, has just begun. The design of MAPS has been optimised for studies of coherent excitations in single-crystals. The principal innovation is the use of position sensitive detectors that provide close to continuos coverage over a large solid angle detector array in the forward direction. The technical description of the spectrometer is presented, and examples from the first scientific experiments are used to illustrate how the position sensitive detectors coupled with easy-to-use visualisation software is already beginning to have an impact in the measurement of excitations in single crystals. (author)

SNP Arrays

Directory of Open Access Journals (Sweden)

Jari Louhelainen

2016-10-01

Full Text Available The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

Optimizing Hash-Array Mapped Tries for Fast and Lean Immutable JVM Collections

NARCIS (Netherlands)

M.J. Steindorfer (Michael); J.J. Vinju (Jurgen)

2015-01-01

textabstractThe data structures under-pinning collection API (e.g. lists, sets, maps) in the standard libraries of programming languages are used intensively in many applications. The standard libraries of recent Java Virtual Machine languages, such as Clojure or Scala, contain scalable and

Using participatory risk mapping (PRM to identify and understand people's perceptions of crop loss to animals in Uganda.

Directory of Open Access Journals (Sweden)

Amanda D Webber

Full Text Available Considering how people perceive risks to their livelihoods from local wildlife is central to (i understanding the impact of crop damage by animals on local people and (ii recognising how this influences their interactions with, and attitudes towards, wildlife. Participatory risk mapping (PRM is a simple, analytical tool that can be used to identify and classify risk within communities. Here we use it to explore local people's perceptions of crop damage by wildlife and the animal species involved. Interviews (n = 93, n = 76 and seven focus groups were conducted in four villages around Budongo Forest Reserve, Uganda during 2004 and 2005. Farms (N = 129 were simultaneously monitored for crop loss. Farmers identified damage by wildlife as the most significant risk to their crops; risk maps highlighted its anomalous status compared to other anticipated challenges to agricultural production. PRM was further used to explore farmers' perceptions of animal species causing crop damage and the results of this analysis compared with measured crop losses. Baboons (Papio anubis were considered the most problematic species locally but measurements of loss indicate this perceived severity was disproportionately high. In contrast goats (Capra hircus were considered only a moderate risk, yet risk of damage by this species was significant. Surprisingly, for wild pigs (Potamochoerus sp, perceptions of severity were not as high as damage incurred might have predicted, although perceived incidence was greater than recorded frequency of damage events. PRM can assist researchers and practitioners to identify and explore perceptions of the risk of crop damage by wildlife. As this study highlights, simply quantifying crop loss does not determine issues that are important to local people nor the complex relationships between perceived risk factors. Furthermore, as PRM is easily transferable it may contribute to the identification and development of

Fine-Scale Mapping at 9p22.2 Identifies Candidate Causal Variants That Modify Ovarian Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

NARCIS (Netherlands)

Vigorito, E.; Kuchenbaecker, K.B.; Beesley, J.; Adlard, J.; Agnarsson, B.A.; Andrulis, I.L.; Arun, B.K.; Barjhoux, L.; Belotti, M.; Benitez, J.; Berger, A.; Bojesen, A.; Bonanni, B.; Brewer, C.; Caldes, T.; Caligo, M.A.; Campbell, I.; Chan, S.B.; Claes, K.B.; Cohn, D.E.; Cook, J.; Daly, M.B.; Damiola, F.; Davidson, R.; Pauw, A. de; Delnatte, C.; Diez, O.; Domchek, S.M.; Dumont, M.; Durda, K.; Dworniczak, B.; Easton, D.F.; Eccles, D.; Edwinsdotter Ardnor, C.; Eeles, R.; Ejlertsen, B.; Ellis, S.; Evans, D.G.; Feliubadalo, L.; Fostira, F.; Foulkes, W.D.; Friedman, E.; Frost, D.; Gaddam, P.; Ganz, P.A.; Garber, J.; Garcia-Barberan, V.; Gauthier-Villars, M.; Gehrig, A.; Gerdes, A.M.; Giraud, S.; Godwin, A.K.; Goldgar, D.E.; Hake, C.R.; Hansen, T.V.; Healey, S.; Hodgson, S.; Hogervorst, F.B.; Houdayer, C.; Hulick, P.J.; Imyanitov, E.N.; Isaacs, C.; Izatt, L.; Izquierdo, A.; Jacobs, L; Jakubowska, A.; Janavicius, R.; Jaworska-Bieniek, K.; Jensen, U.B.; John, E.M.; Vijai, J.; Karlan, B.Y.; Kast, K.; Khan, S.; Kwong, A.; Laitman, Y.; Lester, J.; Lesueur, F.; Liljegren, A.; Lubinski, J.; Mai, P.L.; Manoukian, S.; Mazoyer, S.; Meindl, A.; Mensenkamp, A.R.; Montagna, M.; Nathanson, K.L.; Neuhausen, S.L.; Nevanlinna, H.; Niederacher, D.; Olah, E.; Olopade, O.I.; Ong, K.R.; Osorio, A.; Park, S.K.; Paulsson-Karlsson, Y.; Pedersen, I.S.; Peissel, B.; Peterlongo, P.; et al.,

2016-01-01

Population-based genome wide association studies have identified a locus at 9p22.2 associated with ovarian cancer risk, which also modifies ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. We conducted fine-scale mapping at 9p22.2 to identify potential causal variants in BRCA1 and BRCA2

Fine-Scale Mapping at 9p22.2 Identifies Candidate Causal Variants That Modify Ovarian Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

DEFF Research Database (Denmark)

Vigorito, Elena; Kuchenbaecker, Karoline B; Beesley, Jonathan

2016-01-01

Population-based genome wide association studies have identified a locus at 9p22.2 associated with ovarian cancer risk, which also modifies ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. We conducted fine-scale mapping at 9p22.2 to identify potential causal variants in BRCA1 and BRCA2 ...

A novel method to design sparse linear arrays for ultrasonic phased array.

Science.gov (United States)

Yang, Ping; Chen, Bin; Shi, Ke-Ren

2006-12-22

In ultrasonic phased array testing, a sparse array can increase the resolution by enlarging the aperture without adding system complexity. Designing a sparse array involves choosing the best or a better configuration from a large number of candidate arrays. We firstly designed sparse arrays by using a genetic algorithm, but found that the arrays have poor performance and poor consistency. So, a method based on the Minimum Redundancy Linear Array was then adopted. Some elements are determined by the minimum-redundancy array firstly in order to ensure spatial resolution and then a genetic algorithm is used to optimize the remaining elements. Sparse arrays designed by this method have much better performance and consistency compared to the arrays designed only by a genetic algorithm. Both simulation and experiment confirm the effectiveness.

Localization of canine brachycephaly using an across breed mapping approach.

Directory of Open Access Journals (Sweden)

Danika Bannasch

2010-03-01

Full Text Available The domestic dog, Canis familiaris, exhibits profound phenotypic diversity and is an ideal model organism for the genetic dissection of simple and complex traits. However, some of the most interesting phenotypes are fixed in particular breeds and are therefore less tractable to genetic analysis using classical segregation-based mapping approaches. We implemented an across breed mapping approach using a moderately dense SNP array, a low number of animals and breeds carefully selected for the phenotypes of interest to identify genetic variants responsible for breed-defining characteristics. Using a modest number of affected (10-30 and control (20-60 samples from multiple breeds, the correct chromosomal assignment was identified in a proof of concept experiment using three previously defined loci; hyperuricosuria, white spotting and chondrodysplasia. Genome-wide association was performed in a similar manner for one of the most striking morphological traits in dogs: brachycephalic head type. Although candidate gene approaches based on comparable phenotypes in mice and humans have been utilized for this trait, the causative gene has remained elusive using this method. Samples from nine affected breeds and thirteen control breeds identified strong genome-wide associations for brachycephalic head type on Cfa 1. Two independent datasets identified the same genomic region. Levels of relative heterozygosity in the associated region indicate that it has been subjected to a selective sweep, consistent with it being a breed defining morphological characteristic. Genotyping additional dogs in the region confirmed the association. To date, the genetic structure of dog breeds has primarily been exploited for genome wide association for segregating traits. These results demonstrate that non-segregating traits under strong selection are equally tractable to genetic analysis using small sample numbers.

Intensity correction method customized for multi-animal abdominal MR imaging with 3 T clinical scanner and multi-array coil

International Nuclear Information System (INIS)

Mitsuda, Minoru; Yamaguchi, Masayuki; Nakagami, Ryutaro; Furuta, Toshihiro; Fujii, Hirofumi; Sekine, Norio; Niitsu, Mamoru; Moriyama, Noriyuki

2013-01-01

Simultaneous magnetic resonance (MR) imaging of multiple small animals in a single session increases throughput of preclinical imaging experiments. Such imaging using a 3-tesla clinical scanner with multi-array coil requires correction of intensity variation caused by the inhomogeneous sensitivity profile of the coil. We explored a method for correcting intensity that we customized for multi-animal MR imaging, especially abdominal imaging. Our institutional committee for animal experimentation approved the protocol. We acquired high resolution T 1 -, T 2 -, and T 2 * -weighted images and low resolution proton density-weighted images (PDWIs) of 4 rat abdomens simultaneously using a 3T clinical scanner and custom-made multi-array coil. For comparison, we also acquired T 1 -, T 2 -, and T 2 * -weighted volume coil images in the same rats in 4 separate sessions. We used software created in-house to correct intensity variation. We applied thresholding to the PDWIs to produce binary images that displayed only a signal-producing area, calculated multi-array coil sensitivity maps by dividing low-pass filtered PDWIs by low-pass filtered binary images pixel by pixel, and divided uncorrected T 1 -, T 2 -, or T 2 * -weighted images by those maps to obtain intensity-corrected images. We compared tissue contrast among the liver, spinal canal, and muscle between intensity-corrected multi-array coil images and volume coil images. Our intensity correction method performed well for all pulse sequences studied and corrected variation in original multi-array coil images without deteriorating the throughput of animal experiments. Tissue contrasts were comparable between intensity-corrected multi-array coil images and volume coil images. Our intensity correction method customized for multi-animal abdominal MR imaging using a 3T clinical scanner and dedicated multi-array coil could facilitate image interpretation. (author)

Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization.

