Sample records for genetically guided array
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Ordered nanoparticle arrays formed on engineered chaperonin protein templates
NASA Technical Reports Server (NTRS)
McMillan, R. Andrew; Paavola, Chad D.; Howard, Jeanie; Chan, Suzanne L.; Zaluzec, Nestor J.; Trent, Jonathan D.
2002-01-01
Traditional methods for fabricating nanoscale arrays are usually based on lithographic techniques. Alternative new approaches rely on the use of nanoscale templates made of synthetic or biological materials. Some proteins, for example, have been used to form ordered two-dimensional arrays. Here, we fabricated nanoscale ordered arrays of metal and semiconductor quantum dots by binding preformed nanoparticles onto crystalline protein templates made from genetically engineered hollow double-ring structures called chaperonins. Using structural information as a guide, a thermostable recombinant chaperonin subunit was modified to assemble into chaperonins with either 3 nm or 9 nm apical pores surrounded by chemically reactive thiols. These engineered chaperonins were crystallized into two-dimensional templates up to 20 microm in diameter. The periodic solvent-exposed thiols within these crystalline templates were used to size-selectively bind and organize either gold (1.4, 5 or 10nm) or CdSe-ZnS semiconductor (4.5 nm) quantum dots into arrays. The order within the arrays was defined by the lattice of the underlying protein crystal. By combining the self-assembling properties of chaperonins with mutations guided by structural modelling, we demonstrate that quantum dots can be manipulated using modified chaperonins and organized into arrays for use in next-generation electronic and photonic devices.
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Multiplexed precision genome editing with trackable genomic barcodes in yeast.
Roy, Kevin R; Smith, Justin D; Vonesch, Sibylle C; Lin, Gen; Tu, Chelsea Szu; Lederer, Alex R; Chu, Angela; Suresh, Sundari; Nguyen, Michelle; Horecka, Joe; Tripathi, Ashutosh; Burnett, Wallace T; Morgan, Maddison A; Schulz, Julia; Orsley, Kevin M; Wei, Wu; Aiyar, Raeka S; Davis, Ronald W; Bankaitis, Vytas A; Haber, James E; Salit, Marc L; St Onge, Robert P; Steinmetz, Lars M
2018-07-01
Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess the phenotypic consequences of each perturbation. Here we describe a CRISPR-Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerevisiae. MAGESTIC uses array-synthesized guide-donor oligos for plasmid-based high-throughput editing and features genomic barcode integration to prevent plasmid barcode loss and to enable robust phenotyping. We demonstrate that editing efficiency can be increased more than fivefold by recruiting donor DNA to the site of breaks using the LexA-Fkh1p fusion protein. We performed saturation editing of the essential gene SEC14 and identified amino acids critical for chemical inhibition of lipid signaling. We also constructed thousands of natural genetic variants, characterized guide mismatch tolerance at the genome scale, and ascertained that cryptic Pol III termination elements substantially reduce guide efficacy. MAGESTIC will be broadly useful to uncover the genetic basis of phenotypes in yeast.
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Genetic programming applied to RFI mitigation in radio astronomy
NASA Astrophysics Data System (ADS)
Staats, K.
2016-12-01
Genetic Programming is a type of machine learning that employs a stochastic search of a solutions space, genetic operators, a fitness function, and multiple generations of evolved programs to resolve a user-defined task, such as the classification of data. At the time of this research, the application of machine learning to radio astronomy was relatively new, with a limited number of publications on the subject. Genetic Programming had never been applied, and as such, was a novel approach to this challenging arena. Foundational to this body of research, the application Karoo GP was developed in the programming language Python following the fundamentals of tree-based Genetic Programming described in "A Field Guide to Genetic Programming" by Poli, et al. Karoo GP was tasked with the classification of data points as signal or radio frequency interference (RFI) generated by instruments and machinery which makes challenging astronomers' ability to discern the desired targets. The training data was derived from the output of an observation run of the KAT-7 radio telescope array built by the South African Square Kilometre Array (SKA-SA). Karoo GP, kNN, and SVM were comparatively employed, the outcome of which provided noteworthy correlations between input parameters, the complexity of the evolved hypotheses, and performance of raw data versus engineered features. This dissertation includes description of novel approaches to GP, such as upper and lower limits to the size of syntax trees, an auto-scaling multiclass classifier, and a Numpy array element manager. In addition to the research conducted at the SKA-SA, it is described how Karoo GP was applied to fine-tuning parameters of a weather prediction model at the South African Astronomical Observatory (SAAO), to glitch classification at the Laser Interferometer Gravitational-wave Observatory (LIGO), and to astro-particle physics at The Ohio State University.
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Phased Array Beamforming and Imaging in Composite Laminates Using Guided Waves
NASA Technical Reports Server (NTRS)
Tian, Zhenhua; Leckey, Cara A. C.; Yu, Lingyu
2016-01-01
This paper presents the phased array beamforming and imaging using guided waves in anisotropic composite laminates. A generic phased array beamforming formula is presented, based on the classic delay-and-sum principle. The generic formula considers direction-dependent guided wave properties induced by the anisotropic material properties of composites. Moreover, the array beamforming and imaging are performed in frequency domain where the guided wave dispersion effect has been considered. The presented phased array method is implemented with a non-contact scanning laser Doppler vibrometer (SLDV) to detect multiple defects at different locations in an anisotropic composite plate. The array is constructed of scan points in a small area rapidly scanned by the SLDV. Using the phased array method, multiple defects at different locations are successfully detected. Our study shows that the guided wave phased array method is a potential effective method for rapid inspection of large composite structures.
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Design, implementation and investigation of an image guide-based optical flip-flop array
NASA Technical Reports Server (NTRS)
Griffith, P. C.
1987-01-01
Presented is the design for an image guide-based optical flip-flop array created using a Hughes liquid crystal light valve and a flexible image guide in a feedback loop. This design is used to investigate the application of image guides as a communication mechanism in numerical optical computers. It is shown that image guides can be used successfully in this manner but mismatch match between the input and output fiber arrays is extremely limiting.
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Peace, Cameron; Bassil, Nahla; Main, Dorrie; Ficklin, Stephen; Rosyara, Umesh R.; Stegmeir, Travis; Sebolt, Audrey; Gilmore, Barbara; Lawley, Cindy; Mockler, Todd C.; Bryant, Douglas W.; Wilhelm, Larry; Iezzoni, Amy
2012-01-01
High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group. PMID:23284615
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Testing of a novel pin array guide for accurate three-dimensional glenoid component positioning.
Lewis, Gregory S; Stevens, Nicole M; Armstrong, April D
2015-12-01
A substantial challenge in total shoulder replacement is accurate positioning and alignment of the glenoid component. This challenge arises from limited intraoperative exposure and complex arthritic-driven deformity. We describe a novel pin array guide and method for patient-specific guiding of the glenoid central drill hole. We also experimentally tested the hypothesis that this method would reduce errors in version and inclination compared with 2 traditional methods. Polymer models of glenoids were created from computed tomography scans from 9 arthritic patients. Each 3-dimensional (3D) printed scapula was shrouded to simulate the operative situation. Three different methods for central drill alignment were tested, all with the target orientation of 5° retroversion and 0° inclination: no assistance, assistance by preoperative 3D imaging, and assistance by the pin array guide. Version and inclination errors of the drill line were compared. Version errors using the pin array guide (3° ± 2°) were significantly lower than version errors associated with no assistance (9° ± 7°) and preoperative 3D imaging (8° ± 6°). Inclination errors were also significantly lower using the pin array guide compared with no assistance. The new pin array guide substantially reduced errors in orientation of the central drill line. The guide method is patient specific but does not require rapid prototyping and instead uses adjustments to an array of pins based on automated software calculations. This method may ultimately provide a cost-effective solution enabling surgeons to obtain accurate orientation of the glenoid. Copyright © 2015 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.
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Imputation-Based Genomic Coverage Assessments of Current Human Genotyping Arrays
Nelson, Sarah C.; Doheny, Kimberly F.; Pugh, Elizabeth W.; Romm, Jane M.; Ling, Hua; Laurie, Cecelia A.; Browning, Sharon R.; Weir, Bruce S.; Laurie, Cathy C.
2013-01-01
Microarray single-nucleotide polymorphism genotyping, combined with imputation of untyped variants, has been widely adopted as an efficient means to interrogate variation across the human genome. “Genomic coverage” is the total proportion of genomic variation captured by an array, either by direct observation or through an indirect means such as linkage disequilibrium or imputation. We have performed imputation-based genomic coverage assessments of eight current genotyping arrays that assay from ~0.3 to ~5 million variants. Coverage was determined separately in each of the four continental ancestry groups in the 1000 Genomes Project phase 1 release. We used the subset of 1000 Genomes variants present on each array to impute the remaining variants and assessed coverage based on correlation between imputed and observed allelic dosages. More than 75% of common variants (minor allele frequency > 0.05) are covered by all arrays in all groups except for African ancestry, and up to ~90% in all ancestries for the highest density arrays. In contrast, less than 40% of less common variants (0.01 < minor allele frequency < 0.05) are covered by low density arrays in all ancestries and 50–80% in high density arrays, depending on ancestry. We also calculated genome-wide power to detect variant-trait association in a case-control design, across varying sample sizes, effect sizes, and minor allele frequency ranges, and compare these array-based power estimates with a hypothetical array that would type all variants in 1000 Genomes. These imputation-based genomic coverage and power analyses are intended as a practical guide to researchers planning genetic studies. PMID:23979933
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Accelerated Evolution in the Death Galaxy
NASA Astrophysics Data System (ADS)
Austin, Robert; Tung, Chih-Kuan; Gong, Xiu-Quing; Lambert, Guillaume; Liao, David
2010-03-01
We recall 4 main guiding principles of evolution: 1) instability of defections, 2) stress induced non-random mutations, 3) genetic heterogeneity, and 4) fragmented populations. Our previous preliminary experiments have been relatively simple 1-D stress experiments. We are proceeding with 2-D experiments whose design is guided by these principles. Our new experiment we have dubbed the Death Galaxy because of it's use of these design principles. The ``galaxy'' name comes from the fact that the structure is designed as an interconnected array of micro-ecologies, these micro-ecologies are similar to the stars that comprise an astronomical galaxy, and provide the fragmented small populations. A gradient of the antibiotic Cipro is introduced across the galaxy, and we will present results which show how bacterial evolution resulting in resistance to Cipro is accelerated by the physics principles underlying the device.
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Acoustic Wave Guiding by Reconfigurable Tessellated Arrays
NASA Astrophysics Data System (ADS)
Zou, Chengzhe; Lynd, Danielle T.; Harne, Ryan L.
2018-01-01
The reconfiguration of origami tessellations is a prime vehicle to harness for adapting system properties governed by a structural form. While the knowledge of mechanical property changes associated with origami tessellation folding has been extensively built up, the opportunities to integrate other physics into a framework of tessellated, adaptive structures remain to be fully exploited. Acoustics appears to be a prime domain to marry with origami science. Specifically, deep technical analogies are revealed between wave-guiding properties achieved via digital methods that virtually reposition array elements and the actual repositioning of facets by folding origami-inspired tessellations. Here we capitalize on this analogy to investigate acoustic arrays established upon facet layouts of origami-inspired tessellations. We show that a concept of reconfigurable tessellated arrays may guide waves more effectively than traditional digitally phased arrays using fewer transducer elements. Moreover, we show that the refinement of tessellated arrays trends to the ideal case of classical wave radiators or receivers grounded in principles of geometrical acoustics. By linear wave physics shared among myriad scientific disciplines and across orders of magnitude in length scale, these discoveries may cultivate numerous opportunities for wave-guiding adaptive structures inspired by low-dimensional origami tessellations.
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High-frequency plasma-heating apparatus
Brambilla, Marco; Lallia, Pascal
1978-01-01
An array of adjacent wave guides feed high-frequency energy into a vacuum chamber in which a toroidal plasma is confined by a magnetic field, the wave guide array being located between two toroidal current windings. Waves are excited in the wave guide at a frequency substantially equal to the lower frequency hybrid wave of the plasma and a substantially equal phase shift is provided from one guide to the next between the waves therein. For plasmas of low peripheral density gradient, the guides are excited in the TE.sub.01 mode and the output electric field is parallel to the direction of the toroidal magnetic field. For exciting waves in plasmas of high peripheral density gradient, the guides are excited in the TM.sub.01 mode and the magnetic field at the wave guide outlets is parallel to the direction of the toroidal magnetic field. The wave excited at the outlet of the wave guide array is a progressive wave propagating in the direction opposite to that of the toroidal current and is, therefore, not absorbed by so-called "runaway" electrons.
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Carvalho, Márcia; Muñoz-Amatriaín, María; Castro, Isaura; Lino-Neto, Teresa; Matos, Manuela; Egea-Cortines, Marcos; Rosa, Eduardo; Close, Timothy; Carnide, Valdemar
2017-11-21
Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of genetic diversity among cowpea landraces is important for the preservation of local varieties and is the basis to obtain improved varieties. The aims of this study were to explore diversity and the genetic structure of a set of Iberian Peninsula cowpea accessions in comparison to a worldwide collection and to infer possible dispersion routes of cultivated cowpea. The Illumina Cowpea iSelect Consortium Array containing 51,128 SNPs was used to genotype 96 cowpea accessions including 43 landraces and cultivars from the Iberian Peninsula, and 53 landraces collected worldwide. Four subpopulations were identified. Most Iberian Peninsula accessions clustered together with those from other southern European and northern African countries. Only one accession belonged to another subpopulation, while two accessions were 'admixed'. A lower genetic diversity level was found in the Iberian Peninsula accessions compared to worldwide cowpeas. The genetic analyses performed in this study brought some insights into worldwide genetic diversity and structure and possible dispersion routes of cultivated cowpea. Also, it provided an in-depth analysis of genetic diversity in Iberian Peninsula cowpeas that will help guide crossing strategies in breeding programs.
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Genome-wide investigation of genetic changes during modern breeding of Brassica napus.
Wang, Nian; Li, Feng; Chen, Biyun; Xu, Kun; Yan, Guixin; Qiao, Jiangwei; Li, Jun; Gao, Guizhen; Bancroft, Ian; Meng, Jingling; King, Graham J; Wu, Xiaoming
2014-08-01
Considerable genome variation had been incorporated within rapeseed breeding programs over past decades. In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6-10 % genomic regions revealed high F ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.
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Delamination Detection Using Guided Wave Phased Arrays
NASA Technical Reports Server (NTRS)
Tian, Zhenhua; Yu, Lingyu; Leckey, Cara
2016-01-01
This paper presents a method for detecting multiple delaminations in composite laminates using non-contact phased arrays. The phased arrays are implemented with a non-contact scanning laser Doppler vibrometer (SLDV). The array imaging algorithm is performed in the frequency domain where both the guided wave dispersion effect and direction dependent wave properties are considered. By using the non-contact SLDV array with a frequency domain imaging algorithm, an intensity image of the composite plate can be generated for delamination detection. For the proof of concept, a laboratory test is performed using a non-contact phased array to detect two delaminations (created through quasi-static impact test) at different locations in a composite plate. Using the non-contact phased array and frequency domain imaging, the two impact-induced delaminations are successfully detected. This study shows that the non-contact phased array method is a potentially effective method for rapid delamination inspection in large composite structures.
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Lee, Vivian C Y; Chow, Judy F C; Lau, Estella Y L; Yeung, William S B; Ho, P C; Ng, Ernest H Y
2015-02-01
To compare the pregnancy outcome of the fluorescent in-situ hybridisation and array comparative genomic hybridisation in preimplantation genetic diagnosis of translocation carriers. Historical cohort. A teaching hospital in Hong Kong. All preimplantation genetic diagnosis treatment cycles performed for translocation carriers from 2001 to 2013. Overall, 101 treatment cycles for preimplantation genetic diagnosis in translocation were included: 77 cycles for reciprocal translocation and 24 cycles for Robertsonian translocation. Fluorescent in-situ hybridisation and array comparative genomic hybridisation were used in 78 and 11 cycles, respectively. The ongoing pregnancy rate per initiated cycle after array comparative genomic hybridisation was significantly higher than that after fluorescent in-situ hybridisation in all translocation carriers (36.4% vs 9.0%; P=0.010). The miscarriage rate was comparable with both techniques. The testing method (array comparative genomic hybridisation or fluorescent in-situ hybridisation) was the only significant factor affecting the ongoing pregnancy rate after controlling for the women's age, type of translocation, and clinical information of the preimplantation genetic diagnosis cycles by logistic regression (odds ratio=1.875; P=0.023; 95% confidence interval, 1.090-3.226). This local retrospective study confirmed that comparative genomic hybridisation is associated with significantly higher pregnancy rates versus fluorescent in-situ hybridisation in translocation carriers. Array comparative genomic hybridisation should be the technique of choice in preimplantation genetic diagnosis cycles in translocation carriers.
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Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima
2014-01-01
Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈ 20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers.
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Ramos, Laia; del Rey, Javier; Daina, Gemma; García-Aragonés, Manel; Armengol, Lluís; Fernandez-Encinas, Alba; Parriego, Mònica; Boada, Montserrat; Martinez-Passarell, Olga; Martorell, Maria Rosa; Casagran, Oriol; Benet, Jordi; Navarro, Joaquima
2014-01-01
Comprehensive chromosome analysis techniques such as metaphase-Comparative Genomic Hybridisation (CGH) and array-CGH are available for single-cell analysis. However, while metaphase-CGH and BAC array-CGH have been widely used for Preimplantation Genetic Diagnosis, oligonucleotide array-CGH has not been used in an extensive way. A comparison between oligonucleotide array-CGH and metaphase-CGH has been performed analysing 15 single fibroblasts from aneuploid cell-lines and 18 single blastomeres from human cleavage-stage embryos. Afterwards, oligonucleotide array-CGH and BAC array-CGH were also compared analysing 16 single blastomeres from human cleavage-stage embryos. All three comprehensive analysis techniques provided broadly similar cytogenetic profiles; however, non-identical profiles appeared when extensive aneuploidies were present in a cell. Both array techniques provided an optimised analysis procedure and a higher resolution than metaphase-CGH. Moreover, oligonucleotide array-CGH was able to define extra segmental imbalances in 14.7% of the blastomeres and it better determined the specific unbalanced chromosome regions due to a higher resolution of the technique (≈20 kb). Applicability of oligonucleotide array-CGH for Preimplantation Genetic Diagnosis has been demonstrated in two cases of Robertsonian translocation carriers 45,XY,der(13;14)(q10;q10). Transfer of euploid embryos was performed in both cases and pregnancy was achieved by one of the couples. This is the first time that an oligonucleotide array-CGH approach has been successfully applied to Preimplantation Genetic Diagnosis for balanced chromosome rearrangement carriers. PMID:25415307
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Koning-Boucoiran, Carole F S; Esselink, G Danny; Vukosavljev, Mirjana; van 't Westende, Wendy P C; Gitonga, Virginia W; Krens, Frans A; Voorrips, Roeland E; van de Weg, W Eric; Schulz, Dietmar; Debener, Thomas; Maliepaard, Chris; Arens, Paul; Smulders, Marinus J M
2015-01-01
In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
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USDA-ARS?s Scientific Manuscript database
Carrot is one of the most economically important vegetables worldwide, however, genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to devel...
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Through a glass darkly: economics and personalised medicine.
Haycox, Alan; Pirmohamed, Munir; McLeod, Claire; Houten, Rachel; Richards, Sarah
2014-11-01
Personalised medicine and pharmacogenetic-test-guided treatment strategies will be of increasing importance in the future, both in terms of healthcare provision and evaluation. It is well recognised that significant variability exists in the response of patients to drugs resulting from genetic or biological variations; however, we are only now gradually becoming aware of the complexities involved. Enormous variability occurs in the risk-benefit ratio that will be experienced by each individual patient as a consequence of their overall genetic make-up. Although not a panacea, enhanced scientific knowledge of the genetic basis for such variability offers the potential for a more 'tailored' approach to prescribing in the future, making it more closely attuned to the needs of the individual patient. Such 'personalised' medicine has the potential to revolutionise care provision in a manner that provides a range of challenges to current structures and processes of 'conventional' healthcare delivery. The aim of this paper is to outline such challenges and analyse potential ways in which they may be addressed in the future. It provides non-expert readers with a non-technical case study of the complexities inherent in the evaluation of a pharmacogenetic-test-guided treatment strategy from a health economic perspective. Wherever possible, technical issues have been minimised; however, references are provided for readers who wish to enhance their knowledge of the pharmacological basis of the case study of cytochrome P450 test-guided treatment. The case study aims simply to illustrate the approach and difficulties encountered in the health economic evaluation of complex pharmacogenetic technologies. Such technologies present a range of new and complex issues which have crucial implications for health economists attempting to obtain an accurate assessment of the 'value' of the technology in clinical practice in an array of patient subgroups. Personalised medicine is the future and this paper highlights how pharmaceutical manufacturers, clinicians, regulators and other stakeholders must all play their part in the inevitable and accelerating move into this complex and uncertain future.
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Discovery and Refinement of Loci Associated with Lipid Levels
Peloso, Gina M.; Gustafsson, Stefan; Kanoni, Stavroula; Ganna, Andrea; Chen, Jin; Buchkovich, Martin L.; Mora, Samia; Beckmann, Jacques S.; Bragg-Gresham, Jennifer L.; Chang, Hsing-Yi; Demirkan, Ayşe; Den Hertog, Heleen M.; Do, Ron; Donnelly, Louise A.; Ehret, Georg B.; Esko, Tõnu; Feitosa, Mary F.; Ferreira, Teresa; Fischer, Krista; Fontanillas, Pierre; Fraser, Ross M.; Freitag, Daniel F.; Gurdasani, Deepti; Heikkilä, Kauko; Hyppönen, Elina; Isaacs, Aaron; Jackson, Anne U.; Johansson, Åsa; Johnson, Toby; Kaakinen, Marika; Kettunen, Johannes; Kleber, Marcus E.; Li, Xiaohui; Luan, Jian’an; Lyytikäinen, Leo-Pekka; Magnusson, Patrik K.E.; Mangino, Massimo; Mihailov, Evelin; Montasser, May E.; Müller-Nurasyid, Martina; Nolte, Ilja M.; O’Connell, Jeffrey R.; Palmer, Cameron D.; Perola, Markus; Petersen, Ann-Kristin; Sanna, Serena; Saxena, Richa; Service, Susan K.; Shah, Sonia; Shungin, Dmitry; Sidore, Carlo; Song, Ci; Strawbridge, Rona J.; Surakka, Ida; Tanaka, Toshiko; Teslovich, Tanya M.; Thorleifsson, Gudmar; Van den Herik, Evita G.; Voight, Benjamin F.; Volcik, Kelly A.; Waite, Lindsay L.; Wong, Andrew; Wu, Ying; Zhang, Weihua; Absher, Devin; Asiki, Gershim; Barroso, Inês; Been, Latonya F.; Bolton, Jennifer L.; Bonnycastle, Lori L; Brambilla, Paolo; Burnett, Mary S.; Cesana, Giancarlo; Dimitriou, Maria; Doney, Alex S.F.; Döring, Angela; Elliott, Paul; Epstein, Stephen E.; Ingi Eyjolfsson, Gudmundur; Gigante, Bruna; Goodarzi, Mark O.; Grallert, Harald; Gravito, Martha L.; Groves, Christopher J.; Hallmans, Göran; Hartikainen, Anna-Liisa; Hayward, Caroline; Hernandez, Dena; Hicks, Andrew A.; Holm, Hilma; Hung, Yi-Jen; Illig, Thomas; Jones, Michelle R.; Kaleebu, Pontiano; Kastelein, John J.P.; Khaw, Kay-Tee; Kim, Eric; Klopp, Norman; Komulainen, Pirjo; Kumari, Meena; Langenberg, Claudia; Lehtimäki, Terho; Lin, Shih-Yi; Lindström, Jaana; Loos, Ruth J.F.; Mach, François; McArdle, Wendy L; Meisinger, Christa; Mitchell, Braxton D.; Müller, Gabrielle; Nagaraja, Ramaiah; Narisu, Narisu; Nieminen, Tuomo V.M.; Nsubuga, Rebecca N.; Olafsson, Isleifur; Ong, Ken K.; Palotie, Aarno; Papamarkou, Theodore; Pomilla, Cristina; Pouta, Anneli; Rader, Daniel J.; Reilly, Muredach P.; Ridker, Paul M.; Rivadeneira, Fernando; Rudan, Igor; Ruokonen, Aimo; Samani, Nilesh; Scharnagl, Hubert; Seeley, Janet; Silander, Kaisa; Stančáková, Alena; Stirrups, Kathleen; Swift, Amy J.; Tiret, Laurence; Uitterlinden, Andre G.; van Pelt, L. Joost; Vedantam, Sailaja; Wainwright, Nicholas; Wijmenga, Cisca; Wild, Sarah H.; Willemsen, Gonneke; Wilsgaard, Tom; Wilson, James F.; Young, Elizabeth H.; Zhao, Jing Hua; Adair, Linda S.; Arveiler, Dominique; Assimes, Themistocles L.; Bandinelli, Stefania; Bennett, Franklyn; Bochud, Murielle; Boehm, Bernhard O.; Boomsma, Dorret I.; Borecki, Ingrid B.; Bornstein, Stefan R.; Bovet, Pascal; Burnier, Michel; Campbell, Harry; Chakravarti, Aravinda; Chambers, John C.; Chen, Yii-Der Ida; Collins, Francis S.; Cooper, Richard S.; Danesh, John; Dedoussis, George; de Faire, Ulf; Feranil, Alan B.; Ferrières, Jean; Ferrucci, Luigi; Freimer, Nelson B.; Gieger, Christian; Groop, Leif C.; Gudnason, Vilmundur; Gyllensten, Ulf; Hamsten, Anders; Harris, Tamara B.; Hingorani, Aroon; Hirschhorn, Joel N.; Hofman, Albert; Hovingh, G. Kees; Hsiung, Chao Agnes; Humphries, Steve E.; Hunt, Steven C.; Hveem, Kristian; Iribarren, Carlos; Järvelin, Marjo-Riitta; Jula, Antti; Kähönen, Mika; Kaprio, Jaakko; Kesäniemi, Antero; Kivimaki, Mika; Kooner, Jaspal S.; Koudstaal, Peter J.; Krauss, Ronald M.; Kuh, Diana; Kuusisto, Johanna; Kyvik, Kirsten O.; Laakso, Markku; Lakka, Timo A.; Lind, Lars; Lindgren, Cecilia M.; Martin, Nicholas G.; März, Winfried; McCarthy, Mark I.; McKenzie, Colin A.; Meneton, Pierre; Metspalu, Andres; Moilanen, Leena; Morris, Andrew D.; Munroe, Patricia B.; Njølstad, Inger; Pedersen, Nancy L.; Power, Chris; Pramstaller, Peter P.; Price, Jackie F.; Psaty, Bruce M.; Quertermous, Thomas; Rauramaa, Rainer; Saleheen, Danish; Salomaa, Veikko; Sanghera, Dharambir K.; Saramies, Jouko; Schwarz, Peter E.H.; Sheu, Wayne H-H; Shuldiner, Alan R.; Siegbahn, Agneta; Spector, Tim D.; Stefansson, Kari; Strachan, David P.; Tayo, Bamidele O.; Tremoli, Elena; Tuomilehto, Jaakko; Uusitupa, Matti; van Duijn, Cornelia M.; Vollenweider, Peter; Wallentin, Lars; Wareham, Nicholas J.; Whitfield, John B.; Wolffenbuttel, Bruce H.R.; Ordovas, Jose M.; Boerwinkle, Eric; Palmer, Colin N.A.; Thorsteinsdottir, Unnur; Chasman, Daniel I.; Rotter, Jerome I.; Franks, Paul W.; Ripatti, Samuli; Cupples, L. Adrienne; Sandhu, Manjinder S.; Rich, Stephen S.
2013-01-01
Low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides, and total cholesterol are heritable, modifiable, risk factors for coronary artery disease. To identify new loci and refine known loci influencing these lipids, we examined 188,578 individuals using genome-wide and custom genotyping arrays. We identify and annotate 157 loci associated with lipid levels at P < 5×10−8, including 62 loci not previously associated with lipid levels in humans. Using dense genotyping in individuals of European, East Asian, South Asian, and African ancestry, we narrow association signals in 12 loci. We find that loci associated with blood lipids are often associated with cardiovascular and metabolic traits including coronary artery disease, type 2 diabetes, blood pressure, waist-hip ratio, and body mass index. Our results illustrate the value of genetic data from individuals of diverse ancestries and provide insights into biological mechanisms regulating blood lipids to guide future genetic, biological, and therapeutic research. PMID:24097068
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Discovery and refinement of loci associated with lipid levels.