Science.gov (United States)

Xu, Y; Ehringer, M; Yang, F; Sikela, J M

2001-06-01

Inbred long-sleep (ILS) and short-sleep (ISS) mice show significant central nervous system-mediated differences in sleep time for sedative dose of ethanol and are frequently used as a rodent model for ethanol sensitivity. In this study, we have used complementary DNA (cDNA) array hybridization methodology to identify genes that are differentially expressed between the brains of ILS and ISS mice. To carry out this analysis, we used both the gene discovery array (GDA) and the Mouse GEM 1 Microarray. GDA consists of 18,378 nonredundant mouse cDNA clones on a single nylon filter. Complex probes were prepared from total brain mRNA of ILS or ISS mice by using reverse transcription and 33P labeling. The labeled probes were hybridized in parallel to the gene array filters. Data from GDA experiments were analyzed with SQL-Plus and Oracle 8. The GEM microarray includes 8,730 sequence-verified clones on a glass chip. Two fluorescently labeled probes were used to hybridize a microarray simultaneously. Data from GEM experiments were analyzed by using the GEMTools software package (Incyte). Differentially expressed genes identified from each method were confirmed by relative quantitative reverse transcription-polymerase chain reaction (RT-PCR). A total of 41 genes or expressed sequence tags (ESTs) display significant expression level differences between brains of ILS and ISS mice after GDA, GEM1 hybridization, and quantitative RT-PCR confirmation. Among them, 18 clones were expressed higher in ILS mice, and 23 clones were expressed higher in ISS mice. The individual gene or EST's function and mapping information have been analyzed. This study identified 41 genes that are differentially expressed between brains of ILS and ISS mice. Some of them may have biological relevance in mediation of phenotypic variation between ILS and ISS mice for ethanol sensitivity. This study also demonstrates that parallel gene expression comparison with high-density cDNA arrays is a rapid and

A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat.

Science.gov (United States)

Elbasyoni, Ibrahim S; Lorenz, A J; Guttieri, M; Frels, K; Baenziger, P S; Poland, J; Akhunov, E

2018-05-01

The utilization of DNA molecular markers in plant breeding to maximize selection response via marker-assisted selection (MAS) and genomic selection (GS) has revolutionized plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotyping-by-sequencing scored SNPs (GBS-scored SNPs) provides a large number of markers, albeit with high rates of missing data. Array scored SNPs are of high quality, but the cost per sample is substantially higher. The objectives of this study were 1) compare GBS-scored SNPs, and array scored SNPs for genomic selection applications, and 2) compare estimates of genomic kinship and population structure calculated using the two marker platforms. SNPs were compared in a diversity panel consisting of 299 hard winter wheat (Triticum aestivum L.) accessions that were part of a multi-year, multi-environments association mapping study. The panel was phenotyped in Ithaca, Nebraska for heading date, plant height, days to physiological maturity and grain yield in 2012 and 2013. The panel was genotyped using GBS-scored SNPs, and array scored SNPs. Results indicate that GBS-scored SNPs is comparable to or better than Array-scored SNPs for genomic prediction application. Both platforms identified the same genetic patterns in the panel where 90% of the lines were classified to common genetic groups. Overall, we concluded that GBS-scored SNPs have the potential to be the marker platform of choice for genetic diversity and genomic selection in winter wheat. Copyright © 2018 Elsevier B.V. All rights reserved.

Identifying and classifying water hyacinth (Eichhornia crassipes) using the HyMap sensor

Science.gov (United States)

Rajapakse, Sepalika S.; Khanna, Shruti; Andrew, Margaret E.; Ustin, Susan L.; Lay, Mui

2006-08-01

In recent years, the impact of aquatic invasive species on biodiversity has become a major global concern. In the Sacramento-San Joaquin Delta region in the Central Valley of California, USA, dense infestations of the invasive aquatic emergent weed, water hyacinth (Eichhornia crassipes) interfere with ecosystem functioning. This silent invader constantly encroaches into waterways, eventually making them unusable by people and uninhabitable to aquatic fauna. Quantifying and mapping invasive plant species in aquatic ecosystems is important for efficient management and implementation of mitigation measures. This paper evaluates the ability of hyperspectral imagery, acquired using the HyMap sensor, for mapping water hyacinth in the Sacramento-San Joaquin Delta region. Classification was performed on sixty-four flightlines acquired over the study site using a decision tree which incorporated Spectral Angle Mapper (SAM) algorithm, absorption feature parameters in the spectral region between 0.4 and 2.5μm, and spectral endmembers. The total image dataset was 130GB. Spectral signatures of other emergent aquatic species like pennywort (Hydrocotyle ranunculoides) and water primrose (Ludwigia peploides) showed close similarity with the water hyacinth spectrum, however, the decision tree successfully discriminated water hyacinth from other emergent aquatic vegetation species. The classification algorithm showed high accuracy (κ value = 0.8) in discriminating water hyacinth.

Mapping Local Cytosolic Enzymatic Activity in Human Esophageal Mucosa with Porous Silicon Nanoneedles.

Science.gov (United States)

Chiappini, Ciro; Campagnolo, Paola; Almeida, Carina S; Abbassi-Ghadi, Nima; Chow, Lesley W; Hanna, George B; Stevens, Molly M

2015-09-16

Porous silicon nanoneedles can map Cathepsin B activity across normal and tumor human esophageal mucosa. Assembling a peptide-based Cathepsin B cleavable sensor over a large array of nano-needles allows the discrimination of cancer cells from healthy ones in mixed culture. The same sensor applied to tissue can map Cathepsin B activity with high resolution across the tumor margin area of esophageal adenocarcinoma. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The National Map 2.0 Tactical Plan: "Toward the (Integrated) National Map"

Science.gov (United States)

Zulick, Carl A.

2008-01-01

The National Map's 2-year goal, as described in this plan, is to provide a range of geospatial products and services that meet the basic goals of the original vision for The National Map while furthering the National Spatial Data Infrastructure that underpins U.S. Geological Survey (USGS) science. To accomplish this goal, the National Geospatial Program (NGP) will acquire, store, maintain, and distribute base map data. The management team for the NGP sets priorities for The National Map in three areas: Data and Products, Services, and Management. Priorities for fiscal years 2008 and 2009 (October 1, 2007 through September 30, 2009), involving the current data inventory, data acquisition, and the integration of data, are (1) incorporating current data from Federal, State, and local organizations into The National Map to the degree possible, given data availability and program resources; (2) collaborating with other USGS programs to incorporate data that support the USGS Science Strategy; (3) supporting the Department of the Interior (DOI) high-priority geospatial information needs; (4) emergency response; (5) homeland security, natural hazards; and (6) graphics products delivery. The management team identified known constraints, enablers, and drivers for the acquisition and integration of data. The NGP management team also identified customer-focused products and services of The National Map. Ongoing planning and management activities direct the development and delivery of these products and services. Management of work flow processes to support The National Map priorities are identified and established through a business-driven prioritization process. This tactical plan is primarily for use as a document to guide The National Map program for the next two fiscal years. The document is available to the public because of widespread interest in The National Map. The USGS collaborates with a broad range of customers and partners who are essential to the success of The

Fabrication and characterization of nano-gas sensor arrays

International Nuclear Information System (INIS)

Hassan, H. S.; Kashyout, A. B.; Morsi, I.; Nasser, A. A. A.; Raafat, A.

2015-01-01

A novel structures of Nanomaterials gas sensors array constructed using ZnO, and ZnO doped with Al via sol-gel technique. Two structure arrays are developed; the first one is a double sensor array based on doping with percentages of 1% and 5%. The second is a quadrature sensor array based on several doping ratios concentrations (0%, 1%, 5% and 10%). The morphological structures of prepared ZnO were revealed using scanning electron microscope (SEM). X-ray diffraction (XRD) patterns reveal a highly crystallized wurtzite structure and used for identifying phase structure and chemical state of both ZnO and ZnO doped with Al under different preparation conditions and different doping ratios. Chemical composition of Al-doped ZnO nanopowders was performed using energy dispersive x-ray (EDS) analysis. The electrical characteristics of the sensor are determined by measuring the two terminal sensor’s output resistance for O 2 , H 2 and CO 2 gases as a function of temperature

Fabrication and characterization of nano-gas sensor arrays

Energy Technology Data Exchange (ETDEWEB)

Hassan, H. S., E-mail: hassan.shokry@gmail.com; Kashyout, A. B., E-mail: hady8@yahoo.com [Electronic Materials Researches Department, Advanced Technology and New Materials Research Institute, City of Scientific Researches and technological applications, New Borg El-Arab City, Alexandria (Egypt); Morsi, I., E-mail: drimanmorsi@yahoo.com; Nasser, A. A. A., E-mail: menem-1954@yahoo.com; Raafat, A., E-mail: abrs-218@yahoo.com [Arab Academy for Science and Technology, and Maritime Transport, Alexandria, 21936 (Egypt)

2015-03-30

A novel structures of Nanomaterials gas sensors array constructed using ZnO, and ZnO doped with Al via sol-gel technique. Two structure arrays are developed; the first one is a double sensor array based on doping with percentages of 1% and 5%. The second is a quadrature sensor array based on several doping ratios concentrations (0%, 1%, 5% and 10%). The morphological structures of prepared ZnO were revealed using scanning electron microscope (SEM). X-ray diffraction (XRD) patterns reveal a highly crystallized wurtzite structure and used for identifying phase structure and chemical state of both ZnO and ZnO doped with Al under different preparation conditions and different doping ratios. Chemical composition of Al-doped ZnO nanopowders was performed using energy dispersive x-ray (EDS) analysis. The electrical characteristics of the sensor are determined by measuring the two terminal sensor’s output resistance for O{sub 2}, H{sub 2} and CO{sub 2} gases as a function of temperature.

LES investigation of infinite staggered wind-turbine arrays

International Nuclear Information System (INIS)

Yang, Xiaolei; Sotiropoulos, Fotis

2014-01-01

The layouts of turbines affect the turbine wake interactions and thus the wind farm performance. The wake interactions in infinite staggered wind-turbine arrays are investigated and compared with infinite aligned turbine arrays in this paper. From the numerical results we identify three types of wake behaviours, which are significantly different from wakes in aligned wind-turbine arrays. For the first type, each turbine wake interferes with the pair of staggered downstream turbine wakes and the aligned downstream turbine. For the second type, each turbine wake interacts with the first two downstream turbine wakes but does not show significant interference with the second aligned downstream turbine. For the third type, each turbine wake recovers immediately after passing through the gap of the first two downstream turbines and has little interaction with the second downstream turbine wakes The extracted power density and power efficiency are also studied and compared with aligned wind-turbine arrays

Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species.