Willer, Cristen J; Schmidt, Ellen M; Sengupta, Sebanti; Peloso, Gina M; Gustafsson, Stefan; Kanoni, Stavroula; Ganna, Andrea; Chen, Jin; Buchkovich, Martin L; Mora, Samia; Beckmann, Jacques S; Bragg-Gresham, Jennifer L; Chang, Hsing-Yi; Demirkan, Ayşe; Den Hertog, Heleen M; Do, Ron; Donnelly, Louise A; Ehret, Georg B; Esko, Tõnu; Feitosa, Mary F; Ferreira, Teresa; Fischer, Krista; Fontanillas, Pierre; Fraser, Ross M; Freitag, Daniel F; Gurdasani, Deepti; Heikkilä, Kauko; Hyppönen, Elina; Isaacs, Aaron; Jackson, Anne U; Johansson, Åsa; Johnson, Toby; Kaakinen, Marika; Kettunen, Johannes; Kleber, Marcus E; Li, Xiaohui; Luan, Jian'an; Lyytikäinen, Leo-Pekka; Magnusson, Patrik K E; Mangino, Massimo; Mihailov, Evelin; Montasser, May E; Müller-Nurasyid, Martina; Nolte, Ilja M; O'Connell, Jeffrey R; Palmer, Cameron D; Perola, Markus; Petersen, Ann-Kristin; Sanna, Serena; Saxena, Richa; Service, Susan K; Shah, Sonia; Shungin, Dmitry; Sidore, Carlo; Song, Ci; Strawbridge, Rona J; Surakka, Ida; Tanaka, Toshiko; Teslovich, Tanya M; Thorleifsson, Gudmar; Van den Herik, Evita G; Voight, Benjamin F; Volcik, Kelly A; Waite, Lindsay L; Wong, Andrew; Wu, Ying; Zhang, Weihua; Absher, Devin; Asiki, Gershim; Barroso, Inês; Been, Latonya F; Bolton, Jennifer L; Bonnycastle, Lori L; Brambilla, Paolo; Burnett, Mary S; Cesana, Giancarlo; Dimitriou, Maria; Doney, Alex S F; Döring, Angela; Elliott, Paul; Epstein, Stephen E; Ingi Eyjolfsson, Gudmundur; Gigante, Bruna; Goodarzi, Mark O; Grallert, Harald; Gravito, Martha L; Groves, Christopher J; Hallmans, Göran; Hartikainen, Anna-Liisa; Hayward, Caroline; Hernandez, Dena; Hicks, Andrew A; Holm, Hilma; Hung, Yi-Jen; Illig, Thomas; Jones, Michelle R; Kaleebu, Pontiano; Kastelein, John J P; Khaw, Kay-Tee; Kim, Eric; Klopp, Norman; Komulainen, Pirjo; Kumari, Meena; Langenberg, Claudia; Lehtimäki, Terho; Lin, Shih-Yi; Lindström, Jaana; Loos, Ruth J F; Mach, François; McArdle, Wendy L; Meisinger, Christa; Mitchell, Braxton D; Müller, Gabrielle; Nagaraja, Ramaiah; Narisu, Narisu; Nieminen, Tuomo V M; Nsubuga, Rebecca N; Olafsson, Isleifur; Ong, Ken K; Palotie, Aarno; Papamarkou, Theodore; Pomilla, Cristina; Pouta, Anneli; Rader, Daniel J; Reilly, Muredach P; Ridker, Paul M; Rivadeneira, Fernando; Rudan, Igor; Ruokonen, Aimo; Samani, Nilesh; Scharnagl, Hubert; Seeley, Janet; Silander, Kaisa; Stančáková, Alena; Stirrups, Kathleen; Swift, Amy J; Tiret, Laurence; Uitterlinden, Andre G; van Pelt, L Joost; Vedantam, Sailaja; Wainwright, Nicholas; Wijmenga, Cisca; Wild, Sarah H; Willemsen, Gonneke; Wilsgaard, Tom; Wilson, James F; Young, Elizabeth H; Zhao, Jing Hua; Adair, Linda S; Arveiler, Dominique; Assimes, Themistocles L; Bandinelli, Stefania; Bennett, Franklyn; Bochud, Murielle; Boehm, Bernhard O; Boomsma, Dorret I; Borecki, Ingrid B; Bornstein, Stefan R; Bovet, Pascal; Burnier, Michel; Campbell, Harry; Chakravarti, Aravinda; Chambers, John C; Chen, Yii-Der Ida; Collins, Francis S; Cooper, Richard S; Danesh, John; Dedoussis, George; de Faire, Ulf; Feranil, Alan B; Ferrières, Jean; Ferrucci, Luigi; Freimer, Nelson B; Gieger, Christian; Groop, Leif C; Gudnason, Vilmundur; Gyllensten, Ulf; Hamsten, Anders; Harris, Tamara B; Hingorani, Aroon; Hirschhorn, Joel N; Hofman, Albert; Hovingh, G Kees; Hsiung, Chao Agnes; Humphries, Steve E; Hunt, Steven C; Hveem, Kristian; Iribarren, Carlos; Järvelin, Marjo-Riitta; Jula, Antti; Kähönen, Mika; Kaprio, Jaakko; Kesäniemi, Antero; Kivimaki, Mika; Kooner, Jaspal S; Koudstaal, Peter J; Krauss, Ronald M; Kuh, Diana; Kuusisto, Johanna; Kyvik, Kirsten O; Laakso, Markku; Lakka, Timo A; Lind, Lars; Lindgren, Cecilia M; Martin, Nicholas G; März, Winfried; McCarthy, Mark I; McKenzie, Colin A; Meneton, Pierre; Metspalu, Andres; Moilanen, Leena; Morris, Andrew D; Munroe, Patricia B; Njølstad, Inger; Pedersen, Nancy L; Power, Chris; Pramstaller, Peter P; Price, Jackie F; Psaty, Bruce M; Quertermous, Thomas; Rauramaa, Rainer; Saleheen, Danish; Salomaa, Veikko; Sanghera, Dharambir K; Saramies, Jouko; Schwarz, Peter E H; Sheu, Wayne H-H; Shuldiner, Alan R; Siegbahn, Agneta; Spector, Tim D; Stefansson, Kari; Strachan, David P; Tayo, Bamidele O; Tremoli, Elena; Tuomilehto, Jaakko; Uusitupa, Matti; van Duijn, Cornelia M; Vollenweider, Peter; Wallentin, Lars; Wareham, Nicholas J; Whitfield, John B; Wolffenbuttel, Bruce H R; Ordovas, Jose M; Boerwinkle, Eric; Palmer, Colin N A; Thorsteinsdottir, Unnur; Chasman, Daniel I; Rotter, Jerome I; Franks, Paul W; Ripatti, Samuli; Cupples, L Adrienne; Sandhu, Manjinder S; Rich, Stephen S; Boehnke, Michael; Deloukas, Panos; Kathiresan, Sekar; Mohlke, Karen L; Ingelsson, Erik; Abecasis, Gonçalo R
2013-11-01
Levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides and total cholesterol are heritable, modifiable risk factors for coronary artery disease. To identify new loci and refine known loci influencing these lipids, we examined 188,577 individuals using genome-wide and custom genotyping arrays. We identify and annotate 157 loci associated with lipid levels at P < 5 × 10(-8), including 62 loci not previously associated with lipid levels in humans. Using dense genotyping in individuals of European, East Asian, South Asian and African ancestry, we narrow association signals in 12 loci. We find that loci associated with blood lipid levels are often associated with cardiovascular and metabolic traits, including coronary artery disease, type 2 diabetes, blood pressure, waist-hip ratio and body mass index. Our results demonstrate the value of using genetic data from individuals of diverse ancestry and provide insights into the biological mechanisms regulating blood lipids to guide future genetic, biological and therapeutic research.
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Vertical Si nanowire arrays fabricated by magnetically guided metal-assisted chemical etching
NASA Astrophysics Data System (ADS)
Chun, Dong Won; Kim, Tae Kyoung; Choi, Duyoung; Caldwell, Elizabeth; Kim, Young Jin; Paik, Jae Cheol; Jin, Sungho; Chen, Renkun
2016-11-01
In this work, vertically aligned Si nanowire arrays were fabricated by magnetically guided metal-assisted directional chemical etching. Using an anodized aluminum oxide template as a shadow mask, nanoscale Ni dot arrays were fabricated on an Si wafer to serve as a mask to protect the Si during the etching. For the magnetically guided chemical etching, we deposited a tri-layer metal catalyst (Au/Fe/Au) in a Swiss-cheese configuration and etched the sample under the magnetic field to improve the directionality of the Si nanowire etching and increase the etching rate along the vertical direction. After the etching, the nanowires were dried with minimal surface-tension-induced aggregation by utilizing a supercritical CO2 drying procedure. High-resolution transmission electron microscopy (HR-TEM) analysis confirmed the formation of single-crystal Si nanowires. The method developed here for producing vertically aligned Si nanowire arrays could find a wide range of applications in electrochemical and electronic devices.
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Photoacoustic-guided ultrasound therapy with a dual-mode ultrasound array
NASA Astrophysics Data System (ADS)
Prost, Amaury; Funke, Arik; Tanter, Mickaël; Aubry, Jean-François; Bossy, Emmanuel
2012-06-01
Photoacoustics has recently been proposed as a potential method to guide and/or monitor therapy based on high-intensity focused ultrasound (HIFU). We experimentally demonstrate the creation of a HIFU lesion at the location of an optical absorber, by use of photoacoustic signals emitted by the absorber detected on a dual mode transducer array. To do so, a dedicated ultrasound array intended to both detect photoacoustic waves and emit HIFU with the same elements was used. Such a dual-mode array provides automatically coregistered reference frames for photoacoustic detection and HIFU emission, a highly desired feature for methods involving guidance or monitoring of HIFU by use of photoacoustics. The prototype is first characterized in terms of both photoacoustic and HIFU performances. The probe is then used to perform an idealized scenario of photoacoustic-guided therapy, where photoacoustic signals generated by an absorbing thread embedded in a piece of chicken breast are used to automatically refocus a HIFU beam with a time-reversal mirror and necrose the tissue at the location of the absorber.
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ERIC Educational Resources Information Center
Portland Project Committee, OR.
This teacher's guide contains parts three and four of the four-part first year Portland Project, a three-year secondary integrated science curriculum sequence. Part three of the guide deals with topics such as the cell, reproduction, embryology, genetics, genetic diseases, genetics and change, populations, effects of density on populations,…
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Kocabas, Coskun; Hur, Seung-Hyun; Gaur, Anshu; Meitl, Matthew A; Shim, Moonsub; Rogers, John A
2005-11-01
A convenient process for generating large-scale, horizontally aligned arrays of pristine, single-walled carbon nanotubes (SWNTs) is described. The approach uses guided growth, by chemical vapor deposition (CVD), of SWNTs on miscut single-crystal quartz substrates. Studies of the growth reveal important relationships between the density and alignment of the tubes, the CVD conditions, and the morphology of the quartz. Electrodes and dielectrics patterned on top of these arrays yield thin-film transistors that use the SWNTs as effective thin-film semiconductors. The ability to build high-performance devices of this type suggests significant promise for large-scale aligned arrays of SWNTs in electronics, sensors, and other applications.
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Array-CGH in children with mild intellectual disability: a population-based study.
Coutton, Charles; Dieterich, Klaus; Satre, Véronique; Vieville, Gaëlle; Amblard, Florence; David, Marie; Cans, Christine; Jouk, Pierre-Simon; Devillard, Francoise
2015-01-01
Intellectual disability (ID) is characterized by limitation in intellectual function and adaptive behavior, with onset in childhood. Frequent identifiable causes of ID originate from chromosomal imbalances. During the last years, array-CGH has successfully contributed to improve the diagnostic detection rate of genetic abnormalities in patients with ID. Most array-CGH studies focused on patients with moderate or severe intellectual disability. Studies on genetic etiology in children with mild intellectual disability (ID) are very rare. We performed array-CGH analysis in 66 children with mild intellectual disability assessed in a population-based study and for whom no genetic etiology was identified. We found one or more copy number variations (CNVs) in 20 out of 66 (~30 %) patients with a mild ID. In eight of them (~12 %), the CNVs were certainly responsible for the phenotype and in six they were potentially pathogenic for ID. Altogether, array-CGH helped to determine the etiology of ID in 14 patients (~21 %). Our results underscore the clinical relevance of array-CGH to investigate the etiology of isolated idiopathic mild ID in patients or associated with even subtle dysmorphic features or congenital malformations.
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Synthetic Genetic Arrays: Automation of Yeast Genetics.
Kuzmin, Elena; Costanzo, Michael; Andrews, Brenda; Boone, Charles
2016-04-01
Genome-sequencing efforts have led to great strides in the annotation of protein-coding genes and other genomic elements. The current challenge is to understand the functional role of each gene and how genes work together to modulate cellular processes. Genetic interactions define phenotypic relationships between genes and reveal the functional organization of a cell. Synthetic genetic array (SGA) methodology automates yeast genetics and enables large-scale and systematic mapping of genetic interaction networks in the budding yeast,Saccharomyces cerevisiae SGA facilitates construction of an output array of double mutants from an input array of single mutants through a series of replica pinning steps. Subsequent analysis of genetic interactions from SGA-derived mutants relies on accurate quantification of colony size, which serves as a proxy for fitness. Since its development, SGA has given rise to a variety of other experimental approaches for functional profiling of the yeast genome and has been applied in a multitude of other contexts, such as genome-wide screens for synthetic dosage lethality and integration with high-content screening for systematic assessment of morphology defects. SGA-like strategies can also be implemented similarly in a number of other cell types and organisms, includingSchizosaccharomyces pombe,Escherichia coli, Caenorhabditis elegans, and human cancer cell lines. The genetic networks emerging from these studies not only generate functional wiring diagrams but may also play a key role in our understanding of the complex relationship between genotype and phenotype. © 2016 Cold Spring Harbor Laboratory Press.
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Enhanced Lesion Visualization in Image-Guided Noninvasive Surgery With Ultrasound Phased Arrays
2001-10-25
81, 1995. [4] N. Sanghvi et al., “Noninvasive surgery of prostate tissue by high-intensity focused ultrasound ,” IEEE Trans. UFFC, vol. 43, no. 6, pp...ENHANCED LESION VISUALIZATION IN IMAGE-GUIDED NONINVASIVE SURGERY WITH ULTRASOUND PHASED ARRAYS Hui Yao, Pornchai Phukpattaranont and Emad S. Ebbini...Department of Electrical and Computer Engineering University of Minnesota Minneapolis, MN 55455 Abstract- We describe dual-mode ultrasound phased
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The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers.
Yang, Shi Ying; Saxena, Rachit K; Kulwal, Pawan L; Ash, Gavin J; Dubey, Anuja; Harper, John D I; Upadhyaya, Hari D; Gothalwal, Ragini; Kilian, Andrzej; Varshney, Rajeev K
2011-04-01
With an objective to develop a genetic map in pigeon pea (Cajanus spp.), a total of 554 diversity arrays technology (DArT) markers showed polymorphism in a pigeon pea F(2) mapping population of 72 progenies derived from an interspecific cross of ICP 28 (Cajanus cajan) and ICPW 94 (Cajanus scarabaeoides). Approximately 13% of markers did not conform to expected segregation ratio. The total number of DArT marker loci segregating in Mendelian manner was 405 with 73.1% (P > 0.001) of DArT markers having unique segregation patterns. Two groups of genetic maps were generated using DArT markers. While the maternal genetic linkage map had 122 unique DArT maternal marker loci, the paternal genetic linkage map has a total of 172 unique DArT paternal marker loci. The length of these two maps covered 270.0 cM and 451.6 cM, respectively. These are the first genetic linkage maps developed for pigeon pea, and this is the first report of genetic mapping in any grain legume using diversity arrays technology.
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Directed branch growth in aligned nanowire arrays.
Beaudry, Allan L; LaForge, Joshua M; Tucker, Ryan T; Sorge, Jason B; Adamski, Nicholas L; Li, Peng; Taschuk, Michael T; Brett, Michael J
2014-01-01
Branch growth is directed along two, three, or four in-plane directions in vertically aligned nanowire arrays using vapor-liquid-solid glancing angle deposition (VLS-GLAD) flux engineering. In this work, a dynamically controlled collimated vapor flux guides branch placement during the self-catalyzed epitaxial growth of branched indium tin oxide nanowire arrays. The flux is positioned to grow branches on select nanowire facets, enabling fabrication of aligned nanotree arrays with L-, T-, or X-branching. In addition, a flux motion algorithm is designed to selectively elongate branches along one in-plane axis. Nanotrees are found to be aligned across large areas by X-ray diffraction pole figure analysis and through branch length and orientation measurements collected over 140 μm(2) from scanning electron microscopy images for each array. The pathway to guided assembly of nanowire architectures with controlled interconnectivity in three-dimensions using VLS-GLAD is discussed.
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Patel, Jaina; Mercimek-Mahmutoglu, Saadet
2016-10-01
Epilepsy is one of the most common neurological disorders in childhood. Epilepsy associated with global developmental delay and cognitive dysfunction is defined as epileptic encephalopathy. Certain inherited metabolic disorders presenting with epileptic encephalopathy can be treated with disease specific diet, vitamin, amino acid or cofactor supplementations. In those disorders, disease specific therapy is successful to achieve good seizure control and improve long-term neurodevelopmental outcome. For this reason, intractable epilepsy with global developmental delay or history of developmental regression warrants detailed metabolic investigations for the possibility of an underlying treatable inherited metabolic disorder, which should be undertaken as first line investigations. An underlying genetic etiology in epileptic encephalopathy has been supported by recent studies such as array comparative genomic hybridization, targeted next generation sequencing panels, whole exome and whole genome sequencing. These studies report a diagnostic yield up to 70%, depending on the applied genetic testing as well as number of patients enrolled. In patients with epileptic encephalopathy, a stepwise approach for diagnostic work-up will help to diagnose treatable inherited metabolic disorders quickly. Application of detailed genetic investigations such as targeted next generation sequencing as second line and whole exome sequencing as third line testing will diagnose underlying genetic disease which will help for genetic counseling as well as guide for prenatal diagnosis. Knowledge of underlying genetic cause will provide novel insights into the pathogenesis of epileptic encephalopathy and pave the ground towards the development of targeted neuroprotective treatment strategies to improve the health outcome of children with epileptic encephalopathy.
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Assessing the genetic architecture of epithelial ovarian cancer histological subtypes.
Cuellar-Partida, Gabriel; Lu, Yi; Dixon, Suzanne C; Fasching, Peter A; Hein, Alexander; Burghaus, Stefanie; Beckmann, Matthias W; Lambrechts, Diether; Van Nieuwenhuysen, Els; Vergote, Ignace; Vanderstichele, Adriaan; Doherty, Jennifer Anne; Rossing, Mary Anne; Chang-Claude, Jenny; Rudolph, Anja; Wang-Gohrke, Shan; Goodman, Marc T; Bogdanova, Natalia; Dörk, Thilo; Dürst, Matthias; Hillemanns, Peter; Runnebaum, Ingo B; Antonenkova, Natalia; Butzow, Ralf; Leminen, Arto; Nevanlinna, Heli; Pelttari, Liisa M; Edwards, Robert P; Kelley, Joseph L; Modugno, Francesmary; Moysich, Kirsten B; Ness, Roberta B; Cannioto, Rikki; Høgdall, Estrid; Høgdall, Claus; Jensen, Allan; Giles, Graham G; Bruinsma, Fiona; Kjaer, Susanne K; Hildebrandt, Michelle A T; Liang, Dong; Lu, Karen H; Wu, Xifeng; Bisogna, Maria; Dao, Fanny; Levine, Douglas A; Cramer, Daniel W; Terry, Kathryn L; Tworoger, Shelley S; Stampfer, Meir; Missmer, Stacey; Bjorge, Line; Salvesen, Helga B; Kopperud, Reidun K; Bischof, Katharina; Aben, Katja K H; Kiemeney, Lambertus A; Massuger, Leon F A G; Brooks-Wilson, Angela; Olson, Sara H; McGuire, Valerie; Rothstein, Joseph H; Sieh, Weiva; Whittemore, Alice S; Cook, Linda S; Le, Nhu D; Blake Gilks, C; Gronwald, Jacek; Jakubowska, Anna; Lubiński, Jan; Kluz, Tomasz; Song, Honglin; Tyrer, Jonathan P; Wentzensen, Nicolas; Brinton, Louise; Trabert, Britton; Lissowska, Jolanta; McLaughlin, John R; Narod, Steven A; Phelan, Catherine; Anton-Culver, Hoda; Ziogas, Argyrios; Eccles, Diana; Campbell, Ian; Gayther, Simon A; Gentry-Maharaj, Aleksandra; Menon, Usha; Ramus, Susan J; Wu, Anna H; Dansonka-Mieszkowska, Agnieszka; Kupryjanczyk, Jolanta; Timorek, Agnieszka; Szafron, Lukasz; Cunningham, Julie M; Fridley, Brooke L; Winham, Stacey J; Bandera, Elisa V; Poole, Elizabeth M; Morgan, Terry K; Goode, Ellen L; Schildkraut, Joellen M; Pearce, Celeste L; Berchuck, Andrew; Pharoah, Paul D P; Webb, Penelope M; Chenevix-Trench, Georgia; Risch, Harvey A; MacGregor, Stuart
2016-07-01
Epithelial ovarian cancer (EOC) is one of the deadliest common cancers. The five most common types of disease are high-grade and low-grade serous, endometrioid, mucinous and clear cell carcinoma. Each of these subtypes present distinct molecular pathogeneses and sensitivities to treatments. Recent studies show that certain genetic variants confer susceptibility to all subtypes while other variants are subtype-specific. Here, we perform an extensive analysis of the genetic architecture of EOC subtypes. To this end, we used data of 10,014 invasive EOC patients and 21,233 controls from the Ovarian Cancer Association Consortium genotyped in the iCOGS array (211,155 SNPs). We estimate the array heritability (attributable to variants tagged on arrays) of each subtype and their genetic correlations. We also look for genetic overlaps with factors such as obesity, smoking behaviors, diabetes, age at menarche and height. We estimated the array heritabilities of high-grade serous disease ([Formula: see text] = 8.8 ± 1.1 %), endometrioid ([Formula: see text] = 3.2 ± 1.6 %), clear cell ([Formula: see text] = 6.7 ± 3.3 %) and all EOC ([Formula: see text] = 5.6 ± 0.6 %). Known associated loci contributed approximately 40 % of the total array heritability for each subtype. The contribution of each chromosome to the total heritability was not proportional to chromosome size. Through bivariate and cross-trait LD score regression, we found evidence of shared genetic backgrounds between the three high-grade subtypes: serous, endometrioid and undifferentiated. Finally, we found significant genetic correlations of all EOC with diabetes and obesity using a polygenic prediction approach.
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Guided growth of horizontal GaN nanowires on quartz and their transfer to other substrates.
Goren-Ruck, Lior; Tsivion, David; Schvartzman, Mark; Popovitz-Biro, Ronit; Joselevich, Ernesto
2014-03-25
The guided growth of horizontal nanowires has so far been demonstrated on a limited number of substrates. In most cases, the nanowires are covalently bonded to the substrate where they grow and cannot be transferred to other substrates. Here we demonstrate the guided growth of well-aligned horizontal GaN nanowires on quartz and their subsequent transfer to silicon wafers by selective etching of the quartz while maintaining their alignment. The guided growth was observed on different planes of quartz with varying degrees of alignment. We characterized the crystallographic orientations of the nanowires and proposed a new mechanism of "dynamic graphoepitaxy" for their guided growth on quartz. The transfer of the guided nanowires enabled the fabrication of back-gated field-effect transistors from aligned nanowire arrays on oxidized silicon wafers and the production of crossbar arrays. The guided growth of transferrable nanowires opens up the possibility of massively parallel integration of nanowires into functional systems on virtually any desired substrate.
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USDA-ARS?s Scientific Manuscript database
The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...
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Misfit-guided self-organization of anticorrelated Ge quantum dot arrays on Si nanowires.
Kwon, Soonshin; Chen, Zack C Y; Kim, Ji-Hun; Xiang, Jie
2012-09-12
Misfit-strain guided growth of periodic quantum dot (QD) arrays in planar thin film epitaxy has been a popular nanostructure fabrication method. Engineering misfit-guided QD growth on a nanoscale substrate such as the small curvature surface of a nanowire represents a new approach to self-organized nanostructure preparation. Perhaps more profoundly, the periodic stress underlying each QD and the resulting modulation of electro-optical properties inside the nanowire backbone promise to provide a new platform for novel mechano-electronic, thermoelectronic, and optoelectronic devices. Herein, we report a first experimental demonstration of self-organized and self-limited growth of coherent, periodic Ge QDs on a one-dimensional Si nanowire substrate. Systematic characterizations reveal several distinctively different modes of Ge QD ordering on the Si nanowire substrate depending on the core diameter. In particular, Ge QD arrays on Si nanowires of around 20 nm diameter predominantly exhibit an anticorrelated pattern whose wavelength agrees with theoretical predictions. The correlated pattern can be attributed to propagation and correlation of misfit strain across the diameter of the thin nanowire substrate. The QD array growth is self-limited as the wavelength of the QDs remains unchanged even after prolonged Ge deposition. Furthermore, we demonstrate a direct kinetic transformation from a uniform Ge shell layer to discrete QD arrays by a postgrowth annealing process.
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Kang, Jihoon; Choi, Yong
2016-07-01
Light sharing PET detector configuration coupled with thick light guide and Geiger-mode avalanche photodiode (GAPD) with large-area microcells was proposed to overcome the energy non-linearity problem and to obtain high light collection efficiency (LCE). A Monte-Carlo simulation was conducted for the three types of LSO block, 4 × 4 array of 3 × 3 × 20 mm(3) discrete crystals, 6 × 6 array of 2 × 2 × 20 mm(3) discrete crystals, and 12 × 12 array of 1 × 1 × 20 mm(3) discrete crystals, to investigate the scintillation light distribution after conversion of the γ-rays in LSO. The incident photons were read out by three types of 4 × 4 array photosensors, which were PSPMT of 25% quantum efficiency (QE), GAPD1 with 50 × 50 µm(2) microcells of 30% photon detection efficiency (PDE) and GAPD2 with 100 × 100 µm(2) of 45% PDE. The number of counted photons in each photosensor was analytically calculated. The LCE, linearity and flood histogram were examined for each PET detector module having 99 different configurations as a function of light guide thickness ranging from 0 to 10 mm. The performance of PET detector modules based on GAPDs was considerably improved by using the thick light guide. The LCE was increased from 24 to 30% and from 14 to 41%, and the linearity was also improved from 0.97 to 0.99 and from 0.75 to 0.99, for GAPD1 and GAPD2, respectively. As expected, the performance of PSPMT based detector did not change. The flood histogram of 12 × 12 array PET detector modules using 3 mm light guide coupled with GAPDs was obtained by simulation, and all crystals of 1 × 1 × 20 mm(3) size were clearly identified. PET detector module coupled with thick light guide and GAPD array with large-area microcells was proposed to obtain high QE and high spatial resolution, and its feasibility was verified. This study demonstrated that the overall PET performance of the proposed design was considerably improved, and this approach will provide opportunities to develop GAPD based PET detector with a high LCE. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
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Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus
Slavov, Gancho; Allison, Gordon; Bosch, Maurice
2013-01-01
Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we present a summary of recent and on-going biochemical studies, including prospects and limitations for the development of powerful phenotyping approaches. Second, we review current knowledge about genetic variation for cell wall characteristics of Miscanthus and illustrate how phenotypic data, combined with high-density arrays of single-nucleotide polymorphisms, are being used in genome-wide association studies to generate testable hypotheses and guide biological discovery. Finally, we provide an overview of the current knowledge about the molecular biology of cell wall biosynthesis in Miscanthus and closely related grasses, discuss the key conceptual and technological bottlenecks, and outline the short-term prospects for progress in this field. PMID:23847628
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Kabbaj, Hafssa; Sall, Amadou T; Al-Abdallat, Ayed; Geleta, Mulatu; Amri, Ahmed; Filali-Maltouf, Abdelkarim; Belkadi, Bouchra; Ortiz, Rodomiro; Bassi, Filippo M
2017-01-01
Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.
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Silva, Leonardo W T; Barros, Vitor F; Silva, Sandro G
2014-08-18
In launching operations, Rocket Tracking Systems (RTS) process the trajectory data obtained by radar sensors. In order to improve functionality and maintenance, radars can be upgraded by replacing antennas with parabolic reflectors (PRs) with phased arrays (PAs). These arrays enable the electronic control of the radiation pattern by adjusting the signal supplied to each radiating element. However, in projects of phased array radars (PARs), the modeling of the problem is subject to various combinations of excitation signals producing a complex optimization problem. In this case, it is possible to calculate the problem solutions with optimization methods such as genetic algorithms (GAs). For this, the Genetic Algorithm with Maximum-Minimum Crossover (GA-MMC) method was developed to control the radiation pattern of PAs. The GA-MMC uses a reconfigurable algorithm with multiple objectives, differentiated coding and a new crossover genetic operator. This operator has a different approach from the conventional one, because it performs the crossover of the fittest individuals with the least fit individuals in order to enhance the genetic diversity. Thus, GA-MMC was successful in more than 90% of the tests for each application, increased the fitness of the final population by more than 20% and reduced the premature convergence.
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Silva, Leonardo W. T.; Barros, Vitor F.; Silva, Sandro G.
2014-01-01
In launching operations, Rocket Tracking Systems (RTS) process the trajectory data obtained by radar sensors. In order to improve functionality and maintenance, radars can be upgraded by replacing antennas with parabolic reflectors (PRs) with phased arrays (PAs). These arrays enable the electronic control of the radiation pattern by adjusting the signal supplied to each radiating element. However, in projects of phased array radars (PARs), the modeling of the problem is subject to various combinations of excitation signals producing a complex optimization problem. In this case, it is possible to calculate the problem solutions with optimization methods such as genetic algorithms (GAs). For this, the Genetic Algorithm with Maximum-Minimum Crossover (GA-MMC) method was developed to control the radiation pattern of PAs. The GA-MMC uses a reconfigurable algorithm with multiple objectives, differentiated coding and a new crossover genetic operator. This operator has a different approach from the conventional one, because it performs the crossover of the fittest individuals with the least fit individuals in order to enhance the genetic diversity. Thus, GA-MMC was successful in more than 90% of the tests for each application, increased the fitness of the final population by more than 20% and reduced the premature convergence. PMID:25196013
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Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao
Livingstone, Donald; Royaert, Stefan; Stack, Conrad; Mockaitis, Keithanne; May, Greg; Farmer, Andrew; Saski, Christopher; Schnell, Ray; Kuhn, David; Motamayor, Juan Carlos
2015-01-01
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. PMID:26070980
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Mano, Junichi; Shigemitsu, Natsuki; Futo, Satoshi; Akiyama, Hiroshi; Teshima, Reiko; Hino, Akihiro; Furui, Satoshi; Kitta, Kazumi
2009-01-14
We developed a novel type of real-time polymerase chain reaction (PCR) array with TaqMan chemistry as a platform for the comprehensive and semiquantitative detection of genetically modified (GM) crops. Thirty primer-probe sets for the specific detection of GM lines, recombinant DNA (r-DNA) segments, endogenous reference genes, and donor organisms were synthesized, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The specificity and sensitivity of the array were evaluated. A comparative analysis with the data and publicly available information on GM crops approved in Japan allowed us to assume the possibility of unapproved GM crop contamination. Furthermore, we designed a Microsoft Excel spreadsheet application, Unapproved GMO Checker version 2.01, which helps process all the data of real-time PCR arrays for the easy assumption of unapproved GM crop contamination. The spreadsheet is available free of charge at http://cse.naro.affrc.go.jp/jmano/index.html .
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Wang, Yao; Stephens, Douglas N; O'Donnell, Matthew
2002-12-01
Intravascular ultrasound (IVUS) imaging systems using circumferential arrays mounted on cardiac catheter tips fire beams orthogonal to the principal axis of the catheter. The system produces high resolution cross-sectional images but must be guided by conventional angioscopy. A real-time forward-viewing array, integrated into the same catheter, could greatly reduce radiation exposure by decreasing angiographic guidance. Unfortunately, the mounting requirement of a catheter guide wire prohibits a full-disk imaging aperture. Given only an annulus of array elements, prior theoretical investigations have only considered a circular ring of point transceivers and focusing strategies using all elements in the highly dense array, both impractical assumptions. In this paper, we consider a practical array geometry and signal processing architecture for a forward-viewing IVUS system. Our specific design uses a total of 210 transceiver firings with synthetic reconstruction for a given 3-D image frame. Simulation results demonstrate this design can achieve side-lobes under -40 dB for on-axis situations and under -30 dB for steering to the edge of a 80 degrees cone.
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USDA-ARS?s Scientific Manuscript database
Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applicatio...
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Aviation and Space Curriculum Guide K-3
DOT National Transportation Integrated Search
1992-01-01
The Alabama Aerospace Curriculum Guide is designed for teachers of grades K-3 who have little or no experience in the area of aviation or space. The purpose of this guide is to provide an array of aviation and space activities which may be used by te...
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Aleksandrova, N V; Shubina, E S; Ekimov, A N; Kodyleva, T A; Mukosey, I S; Makarova, N P; Kulakova, E V; Levkov, L A; Barkov, I Yu; Trofimov, D Yu; Sukhikh, G T
2017-01-01
Aneuploidies as quantitative chromosome abnormalities are a main cause of failed development of morphologically normal embryos, implantation failures, and early reproductive losses. Preimplantation genetic screening (PGS) allows a preselection of embryos with a normal karyotype, thus increasing the implantation rate and reducing the frequency of early pregnancy loss after IVF. Modern PGS technologies are based on a genome-wide analysis of the embryo. The first pilot study in Russia was performed to assess the possibility of using semiconductor new-generation sequencing (NGS) as a PGS method. NGS data were collected for 38 biopsied embryos and compared with the data from array comparative genomic hybridization (array-CGH). The concordance between the NGS and array-CGH data was 94.8%. Two samples showed the karyotype 47,XXY by array-CGH and a normal karyotype by NGS. The discrepancies may be explained by loss of efficiency of array-CGH amplicon labeling.
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Guided neuronal growth on arrays of biofunctionalized GaAs/InGaAs semiconductor microtubes
NASA Astrophysics Data System (ADS)
Bausch, Cornelius S.; Koitmäe, Aune; Stava, Eric; Price, Amanda; Resto, Pedro J.; Huang, Yu; Sonnenberg, David; Stark, Yuliya; Heyn, Christian; Williams, Justin C.; Dent, Erik W.; Blick, Robert H.
2013-10-01
We demonstrate embedded growth of cortical mouse neurons in dense arrays of semiconductor microtubes. The microtubes, fabricated from a strained GaAs/InGaAs heterostructure, guide axon growth through them and potentially enable electrical and optical probing of propagating action potentials. The coaxial nature of the microtubes—similar to myelin—is expected to enhance the signal transduction along the axon. We present a technique of suppressing arsenic toxicity and prove the success of this technique by overgrowing neuronal mouse cells.
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NASA Astrophysics Data System (ADS)
Moilanen, Petro; Salmi, Ari; Kilappa, Vantte; Zhao, Zuomin; Timonen, Jussi; Hæggström, Edward
2017-10-01
This paper validates simulation predictions, which state that specific modes could be enhanced in quantitative ultrasonic bone testing. Tunable selection of ultrasonic guided wave excitation is useful in non-destructive testing since it permits the mediation of energy into diagnostically useful modes while reducing the energy mediated into disturbing contributions. For instance, it is often challenging to distinguish and extract the useful modes from ultrasound signals measured in bone covered by a soft tissue. We show that a laser diode array can selectively excite ultrasound in bone mimicking phantoms. A fiber-coupled diode array (4 elements) illuminated two solid tubes (2-3 mm wall thickness) embraced by an opaque soft-tissue mimicking elastomer coating (5 mm thick). A predetermined time delay matching the selected mode and frequency was employed between the outputs of the elements. The generated ultrasound was detected by a 215 kHz piezo receiver. Our results suggest that this array reduces the disturbances caused by the elastomer cover and so pave way to permit non-contacting in vivo guided wave ultrasound assessment of human bones. The implementation is small, inexpensive, and robust in comparison with the conventional pulsed lasers.