Science.gov (United States)

Pottorff, Marti; Ehlers, Jeffrey D; Fatokun, Christian; Roberts, Philip A; Close, Timothy J

2012-06-12

Cowpea [Vigna unguiculata (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa. Leaf morphology was studied in the cowpea RIL population, Sanzi (sub-globose leaf shape) x Vita 7 (hastate leaf shape). A QTL for leaf shape, Hls (hastate leaf shape), was identified on the Sanzi x Vita 7 genetic map spanning from 56.54 cM to 67.54 cM distance on linkage group 15. SNP marker 1_0910 was the most significant over the two experiments, accounting for 74.7% phenotypic variance (LOD 33.82) in a greenhouse experiment and 71.5% phenotypic variance (LOD 30.89) in a field experiment. The corresponding Hls locus was positioned on the cowpea consensus genetic map on linkage group 4, spanning from 25.57 to 35.96 cM. A marker-trait association of the Hls region identified SNP marker 1_0349 alleles co-segregating with either the hastate or sub-globose leaf phenotype. High co-linearity was observed for the syntenic Hls region in Medicago truncatula and Glycine max. One syntenic locus for Hls was identified on Medicago chromosome 7 while syntenic regions for Hls were identified on two soybean chromosomes, 3 and 19. In all three syntenic loci, an ortholog for the EZA1/SWINGER (AT4G02020.1) gene was observed and is the candidate gene for the Hls locus. The Hls locus was identified on the cowpea physical map via SNP markers 1_0910, 1_1013 and 1_0992 which were identified in three BAC contigs; contig926, contig821 and contig25. This study has demonstrated how integrated genomic resources can be utilized for a candidate gene approach. Identification of genes which control leaf morphology may be utilized to improve the quality of cowpea leaves for vegetable and or forage markets as well as contribute to more fundamental research understanding the control of leaf shape in legumes.

Novel Wearable Device for Blood Leakage Detection during Hemodialysis Using an Array Sensing Patch.

Science.gov (United States)

Du, Yi-Chun; Lim, Bee-Yen; Ciou, Wei-Siang; Wu, Ming-Jui

2016-06-09

Hemodialysis (HD) is a clinical treatment that requires the puncturing of the body surface. However, needle dislodgement can cause a high risk of blood leakage and can be fatal to patients. Previous studies proposed several devices for blood leakage detection using optical or electrical techniques. Nonetheless, these methods used single-point detection and the design was not suitable for multi-bed monitoring. This study proposed a novel wearable device for blood leakage monitoring during HD using an array sensing patch. The array sensing patch combined with a mapping circuit and a wireless module could measure and transmit risk levels. The different risk levels could improve the working process of healthcare workers, and enhance their work efficiency and reduce inconvenience due to false alarms. Experimental results showed that each point of the sensing array could detect up to 0.1 mL of blood leakage and the array sensing patch supports a risk level monitoring system up to 8 h to alert healthcare personnel of pertinent danger to the patients.

Novel Wearable Device for Blood Leakage Detection during Hemodialysis Using an Array Sensing Patch

Directory of Open Access Journals (Sweden)

Yi-Chun Du

2016-06-01

Full Text Available Hemodialysis (HD is a clinical treatment that requires the puncturing of the body surface. However, needle dislodgement can cause a high risk of blood leakage and can be fatal to patients. Previous studies proposed several devices for blood leakage detection using optical or electrical techniques. Nonetheless, these methods used single-point detection and the design was not suitable for multi-bed monitoring. This study proposed a novel wearable device for blood leakage monitoring during HD using an array sensing patch. The array sensing patch combined with a mapping circuit and a wireless module could measure and transmit risk levels. The different risk levels could improve the working process of healthcare workers, and enhance their work efficiency and reduce inconvenience due to false alarms. Experimental results showed that each point of the sensing array could detect up to 0.1 mL of blood leakage and the array sensing patch supports a risk level monitoring system up to 8 h to alert healthcare personnel of pertinent danger to the patients.

Synthesis and photoluminescence of a full zinc blende phase ZnO nanorod array

International Nuclear Information System (INIS)

Zhou Shaomin; Gong Hechun; Zhang Bin; Du Zuliang; Zhang Xingtang; Wu Sixin

2008-01-01

A single-crystalline ZnO nanorod array with rectangular cross-sections has been synthesized, in which the as-obtained products are a complete metastable zinc blende (ZB) phase. X-ray powder diffraction, electron microscopy, and elemental maps have been used to show that the ZB-ZnO samples have a lattice constant a = 4.580 A, and are free from contamination by hexagonal wurtzite (HW) ZnO. Based on our experimental data, the associated growth mechanism is tentatively suggested. In addition, the photoluminescence (PL) spectrum (about 400 nm (3.1 eV)) of the as-fabricated ZB-ZnO products was detected; this is the first experimental report of the optical properties of ZB-ZnO nanorod arrays

Genetic Mapping of Novel Loci Affecting Canine Blood Phenotypes.

Directory of Open Access Journals (Sweden)

Michelle E White

Full Text Available Since the publication of the dog genome and the construction of high-quality genome-wide SNP arrays, thousands of dogs have been genotyped for disease studies. For many of these dogs, additional clinical phenotypes are available, such as hematological and clinical chemistry results collected during routine veterinary care. Little is known about the genetic basis of variation in blood phenotypes, but this variation may play an important role in the etiology and progression of many diseases. From a cohort of dogs that had been previously genotyped on a semi-custom Illumina CanineHD array for various genome-wide association studies (GWAS at Cornell University Hospital for Animals, we chose 353 clinically healthy, adult dogs for our analysis of clinical pathologic test results (14 hematological tests and 25 clinical chemistry tests. After correcting for age, body weight and sex, genetic associations were identified for amylase, segmented neutrophils, urea nitrogen, glucose, and mean corpuscular hemoglobin. Additionally, a strong genetic association (P = 8.1×10-13 was evident between a region of canine chromosome 13 (CFA13 and alanine aminotransferase (ALT, explaining 23% of the variation in ALT levels. This region of CFA13 encompasses the GPT gene that encodes the transferase. Dogs homozygous for the derived allele exhibit lower ALT activity, making increased ALT activity a less useful marker of hepatic injury in these individuals. Overall, these associations provide a roadmap for identifying causal variants that could improve interpretation of clinical blood tests and understanding of genetic risk factors associated with diseases such as canine diabetes and anemia, and demonstrate the utility of holistic phenotyping of dogs genotyped for disease mapping studies.

Genetic Mapping of Novel Loci Affecting Canine Blood Phenotypes.

Science.gov (United States)

White, Michelle E; Hayward, Jessica J; Stokol, Tracy; Boyko, Adam R

2015-01-01

Since the publication of the dog genome and the construction of high-quality genome-wide SNP arrays, thousands of dogs have been genotyped for disease studies. For many of these dogs, additional clinical phenotypes are available, such as hematological and clinical chemistry results collected during routine veterinary care. Little is known about the genetic basis of variation in blood phenotypes, but this variation may play an important role in the etiology and progression of many diseases. From a cohort of dogs that had been previously genotyped on a semi-custom Illumina CanineHD array for various genome-wide association studies (GWAS) at Cornell University Hospital for Animals, we chose 353 clinically healthy, adult dogs for our analysis of clinical pathologic test results (14 hematological tests and 25 clinical chemistry tests). After correcting for age, body weight and sex, genetic associations were identified for amylase, segmented neutrophils, urea nitrogen, glucose, and mean corpuscular hemoglobin. Additionally, a strong genetic association (P = 8.1×10-13) was evident between a region of canine chromosome 13 (CFA13) and alanine aminotransferase (ALT), explaining 23% of the variation in ALT levels. This region of CFA13 encompasses the GPT gene that encodes the transferase. Dogs homozygous for the derived allele exhibit lower ALT activity, making increased ALT activity a less useful marker of hepatic injury in these individuals. Overall, these associations provide a roadmap for identifying causal variants that could improve interpretation of clinical blood tests and understanding of genetic risk factors associated with diseases such as canine diabetes and anemia, and demonstrate the utility of holistic phenotyping of dogs genotyped for disease mapping studies.

A high-throughput shotgun mutagenesis approach to mapping B-cell antibody epitopes.

Science.gov (United States)

Davidson, Edgar; Doranz, Benjamin J

2014-09-01

Characterizing the binding sites of monoclonal antibodies (mAbs) on protein targets, their 'epitopes', can aid in the discovery and development of new therapeutics, diagnostics and vaccines. However, the speed of epitope mapping techniques has not kept pace with the increasingly large numbers of mAbs being isolated. Obtaining detailed epitope maps for functionally relevant antibodies can be challenging, particularly for conformational epitopes on structurally complex proteins. To enable rapid epitope mapping, we developed a high-throughput strategy, shotgun mutagenesis, that enables the identification of both linear and conformational epitopes in a fraction of the time required by conventional approaches. Shotgun mutagenesis epitope mapping is based on large-scale mutagenesis and rapid cellular testing of natively folded proteins. Hundreds of mutant plasmids are individually cloned, arrayed in 384-well microplates, expressed within human cells, and tested for mAb reactivity. Residues are identified as a component of a mAb epitope if their mutation (e.g. to alanine) does not support candidate mAb binding but does support that of other conformational mAbs or allows full protein function. Shotgun mutagenesis is particularly suited for studying structurally complex proteins because targets are expressed in their native form directly within human cells. Shotgun mutagenesis has been used to delineate hundreds of epitopes on a variety of proteins, including G protein-coupled receptor and viral envelope proteins. The epitopes mapped on dengue virus prM/E represent one of the largest collections of epitope information for any viral protein, and results are being used to design better vaccines and drugs. © 2014 John Wiley & Sons Ltd.

Asymmetric neighborhood functions accelerate ordering process of self-organizing maps

International Nuclear Information System (INIS)

Ota, Kaiichiro; Aoki, Takaaki; Kurata, Koji; Aoyagi, Toshio

2011-01-01

A self-organizing map (SOM) algorithm can generate a topographic map from a high-dimensional stimulus space to a low-dimensional array of units. Because a topographic map preserves neighborhood relationships between the stimuli, the SOM can be applied to certain types of information processing such as data visualization. During the learning process, however, topological defects frequently emerge in the map. The presence of defects tends to drastically slow down the formation of a globally ordered topographic map. To remove such topological defects, it has been reported that an asymmetric neighborhood function is effective, but only in the simple case of mapping one-dimensional stimuli to a chain of units. In this paper, we demonstrate that even when high-dimensional stimuli are used, the asymmetric neighborhood function is effective for both artificial and real-world data. Our results suggest that applying the asymmetric neighborhood function to the SOM algorithm improves the reliability of the algorithm. In addition, it enables processing of complicated, high-dimensional data by using this algorithm.

Identification and evaluation of resistance to powdery mildew and yellow rust in a wheat mapping population.

Directory of Open Access Journals (Sweden)

Lijun Yang

Full Text Available Deployment of cultivars with genetic resistance is an effective approach to control the diseases of powdery mildew (PM and yellow rust (YR. Chinese wheat cultivar XK0106 exhibits high levels of resistance to both diseases, while cultivar E07901 has partial, adult plant resistance (APR. The aim of this study was to map resistance loci derived from the two cultivars and analyze their effects against PM and YR in a range of environments. A doubled haploid population (388 lines was used to develop a framework map consisting of 117 SSR markers, while a much higher density map using the 90K Illumina iSelect SNP array was produced with a subset of 80 randomly selected lines. Seedling resistance was characterized against a range of PM and YR isolates, while field scores in multiple environments were used to characterize APR. Composite interval mapping (CIM of seedling PM scores identified two QTLs (QPm.haas-6A and QPm.haas-2A, the former being located at the Pm21 locus. These QTLs were also significant in field scores, as were Qpm.haas-3A and QPm.haas-5A. QYr.haas-1B-1 and QYr.haas-2A were identified in field scores of YR and were located at the Yr24/26 and Yr17 chromosomal regions respectively. A second 1B QTL, QYr.haas-1B-2 was also identified. QPm.haas-2A and QYr.haas-1B-2 are likely to be new QTLs that have not been previously identified. Effects of the QTLs were further investigated in multiple environments through the testing of selected lines predicted to contain various QTL combinations. Significant additive interactions between the PM QTLs highlighted the ability to pyramid these loci to provide higher level of resistance. Interactions between the YR QTLs gave insights into the pathogen populations in the different locations as well as showing genetic interactions between these loci.

The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

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Lo Fang-Yi

2012-06-01

Full Text Available Abstract Background Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Methods Array-comparative genomic hybridization (array-CGH was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR, chromogenic in situ hybridization (CISH, reverse transcriptase-qPCR (RT-qPCR, and immunohistochemistry (IHC in more patients. Results We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1 functioning in Rho activity control, FRAT2 (10q24.1 involved in Wnt signaling, PAFAH1B1 (17p13.3 functioning in motility control, and ZNF322A (6p22.1 involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (PP=0.06. In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of

The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

International Nuclear Information System (INIS)

Lo, Fang-Yi; Nandi, Suvobroto; Salgia, Ravi; Wang, Yi-Ching; Chang, Jer-Wei; Chang, I-Shou; Chen, Yann-Jang; Hsu, Han-Shui; Huang, Shiu-Feng Kathy; Tsai, Fang-Yu; Jiang, Shih Sheng; Kanteti, Rajani

2012-01-01

Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68

Mapping the Views of Adolescent Health Stakeholders.

Science.gov (United States)

Ewan, Lindsay A; McLinden, Daniel; Biro, Frank; DeJonckheere, Melissa; Vaughn, Lisa M

2016-01-01

Health research that includes youth and family stakeholders increases the contextual relevance of findings, which can benefit both the researchers and stakeholders involved. The goal of this study was to identify youth and family adolescent health priorities and to explore strategies to address these concerns. Stakeholders identified important adolescent health concerns, perceptions of which were then explored using concept mapping. Concept mapping is a mixed-method participatory research approach that invites input from various stakeholders. In response to prompts, stakeholders suggested ways to address the identified health conditions. Adolescent participants then sorted the statements into groups based on content similarity and rated the statements for importance and feasibility. Multidimensional scaling and cluster analysis were then applied to create the concept maps. Stakeholders identified sexually transmitted infections (STIs) and obesity as the health conditions they considered most important. The concept map for STIs identified 7 clusters: General sex education, support and empowerment, testing and treatment, community involvement and awareness, prevention and protection, parental involvement in sex education, and media. The obesity concept map portrayed 8 clusters: Healthy food choices, obesity education, support systems, clinical and community involvement, community support for exercise, physical activity, nutrition support, and nutrition education. Ratings were generally higher for importance than for feasibility. The concept maps demonstrate stakeholder-driven ideas about approaches to target STIs and obesity in this context. Strategies at multiple social ecological levels were emphasized. The concept maps can be used to generate discussion regarding these topics and to identify interventions. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Environmental Assessment for the Solar Photovoltaic Array at Eglin Air Force Base, Florida

Science.gov (United States)

2014-01-24

fire hazard to solar panel array. ● Where applicable, reduce erosion using rough grade slopes or terrace slopes. ● Identify areas of existing...method would entail the installation of numerous smaller solar PV systems on the roofs of various buildings on the base. This alternative was...panel array.  Where applicable, reduce erosion using rough grade slopes or terrace slopes.  Identify areas of existing vegetation that the proponent

Low Frequency Space Array

International Nuclear Information System (INIS)

Dennison, B.; Weiler, K.W.; Johnston, K.J.

1987-01-01

The Low Frequency Space Array (LFSA) is a conceptual mission to survey the entire sky and to image individual sources at frequencies between 1.5 and 26 MHz, a frequency range over which the earth's ionosphere transmits poorly or not at all. With high resolution, high sensitivity observations, a new window will be opened in the electromagnetic spectrum for astronomical investigation. Also, extending observations down to such low frequencies will bring astronomy to the fundamental limit below which the galaxy becomes optically thick due to free-free absorption. A number of major scientific goals can be pursued with such a mission, including mapping galactic emission and absorption, studies of individual source spectra in a frequency range where a number of important processes may play a role, high resolution imaging of extended sources, localization of the impulsive emission from Jupiter, and a search for coherent emission processes. 19 references

Identifying phenomenal consciousness.

Science.gov (United States)

Schier, Elizabeth

2009-03-01

This paper examines the possibility of finding evidence that phenomenal consciousness is independent of access. The suggestion reviewed is that we should look for isomorphisms between phenomenal and neural activation spaces. It is argued that the fact that phenomenal spaces are mapped via verbal report is no problem for this methodology. The fact that activation and phenomenal space are mapped via different means does not mean that they cannot be identified. The paper finishes by examining how data addressing this theoretical question could be obtained.

Fine-scale mapping of natural variation in fly fecundity identifies neuronal domain of expression and function of an aquaporin.

Directory of Open Access Journals (Sweden)

Alan O Bergland

Full Text Available To gain insight into the molecular genetic basis of standing variation in fitness related traits, we identify a novel factor that regulates the molecular and physiological basis of natural variation in female Drosophila melanogaster fecundity. Genetic variation in female fecundity in flies derived from a wild orchard population is heritable and largely independent of other measured life history traits. We map a portion of this variation to a single QTL and then use deficiency mapping to further refine this QTL to 5 candidate genes. Ubiquitous expression of RNAi against only one of these genes, an aquaporin encoded by Drip, reduces fecundity. Within our mapping population Drip mRNA level in the head, but not other tissues, is positively correlated with fecundity. We localize Drip expression to a small population of corazonin producing neurons located in the dorsolateral posterior compartments of the protocerebrum. Expression of Drip-RNAi using both the pan-neuronal ELAV-Gal4 and the Crz-Gal4 drivers reduces fecundity. Low-fecundity RILs have decreased Crz expression and increased expression of pale, the enzyme encoding the rate-limiting step in the production of dopamine, a modulator of insect life histories. Taken together these data suggest that natural variation in Drip expression in the corazonin producing neurons contributes to standing variation in fitness by altering the concentration of two neurohormones.

Two-dimensional Value Stream Mapping: Integrating the design of the MPC system in the value stream map

DEFF Research Database (Denmark)

Powell, Daryl; Olesen, Peter Bjerg

2013-01-01

Companies use value stream mapping to identify waste, often in the early stages of a lean implementation. Though the tool helps users to visualize material and information flows and to identify improvement opportunities, a limitation of this approach is the lack of an integrated method...... for analysing and re-designing the MPC system in order to support lean improvement. We reflect on the current literature regarding value stream mapping, and use practical insights in order to develop and propose a two-dimensional value stream mapping tool that integrates the design of the MPC system within...... the material and information flow map....

Application of electrical resistivity tomography techniques for mapping man-made sinkholes

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Rey, J.; Martínez, J.; Hidalgo, C.; Dueñas, J.

2012-04-01

The suitability of the geophysical prospecting by electrical resistivity tomography to detect and map man-made subsurface cavities and related sinkholes has been studied in the Linares abandoned mining district (Spain). We have selected for this study four mined sectors constituted of different lithologies: granite and phyllites of Paleozoic age, and Triassic shales and sandstones. In three of these sectors, detail underground topographic surveys were carried out to chart the position and dimensions of the mining voids (galleries and chamber), in order to analyze the resolution of this methodology to characterize these cavities by using different electrode arrays. The results are variable, depending on the depth and diameter of the void, the selected electrode array, the spacing between electrodes, geological complexity and data density. These results also indicate that when the cavity is empty, an anomaly with a steep gradient and high resistivity values is registered, because the air that fills the mining void is dielectric, while when the cavities are filled with fine grain sediments, frequently saturated in water, the electrical resistance is lower. In relation with the three different multi-electrode arrays tested, the Wenner-Schlumberger array has resulted to offer the maximum resolution in all these cases, with lower and more stable values for the RMS than the other arrays. Therefore, this electrode array has been applied in the fourth studied sector, a former mine near the city centre of Linares, in an area of urban expansion in which there are problems of subsidence. Two sets of four electrical tomography profiles have been carried out, perpendicular to each other, and which have allowed reaching depths of research between 30-35 m. This net-array allowed the identification of two shallow anomalies of low resistivity values, interpreted as old mining galleries filled with fine material saturated in water. It also allows detecting two fractures, correlated

A Multi-Modality CMOS Sensor Array for Cell-Based Assay and Drug Screening.

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Chi, Taiyun; Park, Jong Seok; Butts, Jessica C; Hookway, Tracy A; Su, Amy; Zhu, Chengjie; Styczynski, Mark P; McDevitt, Todd C; Wang, Hua

2015-12-01

In this paper, we present a fully integrated multi-modality CMOS cellular sensor array with four sensing modalities to characterize different cell physiological responses, including extracellular voltage recording, cellular impedance mapping, optical detection with shadow imaging and bioluminescence sensing, and thermal monitoring. The sensor array consists of nine parallel pixel groups and nine corresponding signal conditioning blocks. Each pixel group comprises one temperature sensor and 16 tri-modality sensor pixels, while each tri-modality sensor pixel can be independently configured for extracellular voltage recording, cellular impedance measurement (voltage excitation/current sensing), and optical detection. This sensor array supports multi-modality cellular sensing at the pixel level, which enables holistic cell characterization and joint-modality physiological monitoring on the same cellular sample with a pixel resolution of 80 μm × 100 μm. Comprehensive biological experiments with different living cell samples demonstrate the functionality and benefit of the proposed multi-modality sensing in cell-based assay and drug screening.

Multi-colorimetric sensor array for detection of explosives in gas and liquid phase

DEFF Research Database (Denmark)

Kostesha, Natalie; Alstrøm, Tommy Sonne; Johnsen, C.

2011-01-01

In the framework of the research project "Xsense" at the Technical University of Denmark (DTU) we are developing a simple colorimetric sensor array which can be useful in detection of explosives like DNT, TATP, HMX, RDX and identification of reagents needed for making homemade explosives. The tec......In the framework of the research project "Xsense" at the Technical University of Denmark (DTU) we are developing a simple colorimetric sensor array which can be useful in detection of explosives like DNT, TATP, HMX, RDX and identification of reagents needed for making homemade explosives...... to the analytes creates a color difference map which gives a unique fingerprint for each explosive and VOCs. Such sensing technology can be used for screening relevant explosives in a complex background as well as to distinguish mixtures of volatile organic compounds distributed in gas and liquid phases....... This sensor array is inexpensive, and can potentially be produced as single use disposable....

Coupling in reflector arrays

DEFF Research Database (Denmark)

Appel-Hansen, Jørgen

1968-01-01

In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present communic......In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present...