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3D optical coherence tomography image registration for guiding cochlear implant insertion
NASA Astrophysics Data System (ADS)
Cheon, Gyeong-Woo; Jeong, Hyun-Woo; Chalasani, Preetham; Chien, Wade W.; Iordachita, Iulian; Taylor, Russell; Niparko, John; Kang, Jin U.
2014-03-01
In cochlear implant surgery, an electrode array is inserted into the cochlear canal to restore hearing to a person who is profoundly deaf or significantly hearing impaired. One critical part of the procedure is the insertion of the electrode array, which looks like a thin wire, into the cochlear canal. Although X-ray or computed tomography (CT) could be used as a reference to evaluate the pathway of the whole electrode array, there is no way to depict the intra-cochlear canal and basal turn intra-operatively to help guide insertion of the electrode array. Optical coherent tomography (OCT) is a highly effective way of visualizing internal structures of cochlea. Swept source OCT (SSOCT) having center wavelength of 1.3 micron and 2D Galvonometer mirrors was used to achieve 7-mm depth 3-D imaging. Graphics processing unit (GPU), OpenGL, C++ and C# were integrated for real-time volumetric rendering simultaneously. The 3D volume images taken by the OCT system were assembled and registered which could be used to guide a cochlear implant. We performed a feasibility study using both dry and wet temporal bones and the result is presented.
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NASA Astrophysics Data System (ADS)
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.
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Misfit-guided self-organization of anti-correlated Ge quantum dot arrays on Si nanowires
Kwon, Soonshin; Chen, Zack C.Y.; Kim, Ji-Hun; Xiang, Jie
2012-01-01
Misfit-strain guided growth of periodic quantum dot (QD) arrays in planar thin film epitaxy has been a popular nanostructure fabrication method. Engineering misfit-guided QD growth on a nanoscale substrate such as the small curvature surface of a nanowire represents a new approach to self-organized nanostructure preparation. Perhaps more profoundly, the periodic stress underlying each QD and the resulting modulation of electro-optical properties inside the nanowire backbone promise to provide a new platform for novel mechano-electronic, thermoelectronic, and optoelectronic devices. Herein, we report a first experimental demonstration of self-organized and self-limited growth of coherent, periodic Ge QDs on a one dimensional Si nanowire substrate. Systematic characterizations reveal several distinctively different modes of Ge QD ordering on the Si nanowire substrate depending on the core diameter. In particular, Ge QD arrays on Si nanowires of around 20 nm diameter predominantly exhibit an anti-correlated pattern whose wavelength agrees with theoretical predictions. The correlated pattern can be attributed to propagation and correlation of misfit strain across the diameter of the thin nanowire substrate. The QD array growth is self-limited as the wavelength of the QDs remains unchanged even after prolonged Ge deposition. Furthermore, we demonstrate a direct kinetic transformation from a uniform Ge shell layer to discrete QD arrays by a post-growth annealing process. PMID:22889063
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2012-01-01
Background For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficient coverage of genomic sequences, however, none of the expressed sequence tag (EST)-based chips developed to date cover gene expression from the whole genome. The availability of Tobacco Genome Initiative (TGI) sequences provides a useful resource to build a whole genome exon array, even if the assembled sequences are highly fragmented. Here, the design of a Tobacco Exon Array is reported and an application to improve the understanding of genes regulated by cadmium (Cd) in tobacco is described. Results From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon) and tested on two selected tobacco varieties. Two tobacco varieties out of 45 accumulating low and high cadmium in leaf were identified based on the GGE biplot analysis, which is analysis of the genotype main effect (G) plus analysis of the genotype by environment interaction (GE) of eight field trials (four fields over two years) showing reproducibility across the trials. The selected varieties were grown under greenhouse conditions in two different soils and subjected to exon array analyses using root and leaf tissues to understand the genetic make-up of the Cd accumulation. Conclusions An Affymetrix Exon Array was developed to cover a large (~90%) proportion of the tobacco gene space. The Tobacco Exon Array will be available for research use through Affymetrix array catalogue. As a proof of the exon array usability, we have demonstrated that the Tobacco Exon Array is a valuable tool for studying Cd accumulation in tobacco leaves. Data from field and greenhouse experiments supported by gene expression studies strongly suggested that the difference in leaf Cd accumulation between the two specific tobacco cultivars is dependent solely on genetic factors and genetic variability rather than on the environment. PMID:23190529
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Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O’Connor, Timothy D.; Abecasis, Gonçalo R.; Wojcik, Genevieve L; Gignoux, Christopher R.; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E.; Bustamante, Carlos; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Qin, Zhaohui S.; Preethi Boorgula, Meher; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Ruczinski, Ingo; Scott, Alan F.; Taub, Margaret A.; Vergara, Candelaria; Levin, Albert M.; Padhukasahasram, Badri; Williams, L. Keoki; Dunston, Georgia M.; Faruque, Mezbah U.; Gietzen, Kimberly; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-Youn A.; Kumar, Rajesh; Schleimer, Robert; De La Vega, Francisco M.; Shringarpure, Suyash S.; Musharoff, Shaila; Burchard, Esteban G.; Eng, Celeste; Hernandez, Ryan D.; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Maul, Pissamai; Maul, Trevor; Watson, Harold; Ilma Araujo, Maria; Riccio Oliveira, Ricardo; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Francisco Herrera-Paz, Edwin; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Marina Vasquez, Olga; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria
2017-01-01
A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry. PMID:28429804
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Homulle, H A R; Powolny, F; Stegehuis, P L; Dijkstra, J; Li, D-U; Homicsko, K; Rimoldi, D; Muehlethaler, K; Prior, J O; Sinisi, R; Dubikovskaya, E; Charbon, E; Bruschini, C
2016-05-01
In near infrared fluorescence-guided surgical oncology, it is challenging to distinguish healthy from cancerous tissue. One promising research avenue consists in the analysis of the exogenous fluorophores' lifetime, which are however in the (sub-)nanosecond range. We have integrated a single-photon pixel array, based on standard CMOS SPADs (single-photon avalanche diodes), in a compact, time-gated measurement system, named FluoCam. In vivo measurements were carried out with indocyanine green (ICG)-modified derivatives targeting the αvβ 3 integrin, initially on a genetically engineered mouse model of melanoma injected with ICG conjugated with tetrameric cyclic pentapeptide (ICG-E[c(RGD f K)4]), then on mice carrying tumour xenografts of U87-MG (a human primary glioblastoma cell line) injected with monomeric ICG-c(RGD f K). Measurements on tumor, muscle and tail locations allowed us to demonstrate the feasibility of in vivo lifetime measurements with the FluoCam, to determine the characteristic lifetimes (around 500 ps) and subtle lifetime differences between bound and unbound ICG-modified fluorophores (10% level), as well as to estimate the available photon fluxes under realistic conditions.
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New knowledge-based genetic algorithm for excavator boom structural optimization
NASA Astrophysics Data System (ADS)
Hua, Haiyan; Lin, Shuwen
2014-03-01
Due to the insufficiency of utilizing knowledge to guide the complex optimal searching, existing genetic algorithms fail to effectively solve excavator boom structural optimization problem. To improve the optimization efficiency and quality, a new knowledge-based real-coded genetic algorithm is proposed. A dual evolution mechanism combining knowledge evolution with genetic algorithm is established to extract, handle and utilize the shallow and deep implicit constraint knowledge to guide the optimal searching of genetic algorithm circularly. Based on this dual evolution mechanism, knowledge evolution and population evolution can be connected by knowledge influence operators to improve the configurability of knowledge and genetic operators. Then, the new knowledge-based selection operator, crossover operator and mutation operator are proposed to integrate the optimal process knowledge and domain culture to guide the excavator boom structural optimization. Eight kinds of testing algorithms, which include different genetic operators, are taken as examples to solve the structural optimization of a medium-sized excavator boom. By comparing the results of optimization, it is shown that the algorithm including all the new knowledge-based genetic operators can more remarkably improve the evolutionary rate and searching ability than other testing algorithms, which demonstrates the effectiveness of knowledge for guiding optimal searching. The proposed knowledge-based genetic algorithm by combining multi-level knowledge evolution with numerical optimization provides a new effective method for solving the complex engineering optimization problem.
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Arrays of Segmented, Tapered Light Guides for Use With Large, Planar Scintillation Detectors
NASA Astrophysics Data System (ADS)
Raylman, Raymond R.; Vaigneur, Keith; Stolin, Alexander V.; Jaliparthi, Gangadhar
2015-06-01
Metabolic imaging techniques can potentially improve detection and diagnosis of cancer in women with radiodense and/or fibrocystic breasts. Our group has previously developed a high-resolution positron emission tomography imaging and biopsy device (PEM-PET) to detect and guide the biopsy of suspicious breast lesions. Initial testing revealed that the imaging field-of-view (FOV) of the scanner was smaller than the physical size of the detector's active area, which could hinder sampling of breast areas close to the chest wall. The purpose of this work was to utilize segmented, tapered light guides for optically coupling the scintillator arrays to arrays of position-sensitive photomultipliers to increase both the active FOV and identification of individual scintillator elements. Testing of the new system revealed that the optics of these structures made it possible to discern detector elements from the complete active area of the detector face. In the previous system the top and bottom rows and left and right columns were not identifiable. Additionally, use of the new light guides increased the contrast of individual detector elements by up to 129%. Improved element identification led to a spatial resolution increase by approximately 12%. Due to attenuation of light in the light guides the detector energy resolution decreased from 18.5% to 19.1%. Overall, these improvements should increase the field-of-view and spatial resolution of the dedicated breast-PET system.
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Making a chocolate chip: development and evaluation of a 6K SNP array for Theobroma cacao.
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.
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Pratte-Santos, Rodrigo; Ribeiro, Katyanne Heringer; Santos, Thainá Altoe; Cintra, Terezinha Sarquis
2016-01-01
ABSTRACT Objective To investigate chromosomal abnormalities by CGH-array in patients with dysmorphic features and intellectual disability with normal conventional karyotype. Methods Retrospective study, carried out from January 2012 to February 2014, analyzing the CGH-array results of 39 patients. Results Twenty-six (66.7%) patients had normal results and 13 (33.3%) showed abnormal results - in that, 6 (15.4%) had pathogenic variants, 6 (15.4%) variants designated as uncertain and 1 (2.5%) non-pathogenic variants. Conclusion The characterization of the genetic profile by CGH-array in patients with intellectual disability and dysmorphic features enabled making etiologic diagnosis, followed by genetic counseling for families and specific treatment. PMID:27074231
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Ganal, Martin W.; Durstewitz, Gregor; Polley, Andreas; Bérard, Aurélie; Buckler, Edward S.; Charcosset, Alain; Clarke, Joseph D.; Graner, Eva-Maria; Hansen, Mark; Joets, Johann; Le Paslier, Marie-Christine; McMullen, Michael D.; Montalent, Pierre; Rose, Mark; Schön, Chris-Carolin; Sun, Qi; Walter, Hildrun; Martin, Olivier C.; Falque, Matthieu
2011-01-01
SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations – IBM (B73×Mo17) and LHRF (F2×F252) – were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding. PMID:22174790
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Chu, Y; Wu, D; Hou, Q F; Huo, X D; Gao, Y; Wang, T; Wang, H D; Yang, Y L; Liao, S X
2016-08-25
To investigate the value of array-based comparative genomic hybridization (array-CGH) technique for the detection of chromosomal analysis of miscarried embryo, and to provide genetic counseling for couples with spontaneous abortion. Totally 382 patients who underwent miscarriage were enrolled in this study. All aborted tissues were analyzed with conventional cytogenetic karyotyping and array-CGH, respectively. Through genetic analysis, all of the 382 specimens were successfully analyzed by array-CGH (100.0%, 382/382), and the detection rate of chromosomal aberrations was 46.6% (178/382). However, conventional karyotype analysis was successfully performed in 281 cases (73.6%, 281/382), and 113 (40.2%, 113/281) were found with chromosomal aberrations. Of these 178 samples identified by array-CGH, 163 samples (91.6%, 163/178) were aneuploidy, 15 samples (8.4%, 15/178) were segmental deletion and (or) duplication cases. Four of 10 cases with small segmental deletion and duplication were validated to be transferred from their fathers or mathers who were carriers of submicroscopic reciprocal translocation. Of these 113 abnormal karyotypes founded by conventional karyotyping, 108 cases (95.6%, 108/113) were aneuploidy and 5 cases (4.4%, 5/113) had chromosome structural aberrations. Most array-CGH results were consistent with conventional karyotyping but with 3 cases of discrepancy, which included 2 cases of triploids, 1 case of low-level mosaicism that undetcted by array-CGH. Compared with conventional karyotyping, there is an increased detection rate of chromosomal abnormalities when array-CGH is used to analyse the products of conception, primarilly because of its sucess with nonviable tissues. It could be a first-line method to determine the reason of miscarrage with higher accuracy and sensitivity.
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Geraldes, A; Difazio, S P; Slavov, G T; Ranjan, P; Muchero, W; Hannemann, J; Gunter, L E; Wymore, A M; Grassa, C J; Farzaneh, N; Porth, I; McKown, A D; Skyba, O; Li, E; Fujita, M; Klápště, J; Martin, J; Schackwitz, W; Pennacchio, C; Rokhsar, D; Friedmann, M C; Wasteneys, G O; Guy, R D; El-Kassaby, Y A; Mansfield, S D; Cronk, Q C B; Ehlting, J; Douglas, C J; Tuskan, G A
2013-03-01
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids. © 2013 Blackwell Publishing Ltd.
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Song, Junho; Pulkkinen, Aki; Huang, Yuexi; Hynynen, Kullervo
2014-01-01
Standing wave formation in an ex vivo human skull was investigated using a clinical prototype of a 30 cm diameter with 15 cm radius of curvature, low frequency (230 kHz), hemispherical transcranial Magnetic Resonance guided Focused Ultrasound (MRgFUS) phased-array. Experimental and simulation studies were conducted with changing aperture size and f-number configurations of the phased array, and qualitatively and quantitatively examined the acoustic pressure variation at the focus due to standing waves. The results demonstrated that the nodes and anti-nodes of standing wave produced by the small aperture array were clearly seen at approximately every 3 mm. The effect of the standing wave became more pronounced as the focus was moved closer to skull base. However, a sharp focus was seen for the full array, and there was no such standing wave pattern in the acoustic plane or near the skull base. This study showed that the fluctuation pressure amplitude would be greatly reduced by using a large-scale, hemispherical phased array with a low f-number. PMID:22049360
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Diverging diamond interchange : informational guide.
DOT National Transportation Integrated Search
2014-08-01
This document provides information and guidance on the Diverging Diamond Interchange (DDI). To the extent possible, the guide : addresses a variety of conditions found in the United States, to achieve designs suitable for a wide array of potential us...
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Restricted crossing u-turn : informational guide.
DOT National Transportation Integrated Search
2014-08-01
This document provides information and guidance on Restricted Crossing U-Turn (RCUT) intersections. To the extent possible, : the guide addresses a variety of conditions found in the United States, to achieve designs suitable for a wide array of pote...
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Displaced left turn intersection : informational guide.
DOT National Transportation Integrated Search
2014-08-01
This document provides information and guidance on the Displaced Left Turn (DLT) intersection. To the extent possible, the : guide addresses a variety of conditions found in the United States, to achieve designs suitable for a wide array of potential...
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High-intensity focused ultrasound (HIFU) array system for image-guided ablative therapy (IGAT)
NASA Astrophysics Data System (ADS)
Kaczkowski, Peter J.; Keilman, George W.; Cunitz, Bryan W.; Martin, Roy W.; Vaezy, Shahram; Crum, Lawrence A.
2003-06-01
Recent interest in using High Intensity Focused Ultrasound (HIFU) for surgical applications such as hemostasis and tissue necrosis has stimulated the development of image-guided systems for non-invasive HIFU therapy. Seeking an all-ultrasound therapeutic modality, we have developed a clinical HIFU system comprising an integrated applicator that permits precisely registered HIFU therapy delivery and high quality ultrasound imaging using two separate arrays, a multi-channel signal generator and RF amplifier system, and a software program that provides the clinician with a graphical overlay of the ultrasound image and therapeutic protocol controls. Electronic phasing of a 32 element 2 MHz HIFU annular array allows adjusting the focus within the range of about 4 to 12 cm from the face. A central opening in the HIFU transducer permits mounting a commercial medical imaging scanhead (ATL P7-4) that is held in place within a special housing. This mechanical fixture ensures precise coaxial registration between the HIFU transducer and the image plane of the imaging probe. Recent enhancements include development of an acoustic lens using numerical simulations for use with a 5-element array. Our image-guided therapy system is very flexible and enables exploration of a variety of new HIFU therapy delivery and monitoring approaches in the search for safe, effective, and efficient treatment protocols.
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Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed
2014-01-01
Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents. PMID:24718292
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Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed
2014-01-01
Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents.
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Allen, Alexandra M; Winfield, Mark O; Burridge, Amanda J; Downie, Rowena C; Benbow, Harriet R; Barker, Gary L A; Wilkinson, Paul A; Coghill, Jane; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa; Brew, Fiona; Bloor, Claire; Griffiths, Simon; Bentley, Alison R; Alda, Mark; Jack, Peter; Phillips, Andrew L; Edwards, Keith J
2017-03-01
Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom ® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
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Lee, Sandra Soo-Jin; Mountain, Joanna; Koenig, Barbara; Altman, Russ; Brown, Melissa; Camarillo, Albert; Cavalli-Sforza, Luca; Cho, Mildred; Eberhardt, Jennifer; Feldman, Marcus; Ford, Richard; Greely, Henry; King, Roy; Markus, Hazel; Satz, Debra; Snipp, Matthew; Steele, Claude; Underhill, Peter
2008-01-01
We are a multidisciplinary group of Stanford faculty who propose ten principles to guide the use of racial and ethnic categories when characterizing group differences in research into human genetic variation. PMID:18638359
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Wang, Shichen; Wong, Debbie; Forrest, Kerrie; Allen, Alexandra; Chao, Shiaoman; Huang, Bevan E; Maccaferri, Marco; Salvi, Silvio; Milner, Sara G; Cattivelli, Luigi; Mastrangelo, Anna M; Whan, Alex; Stephen, Stuart; Barker, Gary; Wieseke, Ralf; Plieske, Joerg; International Wheat Genome Sequencing Consortium; Lillemo, Morten; Mather, Diane; Appels, Rudi; Dolferus, Rudy; Brown-Guedira, Gina; Korol, Abraham; Akhunova, Alina R; Feuillet, Catherine; Salse, Jerome; Morgante, Michele; Pozniak, Curtis; Luo, Ming-Cheng; Dvorak, Jan; Morell, Matthew; Dubcovsky, Jorge; Ganal, Martin; Tuberosa, Roberto; Lawley, Cindy; Mikoulitch, Ivan; Cavanagh, Colin; Edwards, Keith J; Hayden, Matthew; Akhunov, Eduard
2014-01-01
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat. PMID:24646323
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Genetic Testing as a New Standard for Clinical Diagnosis of Color Vision Deficiencies.
Davidoff, Candice; Neitz, Maureen; Neitz, Jay
2016-09-01
The genetics underlying inherited color vision deficiencies is well understood: causative mutations change the copy number or sequence of the long (L), middle (M), or short (S) wavelength sensitive cone opsin genes. This study evaluated the potential of opsin gene analyses for use in clinical diagnosis of color vision defects. We tested 1872 human subjects using direct sequencing of opsin genes and a novel genetic assay that characterizes single nucleotide polymorphisms (SNPs) using the MassArray system. Of the subjects, 1074 also were given standard psychophysical color vision tests for a direct comparison with current clinical methods. Protan and deutan deficiencies were classified correctly in all subjects identified by MassArray as having red-green defects. Estimates of defect severity based on SNPs that control photopigment spectral tuning correlated with estimates derived from Nagel anomaloscopy. The MassArray assay provides genetic information that can be useful in the diagnosis of inherited color vision deficiency including presence versus absence, type, and severity, and it provides information to patients about the underlying pathobiology of their disease. The MassArray assay provides a method that directly analyzes the molecular substrates of color vision that could be used in combination with, or as an alternative to current clinical diagnosis of color defects.
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Genetic Testing as a New Standard for Clinical Diagnosis of Color Vision Deficiencies
Davidoff, Candice; Neitz, Maureen; Neitz, Jay
2016-01-01
Purpose The genetics underlying inherited color vision deficiencies is well understood: causative mutations change the copy number or sequence of the long (L), middle (M), or short (S) wavelength sensitive cone opsin genes. This study evaluated the potential of opsin gene analyses for use in clinical diagnosis of color vision defects. Methods We tested 1872 human subjects using direct sequencing of opsin genes and a novel genetic assay that characterizes single nucleotide polymorphisms (SNPs) using the MassArray system. Of the subjects, 1074 also were given standard psychophysical color vision tests for a direct comparison with current clinical methods. Results Protan and deutan deficiencies were classified correctly in all subjects identified by MassArray as having red–green defects. Estimates of defect severity based on SNPs that control photopigment spectral tuning correlated with estimates derived from Nagel anomaloscopy. Conclusions The MassArray assay provides genetic information that can be useful in the diagnosis of inherited color vision deficiency including presence versus absence, type, and severity, and it provides information to patients about the underlying pathobiology of their disease. Translational Relevance The MassArray assay provides a method that directly analyzes the molecular substrates of color vision that could be used in combination with, or as an alternative to current clinical diagnosis of color defects. PMID:27622081
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The GenoChip: A New Tool for Genetic Anthropology
Elhaik, Eran; Greenspan, Elliott; Staats, Sean; Krahn, Thomas; Tyler-Smith, Chris; Xue, Yali; Tofanelli, Sergio; Francalacci, Paolo; Cucca, Francesco; Pagani, Luca; Jin, Li; Li, Hui; Schurr, Theodore G.; Greenspan, Bennett; Spencer Wells, R.
2013-01-01
The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are inappropriate for global population genetic studies. GenoChip, the Genographic Project’s new genotyping array, was designed to resolve these issues and enable higher resolution research into outstanding questions in genetic anthropology. The GenoChip includes ancestry informative markers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all known Y-chromosome and mtDNA haplogroups. The chip was carefully vetted to avoid inclusion of medically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPs without any known health, medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics. PMID:23666864
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The GenoChip: a new tool for genetic anthropology.
Elhaik, Eran; Greenspan, Elliott; Staats, Sean; Krahn, Thomas; Tyler-Smith, Chris; Xue, Yali; Tofanelli, Sergio; Francalacci, Paolo; Cucca, Francesco; Pagani, Luca; Jin, Li; Li, Hui; Schurr, Theodore G; Greenspan, Bennett; Spencer Wells, R
2013-01-01
The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are inappropriate for global population genetic studies. GenoChip, the Genographic Project's new genotyping array, was designed to resolve these issues and enable higher resolution research into outstanding questions in genetic anthropology. The GenoChip includes ancestry informative markers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all known Y-chromosome and mtDNA haplogroups. The chip was carefully vetted to avoid inclusion of medically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPs without any known health, medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics.
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Efficient generation and transportation of energetic electrons in a carbon nanotube array target
NASA Astrophysics Data System (ADS)
Ji, Yanling; Jiang, Gang; Wu, Weidong; Wang, Chaoyang; Gu, Yuqiu; Tang, Yongjian
2010-01-01
Laser-driven energetic electron propagation in a carbon nanotube-array target is investigated using two-dimensional particle-in-cell simulations. Energetic electrons are efficiently generated when the array is irradiated by a short intense laser pulse. Confined and guided transportation of energetic electrons in the array is achieved by exploiting strong transient electromagnetic fields created at the wall surfaces of nanotubes. The underlying mechanisms are discussed in detail. Our investigation shows that the laser energy can be transferred more effectively to the target electrons in the array than that of in the flat foil due to the hole structures in the array.
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Wang, Liang; Yang, Die; Fang, Cheng; Chen, Zuliang; Lesniewski, Peter J; Mallavarapu, Megharaj; Naidu, Ravendra
2015-01-01
Sodium potassium absorption ratio (SPAR) is an important measure of agricultural water quality, wherein four exchangeable cations (K(+), Na(+), Ca(2+) and Mg(2+)) should be simultaneously determined. An ISE-array is suitable for this application because its simplicity, rapid response characteristics and lower cost. However, cross-interferences caused by the poor selectivity of ISEs need to be overcome using multivariate chemometric methods. In this paper, a solid contact ISE array, based on a Prussian blue modified glassy carbon electrode (PB-GCE), was applied with a novel chemometric strategy. One of the most popular independent component analysis (ICA) methods, the fast fixed-point algorithm for ICA (fastICA), was implemented by the genetic algorithm (geneticICA) to avoid the local maxima problem commonly observed with fastICA. This geneticICA can be implemented as a data preprocessing method to improve the prediction accuracy of the Back-propagation neural network (BPNN). The ISE array system was validated using 20 real irrigation water samples from South Australia, and acceptable prediction accuracies were obtained. Copyright © 2014 Elsevier B.V. All rights reserved.
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ERIC Educational Resources Information Center
Balan, Hazel R.
2018-01-01
Genetics is considered as one of the topics in science that students have difficulty and trouble in understanding. This study used study guide as an intervention tool to address the difficulties of students in learning genetics concepts. The main purpose of this study was to determine the perceptions of students on the effectiveness of study guide…
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Long range guided wave defect monitoring in rail track
NASA Astrophysics Data System (ADS)
Loveday, Philip W.; Long, Craig S.
2014-02-01
A guided wave ultrasound system was previously developed for monitoring rail track used on heavy duty freight lines. This system operates by transmitting guided waves between permanently installed transmit and receive transducers spaced approximately 1km apart. The system has been proven to reliably detect rail breaks without false alarms. While cracks are sometimes detected there is a trade - off between detecting cracks and the possibility of false alarms. Adding a pulse-echo mode of operation to the system could provide increased functionality by detecting, locating and possibly monitoring cracks. This would require an array of transducers to control the direction and mode of propagation and it would be necessary to detect cracks up to a range of approximately 500 m in either direction along the rail. A four transducer array was designed and full matrix capture was used for field measurements. Post processing of the signals showed that a thermite weld could be detected at a range of 790m from the transducer array. It was concluded that the required range can be achieved in new rail while it would be extremely difficult in very old rail.
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Chen, Justin; Jacox, Laura A; Saldanha, Francesca; Sive, Hazel
2017-09-01
A mouth is present in all animals, and comprises an opening from the outside into the oral cavity and the beginnings of the digestive tract to allow eating. This review focuses on the earliest steps in mouth formation. In the first half, we conclude that the mouth arose once during evolution. In all animals, the mouth forms from ectoderm and endoderm. A direct association of oral ectoderm and digestive endoderm is present even in triploblastic animals, and in chordates, this region is known as the extreme anterior domain (EAD). Further support for a single origin of the mouth is a conserved set of genes that form a 'mouth gene program' including foxA and otx2. In the second half of this review, we discuss steps involved in vertebrate mouth formation, using the frog Xenopus as a model. The vertebrate mouth derives from oral ectoderm from the anterior neural ridge, pharyngeal endoderm and cranial neural crest (NC). Vertebrates form a mouth by breaking through the body covering in a precise sequence including specification of EAD ectoderm and endoderm as well as NC, formation of a 'pre-mouth array,' basement membrane dissolution, stomodeum formation, and buccopharyngeal membrane perforation. In Xenopus, the EAD is also a craniofacial organizer that guides NC, while reciprocally, the NC signals to the EAD to elicit its morphogenesis into a pre-mouth array. Human mouth anomalies are prevalent and are affected by genetic and environmental factors, with understanding guided in part by use of animal models. WIREs Dev Biol 2017, 6:e275. doi: 10.1002/wdev.275 For further resources related to this article, please visit the WIREs website. © 2017 The Authors. WIREs Developmental Biology published by Wiley Periodicals, Inc.
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76 FR 80949 - Request for Nominations for Voting Members on Public Advisory Panels or Committees
Federal Register 2010, 2011, 2012, 2013, 2014
2011-12-27
.... Molecular and Clinical 1 June 1, 2012. Genetics Devices Panel of the Medical Devices Advisory Committee..., biochemical and/or molecular genetics, population genetics, epidemiology and related statistical training, and clinical molecular genetics testing (e.g., genotyping, array CGH, etc.). Individuals with experience in...
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Aviation & Space Curriculum Guide K-3. Revised.
ERIC Educational Resources Information Center
Alabama State Dept. of Education, Montgomery.
This guide is designed for teachers of grades K-3 who have little or no experience in the area of aviation or space. The purpose of this guide is to provide an array of aviation and space activities which may be used by teachers to enrich locally-designed programs. Units in this book include: (1) History of Aerospace; (2) Kinds and Uses of…
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Institutional Protocol to Manage Consanguinity Detected by Genetic Testing in Pregnancy in a Minor
Chen, Laura P.; Beck, Anita E.; Tsuchiya, Karen D.; Chow, Penny M.; Mirzaa, Ghayda M.; Wiester, Rebecca T.
2015-01-01
Single-nucleotide polymorphism arrays and other types of genetic tests have the potential to detect first-degree consanguinity and uncover parental rape in cases of minor teenage pregnancy. We present 2 cases in which genetic testing identified parental rape of a minor teenager. In case 1, single-nucleotide polymorphism array in a patient with multiple developmental abnormalities demonstrated multiple long stretches of homozygosity, revealing parental rape of a teenage mother. In case 2, a vague maternal sexual assault history and diagnosis of Pompe disease by direct gene sequencing identified parental rape of a minor. Given the medical, legal, and ethical implications of such revelations, a protocol was developed at our institution to manage consanguinity identified via genetic testing. PMID:25687148
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Zubair, Niha; Luis Ambite, Jose; Bush, William S.; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H.; Absher, Devin; Assimes, Themistocles L.; Bielinski, Suzette J.; Bottinger, Erwin P.; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W.; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A.; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J.; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H.; Martin, Lisa W.; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P.; Robinson, Jennifer; Rotter, Jerome I.; Ryckman, Kelli K.; Schreiner, Pamela J.; Stahl, Eli; Tao, Ran; Tsai, Michael Y.; Waite, Lindsay L.; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C.; Loos, Ruth J.F.; Rich, Stephen S.; Fornage, Myriam; North, Kari E.; Kooperberg, Charles; Carty, Cara L.
2016-01-01
Abstract Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. PMID:28426890
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Ng, Simon; Lin, Edith; Kitov, Pavel I.; ...
2015-04-10
Here we describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based-discovery (GE-FBD) uses selection of phagedisplayed glycopeptides to dock a glycan fragment at the CRD and guide selection of Synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 10 8 glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40 50-fold enhancement in affinity over methyl α-D-mannopyranoside (MeMan). Lectin array Suggested specificity: Man-WYD derivative bound only to 3more » out of 17 proteins-ConA, LcH, and PSA-that bind to Man. An X-ray structure of ConA.:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking; but their extra-CRD binding modes are significantly. different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry :of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ng, Simon; Lin, Edith; Kitov, Pavel I.
Here we describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based-discovery (GE-FBD) uses selection of phagedisplayed glycopeptides to dock a glycan fragment at the CRD and guide selection of Synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 10 8 glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40 50-fold enhancement in affinity over methyl α-D-mannopyranoside (MeMan). Lectin array Suggested specificity: Man-WYD derivative bound only to 3more » out of 17 proteins-ConA, LcH, and PSA-that bind to Man. An X-ray structure of ConA.:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking; but their extra-CRD binding modes are significantly. different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry :of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.« less
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Functional Analysis With a Barcoder Yeast Gene Overexpression System
Douglas, Alison C.; Smith, Andrew M.; Sharifpoor, Sara; Yan, Zhun; Durbic, Tanja; Heisler, Lawrence E.; Lee, Anna Y.; Ryan, Owen; Göttert, Hendrikje; Surendra, Anu; van Dyk, Dewald; Giaever, Guri; Boone, Charles; Nislow, Corey; Andrews, Brenda J.