Integration of Antibody Array Technology into Drug Discovery and Development.

Science.gov (United States)

Huang, Wei; Whittaker, Kelly; Zhang, Huihua; Wu, Jian; Zhu, Si-Wei; Huang, Ruo-Pan

Antibody arrays represent a high-throughput technique that enables the parallel detection of multiple proteins with minimal sample volume requirements. In recent years, antibody arrays have been widely used to identify new biomarkers for disease diagnosis or prognosis. Moreover, many academic research laboratories and commercial biotechnology companies are starting to apply antibody arrays in the field of drug discovery. In this review, some technical aspects of antibody array development and the various platforms currently available will be addressed; however, the main focus will be on the discussion of antibody array technologies and their applications in drug discovery. Aspects of the drug discovery process, including target identification, mechanisms of drug resistance, molecular mechanisms of drug action, drug side effects, and the application in clinical trials and in managing patient care, which have been investigated using antibody arrays in recent literature will be examined and the relevance of this technology in progressing this process will be discussed. Protein profiling with antibody array technology, in addition to other applications, has emerged as a successful, novel approach for drug discovery because of the well-known importance of proteins in cell events and disease development.

Genetic Linkage Mapping of Economically Important Traits in Cultivated Tetraploid Potato (Solanum tuberosum L.).

Science.gov (United States)

Massa, Alicia N; Manrique-Carpintero, Norma C; Coombs, Joseph J; Zarka, Daniel G; Boone, Anne E; Kirk, William W; Hackett, Christine A; Bryan, Glenn J; Douches, David S

2015-09-14

The objective of this study was to construct a single nucleotide polymorphism (SNP)-based genetic map at the cultivated tetraploid level to locate quantitative trait loci (QTL) contributing to economically important traits in potato (Solanum tuberosum L.). The 156 F1 progeny and parents of a cross (MSL603) between "Jacqueline Lee" and "MSG227-2" were genotyped using the Infinium 8303 Potato Array. Furthermore, the progeny and parents were evaluated for foliar late blight reaction to isolates of the US-8 genotype of Phytophthora infestans (Mont.) de Bary and vine maturity. Linkage analyses and QTL mapping were performed using a novel approach that incorporates allele dosage information. The resulting genetic maps contained 1972 SNP markers with an average density of 1.36 marker per cM. QTL mapping identified the major source of late blight resistance in "Jacqueline Lee." The best SNP marker mapped ~0.54 Mb from a resistance hotspot on the long arm of chromosome 9. For vine maturity, the major-effect QTL was located on chromosome 5 with allelic effects from both parents. A candidate SNP marker for this trait mapped ~0.25 Mb from the StCDF1 gene, which is a candidate gene for the maturity trait. The identification of markers for P. infestans resistance will enable the introgression of multiple sources of resistance through marker-assisted selection. Moreover, the discovery of a QTL for late blight resistance not linked to the QTL for vine maturity provides the opportunity to use marker-assisted selection for resistance independent of the selection for vine maturity classifications. Copyright © 2015 Massa et al.

Performance of UWB Array-Based Radar Sensor in a Multi-Sensor Vehicle-Based Suit for Landmine Detection

NARCIS (Netherlands)

Yarovoy, A.; Savelyev, T.; Zhuge, X.; Aubry, P.; Ligthart, L.; Schavemaker, J.G.M.; Tettelaar, P.; Breejen, E. de

2008-01-01

In this paper, integration of an UWB array-based timedomain radar sensor in a vehicle-mounted multi-sensor system for landmine detection is described. Dedicated real-time signal processing algorithms are developed to compute the radar sensor confidence map which is used for sensor fusion.

Semi-automatic mapping for identifying complex geobodies in seismic images

Science.gov (United States)

Domínguez-C, Raymundo; Romero-Salcedo, Manuel; Velasquillo-Martínez, Luis G.; Shemeretov, Leonid

2017-03-01

Seismic images are composed of positive and negative seismic wave traces with different amplitudes (Robein 2010 Seismic Imaging: A Review of the Techniques, their Principles, Merits and Limitations (Houten: EAGE)). The association of these amplitudes together with a color palette forms complex visual patterns. The color intensity of such patterns is directly related to impedance contrasts: the higher the contrast, the higher the color intensity. Generally speaking, low impedance contrasts are depicted with low tone colors, creating zones with different patterns whose features are not evident for a 3D automated mapping option available on commercial software. In this work, a workflow for a semi-automatic mapping of seismic images focused on those areas with low-intensity colored zones that may be associated with geobodies of petroleum interest is proposed. The CIE L*A*B* color space was used to perform the seismic image processing, which helped find small but significant differences between pixel tones. This process generated binary masks that bound color regions to low-intensity colors. The three-dimensional-mask projection allowed the construction of 3D structures for such zones (geobodies). The proposed method was applied to a set of digital images from a seismic cube and tested on four representative study cases. The obtained results are encouraging because interesting geobodies are obtained with a minimum of information.

X-ray metrology of an array of active edge pixel sensors for use at synchrotron light sources

Science.gov (United States)

Plackett, R.; Arndt, K.; Bortoletto, D.; Horswell, I.; Lockwood, G.; Shipsey, I.; Tartoni, N.; Williams, S.

2018-01-01

We report on the production and testing of an array of active edge silicon sensors as a prototype of a large array. Four Medipix3RX.1 chips were bump bonded to four single chip sized Advacam active edge n-on-n sensors. These detectors were then mounted into a 2 by 2 array and tested on B16 at Diamond Light Source with an x-ray beam spot of 2um. The results from these tests, compared with optical metrology demonstrate that this type of sensor is sensitive to the physical edge of the silicon, with only a modest loss of efficiency in the final two rows of pixels. We present the efficiency maps recorded with the microfocus beam and a sample powder diffraction measurement. These results give confidence that this sensor technology can be used effectively in larger arrays of detectors at synchrotron light sources.

Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

Science.gov (United States)

Galeano, Carlos H; Fernandez, Andrea C; Franco-Herrera, Natalia; Cichy, Karen A; McClean, Phillip E; Vanderleyden, Jos; Blair, Matthew W

2011-01-01

Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

Single Nucleotide Polymorphism Identification, Characterization, and Linkage Mapping in Quinoa

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P. J. Maughan

2012-11-01

Full Text Available Quinoa ( Willd. is an important seed crop throughout the Andean region of South America. It is important as a regional food security crop for millions of impoverished rural inhabitants of the Andean Altiplano (high plains. Efforts to improve the crop have led to an increased focus on genetic research. We report the identification of 14,178 putative single nucleotide polymorphisms (SNPs using a genomic reduction protocol as well as the development of 511 functional SNP assays. The SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 113 quinoa accessions showed that the minor allele frequency (MAF of the SNPs ranged from 0.02 to 0.50, with an average MAF of 0.28. Structure analysis of the quinoa diversity panel uncovered the two major subgroups corresponding to the Andean and coastal quinoa ecotypes. Linkage mapping of the SNPs in two recombinant inbred line populations produced an integrated linkage map consisting of 29 linkage groups with 20 large linkage groups, spanning 1404 cM with a marker density of 3.1 cM per SNP marker. The SNPs identified here represent important genomic tools needed in emerging plant breeding programs for advanced genetic analysis of agronomic traits in quinoa.

Determination of flavonoids in plant material by HPLC with diode-array and electro-array detections.

Science.gov (United States)

Mattila, P; Astola, J; Kumpulainen, J

2000-12-01

A high-performance liquid chromatographic (HPLC) method with in-line connected diode-array (DAD) and electro-array (EC) detection to identify and quantify 17 flavonoids in plant-derived foods is described. Catechins were extracted from the samples using ethyl acetate, and quantification of these compounds was performed with the EC detector. Other flavonoids were quantified with DAD after acid hydrolysis. The methods developed were effective for the determination of catechins and other flavonoids in plant-derived foods. Responses of the detection systems were linear within the range evaluated, 20-200 ng/injection (DAD) and 20-100 ng/injection (EC), with correlation coefficients exceeding 0.999. Coefficient of variation was under 10.5%, and recoveries of flavonoids ranged from 70 to 124%. Purity of the flavonoid peaks was confirmed by combining the spectral and voltammetric data.

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome

Directory of Open Access Journals (Sweden)

Zhang Li

2012-08-01

Full Text Available Abstract Background A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Results Of the 606 markers used to assemble the genetic map, 588 (97% were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT markers, 72 simple sequence repeat (SSR, one insertion site-based polymorphism (ISBP, and two high-molecular-weight glutenin subunit (HMW-GS markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL, including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. Conclusions A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome.

Science.gov (United States)

Zhang, Li; Luo, Jiang-Tao; Hao, Ming; Zhang, Lian-Quan; Yuan, Zhong-Wei; Yan, Ze-Hong; Liu, Ya-Xi; Zhang, Bo; Liu, Bao-Long; Liu, Chun-Ji; Zhang, Huai-Gang; Zheng, You-Liang; Liu, Deng-Cai

2012-08-13

A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population. Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B. A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.

Assessing spacing impact on coherent features in a wind turbine array boundary layer

Directory of Open Access Journals (Sweden)

N. Ali

2018-02-01

Full Text Available As wind farms become larger, the spacing between turbines becomes a significant design consideration that can impose serious economic constraints. To investigate the turbulent flow structures in a 4 × 3 Cartesian wind turbine array boundary layer (WTABL, a wind tunnel experiment was carried out parameterizing the streamwise and spanwise wind turbine spacing. Four cases are chosen spacing turbines by 6 or 3D in the streamwise direction, and 3 or 1.5D in the spanwise direction, where D = 12 cm is the rotor diameter. Data are obtained experimentally using stereo particle image velocimetry. Mean streamwise velocity showed maximum values upstream of the turbine with the spacing of 6 and 3D in the streamwise and spanwise direction, respectively. Fixing the spanwise turbine spacing to 3D, variations in the streamwise spacing influence the turbulent flow structure and the power available to following wind turbines. Quantitative comparisons are made through spatial averaging, shifting measurement data and interpolating to account for the full range between devices to obtain data independent of array spacing. The largest averaged Reynolds stress is seen in cases with spacing of 3D × 3D. Snapshot proper orthogonal decomposition (POD was employed to identify the flow structures based on the turbulence kinetic energy content. The maximum turbulence kinetic energy content in the first POD mode is seen for turbine spacing of 6D × 1.5D. The flow upstream of each wind turbine converges faster than the flow downstream according to accumulation of turbulence kinetic energy by POD modes, regardless of spacing. The streamwise-averaged profile of the Reynolds stress is reconstructed using a specific number of modes for each case; the case of 6D × 1.5D spacing shows the fastest reconstruction to compare the rate of reconstruction of statistical profiles. Intermediate modes are also used to reconstruct the averaged profile and show that the

Children’s Mapping between Non-Symbolic and Symbolic Numerical Magnitudes and Its Association with Timed and Untimed Tests of Mathematics Achievement

Science.gov (United States)

Brankaer, Carmen; Ghesquière, Pol; De Smedt, Bert

2014-01-01

The ability to map between non-symbolic numerical magnitudes and Arabic numerals has been put forward as a key factor in children’s mathematical development. This mapping ability has been mainly examined indirectly by looking at children’s performance on a symbolic magnitude comparison task. The present study investigated mapping in a more direct way by using a task in which children had to choose which of two choice quantities (Arabic digits or dot arrays) matched the target quantity (dot array or Arabic digit), thereby focusing on small quantities ranging from 1 to 9. We aimed to determine the development of mapping over time and its relation to mathematics achievement. Participants were 36 first graders (M = 6 years 8 months) and 46 third graders (M = 8 years 8 months) who all completed mapping tasks, symbolic and non-symbolic magnitude comparison tasks and standardized timed and untimed tests of mathematics achievement. Findings revealed that children are able to map between non-symbolic and symbolic representations and that this mapping ability develops over time. Moreover, we found that children’s mapping ability is related to timed and untimed measures of mathematics achievement, over and above the variance accounted for by their numerical magnitude comparison skills. PMID:24699664

Study of solar array switching power management technology for space power system

Science.gov (United States)

Cassinelli, J. E.