2012-01-01
Systematic analysis of gene overexpression phenotypes provides an insight into gene function, enzyme targets, and biological pathways. Here, we describe a novel functional genomics platform that enables a highly parallel and systematic assessment of overexpression phenotypes in pooled cultures. First, we constructed a genome-level collection of ~5100 yeast barcoder strains, each of which carries a unique barcode, enabling pooled fitness assays with a barcode microarray or sequencing readout. Second, we constructed a yeast open reading frame (ORF) galactose-induced overexpression array by generating a genome-wide set of yeast transformants, each of which carries an individual plasmid-born and sequence-verified ORF derived from the Saccharomyces cerevisiae full-length EXpression-ready (FLEX) collection. We combined these collections genetically using synthetic genetic array methodology, generating ~5100 strains, each of which is barcoded and overexpresses a specific ORF, a set we termed “barFLEX.” Additional synthetic genetic array allows the barFLEX collection to be moved into different genetic backgrounds. As a proof-of-principle, we describe the properties of the barFLEX overexpression collection and its application in synthetic dosage lethality studies under different environmental conditions. PMID:23050238
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Chow, J Fc; Yeung, W Sb; Lee, V Cy; Lau, E Yl; Ho, P C; Ng, E Hy
2017-04-01
Preimplantation genetic screening has been proposed to improve the in-vitro fertilisation outcome by screening for aneuploid embryos or blastocysts. This study aimed to report the outcome of 133 cycles of preimplantation genetic diagnosis and screening by array comparative genomic hybridisation. This study of case series was conducted in a tertiary assisted reproductive centre in Hong Kong. Patients who underwent preimplantation genetic diagnosis for chromosomal abnormalities or preimplantation genetic screening between 1 April 2012 and 30 June 2015 were included. They underwent in-vitro fertilisation and intracytoplasmic sperm injection. An embryo biopsy was performed on day-3 embryos and the blastomere was subject to array comparative genomic hybridisation. Embryos with normal copy numbers were replaced. The ongoing pregnancy rate, implantation rate, and miscarriage rate were studied. During the study period, 133 cycles of preimplantation genetic diagnosis for chromosomal abnormalities or preimplantation genetic screening were initiated in 94 patients. Overall, 112 cycles proceeded to embryo biopsy and 65 cycles had embryo transfer. The ongoing pregnancy rate per transfer cycle after preimplantation genetic screening was 50.0% and that after preimplantation genetic diagnosis was 34.9%. The implantation rates after preimplantation genetic screening and diagnosis were 45.7% and 41.1%, respectively and the miscarriage rates were 8.3% and 28.6%, respectively. There were 26 frozen-thawed embryo transfer cycles, in which vitrified and biopsied genetically transferrable embryos were replaced, resulting in an ongoing pregnancy rate of 36.4% in the screening group and 60.0% in the diagnosis group. The clinical outcomes of preimplantation genetic diagnosis and screening using comparative genomic hybridisation in our unit were comparable to those reported internationally. Genetically transferrable embryos replaced in a natural cycle may improve the ongoing pregnancy rate and implantation rate when compared with transfer in a stimulated cycle.
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Image-guided ultrasound phased arrays are a disruptive technology for non-invasive therapy
NASA Astrophysics Data System (ADS)
Hynynen, Kullervo; Jones, Ryan M.
2016-09-01
Focused ultrasound offers a non-invasive way of depositing acoustic energy deep into the body, which can be harnessed for a broad spectrum of therapeutic purposes, including tissue ablation, the targeting of therapeutic agents, and stem cell delivery. Phased array transducers enable electronic control over the beam geometry and direction, and can be tailored to provide optimal energy deposition patterns for a given therapeutic application. Their use in combination with modern medical imaging for therapy guidance allows precise targeting, online monitoring, and post-treatment evaluation of the ultrasound-mediated bioeffects. In the past there have been some technical obstacles hindering the construction of large aperture, high-power, densely-populated phased arrays and, as a result, they have not been fully exploited for therapy delivery to date. However, recent research has made the construction of such arrays feasible, and it is expected that their continued development will both greatly improve the safety and efficacy of existing ultrasound therapies as well as enable treatments that are not currently possible with existing technology. This review will summarize the basic principles, current statures, and future potential of image-guided ultrasound phased arrays for therapy.
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Image-guided ultrasound phased arrays are a disruptive technology for non-invasive therapy.
Hynynen, Kullervo; Jones, Ryan M
2016-09-07
Focused ultrasound offers a non-invasive way of depositing acoustic energy deep into the body, which can be harnessed for a broad spectrum of therapeutic purposes, including tissue ablation, the targeting of therapeutic agents, and stem cell delivery. Phased array transducers enable electronic control over the beam geometry and direction, and can be tailored to provide optimal energy deposition patterns for a given therapeutic application. Their use in combination with modern medical imaging for therapy guidance allows precise targeting, online monitoring, and post-treatment evaluation of the ultrasound-mediated bioeffects. In the past there have been some technical obstacles hindering the construction of large aperture, high-power, densely-populated phased arrays and, as a result, they have not been fully exploited for therapy delivery to date. However, recent research has made the construction of such arrays feasible, and it is expected that their continued development will both greatly improve the safety and efficacy of existing ultrasound therapies as well as enable treatments that are not currently possible with existing technology. This review will summarize the basic principles, current statures, and future potential of image-guided ultrasound phased arrays for therapy.
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Image-guided ultrasound phased arrays are a disruptive technology for non-invasive therapy
Hynynen, Kullervo; Jones, Ryan M.
2016-01-01
Focused ultrasound offers a non-invasive way of depositing acoustic energy deep into the body, which can be harnessed for a broad spectrum of therapeutic purposes, including tissue ablation, the targeting of therapeutic agents, and stem cell delivery. Phased array transducers enable electronic control over the beam geometry and direction, and can be tailored to provide optimal energy deposition patterns for a given therapeutic application. Their use in combination with modern medical imaging for therapy guidance allows precise targeting, online monitoring, and post-treatment evaluation of the ultrasound-mediated bioeffects. In the past there have been some technical obstacles hindering the construction of large aperture, high-power, densely-populated phased arrays and, as a result, they have not been fully exploited for therapy delivery to date. However, recent research has made the construction of such arrays feasible, and it is expected that their continued development will both greatly improve the safety and efficacy of existing ultrasound therapies as well as enable treatments that are not currently possible with existing technology. This review will summarize the basic principles, current statures, and future potential of image-guided ultrasound phased arrays for therapy. PMID:27494561
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Up-to-date approach to manage keloids and hypertrophic scars: A useful guide
Arno, Anna I.; Gauglitz, Gerd G.; Barret, Juan P.; Jeschke, Marc G.
2014-01-01
Keloids and hypertrophic scars occur anywhere from 30 to 90% of patients, and are characterized by pathologically excessive dermal fibrosis and aberrant wound healing. Both entities have different clinical and histochemical characteristics, and unfortunately still represent a great challenge for clinicians due to lack of efficacious treatments. Current advances in molecular biology and genetics reveal new preventive and therapeutical options which represent a hope to manage this highly prevalent, chronic and disabling problem, with long-term beneficial outcomes and improvement of quality of life. While we wait for these translational clinical products to be marketed, however, it is imperative to know the basics of the currently existing wide array of strategies to deal with excessive scars: from the classical corticotherapy, to the most recent botulinum toxin and lasers. The main aim of this review paper is to offer a useful up-to-date guideline to prevent and treat keloids and hypertrophic scars. PMID:24767715
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Causes of learning disability and epilepsy: a review.
Prince, Elizabeth; Ring, Howard
2011-04-01
Although the association between learning disability and epilepsy is well known, until relatively recently specific processes underlying this association were relatively poorly understood. However, scientific advances in molecular biology are starting to guide researchers towards descriptions of genetic and pathophysiological processes that may explain why syndromes of epilepsy and learning disability often co-exist. This article will focus largely on three areas of advancing knowledge: insights gained from wider use of genome-wide array comparative genomic hybridization (aCGH), specific insights gained from detailed study of Rett syndrome and the role of abnormalities of astrocytic function in predisposing to both epilepsy and learning disability. The enormous complexity of the biological underpinnings of the co-occurrence of epilepsy and learning disability are becoming apparent. In the future it is likely that research into therapeutic approaches will include, amongst other approaches, investigations of gene structure and expression, the role of astrocytes and the stability of dendritic spines.
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Visual short-term memory guides infants' visual attention.
Mitsven, Samantha G; Cantrell, Lisa M; Luck, Steven J; Oakes, Lisa M
2018-08-01
Adults' visual attention is guided by the contents of visual short-term memory (VSTM). Here we asked whether 10-month-old infants' (N = 41) visual attention is also guided by the information stored in VSTM. In two experiments, we modified the one-shot change detection task (Oakes, Baumgartner, Barrett, Messenger, & Luck, 2013) to create a simplified cued visual search task to ask how information stored in VSTM influences where infants look. A single sample item (e.g., a colored circle) was presented at fixation for 500 ms, followed by a brief (300 ms) retention interval and then a test array consisting of two items, one on each side of fixation. One item in the test array matched the sample stimulus and the other did not. Infants were more likely to look at the non-matching item than at the matching item, demonstrating that the information stored rapidly in VSTM guided subsequent looking behavior. Copyright © 2018 Elsevier B.V. All rights reserved.
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Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar).
Houston, Ross D; Taggart, John B; Cézard, Timothé; Bekaert, Michaël; Lowe, Natalie R; Downing, Alison; Talbot, Richard; Bishop, Stephen C; Archibald, Alan L; Bron, James E; Penman, David J; Davassi, Alessandro; Brew, Fiona; Tinch, Alan E; Gharbi, Karim; Hamilton, Alastair
2014-02-06
Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.
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The Contribution of Genetic Recombination to CRISPR Array Evolution
Kupczok, Anne; Landan, Giddy; Dagan, Tal
2015-01-01
CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA. Recognition sequences (spacers) encoded within the CRISPR array mediate the immune reaction in a sequence-specific manner. The known mechanisms for the evolution of CRISPR arrays include spacer acquisition from foreign DNA elements at the time of invasion and array erosion through spacer deletion. Here, we consider the contribution of genetic recombination between homologous CRISPR arrays to the evolution of spacer repertoire. Acquisition of spacers from exogenic arrays via recombination may confer the recipient with immunity against unencountered antagonists. For this purpose, we develop a novel method for the detection of recombination in CRISPR arrays by modeling the spacer order in arrays from multiple strains from the same species. Because the evolutionary signal of spacer recombination may be similar to that of pervasive spacer deletions or independent spacer acquisition, our method entails a robustness analysis of the recombination inference by a statistical comparison to resampled and perturbed data sets. We analyze CRISPR data sets from four bacterial species: two Gammaproteobacteria species harboring CRISPR type I and two Streptococcus species harboring CRISPR type II loci. We find that CRISPR array evolution in Escherichia coli and Streptococcus agalactiae can be explained solely by vertical inheritance and differential spacer deletion. In Pseudomonas aeruginosa, we find an excess of single spacers potentially incorporated into the CRISPR locus during independent acquisition events. In Streptococcus thermophilus, evidence for spacer acquisition by recombination is present in 5 out of 70 strains. Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages. However, for most species under study, we find that CRISPR evolution is shaped mainly by spacer acquisition and loss rather than recombination. Since the evolution of spacer content is characterized by a rapid turnover, it is likely that recombination is not beneficial for improving phage resistance in the strains under study, or that it cannot be detected in the resolution of intraspecies comparisons. PMID:26085541
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Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)
2014-01-01
Background Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array. Results SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex. Conclusions This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection. PMID:24524230
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Nayak, Spurthi N.; Varghese, Nicy; Shah, Trushar M.; Penmetsa, R. Varma; Thirunavukkarasu, Nepolean; Gudipati, Srivani; Gaur, Pooran M.; Kulwal, Pawan L.; Upadhyaya, Hari D.; KaviKishor, Polavarapu B.; Winter, Peter; Kahl, Günter; Town, Christopher D.; Kilian, Andrzej; Cook, Douglas R.; Varshney, Rajeev K.
2011-01-01
Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes. PMID:22102885
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Topic Outlines in Microbiology: An Instructor's Guide for Junior and Community Colleges.
ERIC Educational Resources Information Center
American Society for Microbiology, Washington, DC.
This resource guide presents subject matter organized in outline form for four topical areas: introductory microbiology; medical microbiology; microbial genetics; and microbial physiology. The first two units comprise the two most frequently taught microbiology courses in community and junior colleges. The outlines for microbial genetics and…
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Majewski, Stanislaw; Weisenberger, Andrew G.
2004-06-15
In a camera or similar radiation sensitive device comprising a pixilated scintillation layer, a light guide and an array of position sensitive photomultiplier tubes, wherein there exists so-called dead space between adjacent photomultiplier tubes the improvement comprising a two part light guide comprising a first planar light spreading layer or portion having a first surface that addresses the scintillation layer and optically coupled thereto at a second surface that addresses the photomultiplier tubes, a second layer or portion comprising an array of trapezoidal light collectors defining gaps that span said dead space and are individually optically coupled to individual position sensitive photomultiplier tubes. According to a preferred embodiment, coupling of the trapezoidal light collectors to the position sensitive photomultiplier tubes is accomplished using an optical grease having about the same refractive index as the material of construction of the two part light guide.
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A Beginner's Guide to BASIC Programming, Part 2.
ERIC Educational Resources Information Center
Hughes, Elizabeth
1982-01-01
Discusses a number of important structures which can be used in programming with BASIC, including loops, subroutines, and arrays. To illustrate these structures, a simple grade-averaging program is presented and explained. Commands introduced in Part 1 of the guide are listed in a table. (JL)
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Geraldes, Armando; Hannemann, Jan; Grassa, Chris
2013-01-01
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. Despite the declining costs of genotyping by sequencing, for most studies, the use of large SNP genotyping arrays still offers the most cost-effective solution for large-scale targeted genotyping. Here we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species range. Due to the rapid decay of linkage disequilibrium in P. trichocarpa we adopted a candidate gene approach to the arraymore » design that resulted in the selection of 34,131 SNPs, the majority of which are located in, or within 2 kb, of 3,543 candidate genes. A subset of the SNPs (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%, indicating that high-quality data are generated with this array. We demonstrate that even among small numbers of samples (n=10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that due to ascertainment bias the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca (P. balsamifera and P. angustifolia). Finally, we provide evidence for the utility of the array for intraspecific studies of genetic differentiation and for species assignment and the detection of natural hybrids.« less
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ERIC Educational Resources Information Center
Napoli, Eleonora; Russo, Serena; Casula, Laura; Alesi, Viola; Amendola, Filomena Alessandra; Angioni, Adriano; Novelli, Antonio; Valeri, Giovanni; Menghini, Deny; Vicari, Stefano
2018-01-01
Copy-number variants (CNVs) are associated with susceptibility to autism spectrum disorder (ASD). To detect the presence of CNVs, we conducted an array-comparative genomic hybridization (array-CGH) analysis in 133 children with "essential" ASD phenotype. Genetic analyses documented that 12 children had causative CNVs (C-CNVs), 29…
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NASA Astrophysics Data System (ADS)
Bostron, Jason
Ultrasonic guided waves are becoming more widely used in nondestructive evaluation applications due to their efficiency in defect detection, ability to inspect hidden areas, and other reasons. This dissertation addresses two main topics: ultrasonic guided wave bond evaluation of thin and thick coatings on thick metallic structures, and the use of a novel phased array technique for optimal guided wave mode and frequency selection. (Abstract shortened by UMI.).
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López Ruiz, J A; Zabalza Estévez, I; Mieza Arana, J A
2016-01-01
To evaluate the possibility of determining the genetic profile of primary malignant tumors of the breast from specimens obtained by ultrasound-guided percutaneous biopsies during the diagnostic imaging workup. This is a retrospective study in 13 consecutive patients diagnosed with invasive breast cancer by B-mode ultrasound-guided 12 G core needle biopsy. After clinical indication, the pathologist decided whether the paraffin block specimens seemed suitable (on the basis of tumor size, validity of the sample, and percentage of tumor cells) before sending them for genetic analysis with the MammaPrint® platform. The size of the tumors on ultrasound ranged from 0.6cm to 5cm. In 11 patients the preserved specimen was considered valid and suitable for use in determining the genetic profile. In 1 patient (with a 1cm tumor) the pathologist decided that it was necessary to repeat the core biopsy to obtain additional samples. In 1 patient (with a 5cm tumor) the specimen was not considered valid by the genetic laboratory. The percentage of tumor cells in the samples ranged from 60% to 70%. In 11/13 cases (84.62%) it was possible to do the genetic analysis on the previously diagnosed samples. In most cases, regardless of tumor size, it is possible to obtain the genetic profile from tissue specimens obtained with ultrasound-guided 12 G core biopsy preserved in paraffin blocks. Copyright © 2015 SERAM. Published by Elsevier España, S.L.U. All rights reserved.
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Making Sense of Your Genes: A Guide to Genetic Counseling
... to think about genetic counseling and perhaps genetic testing. A cancer genetic counselor will evaluate your family health history and talk about risks for inherited cancer, as well as screening and ...
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Focusing guided waves using surface bonded elastic metamaterials
NASA Astrophysics Data System (ADS)
Yan, Xiang; Zhu, Rui; Huang, Guoliang; Yuan, Fuh-Gwo
2013-09-01
Bonding a two-dimensional planar array of small lead discs on an aluminum plate with silicone rubber is shown numerically to focus low-frequency flexural guided waves. The "effective mass density profile" of this type of elastic metamaterials (EMMs), perpendicular to wave propagation direction, is carefully tailored and designed, which allows rays of flexural A0 mode Lamb waves to bend in succession and then focus through a 7 × 9 planar array. Numerical simulations show that Lamb waves can be focused beyond EMMs region with amplified displacement and yet largely retained narrow banded waveform, which may have potential application in structural health monitoring.
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Bourret, Vincent; Kent, Matthew P; Primmer, Craig R; Vasemägi, Anti; Karlsson, Sten; Hindar, Kjetil; McGinnity, Philip; Verspoor, Eric; Bernatchez, Louis; Lien, Sigbjørn
2013-02-01
Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this study, we describe the development of a medium-density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP array for conservation, management and aquaculture. © 2012 Blackwell Publishing Ltd.
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Roorkiwal, Manish; Jain, Ankit; Kale, Sandip M; Doddamani, Dadakhalandar; Chitikineni, Annapurna; Thudi, Mahendar; Varshney, Rajeev K
2018-04-01
To accelerate genomics research and molecular breeding applications in chickpea, a high-throughput SNP genotyping platform 'Axiom ® CicerSNP Array' has been designed, developed and validated. Screening of whole-genome resequencing data from 429 chickpea lines identified 4.9 million SNPs, from which a subset of 70 463 high-quality nonredundant SNPs was selected using different stringent filter criteria. This was further narrowed down to 61 174 SNPs based on p-convert score ≥0.3, of which 50 590 SNPs could be tiled on array. Among these tiled SNPs, a total of 11 245 SNPs (22.23%) were from the coding regions of 3673 different genes. The developed Axiom ® CicerSNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15 140 (29.93%; ICCRIL03) and 20 018 (39.57%; ICCRIL04) polymorphic SNPs. High-density genetic maps comprising 13 679 SNPs spanning 1033.67 cM and 7769 SNPs spanning 1076.35 cM were developed for ICCRIL03 and ICCRIL04 populations, respectively. QTL analysis using multilocation, multiseason phenotyping data on these RILs identified 70 (ICCRIL03) and 120 (ICCRIL04) main-effect QTLs on genetic map. Higher precision and potential of this array is expected to advance chickpea genetics and breeding applications. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
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Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing
Wiszniewska, Joanna; Bi, Weimin; Shaw, Chad; Stankiewicz, Pawel; Kang, Sung-Hae L; Pursley, Amber N; Lalani, Seema; Hixson, Patricia; Gambin, Tomasz; Tsai, Chun-hui; Bock, Hans-Georg; Descartes, Maria; Probst, Frank J; Scaglia, Fernando; Beaudet, Arthur L; Lupski, James R; Eng, Christine; Wai Cheung, Sau; Bacino, Carlos; Patel, Ankita
2014-01-01
In clinical diagnostics, both array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping have proven to be powerful genomic technologies utilized for the evaluation of developmental delay, multiple congenital anomalies, and neuropsychiatric disorders. Differences in the ability to resolve genomic changes between these arrays may constitute an implementation challenge for clinicians: which platform (SNP vs array CGH) might best detect the underlying genetic cause for the disease in the patient? While only SNP arrays enable the detection of copy number neutral regions of absence of heterozygosity (AOH), they have limited ability to detect single-exon copy number variants (CNVs) due to the distribution of SNPs across the genome. To provide comprehensive clinical testing for both CNVs and copy-neutral AOH, we enhanced our custom-designed high-resolution oligonucleotide array that has exon-targeted coverage of 1860 genes with 60 000 SNP probes, referred to as Chromosomal Microarray Analysis – Comprehensive (CMA-COMP). Of the 3240 cases evaluated by this array, clinically significant CNVs were detected in 445 cases including 21 cases with exonic events. In addition, 162 cases (5.0%) showed at least one AOH region >10 Mb. We demonstrate that even though this array has a lower density of SNP probes than other commercially available SNP arrays, it reliably detected AOH events >10 Mb as well as exonic CNVs beyond the detection limitations of SNP genotyping. Thus, combining SNP probes and exon-targeted array CGH into one platform provides clinically useful genetic screening in an efficient manner. PMID:23695279
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2007-07-01
been put into place to guide the standards process. 6. If the balloting results in 75% approval then the draft standard is sub- mitted to the IEEE-SA...as functionality and timeliness. Such a design process presumably guided the design for the AMRFC test bed. The multifunction apertures for...Integrated Topside should be guided by the same design process. Engaging in a spiral design process will lead to the most effective selection of research
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NASA Technical Reports Server (NTRS)
Butler, J. K.; Ettenberg, M.; Ackley, D. E.
1985-01-01
The lasing wavelengths and gain characteristics of the modes of phase-locked arrays of channel-substrate-planar (CSP) lasers are presented. The gain values for the array modes are determined from complex coupling coefficients calculated using the fields of neighboring elements of the array. The computations show that, for index guided lasers which have nearly planar phase fronts, the highest order array mode will be preferred. The 'in-phase' or fundamental mode, which produces only one major lobe in the far-field radiation pattern, has the lowest modal gain of all array modes. The modal gain differential between the highest order and fundamental modes is less than 10/cm for weak coupling between the elements.
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The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers.
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-Hohlfeld, Irene; Hicks, Belynda D; Ling, Hua; McGuffog, Lesley; Lee, Andrew; Kuchenbaecker, Karoline; Soucy, Penny; Manz, Judith; Cunningham, Julie M; Butterbach, Katja; Kote-Jarai, Zsofia; Kraft, Peter; FitzGerald, Liesel; Lindström, Sara; Adams, Marcia; McKay, James D; Phelan, Catherine M; Benlloch, Sara; Kelemen, Linda E; Brennan, Paul; Riggan, Marjorie; O'Mara, Tracy A; Shen, Hongbing; 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; Amin Al Olama, Ali; Peters, Ulrike; Eeles, Rosalind A; Seldin, Michael F; Gillanders, Elizabeth; Seminara, Daniela; Antoniou, Antonis C; Pharoah, Paul D P; Chenevix-Trench, Georgia; Chanock, Stephen J; Simard, Jacques; Easton, Douglas F
2017-01-01
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. 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. 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. 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. Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR. ©2016 American Association for Cancer Research.
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The OncoArray Consortium: a Network for Understanding the Genetic Architecture of Common Cancers
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
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Retterer, Kyle; Scuffins, Julie; Schmidt, Daniel; Lewis, Rachel; Pineda-Alvarez, Daniel; Stafford, Amanda; Schmidt, Lindsay; Warren, Stephanie; Gibellini, Federica; Kondakova, Anastasia; Blair, Amanda; Bale, Sherri; Matyakhina, Ludmila; Meck, Jeanne; Aradhya, Swaroop; Haverfield, Eden
2015-08-01
Detection of copy-number variation (CNV) is important for investigating many genetic disorders. Testing a large clinical cohort by array comparative genomic hybridization provides a deep perspective on the spectrum of pathogenic CNV. In this context, we describe a bioinformatics approach to extract CNV information from whole-exome sequencing and demonstrate its utility in clinical testing. Exon-focused arrays and whole-genome chromosomal microarray analysis were used to test 14,228 and 14,000 individuals, respectively. Based on these results, we developed an algorithm to detect deletions/duplications in whole-exome sequencing data and a novel whole-exome array. In the exon array cohort, we observed a positive detection rate of 2.4% (25 duplications, 318 deletions), of which 39% involved one or two exons. Chromosomal microarray analysis identified 3,345 CNVs affecting single genes (18%). We demonstrate that our whole-exome sequencing algorithm resolves CNVs of three or more exons. These results demonstrate the clinical utility of single-exon resolution in CNV assays. Our whole-exome sequencing algorithm approaches this resolution but is complemented by a whole-exome array to unambiguously identify intragenic CNVs and single-exon changes. These data illustrate the next advancements in CNV analysis through whole-exome sequencing and whole-exome array.Genet Med 17 8, 623-629.
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Guidugli, M C; Nazareno, A G; Feres, J M; Contel, E P B; Mestriner, M A; Alzate-Marin, A L
2016-01-01
Here, we explore the mating pattern and genetic structure of a tropical tree species, Cariniana estrellensis, in a small population in which progeny arrays (n=399), all adults (n=28) and all seedlings (n=39) were genotyped at nine highly informative microsatellite loci. From progeny arrays we were able to identify the source tree for at least 78% of pollination events. The gene immigration rates, mainly attributable to pollen, were high, varying from 23.5 to 53%. Although gene dispersal over long distance was observed, the effective gene dispersal distances within the small population were relatively short, with mean pollination distances varying from 69.9 to 146.9 m, and seed dispersal distances occurring up to a mean of 119.6 m. Mating system analyses showed that C. estrellensis is an allogamous species (tm=0.999), with both biparental inbreeding (tm−ts=−0.016) and selfing rates (s=0.001) that are not significantly different from zero. Even though the population is small, the presence of private alleles in both seedlings and progeny arrays and the elevated rates of gene immigration indicate that the C. estrellensis population is not genetically isolated. However, genetic diversity expressed by allelic richness was significantly lower in postfragmentation life stages. Although there was a loss of genetic diversity, indicating susceptibility of C. estrellensis to habitat fragmentation, no evidence of inbreeding or spatial genetic structure was observed across generations. Overall, C. estrellensis showed some resilience to negative genetic effects of habitat fragmentation, but conservation strategies are needed to preserve the remaining genetic diversity of this population. PMID:26732014
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USDA-ARS?s Scientific Manuscript database
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product qua...
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2000-08-30
An overhead crane in the Space Station Processing Facility lifts a solar array as workers stand by to help guide it. The solar array will be installed onto the Integrated Equipment Assembly (IEA). A component of the International Space Station, the solar array is the second one being installed on the IEA. The arrays are scheduled to be launched on mission STS-97 in late November along with the P6 truss. The Station’s electrical power system (EPS) will use eight photovoltaic solar arrays to convert sunlight to electricity. Each of the eight solar arrays will be 112 feet long by 39 feet wide. The solar arrays are mounted on a “blanket” that can be folded like an accordion for delivery. Once in orbit, astronauts will deploy the blankets to their full size. Gimbals will be used to rotate the arrays so that they will face the Sun to provide maximum power to the Space Station
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Automated tetraploid genotype calling by hierarchical clustering
USDA-ARS?s Scientific Manuscript database
SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, however, the relationship between signal intensity and allele dosage must be inferred independently for each marker. We developed an improved computational method to automate this process, ...
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2008-08-28
line array position of Woods Hole Oceanographic Institution (WHOI) during the SWARM experiment by 26 km, and southeast of the AMCOR borehole No. 6010...guided by the stratigraphic constraints provided by closely spaced 50 m chirp seismic reflection profiles that provide pseudo three-dimensional... array is at the center of set of stations at location M. c Geometry showing source position R/V KNORR with respect to the receiving array and the
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2000-08-30
In the Space Station Processing Facility, workers help guide a solar array into position for installation on the Integrated Equipment Assembly. Solar Array Wing-3 is already in place. Components of the International Space Station, the arrays are scheduled to be launched on mission STS-97 in late November along with the P6 truss. The Station’s electrical power system (EPS) will use eight photovoltaic solar arrays to convert sunlight to electricity. Each of the eight solar arrays will be 112 feet long by 39 feet wide. The solar arrays are mounted on a “blanket” that can be folded like an accordion for delivery. Once in orbit, astronauts will deploy the blankets to their full size. Gimbals will be used to rotate the arrays so that they will face the Sun to provide maximum power to the Space Station
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Montanari, Sara; Saeed, Munazza; Knäbel, Mareike; Kim, YoonKyeong; Troggio, Michela; Malnoy, Mickael; Velasco, Riccardo; Fontana, Paolo; Won, KyungHo; Durel, Charles-Eric; Perchepied, Laure; Schaffer, Robert; Wiedow, Claudia; Bus, Vincent; Brewer, Lester; Gardiner, Susan E; Crowhurst, Ross N; Chagné, David
2013-01-01
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.
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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.
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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. PMID:25303088
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The Contribution of Genetic Recombination to CRISPR Array Evolution.
Kupczok, Anne; Landan, Giddy; Dagan, Tal
2015-06-16
CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA. Recognition sequences (spacers) encoded within the CRISPR array mediate the immune reaction in a sequence-specific manner. The known mechanisms for the evolution of CRISPR arrays include spacer acquisition from foreign DNA elements at the time of invasion and array erosion through spacer deletion. Here, we consider the contribution of genetic recombination between homologous CRISPR arrays to the evolution of spacer repertoire. Acquisition of spacers from exogenic arrays via recombination may confer the recipient with immunity against unencountered antagonists. For this purpose, we develop a novel method for the detection of recombination in CRISPR arrays by modeling the spacer order in arrays from multiple strains from the same species. Because the evolutionary signal of spacer recombination may be similar to that of pervasive spacer deletions or independent spacer acquisition, our method entails a robustness analysis of the recombination inference by a statistical comparison to resampled and perturbed data sets. We analyze CRISPR data sets from four bacterial species: two Gammaproteobacteria species harboring CRISPR type I and two Streptococcus species harboring CRISPR type II loci. We find that CRISPR array evolution in Escherichia coli and Streptococcus agalactiae can be explained solely by vertical inheritance and differential spacer deletion. In Pseudomonas aeruginosa, we find an excess of single spacers potentially incorporated into the CRISPR locus during independent acquisition events. In Streptococcus thermophilus, evidence for spacer acquisition by recombination is present in 5 out of 70 strains. Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages. However, for most species under study, we find that CRISPR evolution is shaped mainly by spacer acquisition and loss rather than recombination. Since the evolution of spacer content is characterized by a rapid turnover, it is likely that recombination is not beneficial for improving phage resistance in the strains under study, or that it cannot be detected in the resolution of intraspecies comparisons. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Liu, Jingfei; Foiret, Josquin; Stephens, Douglas N.; Le Baron, Olivier; Ferrara, Katherine W.
2016-01-01
A 1.5 MHz prolate spheroidal therapeutic array with 128 circular elements was designed to accommodate standard imaging arrays for ultrasonic image-guided hyperthermia. The implementation of this dual-array system integrates real-time therapeutic and imaging functions with a single ultrasound system (Vantage 256, Verasonics). To facilitate applications involving small animal imaging and therapy the array was designed to have a beam depth of field smaller than 3.5 mm and to electronically steer over distances greater than 1 cm in both the axial and lateral directions. In order to achieve the required f number of 0.69, 1-3 piezocomposite modules were mated within the transducer housing. The performance of the prototype array was experimentally evaluated with excellent agreement with numerical simulation. A focal volume (2.70 mm (axial) × 0.65 mm (transverse) × 0.35 mm (transverse)) defined by the −6 dB focal intensity was obtained to address the dimensions needed for small animal therapy. An electronic beam steering range defined by the −3 dB focal peak intensity (17 mm (axial) × 14 mm (transverse) × 12 mm (transverse)) and −8 dB lateral grating lobes (24 mm (axial) × 18 mm (transverse) × 16 mm (transverse)) was achieved. The combined testing of imaging and therapeutic functions confirmed well-controlled local heating generation and imaging in a tissue mimicking phantom. This dual-array implementation offers a practical means to achieve hyperthermia and ablation in small animal models and can be incorporated within protocols for ultrasound-mediated drug delivery. PMID:27353347
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A sub-millimeter resolution PET detector module using a multi-pixel photon counter array
NASA Astrophysics Data System (ADS)
Song, Tae Yong; Wu, Heyu; Komarov, Sergey; Siegel, Stefan B.; Tai, Yuan-Chuan
2010-05-01
A PET block detector module using an array of sub-millimeter lutetium oxyorthosilicate (LSO) crystals read out by an array of surface-mount, semiconductor photosensors has been developed. The detector consists of a LSO array, a custom acrylic light guide, a 3 × 3 multi-pixel photon counter (MPPC) array (S10362-11-050P, Hamamatsu Photonics, Japan) and a readout board with a charge division resistor network. The LSO array consists of 100 crystals, each measuring 0.8 × 0.8 × 3 mm3 and arranged in 0.86 mm pitches. A Monte Carlo simulation was used to aid the design and fabrication of a custom light guide to control distribution of scintillation light over the surface of the MPPC array. The output signals of the nine MPPC are multiplexed by a charge division resistor network to generate four position-encoded analog outputs. Flood image, energy resolution and timing resolution measurements were performed using standard NIM electronics. The linearity of the detector response was investigated using gamma-ray sources of different energies. The 10 × 10 array of 0.8 mm LSO crystals was clearly resolved in the flood image. The average energy resolution and standard deviation were 20.0% full-width at half-maximum (FWHM) and ±5.0%, respectively, at 511 keV. The timing resolution of a single MPPC coupled to a LSO crystal was found to be 857 ps FWHM, and the value for the central region of detector module was 1182 ps FWHM when ±10% energy window was applied. The nonlinear response of a single MPPC when used to read out a single LSO was observed among the corner crystals of the proposed detector module. However, the central region of the detector module exhibits significantly less nonlinearity (6.5% for 511 keV). These results demonstrate that (1) a charge-sharing resistor network can effectively multiplex MPPC signals and reduce the number of output signals without significantly degrading the performance of a PET detector and (2) a custom light guide to permit light sharing among multiple MPPC and to diffuse and direct scintillation light can reduce the nonlinearity of the detector response within the limited dynamic range of a typical MPPC. As a result, the proposed PET detector module has the potential to be refined for use in high-resolution PET insert applications.
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A sub-millimeter resolution PET detector module using a multi-pixel photon counter array.
Song, Tae Yong; Wu, Heyu; Komarov, Sergey; Siegel, Stefan B; Tai, Yuan-Chuan
2010-05-07
A PET block detector module using an array of sub-millimeter lutetium oxyorthosilicate (LSO) crystals read out by an array of surface-mount, semiconductor photosensors has been developed. The detector consists of a LSO array, a custom acrylic light guide, a 3 x 3 multi-pixel photon counter (MPPC) array (S10362-11-050P, Hamamatsu Photonics, Japan) and a readout board with a charge division resistor network. The LSO array consists of 100 crystals, each measuring 0.8 x 0.8 x 3 mm(3) and arranged in 0.86 mm pitches. A Monte Carlo simulation was used to aid the design and fabrication of a custom light guide to control distribution of scintillation light over the surface of the MPPC array. The output signals of the nine MPPC are multiplexed by a charge division resistor network to generate four position-encoded analog outputs. Flood image, energy resolution and timing resolution measurements were performed using standard NIM electronics. The linearity of the detector response was investigated using gamma-ray sources of different energies. The 10 x 10 array of 0.8 mm LSO crystals was clearly resolved in the flood image. The average energy resolution and standard deviation were 20.0% full-width at half-maximum (FWHM) and +/-5.0%, respectively, at 511 keV. The timing resolution of a single MPPC coupled to a LSO crystal was found to be 857 ps FWHM, and the value for the central region of detector module was 1182 ps FWHM when +/-10% energy window was applied. The nonlinear response of a single MPPC when used to read out a single LSO was observed among the corner crystals of the proposed detector module. However, the central region of the detector module exhibits significantly less nonlinearity (6.5% for 511 keV). These results demonstrate that (1) a charge-sharing resistor network can effectively multiplex MPPC signals and reduce the number of output signals without significantly degrading the performance of a PET detector and (2) a custom light guide to permit light sharing among multiple MPPC and to diffuse and direct scintillation light can reduce the nonlinearity of the detector response within the limited dynamic range of a typical MPPC. As a result, the proposed PET detector module has the potential to be refined for use in high-resolution PET insert applications.
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A sub-millimeter resolution PET detector module using a multi-pixel photon counter array
Song, Tae Yong; Wu, Heyu; Komarov, Sergey; Siegel, Stefan B; Tai, Yuan-Chuan
2010-01-01
A PET block detector module using an array of sub-millimeter lutetium oxyorthosilicate (LSO) crystals read out by an array of surface-mount, semiconductor photosensors has been developed. The detector consists of a LSO array, a custom acrylic light guide, a 3 × 3 multi-pixel photon counter (MPPC) array (S10362-11-050P, Hamamatsu Photonics, Japan) and a readout board with a charge division resistor network. The LSO array consists of 100 crystals, each measuring 0.8 × 0.8 × 3 mm3 and arranged in 0.86 mm pitches. A Monte Carlo simulation was used to aid the design and fabrication of a custom light guide to control distribution of scintillation light over the surface of the MPPC array. The output signals of the nine MPPC are multiplexed by a charge division resistor network to generate four position-encoded analog outputs. Flood image, energy resolution and timing resolution measurements were performed using standard NIM electronics. The linearity of the detector response was investigated using gamma-ray sources of different energies. The 10 × 10 array of 0.8 mm LSO crystals was clearly resolved in the flood image. The average energy resolution and standard deviation were 20.0% full-width at half-maximum (FWHM) and ±5.0%, respectively, at 511 keV. The timing resolution of a single MPPC coupled to a LSO crystal was found to be 857 ps FWHM, and the value for the central region of detector module was 1182 ps FWHM when ±10% energy window was applied. The nonlinear response of a single MPPC when used to read out a single LSO was observed among the corner crystals of the proposed detector module. However, the central region of the detector module exhibits significantly less nonlinearity (6.5% for 511 keV). These results demonstrate that (1) a charge-sharing resistor network can effectively multiplex MPPC signals and reduce the number of output signals without significantly degrading the performance of a PET detector and (2) a custom light guide to permit light sharing among multiple MPPC and to diffuse and direct scintillation light can reduce the nonlinearity of the detector response within the limited dynamic range of a typical MPPC. As a result, the proposed PET detector module has the potential to be refined for use in high-resolution PET insert applications. PMID:20393236
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NASA Astrophysics Data System (ADS)
Qiu, Zhen; Habeshaw, Roderick; Fortine, Julien; Huang, Zhihong; Démoré, Christine; Cochran, Sandy
2012-11-01
Piezocrystal materials have been recognized as having better performance than piezoelectric ceramics, and have thus been widely adopted in ultrasound imaging arrays. Although their behaviour is susceptible to temperature and pressure, their large electromechanical coupling coefficients and other excellent piezoelectric properties also offer the potential for further improvements in the efficiency of therapeutic ultrasound transducers. Furthermore, new piezocrystals with modified compositions have been developed recently to increase their tolerance to temperature and pressure. In this work, a prototype of faceted bowl transducer was designed and manufactured as a proof of concept to explore practical issues associated with adoption of piezocrystals for magnetic resonance imaging guided focused ultrasound surgery.
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Phase-front measurements of an injection-locked AlGaAs laser-diode array
NASA Technical Reports Server (NTRS)
Cornwell, Donald M., Jr.; Rall, Jonathan A. R.; Abshire, James B.
1989-01-01
The phase-front quality of the primary spatial lobe emitted from an injection-locked gain-guided AlGaAs laser-diode array is measured by using an equal-path, phase-shifting Mach-Zehnder interferometer. Root-mean-square phase errors of 0.037 + or - 0.003 wave are measured for the single spatial lobe, which contained 240-mW cw output power in a single longitudinal mode. This phase-front quality corresponds to a Strehl ratio of S = 0.947, which results in a 0.23-dB power loss from the single lobe's ideal diffraction-limited power. These values are comparable with those measured for single-stripe index-guided AlGaAs lasers.
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Diversity Arrays Technology (DArT) for whole-genome profiling of barley
Wenzl, Peter; Carling, Jason; Kudrna, David; Jaccoud, Damian; Huttner, Eric; Kleinhofs, Andris; Kilian, Andrzej
2004-01-01
Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised ≈385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics. PMID:15192146
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Analysis of copy number variations among cattle breeds
USDA-ARS?s Scientific Manuscript database
Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in the modern domesticated cattle using array comparative genomic hybridization (array CGH) and quanti...
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Genetic variation in the USDA Chamaecrista fasciculata collection
USDA-ARS?s Scientific Manuscript database
Germplasm collections serve as critical repositories of genetic variation. Characterizing genetic diversity in existing collections is necessary to maximize their utility and to guide future collecting efforts. We have used AFLP markers to characterize genetic variation in the USDA germplasm collect...
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Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm.
Kwong, Qi Bin; Teh, Chee Keng; Ong, Ai Ling; Heng, Huey Ying; Lee, Heng Leng; Mohamed, Mohaimi; Low, Joel Zi-Bin; Apparow, Sukganah; Chew, Fook Tim; Mayes, Sean; Kulaveerasingam, Harikrishna; Tammi, Martti; Appleton, David Ross
2016-08-01
High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r(2) = 0.43 to 146 kb at r(2) = 0.50) when compared with the semi-wild populations (19.5 kb at r(2) = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.
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Hulse-Kemp, Amanda M.; Lemm, Jana; Plieske, Joerg; Ashrafi, Hamid; Buyyarapu, Ramesh; Fang, David D.; Frelichowski, James; Giband, Marc; Hague, Steve; Hinze, Lori L.; Kochan, Kelli J.; Riggs, Penny K.; Scheffler, Jodi A.; Udall, Joshua A.; Ulloa, Mauricio; Wang, Shirley S.; Zhu, Qian-Hao; Bag, Sumit K.; Bhardwaj, Archana; Burke, John J.; Byers, Robert L.; Claverie, Michel; Gore, Michael A.; Harker, David B.; Islam, Md S.; Jenkins, Johnie N.; Jones, Don C.; Lacape, Jean-Marc; Llewellyn, Danny J.; Percy, Richard G.; Pepper, Alan E.; Poland, Jesse A.; Mohan Rai, Krishan; Sawant, Samir V.; Singh, Sunil Kumar; Spriggs, Andrew; Taylor, Jen M.; Wang, Fei; Yourstone, Scott M.; Zheng, Xiuting; Lawley, Cindy T.; Ganal, Martin W.; Van Deynze, Allen; Wilson, Iain W.; Stelly, David M.
2015-01-01
High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community. PMID:25908569
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Zubair, Niha; Graff, Mariaelisa; Luis Ambite, Jose; Bush, William S; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H; Absher, Devin; Assimes, Themistocles L; Bielinski, Suzette J; Bottinger, Erwin P; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H; Martin, Lisa W; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P; Robinson, Jennifer; Rotter, Jerome I; Ryckman, Kelli K; Schreiner, Pamela J; Stahl, Eli; Tao, Ran; Tsai, Michael Y; Waite, Lindsay L; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C; Loos, Ruth J F; Rich, Stephen S; Fornage, Myriam; North, Kari E; Kooperberg, Charles; Carty, Cara L
2016-12-15
Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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The therapeutic application of CRISPR/Cas9 technologies for HIV
Saayman, Sheena; Ali, Stuart A.; Morris, Kevin V.; Weinberg, Marc S.
2015-01-01
Introduction The use of antiretroviral therapy (ART) has led to a significant decrease in morbidity and mortality in HIV-infected individuals. Nevertheless gene-based therapies represent a promising therapeutic paradigm for HIV-1, as they have the potential for sustained viral inhibition and reduced treatment interventions. One new method amendable to a gene-based therapy is the clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 gene editing system. Areas covered CRISPR/Cas9 can be engineered to successfully modulate an array of disease-causing genetic elements. We discuss the diverse roles that CRISPR/Cas9 may play in targeting HIV and eradicating infection. The Cas9 nuclease coupled with one or more small guide RNAs (sgRNAs) can target the provirus to mediate excision of the integrated viral genome. Moreover, a modified nuclease deficient Cas9 fused to transcription activating domains may induce targeted activation of proviral gene expression allowing for the purging of the latent reservoirs. These technologies can also be exploited to target host dependency factors such as the co-receptor CCR5, thus preventing cellular entry of the virus. Expert opinion The diversity of the CRISPR/Cas9 technologies hold great promise for targeting different stages of the viral life cycle, and have the capacity for mediating an effective and sustained genetic therapy against HIV. PMID:25865334
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Similar Tensor Arrays - A Framework for Storage of Tensor Array Data
NASA Astrophysics Data System (ADS)
Brun, Anders; Martin-Fernandez, Marcos; Acar, Burak; Munoz-Moreno, Emma; Cammoun, Leila; Sigfridsson, Andreas; Sosa-Cabrera, Dario; Svensson, Björn; Herberthson, Magnus; Knutsson, Hans
This chapter describes a framework for storage of tensor array data, useful to describe regularly sampled tensor fields. The main component of the framework, called Similar Tensor Array Core (STAC), is the result of a collaboration between research groups within the SIMILAR network of excellence. It aims to capture the essence of regularly sampled tensor fields using a minimal set of attributes and can therefore be used as a “greatest common divisor” and interface between tensor array processing algorithms. This is potentially useful in applied fields like medical image analysis, in particular in Diffusion Tensor MRI, where misinterpretation of tensor array data is a common source of errors. By promoting a strictly geometric perspective on tensor arrays, with a close resemblance to the terminology used in differential geometry, (STAC) removes ambiguities and guides the user to define all necessary information. In contrast to existing tensor array file formats, it is minimalistic and based on an intrinsic and geometric interpretation of the array itself, without references to other coordinate systems.
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Pharmacogenetics in clinical practice: how far have we come and where are we going?
Johnson, Julie A
2013-01-01
Recent years have seen great advances in our understanding of genetic contributors to drug response. Drug discovery and development around targeted genetic (somatic) mutations has led to a number of new drugs with genetic indications, particularly for the treatment of cancers. Our knowledge of genetic contributors to variable drug response for existing drugs has also expanded dramatically, such that the evidence now supports clinical use of genetic data to guide treatment in some situations, and across a variety of therapeutic areas. Clinical implementation of pharmacogenetics has seen substantial growth in recent years and groups are working to identify the barriers and best practices for pharmacogenetic-guided treatment. The advances and challenges in these areas are described and predictions about future use of genetics in drug therapy are discussed. PMID:23651030
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Analysis of copy number variations reveals differences among cattle breeds
USDA-ARS?s Scientific Manuscript database
Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in the modern domesticated cattle using array comparative genomic hybridization (array CGH) and quanti...
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NORMAL NASAL GENE EXPRESSION LEVELS USING CDNA ARRAY TECHNOLOGY
Normal Nasal Gene Expression Levels Using cDNA Array Technology.
The nasal epithelium is a target site for chemically-induced toxicity and carcinogenicity. To detect and analyze genetic events which contribute to nasal tumor development, we first defined the gene expressi... -
[Genetic analysis of two cases with Dandy-Walker deformed fetus].
Yao, Juan; Fang, Rong; Shen, Xueping; Shen, Guosong; Zhang, Su
2017-10-10
To explore the genetic etiology of two fetuses with Dandy-Walker malformation using single nucleotide polymorphism microarray (SNP-array). The fetuses and their parents were subjected to G banding karyotype analysis. The fetuses were also subjected to SNP-array analysis. The parents of both fetuses showed a normal karyotype. One fetus has a 46,X,?i(X)(q10), while for another conventional cell culture has failed. SNP-array showed that one fetus carried a 6p25.3p25.2 microdeletion, and another carried a Xp22.33p22.2 deletion and a Yq11.221q11 duplication. The abnormal fragments have involved FOXC1, SHOX and STS genes, which are associated with Dandy-Walker malformation. Alteration of 6p25.3p25.2, Xp22.33p22.2 copy numbers probably underlies the Dandy-Walker syndrome in the fetuses. The disorder may be attributed to abnormal expression of FOXC1, SHOX, and STS genes. SNP-array can provide an important supplement for prenatal diagnosis.
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NASA Astrophysics Data System (ADS)
Holland, Stephen D.; Song, Jun-Ho; Chimenti, D. E.; Roberts, Ron
2006-03-01
We demonstrate an array sensor method intended to locate leaks in manned spacecraft using leak-generated, structure-borne ultrasonic noise. We have developed and tested a method for sensing and processing leak noise to reveal the leak location involving the use of a 64-element phased-array. Cross-correlations of ultrasonic noise waveforms from a leak into vacuum have been used with a phased-array analysis to find the direction from the sensor to the leak. This method measures the propagation of guided ultrasonic Lamb waves passing under the PZT array sensor in the spacecraft skin structure. This paper will describe the custom-designed array with integrated electronics, as well as the performance of the array in prototype applications. We show that this method can be used to successfully locate leaks to within a few millimeters on a 0.6-m square aluminum plate.
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2000-08-30
Workers in the Space Station Processing Facility help guide an overhead crane toward a workstand containing a solar array in order to move it for installation onto the Integrated Equipment Assembly (IEA). A component of the International Space Station, the solar array is the second one being installed on the IEA. The arrays are scheduled to be launched on mission STS-97 in late November along with the P6 truss. The Station’s electrical power system (EPS) will use eight photovoltaic solar arrays to convert sunlight to electricity. Each of the eight solar arrays will be 112 feet long by 39 feet wide. The solar arrays are mounted on a “blanket” that can be folded like an accordion for delivery. Once in orbit, astronauts will deploy the blankets to their full size. Gimbals will be used to rotate the arrays so that they will face the Sun to provide maximum power to the Space Station
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Light Trapping with Silicon Light Funnel Arrays
Nissan, Yuval; Gabay, Tamir; Shalev, Gil
2018-01-01
Silicon light funnels are three-dimensional subwavelength structures in the shape of inverted cones with respect to the incoming illumination. Light funnel (LF) arrays can serve as efficient absorbing layers on account of their light trapping capabilities, which are associated with the presence of high-density complex Mie modes. Specifically, light funnel arrays exhibit broadband absorption enhancement of the solar spectrum. In the current study, we numerically explore the optical coupling between surface light funnel arrays and the underlying substrates. We show that the absorption in the LF array-substrate complex is higher than the absorption in LF arrays of the same height (~10% increase). This, we suggest, implies that a LF array serves as an efficient surface element that imparts additional momentum components to the impinging illumination, and hence optically excites the substrate by near-field light concentration, excitation of traveling guided modes in the substrate, and mode hybridization. PMID:29562685
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Minalga, E.; Payne, A.; Merrill, R.; Todd, N.; Vijayakumar, S.; Kholmovski, E.; Parker, D. L.; Hadley, J. R.
2012-01-01
In this study, a radio-frequency (RF) phased array coil was built to image the breast in conjunction with a Magnetic Resonance guided High Intensity Focused Ultrasound (MRgHIFU) device designed specifically to treat the breast in a treatment cylinder with reduced water volume. The MRgHIFU breast coil was comprised of a 10-channel phased array coil placed around an MRgHIFU treatment cylinder where nearest-neighbor decoupling was achieved with capacitive decoupling in a shared leg. In addition a single loop coil was placed at the chest wall making a total of 11-channels. The RF coil array design presented in this work was chosen based on ease of implementation, increased visualization into the treatment cylinder, image reconstruction speed, temporal resolution, and resulting signal-to-noise-ratio (SNR) profiles. This work presents a dedicated 11-channel coil for imaging of the breast tissue in the MRgHIFU setup without obstruction of the ultrasound beam and, specifically, compares its performance in SNR, overall imaging time, and temperature measurement accuracy to that of the standard single chest-loop coil typically used in breast MRgHIFU. PMID:22431301
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Lugo-Martinez, Jose; Pejaver, Vikas; Pagel, Kymberleigh A.; Mort, Matthew; Cooper, David N.; Mooney, Sean D.; Radivojac, Predrag
2016-01-01
Elucidating the precise molecular events altered by disease-causing genetic variants represents a major challenge in translational bioinformatics. To this end, many studies have investigated the structural and functional impact of amino acid substitutions. Most of these studies were however limited in scope to either individual molecular functions or were concerned with functional effects (e.g. deleterious vs. neutral) without specifically considering possible molecular alterations. The recent growth of structural, molecular and genetic data presents an opportunity for more comprehensive studies to consider the structural environment of a residue of interest, to hypothesize specific molecular effects of sequence variants and to statistically associate these effects with genetic disease. In this study, we analyzed data sets of disease-causing and putatively neutral human variants mapped to protein 3D structures as part of a systematic study of the loss and gain of various types of functional attribute potentially underlying pathogenic molecular alterations. We first propose a formal model to assess probabilistically function-impacting variants. We then develop an array of structure-based functional residue predictors, evaluate their performance, and use them to quantify the impact of disease-causing amino acid substitutions on catalytic activity, metal binding, macromolecular binding, ligand binding, allosteric regulation and post-translational modifications. We show that our methodology generates actionable biological hypotheses for up to 41% of disease-causing genetic variants mapped to protein structures suggesting that it can be reliably used to guide experimental validation. Our results suggest that a significant fraction of disease-causing human variants mapping to protein structures are function-altering both in the presence and absence of stability disruption. PMID:27564311
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Lugo-Martinez, Jose; Pejaver, Vikas; Pagel, Kymberleigh A; Jain, Shantanu; Mort, Matthew; Cooper, David N; Mooney, Sean D; Radivojac, Predrag
2016-08-01
Elucidating the precise molecular events altered by disease-causing genetic variants represents a major challenge in translational bioinformatics. To this end, many studies have investigated the structural and functional impact of amino acid substitutions. Most of these studies were however limited in scope to either individual molecular functions or were concerned with functional effects (e.g. deleterious vs. neutral) without specifically considering possible molecular alterations. The recent growth of structural, molecular and genetic data presents an opportunity for more comprehensive studies to consider the structural environment of a residue of interest, to hypothesize specific molecular effects of sequence variants and to statistically associate these effects with genetic disease. In this study, we analyzed data sets of disease-causing and putatively neutral human variants mapped to protein 3D structures as part of a systematic study of the loss and gain of various types of functional attribute potentially underlying pathogenic molecular alterations. We first propose a formal model to assess probabilistically function-impacting variants. We then develop an array of structure-based functional residue predictors, evaluate their performance, and use them to quantify the impact of disease-causing amino acid substitutions on catalytic activity, metal binding, macromolecular binding, ligand binding, allosteric regulation and post-translational modifications. We show that our methodology generates actionable biological hypotheses for up to 41% of disease-causing genetic variants mapped to protein structures suggesting that it can be reliably used to guide experimental validation. Our results suggest that a significant fraction of disease-causing human variants mapping to protein structures are function-altering both in the presence and absence of stability disruption.
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Resources on Law-Related Education: Documents and Journal Articles in ERIC. Yearbook No. 3.
ERIC Educational Resources Information Center
Healy, Langdon T., Ed.; Vontz, Thomas S., Ed.
This ERIC resource is a guide to the array of law-related education (LRE) resources available to teachers. The annotated bibliography offers resources for essential knowledge of the law, innovative teaching methods, and guides to national LRE programs. Included in this collection are abstracts of LRE documents and journal articles, arranged…
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NASA Astrophysics Data System (ADS)
Kamanin, D. V.; Alexandrov, A. A.; Alexandrova, I. A.; Kondtatyev, N. A.; Kuznetsova, E. A.; Shvetsov, V. N.; Strekalovsky, A. O.; Strekalovsky, O. V.; Zhuchko, V. E.; Pyatkov, Yu. V.; Jacobs, N.; Malaza, V.
2015-06-01
Motivation and status of the VEGA (Velocity-Energy Guide based Array) project is presented. One armed fission fragments spectrometer with an electrostatic guide system is proposed for installation at the vertical experimental channel of the IBR-2 reactor. Scientific program aimed at investigation of new multi-body decays of actinides, shapeisomeric states in fission fragments and fission modes is reported.
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MR-guided noninvasive thermal coagulation of in-vivo liver tissue using ultrasonic phased array
NASA Astrophysics Data System (ADS)
Daum, Douglas R.; Smith, Nadine; McDannold, Nathan; Hynynen, Kullervo H.
1999-05-01
Magnetic resonance (MR) imaging was used to guide and monitor the thermal tissue coagulation of in vivo porcine tissue using a 256 element ultrasonic phased array. The array could coagulate tissue volumes greater than 2 cm3 in liver and 0.5 cm3 in kidney using a single 20 second sonication. This sonication used multiple focus fields which were temporally cycled to heat large tissue volumes simultaneously. Estimates of the coagulated tissue using a thermal dose threshold compare well with T2-weighted images of post sonication lesions. The overlapping large focal volumes could aid in the treatment of large tumor volumes which require multiple overlapping sonications. The ability of MR to detect the presence and undesirable thermal increases at acoustic obstacle such as cartilaginous and bony ribs is demonstrated. This could have a significant impact on the ability to monitor thermal treatments of the liver and other organs which are acoustically blocked.
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Kay, Neil E.; Eckel-Passow, Jeanette E.; Braggio, Esteban; VanWier, Scott; Shanafelt, Tait D.; Van Dyke, Daniel L.; Jelinek, Diane F.; Tschumper, Renee C.; Kipps, Thomas; Byrd, John C.; Fonseca, Rafael
2010-01-01
To better understand the implications of genomic instability and outcome in B-cell CLL, we sought to address genomic complexity as a predictor of chemosensitivity and ultimately clinical outcome in this disease. We employed array-based comparative genomic hybridization (aCGH), using a one-million probe array and identified gains and losses of genetic material in 48 patients treated on a chemoimmunotherapy (CIT) clinical trial. We identified chromosomal gain or loss in ≥6% of the patients on chromosomes 3, 8, 9, 10, 11, 12, 13, 14 and 17. Higher genomic complexity, as a mechanism favoring clonal selection, was associated with shorter progression-free survival and predicted a poor response to treatment. Of interest, CLL cases with loss of p53 surveillance showed more complex genomic features and were found both in patients with a 17p13.1 deletion and in the more favorable genetic subtype characterized by the presence of 13q14.1 deletion. This aCGH study adds information on the association between inferior trial response and increasing genetic complexity as CLL progresses. PMID:21156228
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Ellis, David; Chavez, Oswaldo; Coombs, Joseph J; Soto, Julian V; Gomez, Rene; Douches, David S; Panta, Ana; Silvestre, Rocio; Anglin, Noelle Lynette
2018-05-24
Breeders rely on genetic integrity of material from genebanks, however, mislabeling and errors in original data can occur. Paired samples of original material and their in vitro counterparts from 250 diverse potato landrace accessions from the International Potato Center (CIP), were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity and evaluate genetic diversity. Diploid, triploid, and tetraploid accessions were included representing seven cultivated potato taxa (Hawkes, 1990). Fingerprints between mother field plants and in vitro clones, were used to evaluate identity, relatedness, and ancestry. Clones of the same accession grouped together, however eleven (4.4%) accessions were mismatches genetically. SNP genotypes were used to construct a phylogeny to evaluate inter- and intraspecific relationships and population structure. Data suggests that the triploids evaluated are genetically similar. STRUCTURE analysis identified several putative hybrids and suggests six populations with significant gene flow between. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality and confirmed identity is critical for breeders and other users of these collections, as well as for quality management programs and to provide insights into the diversity of the accessions evaluated.
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Recruitment of CRISPR-Cas systems by Tn7-like transposons.
Peters, Joseph E; Makarova, Kira S; Shmakov, Sergey; Koonin, Eugene V
2017-08-29
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f , cas7f , and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference. Phylogenetic analysis demonstrates that evolution of the CRISPR-Cas-containing transposons included a single, ancestral capture of a type I-F locus and two independent instances of type I-B loci capture. We show that the transposon-associated CRISPR arrays contain spacers homologous to plasmid and temperate phage sequences and, in some cases, chromosomal sequences adjacent to the transposon. We hypothesize that the transposon-encoded CRISPR-Cas systems generate displacement (R-loops) in the cognate DNA sites, targeting the transposon to these sites and thus facilitating their spread via plasmids and phages. These findings suggest the existence of RNA-guided transposition and fit the guns-for-hire concept whereby mobile genetic elements capture host defense systems and repurpose them for different stages in the life cycle of the element.
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Nanostructured optical fibre arrays for high-density biochemical sensing and remote imaging.
Deiss, F; Sojic, N; White, D J; Stoddart, P R
2010-01-01
Optical fibre bundles usually comprise a few thousand to tens of thousands of individually clad glass optical fibres. The ordered arrangement of the fibres enables coherent transmission of an image through the bundle and therefore enables analysis and viewing in remote locations. In fused bundles, this architecture has also been used to fabricate arrays of various micro to nano-scale surface structures (micro/nanowells, nanotips, triangles, etc.) over relatively large areas. These surface structures have been used to obtain new optical and analytical capabilities. Indeed, the imaging bundle can be thought of as a "starting material" that can be sculpted by a combination of fibre drawing and selective wet-chemical etching processes. A large variety of bioanalytical applications have thus been developed, ranging from nano-optics to DNA nanoarrays. For instance, nanostructured optical surfaces with intrinsic light-guiding properties have been exploited as surface-enhanced Raman scattering (SERS) platforms and as near-field probe arrays. They have also been productively associated with electrochemistry to fabricate arrays of transparent nanoelectrodes with electrochemiluminescent imaging properties. The confined geometry of the wells has been loaded with biosensing materials and used as femtolitre-sized vessels to detect single molecules. This review describes the fabrication of high-density nanostructured optical fibre arrays and summarizes the large range of optical and bioanalytical applications that have been developed, reflecting the versatility of this ordered light-guiding platform.
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Implementation of inpatient models of pharmacogenetics programs
Cavallari, Larisa H.; Lee, Craig R.; Duarte, Julio D.; Nutescu, Edith A.; Weitzel, Kristin W.; Stouffer, George A.; Johnson, Julie A.
2017-01-01
Purpose The operational elements essential for establishing an inpatient pharmacogenetic service are reviewed, and the role of the pharmacist in the provision of genotype-guided drug therapy in pharmacogenetics programs at three institutions is highlighted. Summary Pharmacists are well positioned to assume important roles in facilitating the clinical use of genetic information to optimize drug therapy given their expertise in clinical pharmacology and therapeutics. Pharmacists have assumed important roles in implementing inpatient pharmacogenetics programs. This includes programs designed to incorporate genetic test results to optimize antiplatelet drug selection after percutaneous coronary intervention and personalize warfarin dosing. Pharmacist involvement occurs on many levels, including championing and leading pharmacogenetics implementation efforts, establishing clinical processes to support genotype-guided therapy, assisting the clinical staff with interpreting genetic test results and applying them to prescribing decisions, and educating other healthcare providers and patients on genomic medicine. The three inpatient pharmacogenetics programs described use reactive versus preemptive genotyping, the most feasible approach under the current third-party payment structure. All three sites also follow Clinical Pharmacogenetics Implementation Consortium guidelines for drug therapy recommendations based on genetic test results. Conclusion With the clinical emergence of pharmacogenetics into the inpatient setting, it is important that pharmacists caring for hospitalized patients are well prepared to serve as experts in interpreting and applying genetic test results to guide drug therapy decisions. Since genetic test results may not be available until after patient discharge, pharmacists practicing in the ambulatory care setting should also be prepared to assist with genotype-guided drug therapy as part of transitions in care. PMID:27864202
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Implementation of inpatient models of pharmacogenetics programs.
Cavallari, Larisa H; Lee, Craig R; Duarte, Julio D; Nutescu, Edith A; Weitzel, Kristin W; Stouffer, George A; Johnson, Julie A
2016-12-01
The operational elements essential for establishing an inpatient pharmacogenetic service are reviewed, and the role of the pharmacist in the provision of genotype-guided drug therapy in pharmacogenetics programs at three institutions is highlighted. Pharmacists are well positioned to assume important roles in facilitating the clinical use of genetic information to optimize drug therapy given their expertise in clinical pharmacology and therapeutics. Pharmacists have assumed important roles in implementing inpatient pharmacogenetics programs. This includes programs designed to incorporate genetic test results to optimize antiplatelet drug selection after percutaneous coronary intervention and personalize warfarin dosing. Pharmacist involvement occurs on many levels, including championing and leading pharmacogenetics implementation efforts, establishing clinical processes to support genotype-guided therapy, assisting the clinical staff with interpreting genetic test results and applying them to prescribing decisions, and educating other healthcare providers and patients on genomic medicine. The three inpatient pharmacogenetics programs described use reactive versus preemptive genotyping, the most feasible approach under the current third-party payment structure. All three sites also follow Clinical Pharmacogenetics Implementation Consortium guidelines for drug therapy recommendations based on genetic test results. With the clinical emergence of pharmacogenetics into the inpatient setting, it is important that pharmacists caring for hospitalized patients are well prepared to serve as experts in interpreting and applying genetic test results to guide drug therapy decisions. Since genetic test results may not be available until after patient discharge, pharmacists practicing in the ambulatory care setting should also be prepared to assist with genotype-guided drug therapy as part of transitions in care. Copyright © 2016 by the American Society of Health-System Pharmacists, Inc. All rights reserved.