1982-01-01

This report documents work performed on the Solar Array Switching Power Management Study. Mission characteristics for three missions were defined to the depth necessary to determine their power management requirements. Solar array switching concepts which could satisfy the mission requirements were identified. The switching concepts were compared with a conventional buck regulator system for cost, weight and volume, reliability, efficiency and thermal control. Solar array switching provided significant advantages in all areas of comparison for the reviewed missions.

Revision of an automated microseismic location algorithm for DAS - 3C geophone hybrid array

Science.gov (United States)

Mizuno, T.; LeCalvez, J.; Raymer, D.

2017-12-01

Application of distributed acoustic sensing (DAS) has been studied in several areas in seismology. One of the areas is microseismic reservoir monitoring (e.g., Molteni et al., 2017, First Break). Considering the present limitations of DAS, which include relatively low signal-to-noise ratio (SNR) and no 3C polarization measurements, a DAS - 3C geophone hybrid array is a practical option when using a single monitoring well. Considering the large volume of data from distributed sensing, microseismic event detection and location using a source scanning type algorithm is a reasonable choice, especially for real-time monitoring. The algorithm must handle both strain rate along the borehole axis for DAS and particle velocity for 3C geophones. Only a small quantity of large SNR events will be detected throughout a large aperture encompassing the hybrid array; therefore, the aperture is to be optimized dynamically to eliminate noisy channels for a majority of events. For such hybrid array, coalescence microseismic mapping (CMM) (Drew et al., 2005, SPE) was revised. CMM forms a likelihood function of location of event and its origin time. At each receiver, a time function of event arrival likelihood is inferred using an SNR function, and it is migrated to time and space to determine hypocenter and origin time likelihood. This algorithm was revised to dynamically optimize such a hybrid array by identifying receivers where a microseismic signal is possibly detected and using only those receivers to compute the likelihood function. Currently, peak SNR is used to select receivers. To prevent false results due to small aperture, a minimum aperture threshold is employed. The algorithm refines location likelihood using 3C geophone polarization. We tested this algorithm using a ray-based synthetic dataset. Leaney (2014, PhD thesis, UBC) is used to compute particle velocity at receivers. Strain rate along the borehole axis is computed from particle velocity as DAS microseismic

Size dependence in tunneling spectra of PbSe quantum-dot arrays.

Science.gov (United States)

Ou, Y C; Cheng, S F; Jian, W B

2009-07-15

Interdot Coulomb interactions and collective Coulomb blockade were theoretically argued to be a newly important topic, and experimentally identified in semiconductor quantum dots, formed in the gate confined two-dimensional electron gas system. Developments of cluster science and colloidal synthesis accelerated the studies of electron transport in colloidal nanocrystal or quantum-dot solids. To study the interdot coupling, various sizes of two-dimensional arrays of colloidal PbSe quantum dots are self-assembled on flat gold surfaces for scanning tunneling microscopy and scanning tunneling spectroscopy measurements at both room and liquid-nitrogen temperatures. The tip-to-array, array-to-substrate, and interdot capacitances are evaluated and the tunneling spectra of quantum-dot arrays are analyzed by the theory of collective Coulomb blockade. The current-voltage of PbSe quantum-dot arrays conforms properly to a scaling power law function. In this study, the dependence of tunneling spectra on the sizes (numbers of quantum dots) of arrays is reported and the capacitive coupling between quantum dots in the arrays is explored.

Phased Array Antenna Testbed Development at the NASA Glenn Research Center

Science.gov (United States)

Lambert, Kevin M.; Kubat, Gregory; Johnson, Sandra K.; Anzic, Godfrey

2003-01-01

Ideal phased array antennas offer advantages for communication systems, such as wide-angle scanning and multibeam operation, which can be utilized in certain NASA applications. However, physically realizable, electronically steered, phased array antennas introduce additional system performance parameters, which must be included in the evaluation of the system. The NASA Glenn Research Center (GRC) is currently conducting research to identify these parameters and to develop the tools necessary to measure them. One of these tools is a testbed where phased array antennas may be operated in an environment that simulates their use. This paper describes the development of the testbed and its use in characterizing a particular K-Band, phased array antenna.

Using Helicopter Electromagnetic Surveys to Identify Potential Hazards at Mine Waste Impoundments

Energy Technology Data Exchange (ETDEWEB)

Hammack, R.W.

2008-01-01

In July 2003, helicopter electromagnetic surveys were conducted at 14 coal waste impoundments in southern West Virginia. The purpose of the surveys was to detect conditions that could lead to impoundment failure either by structural failure of the embankment or by the flooding of adjacent or underlying mine works. Specifically, the surveys attempted to: 1) identify saturated zones within the mine waste, 2) delineate filtrate flow paths through the embankment or into adjacent strata and receiving streams, and 3) identify flooded mine workings underlying or adjacent to the waste impoundment. Data from the helicopter surveys were processed to generate conductivity/depth images. Conductivity/depth images were then spatially linked to georeferenced air photos or topographic maps for interpretation. Conductivity/depth images were found to provide a snapshot of the hydrologic conditions that exist within the impoundment. This information can be used to predict potential areas of failure within the embankment because of its ability to image the phreatic zone. Also, the electromagnetic survey can identify areas of unconsolidated slurry in the decant basin and beneath the embankment. Although shallow, flooded mineworks beneath the impoundment were identified by this survey, it cannot be assumed that electromagnetic surveys can detect all underlying mines. A preliminary evaluation of the data implies that helicopter electromagnetic surveys can provide a better understanding of the phreatic zone than the piezometer arrays that are typically used.

Micro-dressing of a carbon nanotube array with MoS2 gauze

Science.gov (United States)

Lim, Sharon Xiaodai; Woo, Kah Whye; Ng, Junju; Lu, Junpeng; Kwang, Siu Yi; Zhang, Zheng; Tok, Eng Soon; Sow, Chorng-Haur

2015-10-01

Few-layer MoS2 film has been successfully assembled over an array of CNTs. Using different focused laser beams with different wavelengths, site selective patterning of either the MoS2 film or the supporting CNT array is achieved. This paves the way for applications and investigations into the fundamental properties of the hybrid MoS2/CNT material with a controlled architecture. Through Raman mapping, straining and electron doping of the MoS2 film as a result of interaction with the supporting CNT array are detected. The role of the MoS2 film was further emphasized with a lower work function being detected from Ultra-violet Photoelectron Spectrsocopy (UPS) measurements of the hybrid material, compared to the CNT array. The effect of the changes in the work function was illustrated through the optoelectronic behavior of the hybrid material. At 0 V, 3.49 nA of current is measured upon illuminating the sample with a broad laser beam emitting laser light with a wavelength of 532 nm. With a strong response to external irradiation of different wavelengths, and changes to the power of the excitation source, the hybrid material has shown potential for applications in optoelectronic devices.

Mapping Weathering and Alteration Minerals in the Comstock and Geiger Grade Areas using Visible to Thermal Infrared Airborne Remote Sensing Data

Science.gov (United States)

Vaughan, Greg R.; Calvin, Wendy M.

2005-01-01

To support research into both precious metal exploration and environmental site characterization a combination of high spatial/spectral resolution airborne visible, near infrared, short wave infrared (VNIR/SWIR) and thermal infrared (TIR) image data were acquired to remotely map hydrothermal alteration minerals around the Geiger Grade and Comstock alteration regions, and map the mineral by-products of weathered mine dumps in Virginia City. Remote sensing data from the Airborne Visible Infrared Imaging Spectrometer (AVIRIS), SpecTIR Corporation's airborne hyperspectral imager (HyperSpecTIR), the MODIS-ASTER airborne simulator (MASTER), and the Spatially Enhanced Broadband Array Spectrograph System (SEBASS) were acquired and processed into mineral maps based on the unique spectral signatures of image pixels. VNIR/SWIR and TIR field spectrometer data were collected for both calibration and validation of the remote data sets, and field sampling, laboratory spectral analyses and XRD analyses were made to corroborate the surface mineralogy identified by spectroscopy. The resulting mineral maps show the spatial distribution of several important alteration minerals around each study area including alunite, quartz, pyrophyllite, kaolinite, montmorillonite/muscovite, and chlorite. In the Comstock region the mineral maps show acid-sulfate alteration, widespread propylitic alteration and extensive faulting that offsets the acid-sulfate areas, in contrast to the larger, dominantly acid-sulfate alteration exposed along Geiger Grade. Also, different mineral zones within the intense acid-sulfate areas were mapped. In the Virginia City historic mining district the important weathering minerals mapped include hematite, goethite, jarosite and hydrous sulfate minerals (hexahydrite, alunogen and gypsum) located on mine dumps. Sulfate minerals indicate acidic water forming in the mine dump environment. While there is not an immediate threat to the community, there are clearly sources of

Concurrent array-based queue

Science.gov (United States)

Heidelberger, Philip; Steinmacher-Burow, Burkhard

2015-01-06

According to one embodiment, a method for implementing an array-based queue in memory of a memory system that includes a controller includes configuring, in the memory, metadata of the array-based queue. The configuring comprises defining, in metadata, an array start location in the memory for the array-based queue, defining, in the metadata, an array size for the array-based queue, defining, in the metadata, a queue top for the array-based queue and defining, in the metadata, a queue bottom for the array-based queue. The method also includes the controller serving a request for an operation on the queue, the request providing the location in the memory of the metadata of the queue.