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Large-area, laterally-grown epitaxial semiconductor layers
Han, Jung; Song, Jie; Chen, Danti
2017-07-18
Structures and methods for confined lateral-guided growth of a large-area semiconductor layer on an insulating layer are described. The semiconductor layer may be formed by heteroepitaxial growth from a selective growth area in a vertically-confined, lateral-growth guiding structure. Lateral-growth guiding structures may be formed in arrays over a region of a substrate, so as to cover a majority of the substrate region with laterally-grown epitaxial semiconductor tiles. Quality regions of low-defect, stress-free GaN may be grown on silicon.
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Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds.
Dash, S; Singh, A; Bhatia, A K; Jayakumar, S; Sharma, A; Singh, S; Ganguly, I; Dixit, S P
2018-04-03
In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0.007, and 0.242 ± 0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold's genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r 2 < 0.2) at 140 kb inter-marker distance and, hence, a 20K low density customized SNP array from HD chip could be designed for genomic selection in these cattle else the 54K Bead Chip as such will be useful.
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Bassil, Nahla V; Davis, Thomas M; Zhang, Hailong; Ficklin, Stephen; Mittmann, Mike; Webster, Teresa; Mahoney, Lise; Wood, David; Alperin, Elisabeth S; Rosyara, Umesh R; Koehorst-Vanc Putten, Herma; Monfort, Amparo; Sargent, Daniel J; Amaya, Iraida; Denoyes, Beatrice; Bianco, Luca; van Dijk, Thijs; Pirani, Ali; Iezzoni, Amy; Main, Dorrie; Peace, Cameron; Yang, Yilong; Whitaker, Vance; Verma, Sujeet; Bellon, Laurent; Brew, Fiona; Herrera, Raul; van de Weg, Eric
2015-03-07
A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
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Three Women Scientists and Their Role in the History of Genetics.
ERIC Educational Resources Information Center
Venville, Grady; Milne, Catherine
1999-01-01
Draws on an array of historical documents to delve into the history of genetics and the lives and scientific accomplishments of female geneticists that include Nettie Stevens, Rosalind Franklin, and Barbara McClintock. (Contains 20 references.) (Author/WRM)
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Troggio, Michela; Malnoy, Mickael; Velasco, Riccardo; Fontana, Paolo; Won, KyungHo; Durel, Charles-Eric; Perchepied, Laure; Schaffer, Robert; Wiedow, Claudia; Bus, Vincent; Brewer, Lester; Gardiner, Susan E.; Crowhurst, Ross N.; Chagné, David
2013-01-01
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear (‘Old Home’בLouise Bon Jersey’) and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality. PMID:24155917
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Amrhein, P; Sittel, C; Spaich, C; Kohlhase, J; Boppert, R; Kohlhof, P; Koitschev, A
2014-05-01
Branchio-oto-renal (BOR) syndrome is characterized by ear malformations associated with sensorineural or mixed hearing loss. In addition, preauricular tags, preauricular pits, branchial cleft fistulas and cysts, as well as renal dysplasia are seen. A genetic mutation on chromosome 8, either autosomal dominantly inherited or occuring as a spontaneous mutation, is the cause in the majority of cases. Using array-based comparative genomic hybridization (CGH), it is possible to detect even the smallest genetic changes. Salivary gland choristoma in the middle ear is very rare. Surgical removal and histological clarification are required.
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NASA Astrophysics Data System (ADS)
Liu, Jingfei; Foiret, Josquin; Stephens, Douglas N.; Le Baron, Olivier; Ferrara, Katherine W.
2016-07-01
A 1.5 MHz prolate spheroidal therapeutic array with 128 circular elements was designed to accommodate standard imaging arrays for ultrasonic image-guided hyperthermia. The implementation of this dual-array system integrates real-time therapeutic and imaging functions with a single ultrasound system (Vantage 256, Verasonics). To facilitate applications involving small animal imaging and therapy the array was designed to have a beam depth of field smaller than 3.5 mm and to electronically steer over distances greater than 1 cm in both the axial and lateral directions. In order to achieve the required f number of 0.69, 1-3 piezocomposite modules were mated within the transducer housing. The performance of the prototype array was experimentally evaluated with excellent agreement with numerical simulation. A focal volume (2.70 mm (axial) × 0.65 mm (transverse) × 0.35 mm (transverse)) defined by the -6 dB focal intensity was obtained to address the dimensions needed for small animal therapy. An electronic beam steering range defined by the -3 dB focal peak intensity (17 mm (axial) × 14 mm (transverse) × 12 mm (transverse)) and -8 dB lateral grating lobes (24 mm (axial) × 18 mm (transverse) × 16 mm (transverse)) was achieved. The combined testing of imaging and therapeutic functions confirmed well-controlled local heating generation and imaging in a tissue mimicking phantom. This dual-array implementation offers a practical means to achieve hyperthermia and ablation in small animal models and can be incorporated within protocols for ultrasound-mediated drug delivery.
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Liu, Jingfei; Foiret, Josquin; Stephens, Douglas N; Le Baron, Olivier; Ferrara, Katherine W
2016-07-21
A 1.5 MHz prolate spheroidal therapeutic array with 128 circular elements was designed to accommodate standard imaging arrays for ultrasonic image-guided hyperthermia. The implementation of this dual-array system integrates real-time therapeutic and imaging functions with a single ultrasound system (Vantage 256, Verasonics). To facilitate applications involving small animal imaging and therapy the array was designed to have a beam depth of field smaller than 3.5 mm and to electronically steer over distances greater than 1 cm in both the axial and lateral directions. In order to achieve the required f number of 0.69, 1-3 piezocomposite modules were mated within the transducer housing. The performance of the prototype array was experimentally evaluated with excellent agreement with numerical simulation. A focal volume (2.70 mm (axial) × 0.65 mm (transverse) × 0.35 mm (transverse)) defined by the -6 dB focal intensity was obtained to address the dimensions needed for small animal therapy. An electronic beam steering range defined by the -3 dB focal peak intensity (17 mm (axial) × 14 mm (transverse) × 12 mm (transverse)) and -8 dB lateral grating lobes (24 mm (axial) × 18 mm (transverse) × 16 mm (transverse)) was achieved. The combined testing of imaging and therapeutic functions confirmed well-controlled local heating generation and imaging in a tissue mimicking phantom. This dual-array implementation offers a practical means to achieve hyperthermia and ablation in small animal models and can be incorporated within protocols for ultrasound-mediated drug delivery.
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High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)
USDA-ARS?s Scientific Manuscript database
Implementation of molecular methods in hop breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. Diversity Arrays Technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of...
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Rao, Jing; Ratassepp, Madis; Lisevych, Danylo; Hamzah Caffoor, Mahadhir; Fan, Zheng
2017-12-12
Corrosion is a major safety and economic concern to various industries. In this paper, a novel ultrasonic guided wave tomography (GWT) system based on self-designed piezoelectric sensors is presented for on-line corrosion monitoring of large plate-like structures. Accurate thickness reconstruction of corrosion damages is achieved by using the dispersive regimes of selected guided waves and a reconstruction algorithm based on full waveform inversion (FWI). The system makes use of an array of miniaturised piezoelectric transducers that are capable of exciting and receiving highly dispersive A0 Lamb wave mode at low frequencies. The scattering from transducer array has been found to have a small effect on the thickness reconstruction. The efficiency and the accuracy of the new system have been demonstrated through continuous forced corrosion experiments. The FWI reconstructed thicknesses show good agreement with analytical predictions obtained by Faraday's law and laser measurements, and more importantly, the thickness images closely resemble the actual corrosion sites.
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Energy Guiding and Harvesting through Phonon-Engineered Graphene
2016-01-28
improve the performance of carbon nanotube array transistors. Such transistors suffer about two orders of magnitude performance penalty due to high... nanotube - nanotube resistances in the current pathways from source to drain. Thus, under normal operation CNT array 1. REPORT DATE (DD-MM-YYYY) 4. TITLE...Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 Carbon Nanotubes , FETs, Nanosoldering REPORT DOCUMENTATION PAGE 11. SPONSOR
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Guided-Wave Optic Devices for Integrated Optic Information Processing.
1984-08-08
Modulation and switching of light waves in Yttrium iron garnet (YIG)- Gadolinium gallium garnet (GGG) waveguides using Farady rotation , and light...switch, an electrooptic analog-to-digital converter using a Fabry -Perot modula- tor array, and a noncollinear magnetooptic modulator using magnetostatic...data routing in electronic computer networks. ELECTROOPTIC ANALOG-TO-DIGITAL CONVERTER USING CHANNEL WAVEGUIDE FABRY -PEROT MODULATOR ARRAY One of the
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Up-to-date approach to manage keloids and hypertrophic scars: a useful guide.
Arno, Anna I; Gauglitz, Gerd G; Barret, Juan P; Jeschke, Marc G
2014-11-01
Keloids and hypertrophic scars occur anywhere from 30 to 90% of patients, and are characterized by pathologically excessive dermal fibrosis and aberrant wound healing. Both entities have different clinical and histochemical characteristics, and unfortunately still represent a great challenge for clinicians due to lack of efficacious treatments. Current advances in molecular biology and genetics reveal new preventive and therapeutical options which represent a hope to manage this highly prevalent, chronic and disabling problem, with long-term beneficial outcomes and improvement of quality of life. While we wait for these translational clinical products to be marketed, however, it is imperative to know the basics of the currently existing wide array of strategies to deal with excessive scars: from the classical corticotherapy, to the most recent botulinum toxin and lasers. The main aim of this review paper is to offer a useful up-to-date guideline to prevent and treat keloids and hypertrophic scars. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.
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NASA Astrophysics Data System (ADS)
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 ultrasound enhanced (echogenic) needle.
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Top-down contextual knowledge guides visual attention in infancy.
Tummeltshammer, Kristen; Amso, Dima
2017-10-26
The visual context in which an object or face resides can provide useful top-down information for guiding attention orienting, object recognition, and visual search. Although infants have demonstrated sensitivity to covariation in spatial arrays, it is presently unclear whether they can use rapidly acquired contextual knowledge to guide attention during visual search. In this eye-tracking experiment, 6- and 10-month-old infants searched for a target face hidden among colorful distracter shapes. Targets appeared in Old or New visual contexts, depending on whether the visual search arrays (defined by the spatial configuration, shape and color of component items in the search display) were repeated or newly generated throughout the experiment. Targets in Old contexts appeared in the same location within the same configuration, such that context covaried with target location. Both 6- and 10-month-olds successfully distinguished between Old and New contexts, exhibiting faster search times, fewer looks at distracters, and more anticipation of targets when contexts repeated. This initial demonstration of contextual cueing effects in infants indicates that they can use top-down information to facilitate orienting during memory-guided visual search. © 2017 John Wiley & Sons Ltd.
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Damage Detection in Composite Structures with Wavenumber Array Data Processing
NASA Technical Reports Server (NTRS)
Tian, Zhenhua; Leckey, Cara; Yu, Lingyu
2013-01-01
Guided ultrasonic waves (GUW) have the potential to be an efficient and cost-effective method for rapid damage detection and quantification of large structures. Attractive features include sensitivity to a variety of damage types and the capability of traveling relatively long distances. They have proven to be an efficient approach for crack detection and localization in isotropic materials. However, techniques must be pushed beyond isotropic materials in order to be valid for composite aircraft components. This paper presents our study on GUW propagation and interaction with delamination damage in composite structures using wavenumber array data processing, together with advanced wave propagation simulations. Parallel elastodynamic finite integration technique (EFIT) is used for the example simulations. Multi-dimensional Fourier transform is used to convert time-space wavefield data into frequency-wavenumber domain. Wave propagation in the wavenumber-frequency domain shows clear distinction among the guided wave modes that are present. This allows for extracting a guided wave mode through filtering and reconstruction techniques. Presence of delamination causes spectral change accordingly. Results from 3D CFRP guided wave simulations with delamination damage in flat-plate specimens are used for wave interaction with structural defect study.
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Portable Ultrasonic Guided Wave Inspection with MACRO Fiber Composite Actuators
NASA Astrophysics Data System (ADS)
Haig, A.; Mudge, P.; Catton, P.; Balachandran, W.
2010-02-01
The development of portable ultrasonic guided wave transducer arrays that utilize Macro Fiber Composite actuators (MFCs) is described. Portable inspection equipment can make use of ultrasonic guided waves to rapidly screen large areas of many types of engineering structures for defects. The defect finding performance combined with the difficulty of application determines how much the engineering industry makes use of this non-destructive, non-disruptive technology. The developments with MFCs have the potential to make considerable improvements in both these aspects. MFCs are highly efficient because they use interdigital electrodes to facilitate the extensional, d33 displacement mode. Their fiber composite design allows them to be thin, lightweight, flexible and durable. The flexibility affords them conformance with curved surfaces, which can facilitate good mechanical coupling. The suitability of a given transducer for Long Range Ultrasonic Testing is governed by the nature and amplitude of the displacement that it excites/senses in the contact area of the target structure. This nature is explored for MFCs through directional sensitivity analysis and empirical testing. Housing methods that facilitate non-permanent coupling techniques are discussed. Finally, arrangements of arrays of MFCs for the guided wave inspection of plates and pipes are considered and some broad design criteria are given.
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Scalabrin, Simone; Gilmore, Barbara; Lawley, Cynthia T.; Gasic, Ksenija; Micheletti, Diego; Rosyara, Umesh R.; Cattonaro, Federica; Vendramin, Elisa; Main, Dorrie; Aramini, Valeria; Blas, Andrea L.; Mockler, Todd C.; Bryant, Douglas W.; Wilhelm, Larry; Troggio, Michela; Sosinski, Bryon; Aranzana, Maria José; Arús, Pere; Iezzoni, Amy; Morgante, Michele; Peace, Cameron
2012-01-01
Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ∼75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species. PMID:22536421
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Directional antenna array (DAA) for communications, control, and data link protection
NASA Astrophysics Data System (ADS)
Molchanov, Pavlo A.; Contarino, Vincent M.
2013-06-01
A next generation of Smart antennas with point-to-point communication and jam, spoof protection capability by verification of spatial position is offered. A directional antenna array (DAA) with narrow irradiation beam provides counter terrorism protection for communications, data link, control and GPS. Communications are "invisible" to guided missiles because of 20 dB smaller irradiation outside the beam and spatial separation. This solution can be implemented with current technology. Directional antennas have higher gain and can be multi-frequency or have wide frequency band in contrast to phase antenna arrays. This multi-directional antenna array provides a multi-functional communication network and simultaneously can be used for command control, data link and GPS.
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Guided wave phased array sensor tuning for improved defect detection and characterization
NASA Astrophysics Data System (ADS)
Philtron, Jason H.; Rose, Joseph L.
2014-03-01
Ultrasonic guided waves are finding increased use in a variety of Nondestructive Evaluation and Structural Health Monitoring applications due to their efficiency in defect detection using a sensor at a single location to inspect a large area of a structure and an ability to inspect hidden and coated areas for example. With a thorough understanding of guided wave mechanics, researchers can predict which guided wave modes will have a high probability of success in a particular nondestructive evaluation application. For example, in a sample problem presented here to access bond integrity, researchers may choose to use a guided wave mode which has high in-plane displacement, stress, or other feature at the interface. However, since material properties used for modeling work may not be precise for the development of dispersion curves, in many cases guided wave mode and frequency selection should be adjusted for increased inspection efficiency in the field. In this work, a phased array comb transducer is used to sweep over phase velocity - frequency space to tune mode excitation for improved defect characterization performance. A thin polycarbonate layer bonded to a thick metal plate is considered with a contaminated surface prior to bonding. Physicallybased features are used to correlate wave signals with defect detection. Features assessed include arrival time and the frequency of maximum amplitude. A pseudo C-scan plot is presented which can be used to simplify data analysis. Excellent results are obtained.
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Briegel, Ariane; Ortega, Davi R; Mann, Petra; Kjær, Andreas; Ringgaard, Simon; Jensen, Grant J
2016-09-13
Nearly all motile bacterial cells use a highly sensitive and adaptable sensory system to detect changes in nutrient concentrations in the environment and guide their movements toward attractants and away from repellents. The best-studied bacterial chemoreceptor arrays are membrane-bound. Many motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae's cytoplasmic chemoreceptor array and establish that it is formed by proteins from cluster I. We further identify a chemoreceptor with an unusual domain architecture, DosM, which is essential for formation of the cytoplasmic arrays. DosM contains two signaling domains and spans the two-layered cytoplasmic arrays. Finally, we present evidence suggesting that this type of receptor is important for the structural stability of the cytoplasmic array.
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Porous microwells for geometry-selective, large-scale microparticle arrays
NASA Astrophysics Data System (ADS)
Kim, Jae Jung; Bong, Ki Wan; Reátegui, Eduardo; Irimia, Daniel; Doyle, Patrick S.
2017-01-01
Large-scale microparticle arrays (LSMAs) are key for material science and bioengineering applications. However, previous approaches suffer from trade-offs between scalability, precision, specificity and versatility. Here, we present a porous microwell-based approach to create large-scale microparticle arrays with complex motifs. Microparticles are guided to and pushed into microwells by fluid flow through small open pores at the bottom of the porous well arrays. A scaling theory allows for the rational design of LSMAs to sort and array particles on the basis of their size, shape, or modulus. Sequential particle assembly allows for proximal and nested particle arrangements, as well as particle recollection and pattern transfer. We demonstrate the capabilities of the approach by means of three applications: high-throughput single-cell arrays; microenvironment fabrication for neutrophil chemotaxis; and complex, covert tags by the transfer of an upconversion nanocrystal-laden LSMA.
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Beaney, Katherine E; Ward, Claire E; Bappa, Dauda A S; McGale, Nadine; Davies, Anna K; Hirani, Shashivadan P; Li, KaWah; Howard, Philip; Vance, Dwaine R; Crockard, Martin A; Lamont, John V; Newman, Stanton; Humphries, Steve E
2016-10-03
The coronary risk in diabetes (CoRDia) trial (n = 211) compares the effectiveness of usual diabetes care with a self-management intervention (SMI), with and without personalised risk information (including genetics), on clinical and behavioural outcomes. Here we present an assessment of randomisation, the cardiac risk genotyping assay, and the genetic characteristics of the recruits. Ten-year coronary heart disease (CHD) risk was calculated using the UKPDS score. Genetic CHD risk was determined by genotyping 19 single nucleotide polymorphisms (SNPs) using Randox's Cardiac Risk Prediction Array and calculating a gene score (GS). Accuracy of the array was assessed by genotyping a subset of pre-genotyped samples (n = 185). Overall, 10-year CHD risk ranged from 2-72 % but did not differ between the randomisation groups (p = 0.13). The array results were 99.8 % concordant with the pre-determined genotypes. The GS did not differ between the Caucasian participants in the CoRDia SMI plus risk group (n = 66) (p = 0.80) and a sample of UK healthy men (n = 1360). The GS was also associated with LDL-cholesterol (p = 0.05) and family history (p = 0.03) in a sample of UK healthy men (n = 1360). CHD risk is high in this group of T2D subjects. The risk array is an accurate genotyping assay, and is suitable for estimating an individual's genetic CHD risk. Trial registration This study has been registered at ClinicalTrials.gov; registration identifier NCT01891786.
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A guided search genetic algorithm using mined rules for optimal affective product design
NASA Astrophysics Data System (ADS)
Fung, Chris K. Y.; Kwong, C. K.; Chan, Kit Yan; Jiang, H.
2014-08-01
Affective design is an important aspect of new product development, especially for consumer products, to achieve a competitive edge in the marketplace. It can help companies to develop new products that can better satisfy the emotional needs of customers. However, product designers usually encounter difficulties in determining the optimal settings of the design attributes for affective design. In this article, a novel guided search genetic algorithm (GA) approach is proposed to determine the optimal design attribute settings for affective design. The optimization model formulated based on the proposed approach applied constraints and guided search operators, which were formulated based on mined rules, to guide the GA search and to achieve desirable solutions. A case study on the affective design of mobile phones was conducted to illustrate the proposed approach and validate its effectiveness. Validation tests were conducted, and the results show that the guided search GA approach outperforms the GA approach without the guided search strategy in terms of GA convergence and computational time. In addition, the guided search optimization model is capable of improving GA to generate good solutions for affective design.
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2011-06-13
BALL AEROSPACE ENGINEER DAVE CHANEY, (L), AND MARSHALL ENGINEER HARLAN HAIGHT, (R), GUIDE ARRAY OF SIX GOLD-PLATED JAMES WEBB SPACE TELESCOPE MIRRORS AFTER FINAL ACCEPTANCE TESTING AT MARSHALL'S X-RAY AND CRYOGENIC FACILITY
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2011-06-13
BALL AEROSPACE ENGINEER DAVE CHANEY, (L), AND MARSHALL ENGINEER HARLAN HAIGHT, (R), GUIDE ARRAY OF SIX GOLD-PLATED JAMES WEBB SPACE TELESCOPE MIRRORS AFTER FINAL ACCEPTANCE TESTING AT MARSHALL'S X-RAY AND CRYOGENIC FACILITY
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2011-06-13
BALL AEROSPACE ENGINEER DAVE CHANEY, (L), AND MARSHALL ENGINEER HARLAN HAIGHT, (R), GUIDE ARRAY OF SIX GOLD-PLATED JAMES WEBB SPACE TELESCOPE MIRRORS AFTER FINAL ACCEPTANCE TESTING AT MARSHALL'S X-RAY AND CRYOGENIC FACILITY
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2011-06-13
BALL AEROSPACE ENGINEER DAVE CHANEY, (L), AND MARSHALL ENGINEER HARLAN HAIGHT, (R), GUIDE ARRAY OF SIX GOLD-PLATED JAMES WEBB SPACE TELESCOPE MIRRORS AFTER FINAL ACCEPTANCE TESTING AT MARSHALL'S X-RAY AND CRYOGENIC FACILITY
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2011-06-13
BALL AEROSPACE ENGINEER DAVE CHANEY, (L), AND MARSHALL ENGINEER HARLAN HAIGHT, (R), GUIDE ARRAY OF SIX GOLD-PLATED JAMES WEBB SPACE TELESCOPE MIRRORS AFTER FINAL ACCEPTANCE TESTING AT MARSHALL'S X-RAY AND CRYOGENIC FACILITY
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2011-06-13
BALL AEROSPACE ENGINEER DAVE CHANEY, (L), AND MARSHALL ENGINEER HARLAN HAIGHT, (R), GUIDE ARRAY OF SIX GOLD-PLATED JAMES WEBB SPACE TELESCOPE MIRRORS AFTER FINAL ACCEPTANCE TESTING AT MARSHALL'S X-RAY AND CRYOGENIC FACILITY
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2011-06-13
BALL AEROSPACE ENGINEER DAVE CHANEY, (L), AND MARSHALL ENGINEER HARLAN HAIGHT, (R), GUIDE ARRAY OF SIX GOLD-PLATED JAMES WEBB SPACE TELESCOPE MIRRORS AFTER FINAL ACCEPTANCE TESTING AT MARSHALL'S X-RAY AND CRYOGENIC FACILITY
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2011-06-13
BALL AEROSPACE ENGINEER DAVE CHANEY, (L), AND MARSHALL ENGINEER HARLAN HAIGHT, (R), GUIDE ARRAY OF SIX GOLD-PLATED JAMES WEBB SPACE TELESCOPE MIRRORS AFTER FINAL ACCEPTANCE TESTING AT MARSHALL'S X-RAY AND CRYOGENIC FACILITY
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P450 GENETIC VARIATION: IMPLICATIONS FOR ENVIRONMENTAL AND WORKPLACE EXPOSURE
The Cytochrome P450 array detoxifies many chemicals by catalyzing the conversion of mostly hydrophobic chemicals into more hydrophilic forms that can subsequently be excreted by the body. Human genetic variation in the genes for these enzymes produces wide variations in the abili...
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The National Plant Germplasm System and GRIN-Global
USDA-ARS?s Scientific Manuscript database
The National Plant Germplasm System (NPGS) is a cooperative effort by public and private organizations to preserve plant genetic diversity. Federal and State personnel at 20 sites are responsible for approximately 547,000 unique accessions of a wide array of plant genetic resources (PGR) representi...
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Towards a Reduced-Wire Interface for CMUT-Based Intravascular Ultrasound Imaging Systems
Lim, Jaemyung; Tekes, Coskun; Degertekin, F. Levent; Ghovanloo, Maysam
2016-01-01
Having intravascular ultrasound (IVUS) imaging capability on guide wires used in cardiovascular interventions may eliminate the need for separate IVUS catheters and expand the use of IVUS in a larger portion of the vasculature. High frequency capacitive micro machined ultrasonic transducer (CMUT) arrays should be integrated with interface electronics and placed on the guide wire for this purpose. Besides small size, this system-on-a-chip (SoC) front-end should connect to the back-end imaging system with a minimum number of wires to preserve the critical mechanical properties of the guide wire. We present a 40 MHz CMUT array interface SoC, which will eventually use only two wires for power delivery and transmits image data using a combination of analog-to-time conversion (ATC) and an impulse radio ultra-wideband (IR-UWB) wireless link. The proof-of-concept prototype ASIC consumes only 52.8 mW and occupies 4.07 mm2 in a 0.35-μm standard CMOS process. A rectifier and regulator power the rest of the SoC at 3.3 V from a 10 MHz power carrier that is supplied through a 2.4 m micro-coax cable with an overall efficiency of 49.1%. Echo signals from an 8-element CMUT array are amplified by a transimpedance amplifier (TIA) array and down-converted to baseband by quadrature sampling using a 40 MHz clock, derived from the power carrier. The ATC generates pulse-width-modulated (PWM) samples at 2 × 10 MS/s with 6 bit resolution, while the entire system achieved 5.1 ENOB. Preliminary images from the prototype system are presented, and alternative data transmission and possible future directions towards practical implementation are discussed. PMID:27662686
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Towards a Reduced-Wire Interface for CMUT-Based Intravascular Ultrasound Imaging Systems.
Lim, Jaemyung; Tekes, Coskun; Degertekin, F Levent; Ghovanloo, Maysam
2017-04-01
Having intravascular ultrasound (IVUS) imaging capability on guide wires used in cardiovascular interventions may eliminate the need for separate IVUS catheters and expand the use of IVUS in a larger portion of the vasculature. High frequency capacitive micro machined ultrasonic transducer (CMUT) arrays should be integrated with interface electronics and placed on the guide wire for this purpose. Besides small size, this system-on-a-chip (SoC) front-end should connect to the back-end imaging system with a minimum number of wires to preserve the critical mechanical properties of the guide wire. We present a 40 MHz CMUT array interface SoC, which will eventually use only two wires for power delivery and transmits image data using a combination of analog-to-time conversion (ATC) and an impulse radio ultra-wideband (IR-UWB) wireless link. The proof-of-concept prototype ASIC consumes only 52.8 mW and occupies 4.07 [Formula: see text] in a 0.35- [Formula: see text] standard CMOS process. A rectifier and regulator power the rest of the SoC at 3.3 V from a 10 MHz power carrier that is supplied through a 2.4 m micro-coax cable with an overall efficiency of 49.1%. Echo signals from an 8-element CMUT array are amplified by a transimpedance amplifier (TIA) array and down-converted to baseband by quadrature sampling using a 40 MHz clock, derived from the power carrier. The ATC generates pulse-width-modulated (PWM) samples at 2 × 10 MS/s with 6 bit resolution, while the entire system achieved 5.1 ENOB. Preliminary images from the prototype system are presented, and alternative data transmission and possible future directions towards practical implementation are discussed.
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USDA-ARS?s Scientific Manuscript database
A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification o...
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Endophenotypes, Epigenetics, Polygenicity and More: Irv Gottesman’s Dynamic Legacy
Braff, David L.; Tamminga, Carol A.
2017-01-01
First, we describe the hallmark contributions of Irv Gottesman’s pioneering scholarship for schizophrenia research including concepts of polygenicity, gene × environment interactions, epigenetics and the endophenotype concept. Gottesman and colleagues’ twin studies showed that genes, not social factors, mediate schizophrenia risk. He then showed that schizophrenia is highly polygenic. Next, he introduced the concept of epigenetics into schizophrenia research. Gottesman then introduced the quantitative endophenotype concept. Endophenotypes are laboratory-based measures that show deficits in schizophrenia patients and lesser deficits in their first degree “unaffected” relatives and are viewed as being more proximal to genes and having a simpler genetic architecture than are “fuzzy” qualitative diagnostic disorders. Endophenotypes offer an exciting path to gene discovery, neural circuits, genetic architecture and new treatment pathways of schizophrenia and related psychotic disorders. Second, we were asked to discuss 2 of many endophenotype Consortia and related studies, in order to illustrate the impact of Gottesman’s work. We describe the Consortium on the Genetics of Schizophrenia (COGS) exploring neurocognitive and neurophysiological endophenotypes in family and case-control studies. Association, linkage, sequencing and epigenetic studies are described. The Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP) uses an array of endophenotypes including brain imaging in studies across the psychosis dimension, allowing for dimensional analyses. BSNIP results have led to the concept of biotypes, advancing the field. Irv Gottesman was imaginatively prescient in generating novel insights and predicting many major issues which challenge schizophrenia researchers who still use his concepts to guide current research approaches. PMID:27872267
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Griffel, G; Marshall, W K; Gravé, I; Yariv, A; Nabiev, R
1991-08-01
Frequency selectivity of a novel type of multielement, multisection laterally coupled semiconductor laser array is studied using the round-trip method. It is found that such a structure should lead to a strong frequency selectivity owing to a periodic dependency of the threshold gain on the frequency. A gain-guided two-coupledcavity device was fabricated. The experimental results show excellent agreement with the theoretical prediction.
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Photoacoustic and Ultrasonic Image-Guided Needle Biopsy of the Prostate
2015-02-01
demonstrated in Figures 2 & 3 were performed with a linear array coupled with a Verasonics Vantage 128 US system ( Verasonics Inc., Redmond, WA...the Verasonics ultrasound platform, is suited for eventual clinical trials. The Verasonics acquisition is coordinated with a LabVIEW data...Recently we acquired and integrated an ATL C9-5 end-fire transrectal array (Philips Medical Systems, Bothell, WA) with our Verasonics system. Figure 3
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Uwineza, Annette; Caberg, Jean-Hubert; Hitayezu, Janvier; Hellin, Anne Cecile; Jamar, Mauricette; Dideberg, Vinciane; Rusingiza, Emmanuel K; Bours, Vincent; Mutesa, Leon
2014-07-12
Array-CGH is considered as the first-tier investigation used to identify copy number variations. Right now, there is no available data about the genetic etiology of patients with development delay/intellectual disability and congenital malformation in East Africa. Array comparative genomic hybridization was performed in 50 Rwandan patients with development delay/intellectual disability and multiple congenital abnormalities, using the Agilent's 180 K microarray platform. Fourteen patients (28%) had a global development delay whereas 36 (72%) patients presented intellectual disability. All patients presented multiple congenital abnormalities. Clinically significant copy number variations were found in 13 patients (26%). Size of CNVs ranged from 0,9 Mb to 34 Mb. Six patients had CNVs associated with known syndromes, whereas 7 patients presented rare genomic imbalances. This study showed that CNVs are present in African population and show the importance to implement genetic testing in East-African countries.
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Bai, Mingsian R; Tung, Chih-Wei; Lee, Chih-Chung
2005-05-01
An optimal design technique of loudspeaker arrays for cross-talk cancellation with application in three-dimensional audio is presented. An array focusing scheme is presented on the basis of the inverse propagation that relates the transducers to a set of chosen control points. Tikhonov regularization is employed in designing the inverse cancellation filters. An extensive analysis is conducted to explore the cancellation performance and robustness issues. To best compromise the performance and robustness of the cross-talk cancellation system, optimal configurations are obtained with the aid of the Taguchi method and the genetic algorithm (GA). The proposed systems are further justified by physical as well as subjective experiments. The results reveal that large number of loudspeakers, closely spaced configuration, and optimal control point design all contribute to the robustness of cross-talk cancellation systems (CCS) against head misalignment.
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Campoy, José Antonio; Lerigoleur-Balsemin, Emilie; Christmann, Hélène; Beauvieux, Rémi; Girollet, Nabil; Quero-García, José; Dirlewanger, Elisabeth; Barreneche, Teresa
2016-02-24
Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity and to detect the patterns of LD, (ii) to estimate the levels of population structure and (iii) to identify a 'core collection' suitable for association genetic studies in sweet cherry. A total of 210 genotypes including modern cultivars and landraces from 16 countries were genotyped using the RosBREED cherry 6 K SNP array v1. Two groups, mainly bred cultivars and landraces, respectively, were first detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA). Further analyses identified nine subgroups using STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Several sub-groups correspond to different eco-geographic regions of landraces distribution. Linkage disequilibrium was evaluated showing lower values than in peach, the reference Prunus species. A 'core collection' containing 156 accessions was selected using the maximum length sub tree method. The present study constitutes the first population genetics analysis in cultivated sweet cherry using a medium-density SNP (single nucleotide polymorphism) marker array. We provided estimations of linkage disequilibrium, genetic structure and the definition of a first INRA's Sweet Cherry core collection useful for breeding programs, germplasm management and association genetics studies.
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Dynamic characteristics of far-field radiation of current modulated phase-locked diode laser arrays
NASA Technical Reports Server (NTRS)
Elliott, R. A.; Hartnett, K.
1987-01-01
A versatile and powerful streak camera/frame grabber system for studying the evolution of the near and far field radiation patterns of diode lasers was assembled and tested. Software needed to analyze and display the data acquired with the steak camera/frame grabber system was written and the total package used to record and perform preliminary analyses on the behavior of two types of laser, a ten emitter gain guided array and a flared waveguide Y-coupled array. Examples of the information which can be gathered with this system are presented.
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Optical Phased Array Using Guided Resonance with Backside Reflectors
NASA Technical Reports Server (NTRS)
Horie, Yu (Inventor); Arbabi, Amir (Inventor); Faraon, Andrei (Inventor)
2016-01-01
Methods and systems for controlling the phase of electromagnetic waves are disclosed. A device can consist of a guided resonance grating layer, a spacer, and a reflector. A plurality of devices, arranged in a grid pattern, can control the phase of reflected electromagnetic phase, through refractive index control. Carrier injection, temperature control, and optical beams can be applied to control the refractive index.
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Optical phased array using guided resonance with backside reflectors
Horie, Yu; Arbabi, Amir; Faraon, Andrei
2016-11-01
Methods and systems for controlling the phase of electromagnetic waves are disclosed. A device can consist of a guided resonance grating layer, a spacer, and a reflector. A plurality of devices, arranged in a grid pattern, can control the phase of reflected electromagnetic phase, through refractive index control. Carrier injection, temperature control, and optical beams can be applied to control the refractive index.
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Optical phased array using guided resonance with backside reflectors
DOE Office of Scientific and Technical Information (OSTI.GOV)
Horie, Yu; Arbabi, Amir; Faraon, Andrei
2018-03-13
Methods and systems for controlling the phase of electromagnetic waves are disclosed. A device can consist of a guided resonance grating layer, a spacer, and a reflector. A plurality of devices, arranged in a grid pattern, can control the phase of reflected electromagnetic phase, through refractive index control. Carrier injection, temperature control, and optical beams can be applied to control the refractive index.
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Optical Phased Array Using Guided Resonance with Backside Reflectors
NASA Technical Reports Server (NTRS)
Horie, Yu (Inventor); Arbabi, Amir (Inventor); Faraon, Andrei (Inventor)
2018-01-01
Methods and systems for controlling the phase of electromagnetic waves are disclosed. A device can consist of a guided resonance grating layer, a spacer, and a reflector. A plurality of devices, arranged in a grid pattern, can control the phase of reflected electromagnetic phase, through refractive index control. Carrier injection, temperature control, and optical beams can be applied to control the refractive index.
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Lithium niobate guided-wave beam former for steering phased-array antennas.
Armenise, M N; Passaro, V M; Noviello, G
1994-09-10
We present the theoretical investigation, design, and simulation of a novel guided-wave optical processor for L-band-transmission beam forming in a linear array of phased active antennas. The proposed configuration includes two contradirectional surface acoustic-wave transducers, and it is based on a Y-cut, X-propagating Ti:LiNbO(3) planar waveguide supporting the lowest-order modes of both polarizations (TE(0) and TM(0)) at the free-space wavelength λ = 0.85 µm. A detailed comparison between the processor we propose and other optical and electronic architectures reported in the literature is carried out, exhibiting a number of significant advantages in terms of weight, total chip size, and power consumption, when the number of antenna elements is greater than 50.
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Systolic array IC for genetic computation
NASA Technical Reports Server (NTRS)
Anderson, D.
1991-01-01
Measuring similarities between large sequences of genetic information is a formidable task requiring enormous amounts of computer time. Geneticists claim that nearly two months of CRAY-2 time are required to run a single comparison of the known database against the new bases that will be found this year, and more than a CRAY-2 year for next year's genetic discoveries, and so on. The DNA IC, designed at HP-ICBD in cooperation with the California Institute of Technology and the Jet Propulsion Laboratory, is being implemented in order to move the task of genetic comparison onto workstations and personal computers, while vastly improving performance. The chip is a systolic (pumped) array comprised of 16 processors, control logic, and global RAM, totaling 400,000 FETS. At 12 MHz, each chip performs 2.7 billion 16 bit operations per second. Using 35 of these chips in series on one PC board (performing nearly 100 billion operations per second), a sequence of 560 bases can be compared against the eventual total genome of 3 billion bases, in minutes--on a personal computer. While the designed purpose of the DNA chip is for genetic research, other disciplines requiring similarity measurements between strings of 7 bit encoded data could make use of this chip as well. Cryptography and speech recognition are two examples. A mix of full custom design and standard cells, in CMOS34, were used to achieve these goals. Innovative test methods were developed to enhance controllability and observability in the array. This paper describes these techniques as well as the chip's functionality. This chip was designed in the 1989-90 timeframe.
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Flexible nanopillar-based electrochemical sensors for genetic detection of foodborne pathogens
NASA Astrophysics Data System (ADS)
Park, Yoo Min; Lim, Sun Young; Jeong, Soon Woo; Song, Younseong; Bae, Nam Ho; Hong, Seok Bok; Choi, Bong Gill; Lee, Seok Jae; Lee, Kyoung G.
2018-06-01
Flexible and highly ordered nanopillar arrayed electrodes have brought great interest for many electrochemical applications, especially to the biosensors, because of its unique mechanical and topological properties. Herein, we report an advanced method to fabricate highly ordered nanopillar electrodes produced by soft-/photo-lithography and metal evaporation. The highly ordered nanopillar array exhibited the superior electrochemical and mechanical properties in regard with the wide space to response with electrolytes, enabling the sensitive analysis. As-prepared gold and silver electrodes on nanopillar arrays exhibit great and stable electrochemical performance to detect the amplified gene from foodborne pathogen of Escherichia coli O157:H7. Additionally, lightweight, flexible, and USB-connectable nanopillar-based electrochemical sensor platform improves the connectivity, portability, and sensitivity. Moreover, we successfully confirm the performance of genetic analysis using real food, specially designed intercalator, and amplified gene from foodborne pathogens with high reproducibility (6% standard deviation) and sensitivity (10 × 1.01 CFU) within 25 s based on the square wave voltammetry principle. This study confirmed excellent mechanical and chemical characteristics of nanopillar electrodes have a great and considerable electrochemical activity to apply as genetic biosensor platform in the fields of point-of-care testing (POCT).
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Arraying proteins by cell-free synthesis.
He, Mingyue; Wang, Ming-Wei
2007-10-01
Recent advances in life science have led to great motivation for the development of protein arrays to study functions of genome-encoded proteins. While traditional cell-based methods have been commonly used for generating protein arrays, they are usually a time-consuming process with a number of technical challenges. Cell-free protein synthesis offers an attractive system for making protein arrays, not only does it rapidly converts the genetic information into functional proteins without the need for DNA cloning, but also presents a flexible environment amenable to production of folded proteins or proteins with defined modifications. Recent advancements have made it possible to rapidly generate protein arrays from PCR DNA templates through parallel on-chip protein synthesis. This article reviews current cell-free protein array technologies and their proteomic applications.
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[Characterization of genetic alterations in primary human melanomas carrying BRAF or NRAS mutation].
Lázár, Viktória
2013-06-01
Human malignant melanoma is one of the most aggressive forms of skin cancer with an exceptionally bad prognosis. Melanoma often displays constitutively activated MAPK pathway through BRAF or NRAS mutations. It is also known that these mutations are almost never simultaneously present and that they appear at early stages and preserved throughout tumor progression, although it is proved that these alterations alone are insufficient to cause tumor progression. Therefore the first aim of our study was to evaluate those distinct genetic alterations which can properly differentiate the three important molecular subtypes of primary melanomas with a) BRAF, b) NRAS mutation and c) WT (wild type for both loci). High-resolution array comparative genomic hybridization (array CGH) was used to assess genome-wide analysis of DNA copy number alterations. Primary melanomas with BRAF mutation more frequently exhibited losses on 10q23-10q26 and gains on chromosome 7 and 1q23-1q25 compared to melanomas with NRAS mutation. Loss on the 11q23-11q25 sequence was found mainly in conjunction with NRAS mutation. Based on these results, we proved the existence of marked differences in the genetic pattern of the BRAF and NRAS mutated melanoma subgroups, which might suggest that these mutations contribute to the development of malignant melanoma in conjunction with distinct cooperating oncogenic events. In general, it is an interesting phenomenon suggesting that these mutations provide probably the "guiding force" for these tumors and it also suggests that there are alternative genetic pathways to melanoma. These additional oncogenic events which are associated with BRAF or NRAS mutations can provide rational additional targets for a combination therapy with kinase inhibitors. In this study we also investigated the specific dynamic activities among different signalling pathways highlighting the frequent alterations of genes involved in the signalling interactions between the MAPK-JAK pathways in BRAF mutated melanomas. Using a data mining algorithm we also found a gene alteration signature in the MAPK pathway that was commonly related to the presence of BRAF mutation in our melanoma cohorts. The second aim of this study was to develop an accurate Q-PCR method for determining the co-amplification pattern of six candidate genes that reside in the 11q13 amplicon core. We found that co-amplification of these candidate genes or the CCND1 amplification along with either BRAF or NRAS mutations might be more important for prognosis than the presence of these alterations alone.
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Yang, Daejong; Kang, Kyungnam; Kim, Donghwan; Li, Zhiyong; Park, Inkyu
2015-01-01
A facile top-down/bottom-up hybrid nanofabrication process based on programmable temperature control and parallel chemical supply within microfluidic platform has been developed for the all liquid-phase synthesis of heterogeneous nanomaterial arrays. The synthesized materials and locations can be controlled by local heating with integrated microheaters and guided liquid chemical flow within microfluidic platform. As proofs-of-concept, we have demonstrated the synthesis of two types of nanomaterial arrays: (i) parallel array of TiO2 nanotubes, CuO nanospikes and ZnO nanowires, and (ii) parallel array of ZnO nanowire/CuO nanospike hybrid nanostructures, CuO nanospikes and ZnO nanowires. The laminar flow with negligible ionic diffusion between different precursor solutions as well as localized heating was verified by numerical calculation and experimental result of nanomaterial array synthesis. The devices made of heterogeneous nanomaterial array were utilized as a multiplexed sensor for toxic gases such as NO2 and CO. This method would be very useful for the facile fabrication of functional nanodevices based on highly integrated arrays of heterogeneous nanomaterials. PMID:25634814
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Botanic garden genetics: comparison of two cyacad conservation collections
USDA-ARS?s Scientific Manuscript database
Genetic data can guide the management of plant conservation collections. Direct assay of an ex situ collection’s genetic diversity, measured against wild plant populations, offers insight for conservation efforts. Here we present a carefully chosen case study, Zamia lucayana, selected for its contra...
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Development and mapping of DArT markers within the Festuca - Lolium complex
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
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Gao, Yang; Hassett, Daniel J.; Choi, Seokheun
2017-01-01
Electrogenicity, or bacterial electron transfer capacity, is an important application which offers environmentally sustainable advances in the fields of biofuels, wastewater treatment, bioremediation, desalination, and biosensing. Significant boosts in this technology can be achieved with the growth of synthetic biology that manipulates microbial electron transfer pathways, thereby potentially significantly improving their electrogenic potential. There is currently a need for a high-throughput, rapid, and highly sensitive test array to evaluate the electrogenic properties of newly discovered and/or genetically engineered bacterial species. In this work, we report a single-sheet, paper-based electrofluidic (incorporating both electronic and fluidic structure) screening platform for rapid, sensitive, and potentially high-throughput characterization of bacterial electrogenicity. This novel screening array uses (i) a commercially available wax printer for hydrophobic wax patterning on a single sheet of paper and (ii) water-dispersed electrically conducting polymer mixture, poly(3,4-ethylenedioxythiophene):polystyrene sulfonate, for full integration of electronic and fluidic components into the paper substrate. The engineered 3-D, microporous, hydrophilic, and conductive paper structure provides a large surface area for efficient electron transfer. This results in rapid and sensitive power assessment of electrogenic bacteria from a microliter sample volume. We validated the effectiveness of the sensor array using hypothesis-driven genetically modified Pseudomonas aeruginosa mutant strains. Within 20 min, we observed that the sensor platform successfully measured the electricity-generating capacities of five isogenic mutants of P. aeruginosa while distinguishing their differences from genetically unmodified bacteria. PMID:28798914
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Optimization of the Hartmann-Shack microlens array
NASA Astrophysics Data System (ADS)
de Oliveira, Otávio Gomes; de Lima Monteiro, Davies William
2011-04-01
In this work we propose to optimize the microlens-array geometry for a Hartmann-Shack wavefront sensor. The optimization makes possible that regular microlens arrays with a larger number of microlenses are replaced by arrays with fewer microlenses located at optimal sampling positions, with no increase in the reconstruction error. The goal is to propose a straightforward and widely accessible numerical method to calculate an optimized microlens array for a known aberration statistics. The optimization comprises the minimization of the wavefront reconstruction error and/or the number of necessary microlenses in the array. We numerically generate, sample and reconstruct the wavefront, and use a genetic algorithm to discover the optimal array geometry. Within an ophthalmological context, as a case study, we demonstrate that an array with only 10 suitably located microlenses can be used to produce reconstruction errors as small as those of a 36-microlens regular array. The same optimization procedure can be employed for any application where the wavefront statistics is known.
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A comparison of individual-based genetic distance metrics for landscape genetics
A. J. Shirk; E. L. Landguth; S. A. Cushman
2017-01-01
A major aim of landscape genetics is to understand how landscapes resist gene flow and thereby influence population genetic structure. An empirical understanding of this process provides a wealth of information that can be used to guide conservation and management of species in fragmented landscapes and also to predict how landscape change may affect population...
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Guidelines on the use of molecular genetics in reintroduction programs
Michael K. Schwartz
2005-01-01
The use of molecular genetics can play a key role in reintroduction efforts. Prior to the introduction of any individuals, molecular genetics can be used to identify the most appropriate source population for the reintroduction, ensure that no relic populations exist in the reintroduction area, and guide captive breeding programs. The use of molecular genetics post-...
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Kim, Joshua; Lu, Weiguo; Zhang, Tiezhi
2014-02-07
Cone-beam computed tomography (CBCT) is an important online imaging modality for image guided radiotherapy. But suboptimal image quality and the lack of a real-time stereoscopic imaging function limit its implementation in advanced treatment techniques, such as online adaptive and 4D radiotherapy. Tetrahedron beam computed tomography (TBCT) is a novel online imaging modality designed to improve on the image quality provided by CBCT. TBCT geometry is flexible, and multiple detector and source arrays can be used for different applications. In this paper, we describe a novel dual source-dual detector TBCT system that is specially designed for LINAC radiation treatment machines. The imaging system is positioned in-line with the MV beam and is composed of two linear array x-ray sources mounted aside the electrical portal imaging device and two linear arrays of x-ray detectors mounted below the machine head. The detector and x-ray source arrays are orthogonal to each other, and each pair of source and detector arrays forms a tetrahedral volume. Four planer images can be obtained from different view angles at each gantry position at a frame rate as high as 20 frames per second. The overlapped regions provide a stereoscopic field of view of approximately 10-15 cm. With a half gantry rotation, a volumetric CT image can be reconstructed having a 45 cm field of view. Due to the scatter rejecting design of the TBCT geometry, the system can potentially produce high quality 2D and 3D images with less radiation exposure. The design of the dual source-dual detector system is described, and preliminary results of studies performed on numerical phantoms and simulated patient data are presented.
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NASA Astrophysics Data System (ADS)
Kim, Joshua; Lu, Weiguo; Zhang, Tiezhi
2014-02-01
Cone-beam computed tomography (CBCT) is an important online imaging modality for image guided radiotherapy. But suboptimal image quality and the lack of a real-time stereoscopic imaging function limit its implementation in advanced treatment techniques, such as online adaptive and 4D radiotherapy. Tetrahedron beam computed tomography (TBCT) is a novel online imaging modality designed to improve on the image quality provided by CBCT. TBCT geometry is flexible, and multiple detector and source arrays can be used for different applications. In this paper, we describe a novel dual source-dual detector TBCT system that is specially designed for LINAC radiation treatment machines. The imaging system is positioned in-line with the MV beam and is composed of two linear array x-ray sources mounted aside the electrical portal imaging device and two linear arrays of x-ray detectors mounted below the machine head. The detector and x-ray source arrays are orthogonal to each other, and each pair of source and detector arrays forms a tetrahedral volume. Four planer images can be obtained from different view angles at each gantry position at a frame rate as high as 20 frames per second. The overlapped regions provide a stereoscopic field of view of approximately 10-15 cm. With a half gantry rotation, a volumetric CT image can be reconstructed having a 45 cm field of view. Due to the scatter rejecting design of the TBCT geometry, the system can potentially produce high quality 2D and 3D images with less radiation exposure. The design of the dual source-dual detector system is described, and preliminary results of studies performed on numerical phantoms and simulated patient data are presented.
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NaI(Tl) scintillator read out with SiPM array for gamma spectrometer
NASA Astrophysics Data System (ADS)
Huang, Tuchen; Fu, Qibin; Lin, Shaopeng; Wang, Biao
2017-04-01
The NaI(Tl) scintillator is widely used in gamma spectrometer with photomultiplier tube (PMT) readout. Recently developed silicon photomultiplier (SiPM) offers gain and efficiency similar to those of PMT, but with merits such as low bias voltage, compact volume, low cost, high ruggedness and magnetic resonance compatibility. In this study, 2-in. and 1-in. NaI(Tl) scintillators were readout with SiPM arrays, which were made by tiling multiple SiPMs each with an active area of 6×6 mm2 on a printed circuit board. The energy resolutions for 661.6 keV gamma rays, obtained with Φ2×2 in. scintillator coupled to 6×6 ch SiPM array and Φ1×1 in. scintillator coupled to 4×4 ch SiPM array were 7.6% and 7.8%, respectively, and were very close to the results obtained with traditional bialkali PMT (7.3% and 7.6%, respectively). Scintillator coupled to photodetector with smaller area was also studied by adding a light guide or using scintillator with tapered head. The latter showed better performance than using light guide. The 1-in. NaI(Tl) scintillator with tapered head coupled to 2×2 ch SiPM array achieved 7.7% energy resolution at 661.6 keV, the same as that obtained with standard Φ1×1 in. scintillator coupled to 4×4 ch SiPM array. While the 2-in. scintillator with similar geometry showed degraded energy resolution, 10.2% at 661.6 keV, but could still be used when high efficiency is preferred over energy resolution.
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Resiliency to Victimization: The Role of Genetic Factors
ERIC Educational Resources Information Center
Beaver, Kevin M.; Mancini, Christina; DeLisi, Matt; Vaughn, Michael G.
2011-01-01
There is a burgeoning line of criminological research examining the genetic underpinnings to a wide array of antisocial phenotypes. From this perspective, genes are typically viewed as risk factors that increase the odds of various maladaptive behaviors. However, genes can also have protective effects that insulate against the deleterious effects…
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USDA-ARS?s Scientific Manuscript database
High-throughput genotyping arrays provide a standardized resource for crop research communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), candidate marker and quantitative trait loci (QTL) ide...
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Solís, D; Jiménez-Barbero, J; Kaltner, H; Romero, A; Siebert, H C; von der Lieth, C W; Gabius, H J
2001-01-01
The term 'code' in biological information transfer appears to be tightly and hitherto exclusively connected with the genetic code based on nucleotides and translated into functional activities via proteins. However, the recent appreciation of the enormous coding capacity of oligosaccharide chains of natural glycoconjugates has spurred to give heed to a new concept: versatile glycan assembly by the genetically encoded glycosyltransferases endows cells with a probably not yet fully catalogued array of meaningful messages. Enciphered by sugar receptors such as endogenous lectins the information of code words established by a series of covalently linked monosaccharides as letters for example guides correct intra- and intercellular routing of glycoproteins, modulates cell proliferation or migration and mediates cell adhesion. Evidently, the elucidation of the structural frameworks and the recognition strategies within the operation of the sugar code poses a fascinating conundrum. The far-reaching impact of this recognition mode on the level of cells, tissues and organs has fueled vigorous investigations to probe the subtleties of protein-carbohydrate interactions. This review presents information on the necessarily concerted approach using X-ray crystallography, molecular modeling, nuclear magnetic resonance spectroscopy, thermodynamic analysis and engineered ligands and receptors. This part of the treatise is flanked by exemplarily chosen insights made possible by these techniques. Copyright 2001 S. Karger AG, Basel
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Image-Guided Surgery of Primary Breast Cancer Using Ultrasound Phased Arrays
2004-07-01
applications using high-intensity focused ultrasound ( HIFU ). We tems, Once the real-time imaging capability is available for have shown that this dual-mode...Arrays Emad S. Ebbini, PI Introduction High-intensity focus ultrasound ( HIFU ) is gaining wider acceptance in noninvasive or minimally invasive targeting of...Methods in Ultrasound Imaging, ISBI 2004, Arlington, VA, April 2004. III. Yao and Ebbini, "Real-Time Monitoring of the Transients of HIFU -Induced Lesions
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An Ultrasonic Guided Wave Method to Estimate Applied Biaxial Loads (Preprint)
2011-11-01
VALIDATION A fatigue test was performed with an array of six surface-bonded PZT transducers on a 6061 aluminum plate as shown in Figure 4. The specimen...direct paths of propagation are oriented at different angles. This method is applied to experimental sparse array data recorded during a fatigue test...and the additional complication of the resulting fatigue cracks interfering with some of the direct arrivals is addressed via proper selection of
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Fiber-linked telescope array: description and laboratory tests of a two-channel prototype
NASA Astrophysics Data System (ADS)
Alleman, J. J.; Reynaud, F.; Connes, P.
1995-05-01
We present a complete two-telescope version of a fiber-linked coherent array that is meant to be used for mounting on the dish of a radio telescope. This was built with 20-cm amateur telescopes and includes three different servo subsystems for guiding, nulling of the air path difference, and fiber length control. Laboratory tests of the fully integrated system in front of a star simulator are described.
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NASA Astrophysics Data System (ADS)
Yoo, Byungseok
2011-12-01
In almost all industries of mechanical, aerospace, and civil engineering fields, structural health monitoring (SHM) technology is essentially required for providing the reliable information of structural integrity of safety-critical structures, which can help reduce the risk of unexpected and sometimes catastrophic failures, and also offer cost-effective inspection and maintenance of the structures. State of the art SHM research on structural damage diagnosis is focused on developing global and real-time technologies to identify the existence, location, extent, and type of damage. In order to detect and monitor the structural damage in plate-like structures, SHM technology based on guided Lamb wave (GLW) interrogation is becoming more attractive due to its potential benefits such as large inspection area coverage in short time, simple inspection mechanism, and sensitivity to small damage. However, the GLW method has a few critical issues such as dispersion nature, mode conversion and separation, and multiple-mode existence. Phased array technique widely used in all aspects of civil, military, science, and medical industry fields may be employed to resolve the drawbacks of the GLW method. The GLW-based phased array approach is able to effectively examine and analyze complicated structural vibration responses in thin plate structures. Because the phased sensor array operates as a spatial filter for the GLW signals, the array signal processing method can enhance a desired signal component at a specific direction while eliminating other signal components from other directions. This dissertation presents the development, the experimental validation, and the damage detection applications of an innovative signal processing algorithm based on two-dimensional (2-D) spiral phased array in conjunction with the GLW interrogation technique. It starts with general backgrounds of SHM and the associated technology including the GLW interrogation method. Then, it is focused on the fundamentals of the GLW-based phased array approach and the development of an innovative signal processing algorithm associated with the 2-D spiral phased sensor array. The SHM approach based on array responses determined by the proposed phased array algorithm implementation is addressed. The experimental validation of the GLW-based 2-D spiral phased array technology and the associated damage detection applications to thin isotropic plate and anisotropic composite plate structures are presented.
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ERIC Educational Resources Information Center
Koyanagi, Chris; Gaines, Sam
This report documents the failure of the educational and mental health systems to meet the needs of children with severe emotional disturbances and provides a guide for advocates at both the state and local levels. Part 1 identifies priorities obtained through a national survey and reports major thrusts, including a wider array of services,…
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Simplifying applications software for vision guided robot implementation
NASA Technical Reports Server (NTRS)
Duncheon, Charlie
1994-01-01
A simple approach to robot applications software is described. The idea is to use commercially available software and hardware wherever possible to minimize system costs, schedules and risks. The U.S. has been slow in the adaptation of robots and flexible automation compared to the fluorishing growth of robot implementation in Japan. The U.S. can benefit from this approach because of a more flexible array of vision guided robot technologies.
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ERIC Educational Resources Information Center
Federal Aviation Administration (DOT), Washington, DC.
Provided in this guide is an array of supplementary activities centered around the topic of aviation. Although the activities are designed for students in grades 2 to 6, teachers are encouraged to adapt them to other grade levels or to the individual abilities of students. The activities are presented in five parts by subject area and within these…
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Kim, Hwi; Hahn, Joonku; Choi, Hee-Jin
2011-04-10
We investigate the viewing angle enhancement of a lenticular three-dimensional (3D) display with a triplet lens array. The theoretical limitations of the viewing angle and view number of the lenticular 3D display with the triplet lens array are analyzed numerically. For this, the genetic-algorithm-based design method of the triplet lens is developed. We show that a lenticular 3D display with viewing angle of 120° and 144 views without interview cross talk can be realized with the use of an optimally designed triplet lens array. © 2011 Optical Society of America
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Cowell, John K; Matsui, Sei-Ichi; Wang, Yong D; LaDuca, Jeffrey; Conroy, Jeffrey; McQuaid, Devin; Nowak, Norma J
2004-05-01
Identification of genetic losses and gains is valuable in analysis of brain tumors. Locus-by-locus analyses have revealed correlations between prognosis and response to chemotherapy and loss or gain of specific genes and loci. These approaches are labor intensive and do not provide a global view of the genetic changes within the tumor cells. Bacterial artificial chromosome (BAC) arrays, which cover the genome with an average resolution of less than 1 MbP, allow defining the sum total of these genetic changes in a single comparative genomic hybridization (CGH) experiment. These changes are directly overlaid on the human genome sequence, thus providing the extent of the amplification or deletion, reflected by a megabase position, and gene content of the abnormal region. Although this array-based CGH approach (CGHa) seems to detect the extent of the genetic changes in tumors reliably, it has not been robustly tested. We compared genetic changes in four newly derived, early-passage glioma cell lines, using spectral karyotyping (SKY) and CGHa. Chromosome changes seen in cell lines under SKY analysis were also detected with CGHa. In addition, CGHa detected cryptic genetic gains and losses and resolved the nature of subtle marker chromosomes that could not be resolved with SKY, thus providing distinct advantages over previous technologies. There was remarkable general concordance between the CGHa results comparing the cell lines to the original tumor, except that the magnitude of the changes seen in the tumor sample was generally suppressed compared with the cell lines, a consequence of normal cells contaminating the tumor sample. CGHa revealed changes in cell lines that were not present in the original tumors and vice versa, even when analyzed at the earliest passage possible, which highlights the adaptation of the cells to in vitro culture. CGHa proved to be highly accurate and efficient for identifying genetic changes in tumor cells. This approach can accurately identify subtle, novel genetic abnormalities in tumors directly linked to the human genome sequence. CGHa far surpasses the resolution and information provided by conventional metaphase CGH, without relying on in vitro culture of tumors for metaphase spreads.
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Horvai, Andrew E; DeVries, Sandy; Roy, Ritu; O'Donnell, Richard J; Waldman, Frederic
2009-11-01
Liposarcoma represents a unique model insofar as some well-differentiated liposarcomas progress to non-lipogenic, so-called 'dedifferentiated,' forms. The well-differentiated and dedifferentiated family of liposarcomas demonstrates amplification of the chromosome subregion 12q13-q15 with resultant amplification of the MDM2 and CDK4 genes. However, the specific genetic changes that distinguish between well-differentiated and dedifferentiated liposarcomas are less well understood. To study the genetic changes in dedifferentiated liposarcomas, paired well-differentiated and dedifferentiated components of 29 tumors were analyzed separately by array-based comparative genomic hybridization. A bacterial artificial chromosome array at approximately 1-Mb resolution was used. The genetic changes were compared with clinical presentation, grade of the dedifferentiated component and overexpression of MDM2 and CDK4. Most tumors (n=21, 72%) were retroperitoneal, with both components present at initial diagnosis (n=25, 86%). Eight tumors (28%) were classified as low-grade dedifferentiation. In four cases (14%), a well-differentiated liposarcoma preceded the presentation of the dedifferentiated tumor by 1-5 years. 12q13-q15 was amplified in all tumors. Using unsupervised hierarchical clustering of copy-number changes, all but two tumors showed close similarities between well-differentiated and dedifferentiated components, and segregated as pairs. Dedifferentiated components had more total amplifications (P=0.008) and a trend for gain at 19q13.2, but no genetic changes were significant in distinguishing between the two components. High-level amplifications of 1p21-32 (n=7, 24%), 1q21-23 (n=9, 31%), 6q23-24 (n=6, 21%) and 12q24 (n=3, 10%) were common, but none significantly correlated with differentiation. Presentation and grade correlated with the frequency of changes at a number of genetic loci (P<0.001), whereas CDK4 immunostaining showed negative correlation with 12q13.13 amplification. The genotypic similarity, at the limit of the array's resolution, between components implies that most genetic changes precede phenotypic 'progression,' early in tumorigenesis. The relationship between genetic changes and presentation or grade may reflect differences in factors that control genomic instability or the background genotype of the tumor.
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A Ground-Based Near Infrared Camera Array System for UAV Auto-Landing in GPS-Denied Environment.
Yang, Tao; Li, Guangpo; Li, Jing; Zhang, Yanning; Zhang, Xiaoqiang; Zhang, Zhuoyue; Li, Zhi
2016-08-30
This paper proposes a novel infrared camera array guidance system with capability to track and provide real time position and speed of a fixed-wing Unmanned air vehicle (UAV) during a landing process. The system mainly include three novel parts: (1) Infrared camera array and near infrared laser lamp based cooperative long range optical imaging module; (2) Large scale outdoor camera array calibration module; and (3) Laser marker detection and 3D tracking module. Extensive automatic landing experiments with fixed-wing flight demonstrate that our infrared camera array system has the unique ability to guide the UAV landing safely and accurately in real time. Moreover, the measurement and control distance of our system is more than 1000 m. The experimental results also demonstrate that our system can be used for UAV automatic accurate landing in Global Position System (GPS)-denied environments.
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Mission applications for advanced photovoltaic solar arrays
NASA Technical Reports Server (NTRS)
Stella, Paul M.; West, John L.; Chave, Robert G.; Mcgee, David P.; Yen, Albert S.