Long term economic relationships from cointegration maps

Science.gov (United States)

Vicente, Renato; Pereira, Carlos de B.; Leite, Vitor B. P.; Caticha, Nestor

2007-07-01

We employ the Bayesian framework to define a cointegration measure aimed to represent long term relationships between time series. For visualization of these relationships we introduce a dissimilarity matrix and a map based on the sorting points into neighborhoods (SPIN) technique, which has been previously used to analyze large data sets from DNA arrays. We exemplify the technique in three data sets: US interest rates (USIR), monthly inflation rates and gross domestic product (GDP) growth rates.

Classical mapping for Hubbard operators: Application to the double-Anderson model

Energy Technology Data Exchange (ETDEWEB)

Li, Bin; Miller, William H. [Department of Chemistry and Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Levy, Tal J.; Rabani, Eran [School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel)

2014-05-28

A classical Cartesian mapping for Hubbard operators is developed to describe the nonequilibrium transport of an open quantum system with many electrons. The mapping of the Hubbard operators representing the many-body Hamiltonian is derived by using analogies from classical mappings of boson creation and annihilation operators vis-à-vis a coherent state representation. The approach provides qualitative results for a double quantum dot array (double Anderson impurity model) coupled to fermionic leads for a range of bias voltages, Coulomb couplings, and hopping terms. While the width and height of the conduction peaks show deviations from the master equation approach considered to be accurate in the limit of weak system-leads couplings and high temperatures, the Hubbard mapping captures all transport channels involving transition between many electron states, some of which are not captured by approximate nonequilibrium Green function closures.

Array-based molecular karyotyping in 115 VATER/VACTERL and VATER/VACTERL-like patients identifies disease-causing copy number variations.

Science.gov (United States)

Zhang, Rong; Marsch, Florian; Kause, Franziska; Degenhardt, Franziska; Schmiedeke, Eeberhard; Märzheuser, Stefanie; Hoppe, Bernd; Bachour, Haitham; Boemers, Thomas M; Schäfer, Matthias; Spychalski, Nicole; Neser, Jörg; Leonhardt, Johannes; Kosch, Ferdinand; Ure, Benno; Gómez, Barbara; Lacher, Martin; Deffaa, Oliver J; Palta, Markus; Wittekindt, Boris; Kleine, Katharina; Schmedding, Andrea; Grasshoff-Derr, Sabine; Ven, Amelie van der; Heilmann-Heimbach, Stefanie; Zwink, Nadine; Jenetzky, Ekkehart; Ludwig, Michael; Reutter, Heiko

2017-07-17

The acronym VATER/VACTERL refers to the rare nonrandom association of the following component features (CF): vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia, renal malformations (R), and limb defects (L). Patients presenting with at least three CFs are diagnosed as having VATER/VACTERL association while patients presenting with only two CFs are diagnosed as having VATER/VACTERL-like phenotypes. Recently, rare causative copy number variations (CNVs) have been identified in patients with VATER/VACTERL association and VATER/VACTERL-like phenotypes. To detect further causative CNVs we performed array based molecular karyotyping in 75 VATER/VACTERL and 40 VATER/VACTERL-like patients. Following the application of stringent filter criteria, we identified 13 microdeletions and seven microduplications in 20 unrelated patients all of which were absent in 1,307 healthy inhouse controls (n microdeletion at 17q12 was confirmed to be de novo. Three microdeletions at 5q23.1, 16q23.3, 22q11.21, and one microduplication at 10q11.21 were all absent in the available parent. Microdeletion of chromosomal region 22q11.21 was previously found in VATER/VACTERL patients rendering it to be causative in our patient. The remaining 15 CNVs were inherited from a healthy parent. In two of 115 patients' causative CNVs were found (2%). The remaining identified rare CNVs represent candidates for further evaluation. Rare inherited CNVs may constitute modifiers of, or contributors to, multifactorial VATER/VACTERL or VATER/VACTERL-like phenotypes. Birth Defects Research 109:1063-1069, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Flexible microelectrode array for interfacing with the surface of neural ganglia

Science.gov (United States)

Sperry, Zachariah J.; Na, Kyounghwan; Parizi, Saman S.; Chiel, Hillel J.; Seymour, John; Yoon, Euisik; Bruns, Tim M.

2018-06-01

Objective. The dorsal root ganglia (DRG) are promising nerve structures for sensory neural interfaces because they provide centralized access to primary afferent cell bodies and spinal reflex circuitry. In order to harness this potential, new electrode technologies are needed which take advantage of the unique properties of DRG, specifically the high density of neural cell bodies at the dorsal surface. Here we report initial in vivo results from the development of a flexible non-penetrating polyimide electrode array interfacing with the surface of ganglia. Approach. Multiple layouts of a 64-channel iridium electrode (420 µm2) array were tested, with pitch as small as 25 µm. The buccal ganglia of invertebrate sea slug Aplysia californica were used to develop handling and recording techniques with ganglionic surface electrode arrays (GSEAs). We also demonstrated the GSEA’s capability to record single- and multi-unit activity from feline lumbosacral DRG related to a variety of sensory inputs, including cutaneous brushing, joint flexion, and bladder pressure. Main results. We recorded action potentials from a variety of Aplysia neurons activated by nerve stimulation, and units were observed firing simultaneously on closely spaced electrode sites. We also recorded single- and multi-unit activity associated with sensory inputs from feline DRG. We utilized spatial oversampling of action potentials on closely-spaced electrode sites to estimate the location of neural sources at between 25 µm and 107 µm below the DRG surface. We also used the high spatial sampling to demonstrate a possible spatial sensory map of one feline’s DRG. We obtained activation of sensory fibers with low-amplitude stimulation through individual or groups of GSEA electrode sites. Significance. Overall, the GSEA has been shown to provide a variety of information types from ganglia neurons and to have significant potential as a tool for neural mapping and interfacing.

In vivo sensitivity estimation and imaging acceleration with rotating RF coil arrays at 7 Tesla

Science.gov (United States)

Li, Mingyan; Jin, Jin; Zuo, Zhentao; Liu, Feng; Trakic, Adnan; Weber, Ewald; Zhuo, Yan; Xue, Rong; Crozier, Stuart

2015-03-01

Using a new rotating SENSitivity Encoding (rotating-SENSE) algorithm, we have successfully demonstrated that the rotating radiofrequency coil array (RRFCA) was capable of achieving a significant reduction in scan time and a uniform image reconstruction for a homogeneous phantom at 7 Tesla. However, at 7 Tesla the in vivo sensitivity profiles (B1-) become distinct at various angular positions. Therefore, sensitivity maps at other angular positions cannot be obtained by numerically rotating the acquired ones. In this work, a novel sensitivity estimation method for the RRFCA was developed and validated with human brain imaging. This method employed a library database and registration techniques to estimate coil sensitivity at an arbitrary angular position. The estimated sensitivity maps were then compared to the acquired sensitivity maps. The results indicate that the proposed method is capable of accurately estimating both magnitude and phase of sensitivity at an arbitrary angular position, which enables us to employ the rotating-SENSE algorithm to accelerate acquisition and reconstruct image. Compared to a stationary coil array with the same number of coil elements, the RRFCA was able to reconstruct images with better quality at a high reduction factor. It is hoped that the proposed rotation-dependent sensitivity estimation algorithm and the acceleration ability of the RRFCA will be particularly useful for ultra high field MRI.

In vivo sensitivity estimation and imaging acceleration with rotating RF coil arrays at 7 Tesla.

Science.gov (United States)

Li, Mingyan; Jin, Jin; Zuo, Zhentao; Liu, Feng; Trakic, Adnan; Weber, Ewald; Zhuo, Yan; Xue, Rong; Crozier, Stuart

2015-03-01

Using a new rotating SENSitivity Encoding (rotating-SENSE) algorithm, we have successfully demonstrated that the rotating radiofrequency coil array (RRFCA) was capable of achieving a significant reduction in scan time and a uniform image reconstruction for a homogeneous phantom at 7 Tesla. However, at 7 Tesla the in vivo sensitivity profiles (B1(-)) become distinct at various angular positions. Therefore, sensitivity maps at other angular positions cannot be obtained by numerically rotating the acquired ones. In this work, a novel sensitivity estimation method for the RRFCA was developed and validated with human brain imaging. This method employed a library database and registration techniques to estimate coil sensitivity at an arbitrary angular position. The estimated sensitivity maps were then compared to the acquired sensitivity maps. The results indicate that the proposed method is capable of accurately estimating both magnitude and phase of sensitivity at an arbitrary angular position, which enables us to employ the rotating-SENSE algorithm to accelerate acquisition and reconstruct image. Compared to a stationary coil array with the same number of coil elements, the RRFCA was able to reconstruct images with better quality at a high reduction factor. It is hoped that the proposed rotation-dependent sensitivity estimation algorithm and the acceleration ability of the RRFCA will be particularly useful for ultra high field MRI. Copyright © 2014 Elsevier Inc. All rights reserved.

Road map for photovoltaic electricity; Feuille de route sur l'electricite photovoltaique

Energy Technology Data Exchange (ETDEWEB)

NONE

2011-02-15

This road map aims at highlighting industrial, technological and social challenges, at elaborating comprehensive visions, at highlighting technological locks, and at outlining research needs for the photovoltaic sector. It considers the following sector components: preparation of photo-sensitive materials, manufacturing of photovoltaic cells, manufacturing of photovoltaic arrays, design and manufacturing of electric equipment to control photovoltaic arrays and to connect them to the grid. It highlights the demand for photovoltaic installations, analyzes the value chain, proposes a vision of the sector by 2050 and defines target for 2020, discusses needs for demonstration and experimentation

System and method employing a self-organizing map load feature database to identify electric load types of different electric loads

Science.gov (United States)

Lu, Bin; Harley, Ronald G.; Du, Liang; Yang, Yi; Sharma, Santosh K.; Zambare, Prachi; Madane, Mayura A.

2014-06-17

A method identifies electric load types of a plurality of different electric loads. The method includes providing a self-organizing map load feature database of a plurality of different electric load types and a plurality of neurons, each of the load types corresponding to a number of the neurons; employing a weight vector for each of the neurons; sensing a voltage signal and a current signal for each of the loads; determining a load feature vector including at least four different load features from the sensed voltage signal and the sensed current signal for a corresponding one of the loads; and identifying by a processor one of the load types by relating the load feature vector to the neurons of the database by identifying the weight vector of one of the neurons corresponding to the one of the load types that is a minimal distance to the load feature vector.

IRIS Arrays: Observing Wavefields at Multiple Scales and Frequencies

Science.gov (United States)

Sumy, D. F.; Woodward, R.; Frassetto, A.

2014-12-01

The Incorporated Research Institutions for Seismology (IRIS) provides instruments for creating and operating seismic arrays at a wide range of scales. As an example, for over thirty years the IRIS PASSCAL program has provided instruments to individual Principal Investigators to deploy arrays of all shapes and sizes on every continent. These arrays have ranged from just a few sensors to hundreds or even thousands of sensors, covering areas with dimensions of meters to thousands of kilometers. IRIS also operates arrays directly, such as the USArray Transportable Array (TA) as part of the EarthScope program. Since 2004, the TA has rolled across North America, at any given time spanning a swath of approximately 800 km by 2,500 km, and thus far sampling 2% of the Earth's surface. This achievement includes all of the lower-48 U.S., southernmost Canada, and now parts of Alaska. IRIS has also facilitated specialized arrays in polar environments and on the seafloor. In all cases, the data from these arrays are freely available to the scientific community. As the community of scientists who use IRIS facilities and data look to the future they have identified a clear need for new array capabilities. In particular, as part of its Wavefields Initiative, IRIS is exploring new technologies that can enable large, dense array deployments to record unaliased wavefields at a wide range of frequencies. Large-scale arrays might utilize multiple sensor technologies to best achieve observing objectives and optimize equipment and logistical costs. Improvements in packaging and power systems can provide equipment with reduced size, weight, and power that will reduce logistical constraints for large experiments, and can make a critical difference for deployments in harsh environments or other situations where rapid deployment is required. We will review the range of existing IRIS array capabilities with an overview of previous and current deployments and examples of data and results. We

Intracellular recording, sensory field mapping, and culturing identified neurons in the leech, Hirudo medicinalis.

Science.gov (United States)

Titlow, Josh; Majeed, Zana R; Nicholls, John G; Cooper, Robin L

2013-11-04

The freshwater leech, Hirudo medicinalis, is a versatile model organism that has been used to address scientific questions in the fields of neurophysiology, neuroethology, and developmental biology. The goal of this report is to consolidate experimental techniques from the leech system into a single article that will be of use to physiologists with expertise in other nervous system preparations, or to biology students with little or no electrophysiology experience. We demonstrate how to dissect the leech for recording intracellularly from identified neural circuits in the ganglion. Next we show how individual cells of known function can be removed from the ganglion to be cultured in a Petri dish, and how to record from those neurons in culture. Then we demonstrate how to prepare a patch of innervated skin to be used for mapping sensory or motor fields. These leech preparations are still widely used to address basic electrical properties of neural networks, behavior, synaptogenesis, and development. They are also an appropriate training module for neuroscience or physiology teaching laboratories.

Programmable cellular arrays. Faults testing and correcting in cellular arrays

International Nuclear Information System (INIS)

Cercel, L.

1978-03-01

A review of some recent researches about programmable cellular arrays in computing and digital processing of information systems is presented, and includes both combinational and sequential arrays, with full arbitrary behaviour, or which can realize better implementations of specialized blocks as: arithmetic units, counters, comparators, control systems, memory blocks, etc. Also, the paper presents applications of cellular arrays in microprogramming, in implementing of a specialized computer for matrix operations, in modeling of universal computing systems. The last section deals with problems of fault testing and correcting in cellular arrays. (author)

Towards local oscillators based on arrays of niobium Josephson junctions

International Nuclear Information System (INIS)

Galin, M A; Klushin, A M; Kurin, V V; Seliverstov, S V; Finkel, M I; Goltsman, G N; Müller, F; Scheller, T; Semenov, A D

2015-01-01

Various applications in the field of terahertz technology are in urgent need of compact, wide-tunable solid-state continuous wave radiation sources with a moderate power. However, satisfactory solutions for the THz frequency range are scarce yet. Here we report on coherent radiation from a large planar array of Josephson junctions (JJs) in the frequency range between 0.1 and 0.3 THz. The external resonator providing the synchronization of JJ array is identified as a straight fragment of a single-strip-line containing the junctions themselves. We demonstrate a prototype of the quasioptical heterodyne receiver with the JJ array as a local oscillator and a hot-electron bolometer mixer. (paper)

Homozygosity mapping and targeted sanger sequencing reveal genetic defects underlying inherited retinal disease in families from pakistan.

Directory of Open Access Journals (Sweden)

Maleeha Maria

Full Text Available Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD.We genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA, retinitis pigmentosa (RP, congenital stationary night blindness (CSNB, or cone dystrophy (CD. We employed genome-wide single nucleotide polymorphism (SNP array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families.Homozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1.Homozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future.

Building Quality Report Cards for Geriatric Care in The Netherlands: Using Concept Mapping to Identify the Appropriate "Building Blocks" from the Consumer's Perspective

Science.gov (United States)

Groenewoud, A. Stef; van Exel, N. Job A.; Berg, Marc; Huijsman, Robbert

2008-01-01

Purpose: This article reports on a study to identify "building blocks" for quality report cards for geriatric care. Its aim is to present (a) the results of the study and (b) the innovative step-by-step approach that was developed to arrive at these results. Design and Methods: We used Concept Mapping/Structured Conceptualization to…

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Directory of Open Access Journals (Sweden)

Ashley S. Chaffin

2016-07-01

Full Text Available Hexaploid oat ( L., 2 = 6 = 42 is a member of the Poaceae family and has a large genome (∼12.5 Gb containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP array and genotyping-by-sequencing (GBS were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L. reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

Seismometer array station processors

International Nuclear Information System (INIS)

Key, F.A.; Lea, T.G.; Douglas, A.

1977-01-01

A description is given of the design, construction and initial testing of two types of Seismometer Array Station Processor (SASP), one to work with data stored on magnetic tape in analogue form, the other with data in digital form. The purpose of a SASP is to detect the short period P waves recorded by a UK-type array of 20 seismometers and to edit these on to a a digital library tape or disc. The edited data are then processed to obtain a rough location for the source and to produce seismograms (after optimum processing) for analysis by a seismologist. SASPs are an important component in the scheme for monitoring underground explosions advocated by the UK in the Conference of the Committee on Disarmament. With digital input a SASP can operate at 30 times real time using a linear detection process and at 20 times real time using the log detector of Weichert. Although the log detector is slower, it has the advantage over the linear detector that signals with lower signal-to-noise ratio can be detected and spurious large amplitudes are less likely to produce a detection. It is recommended, therefore, that where possible array data should be recorded in digital form for input to a SASP and that the log detector of Weichert be used. Trial runs show that a SASP is capable of detecting signals down to signal-to-noise ratios of about two with very few false detections, and at mid-continental array sites it should be capable of detecting most, if not all, the signals with magnitude above msub(b) 4.5; the UK argues that, given a suitable network, it is realistic to hope that sources of this magnitude and above can be detected and identified by seismological means alone. (author)

Land use map, Finney County, Kansas

Science.gov (United States)

Morain, S. A. (Principal Investigator); Williams, D. L.; Coiner, J. C.

1973-01-01

The author has identified the following significant results. Methods for the mapping of land use in agricultural regions are developed and applied to preparation of a land use map of Finney County, Kanas. Six land use categories were identified from an MSS-5 image. These categories are: (1) large field irrigation; (2) small field irrigation; (3) dryland cultivation; (4) rangeland; (5) cultural features; and (6) riverine land. The map is composed of basically homogeneous regions with definable mixtures of the six categories. Each region is bounded by an ocularly evident change in land use.

Shark Attack Project - Marine Attack at Towed Hydrophone Arrays

National Research Council Canada - National Science Library

Kalmijn, Adrianus J

2005-01-01

The original objective of the SIO Marine Attack project was to identify the electric and magnetic fields causing sharks to inflict serious damage upon the towed hydrophone arrays of US Navy submarines...

Characteristics of VCSELs and VCSEL arrays for optical data links

Science.gov (United States)

Gaw, Craig A.; Jiang, Wenbin; Lebby, Michael S.; Kiely, Philip A.; Claisse, Paul R.

1997-05-01

High performance, low cost, and highly reliable vertical cavity surface emitting lasers (VCSELs) have been developed and are currently being used in both parallel and serial optical interconnect applications. For example, Motorola's OPTOBUSTM parallel optical interconnect relies heavily on the unique characteristics of arrays of GaAs based VCSELs emitting at 850 nm to achieve its stringent performance goals at low cost. Representative parametric results of discrete VCSELs and VCSEL arrays will be compared, including `optical power output-current' and `current-voltage' curves, optical wall plug efficiencies, and modulation characteristics. The use of statistical parameter analysis across a wafer and subsequent parametric wafer maps has proven to be a valuable tool for maintaining control of the fabrication process. The consistency of VCSEL parameters across individual VCSEL arrays will be discussed. VCSELs are very robust devices. Life times at room ambient in excess of 3E6 hours have been reported by several groups. Degradation behavior of selected device parameters will be discussed. Failure analysis demonstrating the effect of proton implant depth on reliability will be presented. ESD damage at forward bias is shown to be process related, while ESD damage at reverse bias is shown to be material related. These VCSELs are ESD Class 1 devices.

First light from a kilometer-baseline Scintillation Auroral GPS Array.

Science.gov (United States)

Datta-Barua, S; Su, Y; Deshpande, K; Miladinovich, D; Bust, G S; Hampton, D; Crowley, G

2015-05-28

We introduce and analyze the first data from an array of closely spaced Global Positioning System (GPS) scintillation receivers established in the auroral zone in late 2013 to measure spatial and temporal variations in L band signals at 100-1000 m and subsecond scales. The seven receivers of the Scintillation Auroral GPS Array (SAGA) are sited at Poker Flat Research Range, Alaska. The receivers produce 100 s scintillation indices and 100 Hz carrier phase and raw in-phase and quadrature-phase samples. SAGA is the largest existing array with baseline lengths of the ionospheric diffractive Fresnel scale at L band. With an initial array of five receivers, we identify a period of simultaneous amplitude and phase scintillation. We compare SAGA power and phase data with collocated 630.0 nm all-sky images of an auroral arc and incoherent scatter radar electron precipitation measurements, to illustrate how SAGA can be used in multi-instrument observations for subkilometer-scale studies. A seven-receiver Scintillation Auroral GPS Array (SAGA) is now at Poker Flat, Alaska SAGA is the largest subkilometer array to enable phase/irregularities studies Simultaneous scintillation, auroral arc, and electron precipitation are observed.

Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).

Science.gov (United States)

Bianco, Luca; Cestaro, Alessandro; Sargent, Daniel James; Banchi, Elisa; Derdak, Sophia; Di Guardo, Mario; Salvi, Silvio; Jansen, Johannes; Viola, Roberto; Gut, Ivo; Laurens, Francois; Chagné, David; Velasco, Riccardo; van de Weg, Eric; Troggio, Michela

2014-01-01

High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

Development and validation of a 20K single nucleotide polymorphism (SNP whole genome genotyping array for apple (Malus × domestica Borkh.

Directory of Open Access Journals (Sweden)

Luca Bianco

Full Text Available High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus. A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs. Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

Science.gov (United States)

Bianco, Luca; Cestaro, Alessandro; Sargent, Daniel James; Banchi, Elisa; Derdak, Sophia; Di Guardo, Mario; Salvi, Silvio; Jansen, Johannes; Viola, Roberto; Gut, Ivo; Laurens, Francois; Chagné, David; Velasco, Riccardo; van de Weg, Eric; Troggio, Michela