1990-01-01
The suitability of the Advanced Photovoltaic Solar Array (APSA) for future space missions was examined by considering the impact on the spacecraft system in general. The lightweight flexible blanket array system was compared to rigid arrays and a radio-isotope thermoelectric generator (RTG) static power source for a wide range of assumed future earth orbiting and interplanetary mission applications. The study approach was to establish assessment criteria and a rating scheme, identify a reference mission set, perform the power system assessment for each mission, and develop conclusions and recommendations to guide future APSA technology development. The authors discuss the three selected power sources, the assessment criteria and rating definitions, and the reference missions. They present the assessment results in a convenient tabular format. It is concluded that the three power sources examined, APSA, conventional solar arrays, and RTGs, can be considered to complement each other. Each power technology has its own range of preferred applications.
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Diversity arrays technology (DArT) markers in apple for genetic linkage maps.
Schouten, Henk J; van de Weg, W Eric; Carling, Jason; Khan, Sabaz Ali; McKay, Steven J; van Kaauwen, Martijn P W; Wittenberg, Alexander H J; Koehorst-van Putten, Herma J J; Noordijk, Yolanda; Gao, Zhongshan; Rees, D Jasper G; Van Dyk, Maria M; Jaccoud, Damian; Considine, Michael J; Kilian, Andrzej
2012-03-01
Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.
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Wallenborn, M; Petters, O; Rudolf, D; Hantmann, H; Richter, M; Ahnert, P; Rohani, L; Smink, J J; Bulwin, G C; Krupp, W; Schulz, R M; Holland, H
2018-04-23
In the development of cell-based medicinal products, it is crucial to guarantee that the application of such an advanced therapy medicinal product (ATMP) is safe for the patients. The consensus of the European regulatory authorities is: "In conclusion, on the basis of the state of art, conventional karyotyping can be considered a valuable and useful technique to analyse chromosomal stability during preclinical studies". 408 chondrocyte samples (84 monolayers and 324 spheroids) from six patients were analysed using trypsin-Giemsa staining, spectral karyotyping and fluorescence in situ hybridisation, to evaluate the genetic stability of chondrocyte samples from non-clinical studies. Single nucleotide polymorphism (SNP) array analysis was performed on chondrocyte spheroids from five of the six donors. Applying this combination of techniques, the genetic analyses performed revealed no significant genetic instability until passage 3 in monolayer cells and interphase cells from spheroid cultures at different time points. Clonal occurrence of polyploid metaphases and endoreduplications were identified associated with prolonged cultivation time. Also, gonosomal losses were observed in chondrocyte spheroids, with increasing passage and duration of the differentiation phase. Interestingly, in one of the donors, chromosomal aberrations that are also described in extraskeletal myxoid chondrosarcoma were identified. The SNP array analysis exhibited chromosomal aberrations in two donors and copy neutral losses of heterozygosity regions in four donors. This study showed the necessity of combined genetic analyses at defined cultivation time points in quality studies within the field of cell therapy.
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Reconfigurable optical interconnection network for multimode optical fiber sensor arrays
NASA Technical Reports Server (NTRS)
Chen, R. T.; Robinson, D.; Lu, H.; Wang, M. R.; Jannson, T.; Baumbick, R.
1992-01-01
A single-source, single-detector architecture has been developed to implement a reconfigurable optical interconnection network multimode optical fiber sensor arrays. The network was realized by integrating LiNbO3 electrooptic (EO) gratings working at the Raman Na regime and a massive fan-out waveguide hologram (WH) working at the Bragg regime onto a multimode glass waveguide. The glass waveguide utilized the whole substrate as a guiding medium. A 1-to-59 massive waveguide fan-out was demonstrated using a WH operating at 514 nm. Measured diffraction efficiency of 59 percent was experimentally confirmed. Reconfigurability of the interconnection was carried out by generating an EO grating through an externally applied electric field. Unlike conventional single-mode integrated optical devices, the guided mode demonstrated has an azimuthal symmetry in mode profile which is the same as that of a fiber mode.
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A Practical Guide To Solar Array Simulation And PCDU Test
NASA Astrophysics Data System (ADS)
Schmitz, Noah; Carroll, Greg; Clegg, Russell
2011-10-01
Solar arrays consisting of multiple photovoltaic segments provide power to satellites and charge internal batteries for use during eclipse. Solar arrays have unique I-V characteristics and output power which vary with environmental and operational conditions such as temperature, irradiance, spin, and eclipse. Therefore, specialty power solutions are needed to properly test the satellite on the ground, especially the Power Control and Distribution Unit (PCDU) and the Array Power Regulator (APR.) This paper explores some practical and theoretical considerations that should be taken into account when choosing a commercial, off-the-shelf solar array simulator (SAS) for verification of the satellite PCDU. An SAS is a unique power supply with I-V output characteristics that emulate the solar arrays used to power a satellite. It is important to think about the strengths and the limitations of this emulation capability, how closely the SAS approximates a real solar panel, and how best to design a system using SAS as components.
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NASA Technical Reports Server (NTRS)
McMillan, R. Andrew; Howard, Jeanie; Zaluzec, Nestor J.; Kagawa, Hiromi K.; Li, Yi-Fen; Paavola, Chad D.; Trent, Jonathan D.
2004-01-01
Self-assembling biomolecules that form highly ordered structures have attracted interest as potential alternatives to conventional lithographic processes for patterning materials. Here we introduce a general technique for patterning materials on the nanoscale using genetically modified protein cage structures called chaperonins that self-assemble into crystalline templates. Constrained chemical synthesis of transition metal nanoparticles is specific to templates genetically functionalized with poly-Histidine sequences. These arrays of materials are ordered by the nanoscale structure of the crystallized protein. This system may be easily adapted to pattern a variety of materials given the rapidly growing list of peptide sequences selected by screening for specificity for inorganic materials.
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2013-01-01
Background Bacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders' sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units. When spacers are expressed, they direct CRISPR-associated (Cas) proteins to silence complementary invading DNA. In order to characterize the invaders of human microbiomes, we use spacers from CRISPR arrays that we had previously assembled from shotgun metagenomic datasets, and identify contigs that contain these spacers' targets. Results We discover 95,000 contigs that are putative invasive mobile genetic elements, some targeted by hundreds of CRISPR spacers. We find that oral sites in healthy human populations have a much greater variety of mobile genetic elements than stool samples. Mobile genetic elements carry genes encoding diverse functions: only 7% of the mobile genetic elements are similar to known phages or plasmids, although a much greater proportion contain phage- or plasmid-related genes. A small number of contigs share similarity with known integrative and conjugative elements, providing the first examples of CRISPR defenses against this class of element. We provide detailed analyses of a few large mobile genetic elements of various types, and a relative abundance analysis of mobile genetic elements and putative hosts, exploring the dynamic activities of mobile genetic elements in human microbiomes. A joint analysis of mobile genetic elements and CRISPRs shows that protospacer-adjacent motifs drive their interaction network; however, some CRISPR-Cas systems target mobile genetic elements lacking motifs. Conclusions We identify a large collection of invasive mobile genetic elements in human microbiomes, an important resource for further study of the interaction between the CRISPR-Cas immune system and invaders. PMID:23628424
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Lala, A; Berger, J S; Sharma, G; Hochman, J S; Scott Braithwaite, R; Ladapo, J A
2013-01-01
The CYP2C19 genotype is a predictor of adverse cardiovascular events in acute coronary syndrome (ACS) patients undergoing percutaneous coronary intervention (PCI) treated with clopidogrel. We aimed to evaluate the cost-effectiveness of a CYP2C19*2 genotype-guided strategy of antiplatelet therapy in ACS patients undergoing PCI, compared with two 'no testing' strategies (empiric clopidogrel or prasugrel). We developed a Markov model to compare three strategies. The model captured adverse cardiovascular events and antiplatelet-related complications. Costs were expressed in 2010 US dollars and estimated using diagnosis-related group codes and Medicare reimbursement rates. The net wholesale price for prasugrel was estimated as $5.45 per day. A generic estimate for clopidogrel of $1.00 per day was used and genetic testing was assumed to cost $500. Base case analyses demonstrated little difference between treatment strategies. The genetic testing-guided strategy yielded the most QALYs and was the least costly. Over 15 months, total costs were $18 lower with a gain of 0.004 QALY in the genotype-guided strategy compared with empiric clopidogrel, and $899 lower with a gain of 0.0005 QALY compared with empiric prasugrel. The strongest predictor of the preferred strategy was the relative risk of thrombotic events in carriers compared with wild-type individuals treated with clopidogrel. Above a 47% increased risk, a genotype-guided strategy was the dominant strategy. Above a clopidogrel cost of $3.96 per day, genetic testing was no longer dominant but remained cost-effective. Among ACS patients undergoing PCI, a genotype-guided strategy yields similar outcomes to empiric approaches to treatment, but is marginally less costly and more effective. © 2012 International Society on Thrombosis and Haemostasis.
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Gutierrez, Alejandro P; Turner, Frances; Gharbi, Karim; Talbot, Richard; Lowe, Natalie R; Peñaloza, Carolina; McCullough, Mark; Prodöhl, Paulo A; Bean, Tim P; Houston, Ross D
2017-07-05
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species, medium density SNP array for Pacific oyster ( Crassostrea gigas ) and European flat oyster ( Ostrea edulis ), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations. SNP discovery was carried out by whole-genome sequencing (WGS) of pooled genomic DNA samples from eight C. gigas populations, and restriction site-associated DNA sequencing (RAD-Seq) of 11 geographically diverse O. edulis populations. Nearly 12 million candidate SNPs were discovered and filtered based on several criteria, including preference for SNPs segregating in multiple populations and SNPs with monomorphic flanking regions. An Affymetrix Axiom Custom Array was created and tested on a diverse set of samples ( n = 219) showing ∼27 K high quality SNPs for C. gigas and ∼11 K high quality SNPs for O. edulis segregating in these populations. A high proportion of SNPs were segregating in each of the populations, and the array was used to detect population structure and levels of linkage disequilibrium (LD). Further testing of the array on three C. gigas nuclear families ( n = 165) revealed that the array can be used to clearly distinguish between both families based on identity-by-state (IBS) clustering parental assignment software. This medium density, combined-species array will be publicly available through Affymetrix, and will be applied for genome-wide association and evolutionary genetic studies, and for genomic selection in oyster breeding programs. Copyright © 2017 Gutierrez et al.
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Gao, Z J; Jiang, Q; Cheng, D Z; Yan, X X; Chen, Q; Xu, K M
2016-10-02
Objective: To evaluate the application of single nucleotide polymorphism (SNP)-microarray and target gene sequencing technology in the clinical molecular genetic diagnosis of unexplained intellectual disability(ID) or developmental delay (DD). Method: Patients with ID or DD were recruited in the Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics between September 2015 and February 2016. The intellectual assessment of the patients was performed using 0-6-year-old pediatric examination table of neuropsychological development or Wechsler intelligence scale (>6 years). Patients with a DQ less than 49 or IQ less than 51 were included in this study. The patients were scanned by SNP-array for detection of genomic copy number variations (CNV), and the revealed genomic imbalance was confirmed by quantitative real time-PCR. Candidate gene mutation screening was carried out by target gene sequencing technology.Causal mutations or likely pathogenic variants were verified by polymerase chain reaction and direct sequencing. Result: There were 15 children with ID or DD enrolled, 9 males and 6 females. The age of these patients was 7 months-16 years and 9 months. SNP-array revealed that two of the 15 patients had genomic CNV. Both CNV were de novo micro deletions, one involved 11q24.1q25 and the other micro deletion located on 21q22.2q22.3. Both micro deletions were proved to have a clinical significance due to their association with ID, brain DD, unusual faces etc. by querying Decipher database. Thirteen patients with negative findings in SNP-array were consequently examined with target gene sequencing technology, genotype-phenotype correlation analysis and genetic analysis. Five patients were diagnosed with monogenic disorder, two were diagnosed with suspected genetic disorder and six were still negative. Conclusion: Sequential use of SNP-array and target gene sequencing technology can significantly increase the molecular genetic etiologic diagnosis rate of the patients with unexplained ID or DD. Combined use of these technologies can serve as a useful examinational method in assisting differential diagnosis of children with unexplained ID or DD.
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Lacroix, Fréderic; Archambault, Louis; Gingras, Luc; Guillot, Mathieu; Beddar, A Sam; Beaulieu, Luc
2008-08-01
A clinical prototype of a scintillating fiber dosimeter array for quality assurance applications is presented. The array consists of a linear array of 29 plastic scintillation detectors embedded in a water-equivalent plastic sheet coupled to optical fibers used to guide optical photons to a charge coupled device (CCD) camera. The CCD is packaged in a light-tight, radiation-shielded housing designed for convenient transport. A custom designed connector is used to ensure reproducible mechanical positioning of the optical fibers relative to the CCD. Profile and depth dose characterization measurements are presented and show that the prototype provides excellent dose measurement reproducibility (+/-0.8%) in-field and good accuracy (+/-1.6% maximum deviation) relative to the dose measured with an IC10 ionization chamber.
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Hu, Kexiang; Ding, Enjie; Wangyang, Peihua; Wang, Qingkang
2016-06-01
The electromagnetic spectrum and the photoelectric conversion efficiency of the silicon hexagonal nanoconical hole (SiHNH) arrays based solar cells is systematically analyzed according to Rigorous Coupled Wave Analysis (RCWA) and Modal Transmission Line (MTL) theory. An ultimate efficiency of the optimized SiHNH arrays based solar cell is up to 31.92% in consideration of the absorption spectrum, 4.52% higher than that of silicon hexagonal nanoconical frustum (SiHNF) arrays. The absorption enhancement of the SiHNH arrays is due to its lower reflectance and more supported guided-mode resonances, and the enhanced ultimate efficiency is insensitive to bottom diameter (D(bot)) of nanoconical hole and the incident angle. The result provides an additional guideline for the nanostructure surface texturing fabrication design for photovoltaic applications.
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ERIC Educational Resources Information Center
Ansermet, Francois; Lespinasse, James; Gimelli, Stefania; Bena, Frederique; Paoloni-Giacobino, Ariane
2010-01-01
We report the case of a 34-year-old female resulting from a father-daughter sexual abuse and presenting a phenotype of mild intellectual disability with minor dysmorphic features. Karyotyping showed a normal 46, XX constitution. Array-based comparative genomic hybridization (array-CGH) revealed a heterozygote 320kb 6p22.3 microdeletion in the…
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A Novel 6.14 Mb Duplication of Chromosome 8p21 in a Patient with Autism and Self Mutilation
ERIC Educational Resources Information Center
Ozgen, Heval M.; Staal, Wouter G.; Barber, John C.; de Jonge, Maretha V.; Eleveld, Marc J.; Beemer, Frits A.; Hochstenbach, Ron; Poot, Martin
2009-01-01
Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders with a strong genetic etiology. Cytogenetic abnormalities have been detected in 5-10% of the patients with autism. In this study, we present the clinical, cytogenetic and array-comparative genomic hybridization (array-CGH) evaluation of a 13-year-old male with severe…
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Di Gregorio, E; Riberi, E; Belligni, E F; Biamino, E; Spielmann, M; Ala, U; Calcia, A; Bagnasco, I; Carli, D; Gai, G; Giordano, M; Guala, A; Keller, R; Mandrile, G; Arduino, C; Maffè, A; Naretto, V G; Sirchia, F; Sorasio, L; Ungari, S; Zonta, A; Zacchetti, G; Talarico, F; Pappi, P; Cavalieri, S; Giorgio, E; Mancini, C; Ferrero, M; Brussino, A; Savin, E; Gandione, M; Pelle, A; Giachino, D F; De Marchi, M; Restagno, G; Provero, P; Cirillo Silengo, M; Grosso, E; Buxbaum, J D; Pasini, B; De Rubeis, S; Brusco, A; Ferrero, G B
2017-10-01
Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect copy number variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). Identification of genomic disorders in DD/ID. We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes. We further identified and discussed 51 cases with likely pathogenic CNVs spanning novel candidate genes, including genes encoding synaptic components and/or proteins involved in corticogenesis. Additionally, we identified two deletions spanning potential Topological Associated Domain (TAD) boundaries probably affecting the regulatory landscape. We show how phenotypic and genetic analyses of array-CGH data allow unraveling complex cases, identifying rare disease genes, and revealing unexpected position effects. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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Image-Guided Surgery of Primary Breast Cancer Using Ultrasound Phased Arrays
2005-07-01
dual-mode array is ing high-intensity focused ultrasound ( HIFU ) exhibit non- is used), perhaps a result of rectified diffusion. linear behavior that...applications using high-intensity focused ultrasound ( HIFU ). We tems. Once the real-time imaging capability is available for have shown that this dual-mode...INTRODUCTION two effects lead to echo time-shift that can be estimated High intensity focused ultrasound ( HIFU ) is a and have been shown to be related local
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ATLAS, an integrated structural analysis and design system. Volume 1: ATLAS user's guide
NASA Technical Reports Server (NTRS)
Dreisbach, R. L. (Editor)
1979-01-01
Some of the many analytical capabilities provided by the ATLAS Version 4.0 System in the logical sequence are described in which model-definition data are prepared and the subsequent computer job is executed. The example data presented and the fundamental technical considerations that are highlighted can be used as guides during the problem solving process. This guide does not describe the details of the ATLAS capabilities, but provides an introduction to the new user of ATLAS to the level at which the complete array of capabilities described in the ATLAS User's Manual can be exploited fully.
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Historical development of world wide guided missiles
NASA Technical Reports Server (NTRS)
Spearman, M. L.
1978-01-01
This paper attempts to put in perspective the development of missiles from early history to present time. The influence of World War II in accelerating the development of guided missiles, particularly through German scientists, is discussed. The dispersion of German scientists to other countries and the coupling of their work with native talent to develop guided missiles is traced. Particular emphasis is placed on the evolution of the missile in the U.S. and the U.S.S.R. Since the Soviets possess what is probably the world's most complete array of dedicated missile system types, their known inventory is reviewed in some detail.
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Editorial overview: Molecular and genetic bases of disease: the double life of DNA.
McMurray, Cynthia T; Vijg, Jan
2014-06-01
This issue of Current Opinions focuses on the dual role of DNA in life and death. In ancient Roman religion and myth, Janus is the god who looks both to the past and to the future. He guides the beginnings of life, its progression from one condition to another, and he foresees distant events. The analogy to DNA could not be stronger. Closely interacting with the environment, our basic genetics provides the origin of life, guides the quality of health with age, predicts disease, and ultimately foresees our end. A shared and deep interest with the origin of life has long prompted our desire to define aging, and, ultimately, to understand whether it can be reversed. In this special issue, the authors collectively review concepts of normative aging, DNA instability, DNA repair, the genetic contribution of age and diet to disease, and how the basic molecular transactions of DNA guide both the transitions to life as well as the transitions to death. Published by Elsevier Ltd.
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Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening
Joung, Julia; Konermann, Silvana; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Platt, Randall J.; Brigham, Mark D.; Sanjana, Neville E.; Zhang, Feng
2017-01-01
Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeats) immune system has been adapted for genome-scale screening by combining Cas9 with pooled guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom- or ready-made guide RNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening. As each screen is unique, we provide guidelines for determining screening parameters and maintaining sufficient coverage. To validate candidate genes identified from the screen, we further describe strategies for confirming the screening phenotype as well as genetic perturbation through analysis of indel rate and transcriptional activation. Beginning with library design, a genome-scale screen can be completed in 9–15 weeks followed by 4–5 weeks of validation. PMID:28333914
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Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening.
Joung, Julia; Konermann, Silvana; Gootenberg, Jonathan S; Abudayyeh, Omar O; Platt, Randall J; Brigham, Mark D; Sanjana, Neville E; Zhang, Feng
2017-04-01
Forward genetic screens are powerful tools for the unbiased discovery and functional characterization of specific genetic elements associated with a phenotype of interest. Recently, the RNA-guided endonuclease Cas9 from the microbial CRISPR (clustered regularly interspaced short palindromic repeats) immune system has been adapted for genome-scale screening by combining Cas9 with pooled guide RNA libraries. Here we describe a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system. Custom- or ready-made guide RNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening. As each screen is unique, we provide guidelines for determining screening parameters and maintaining sufficient coverage. To validate candidate genes identified by the screen, we further describe strategies for confirming the screening phenotype, as well as genetic perturbation, through analysis of indel rate and transcriptional activation. Beginning with library design, a genome-scale screen can be completed in 9-15 weeks, followed by 4-5 weeks of validation.
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Heep, Madeleine; Mach, Pia; Reautschnig, Philipp; Wettengel, Jacqueline; Stafforst, Thorsten
2017-01-14
Site-directed RNA editing is an approach to reprogram genetic information at the RNA level. We recently introduced a novel guideRNA that allows for the recruitment of human ADAR2 to manipulate genetic information. Here, we show that the current guideRNA design is already able to recruit another human deaminase, ADAR1, in both isoforms, p110 and p150. However, further optimization seems necessary as the current design is less efficient for ADAR1 isoforms. Furthermore, we describe hotspots at which the guideRNA itself is edited and show a way to circumvent this auto-editing without losing editing efficiency at the target. Both findings are important for the advancement of site-directed RNA editing as a tool in basic biology or as a platform for therapeutic editing.
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ERIC Educational Resources Information Center
Baker, Andy; And Others
This instructor guide and the corresponding student reference contain 4 units that include 30 lessons for a course in animal science for 11th- and 12th-grade agriculture science students. The units cover nutrition, genetics, reproduction, and animal health. The instructor's guide contains the following: objectives, competencies, motivational…
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Ensuring Operational Readiness: Private Military Contractor Support for the United States Air Force
2017-03-15
range, supersonic, low altitude terrain following bomber that could evade Soviet detection. It is now loaded with conventional bombs and flown hundreds... bombs that commercially available single engine propeller planes can employ. The Airmen who perform this endeavor are America’s finest. They...array of weapons, to include laser, electro optical, and infrared guided missiles, laser and GPS guided bombs , 2.75” rockets, and a 20mm Gatling gun
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Dang, Fuquan; Tabata, Osamu; Kurokawa, Masaya; Ewis, Ashraf A; Zhang, Lihua; Yamaoka, Yoshihisa; Shinohara, Shouji; Shinohara, Yasuo; Ishikawa, Mitsuru; Baba, Yoshinobu
2005-04-01
We have developed a novel technique for mass production of microfabricated capillary array electrophoresis (mu-CAE) plastic chips for high-speed, high-throughput genetic analysis. The mu-CAE chips, containing 10 individual separation channels of 50-microm width, 50-microm depth, and a 100-microm lane-to-lane spacing at the detection region and a sacrificial channel network, were fabricated on a poly(methyl methacrylate) substrate by injection molding and then bonded manually using a pressure-sensitive sealing tape within several seconds at room temperature. The conditions for injection molding and bonding were carefully characterized to yield mu-CAE chips with well-defined channel and injection structures. A CCD camera equipped with an image intensifier was used to monitor simultaneously the separation in a 10-channel array with laser-induced fluorescence detection. High-performance electrophoretic separations of phiX174 HaeIII DNA restriction fragments and PCR products related to the human beta-globin gene and SP-B gene (the surfactant protein B) have been demonstrated on mu-CAE plastic chips using a methylcellulose sieving matrix in individual channels. The current work demonstrated greatly simplified the fabrication process as well as a detection scheme for mu-CAE chips and will bring the low-cost mass production and application of mu-CAE plastic chips for genetic analysis.
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Unique volatolomic signatures of TP53 and KRAS in lung cells
Davies, M P A; Barash, O; Jeries, R; Peled, N; Ilouze, M; Hyde, R; Marcus, M W; Field, J K; Haick, H
2014-01-01
Background: Volatile organic compounds (VOCs) are potential biomarkers for cancer detection in breath, but it is unclear if they reflect specific mutations. To test this, we have compared human bronchial epithelial cell (HBEC) cell lines carrying the KRASV12 mutation, knockdown of TP53 or both with parental HBEC cells. Methods: VOC from headspace above cultured cells were collected by passive sampling and analysed by thermal desorption gas chromatography mass spectrometry (TD-GC–MS) or sensor array with discriminant factor analysis (DFA). Results: In TD-GC–MS analysis, individual compounds had limited ability to discriminate between cell lines, but by applying DFA analysis combinations of 20 VOCs successfully discriminated between all cell types (accuracies 80–100%, with leave-one-out cross validation). Sensor array detection DFA demonstrated the ability to discriminate samples based on their cell type for all comparisons with accuracies varying between 77% and 93%. Conclusions: Our results demonstrate that minimal genetic changes in bronchial airway cells lead to detectable differences in levels of specific VOCs identified by TD-GC–MS or of patterns of VOCs identified by sensor array output. From the clinical aspect, these results suggest the possibility of breath analysis for detection of minimal genetic changes for earlier diagnosis or for genetic typing of lung cancers. PMID:25051409
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Emergence of antibiotic-resistant extremophiles (AREs).
Gabani, Prashant; Prakash, Dhan; Singh, Om V
2012-09-01
Excessive use of antibiotics in recent years has produced bacteria that are resistant to a wide array of antibiotics. Several genetic and non-genetic elements allow microorganisms to adapt and thrive under harsh environmental conditions such as lethal doses of antibiotics. We attempt to classify these microorganisms as antibiotic-resistant extremophiles (AREs). AREs develop strategies to gain greater resistance to antibiotics via accumulation of multiple genes or plasmids that harbor genes for multiple drug resistance (MDR). In addition to their altered expression of multiple genes, AREs also survive by producing enzymes such as penicillinase that inactivate antibiotics. It is of interest to identify the underlying molecular mechanisms by which the AREs are able to survive in the presence of wide arrays of high-dosage antibiotics. Technologically, "omics"-based approaches such as genomics have revealed a wide array of genes differentially expressed in AREs. Proteomics studies with 2DE, MALDI-TOF, and MS/MS have identified specific proteins, enzymes, and pumps that function in the adaptation mechanisms of AREs. This article discusses the molecular mechanisms by which microorganisms develop into AREs and how "omics" approaches can identify the genetic elements of these adaptation mechanisms. These objectives will assist the development of strategies and potential therapeutics to treat outbreaks of pathogenic microorganisms in the future.
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Tang, Shaohua; Lv, Jiaojiao; Chen, Xiangnan; Bai, Lili; Li, Huanzheng; Chen, Chong; Wang, Ping; Xu, Xueqin; Lu, Jianxin
2016-01-01
To evaluate the usefulness of single-nucleotide polymorphism (SNP) array for prenatal genetic diagnosis of congenital heart defect (CHD), we used this approach to detect clinically significant copy number variants (CNVs) in fetuses with CHDs. A HumanCytoSNP-12 array was used to detect genomic samples obtained from 39 fetuses that exhibited cardiovascular abnormalities on ultrasound and had a normal karyotype. The relationship between CNVs and CHDs was identified by using genotype-phenotype comparisons and searching of chromosomal databases. All clinically significant CNVs were confirmed by real-time PCR. CNVs were detected in 38/39 (97.4%) fetuses: variants of unknown significance were detected in 2/39 (5.1%), and clinically significant CNVs were identified in 7/39 (17.9%). In 3 of the 7 fetuses with clinically significant CNVs, 3 rare and previously undescribed CNVs were detected, and these CNVs encompassed the CHD candidate genes FLNA (Xq28 dup), BCOR (Xp11.4 dup), and RBL2 (16q12.2 del). Compared with conventional cytogenetic genomics, SNP array analysis provides significantly improved detection of submicroscopic genomic aberrations in pregnancies with CHDs. Based on these results, we propose that genomic SNP array is an effective method which could be used in the prenatal diagnostic test to assist genetic counseling for pregnancies with CHDs. © 2015 S. Karger AG, Basel.
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Schaeffer, Anthony J. ; Chung, June ; Heretis, Konstantina ; Wong, Andrew ; Ledbetter, David H. ; Lese Martin, Christa
2004-01-01
Miscarriage is a condition that affects 10%–15% of all clinically recognized pregnancies, most of which occur in the first trimester. Approximately 50% of first-trimester miscarriages result from fetal chromosome abnormalities. Currently, G-banded chromosome analysis is used to determine if large-scale genetic imbalances are the cause of these pregnancy losses. This technique relies on the culture of cells derived from the fetus, a technique that has many limitations, including a high rate of culture failure, maternal overgrowth of fetal cells, and poor chromosome morphology. Comparative genomic hybridization (CGH)–array analysis is a powerful new molecular cytogenetic technique that allows genomewide analysis of DNA copy number. By hybridizing patient DNA and normal reference DNA to arrays of genomic clones, unbalanced gains or losses of genetic material across the genome can be detected. In this study, 41 product-of-conception (POC) samples, which were previously analyzed by G-banding, were tested using CGH arrays to determine not only if the array could identify all reported abnormalities, but also whether any previously undetected genomic imbalances would be discovered. The array methodology detected all abnormalities as reported by G-banding analysis and revealed new abnormalities in 4/41 (9.8%) cases. Of those, one trisomy 21 POC was also mosaic for trisomy 20, one had a duplication of the 10q telomere region, one had an interstitial deletion of chromosome 9p, and the fourth had an interstitial duplication of the Prader-Willi/Angelman syndrome region on chromosome 15q, which, if maternally inherited, has been implicated in autism. This retrospective study demonstrates that the DNA-based CGH-array technology overcomes many of the limitations of routine cytogenetic analysis of POC samples while enhancing the detection of fetal chromosome aberrations. PMID:15127362
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Troggio, Michela; Surbanovski, Nada; Bianco, Luca; Moretto, Marco; Giongo, Lara; Banchi, Elisa; Viola, Roberto; Fernández, Felicdad Fernández; Costa, Fabrizio; Velasco, Riccardo; Cestaro, Alessandro; Sargent, Daniel James
2013-01-01
High throughput arrays for the simultaneous genotyping of thousands of single-nucleotide polymorphisms (SNPs) have made the rapid genetic characterisation of plant genomes and the development of saturated linkage maps a realistic prospect for many plant species of agronomic importance. However, the correct calling of SNP genotypes in divergent polyploid genomes using array technology can be problematic due to paralogy, and to divergence in probe sequences causing changes in probe binding efficiencies. An Illumina Infinium II whole-genome genotyping array was recently developed for the cultivated apple and used to develop a molecular linkage map for an apple rootstock progeny (M432), but a large proportion of segregating SNPs were not mapped in the progeny, due to unexpected genotype clustering patterns. To investigate the causes of this unexpected clustering we performed BLAST analysis of all probe sequences against the 'Golden Delicious' genome sequence and discovered evidence for paralogous annealing sites and probe sequence divergence for a high proportion of probes contained on the array. Following visual re-evaluation of the genotyping data generated for 8,788 SNPs for the M432 progeny using the array, we manually re-scored genotypes at 818 loci and mapped a further 797 markers to the M432 linkage map. The newly mapped markers included the majority of those that could not be mapped previously, as well as loci that were previously scored as monomorphic, but which segregated due to divergence leading to heterozygosity in probe annealing sites. An evaluation of the 8,788 probes in a diverse collection of Malus germplasm showed that more than half the probes returned genotype clustering patterns that were difficult or impossible to interpret reliably, highlighting implications for the use of the array in genome-wide association studies.
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Poćwierz-Kotus, Anita; Bernaś, Rafał; Kent, Matthew P; Lien, Sigbjørn; Leliűna, Egidijus; Dębowski, Piotr; Wenne, Roman
2015-05-06
Native populations of Atlantic salmon in Poland, from the southern Baltic region, became extinct in the 1980s. Attempts to restitute salmon populations in Poland have been based on a Latvian salmon population from the Daugava river. Releases of hatchery reared smolts started in 1986, but to date, only one population with confirmed natural reproduction has been observed in the Slupia river. Our aim was to investigate the genetic differentiation of salmon populations in the southern Baltic using a 7K SNP (single nucleotide polymorphism) array in order to assess the impact of salmon restitution in Poland. One hundred and forty salmon samples were collected from: the Polish Slupia river including wild salmon and individuals from two hatcheries, the Swedish Morrum river and the Lithuanian Neman river. All samples were genotyped using an Atlantic salmon 7K SNP array. A set of 3218 diagnostic SNPs was used for genetic analyses. Genetic structure analyses indicated that the individuals from the investigated populations were clustered into three groups i.e. one clade that included individuals from both hatcheries and the wild population from the Polish Slupia river, which was clearly separated from the other clades. An assignment test showed that there were no stray fish from the Morrum or Neman rivers in the sample analyzed from the Slupia river. Global FST over polymorphic loci was high (0.177). A strong genetic differentiation was observed between the Lithuanian and Swedish populations (FST = 0.28). Wild juvenile salmon specimens that were sampled from the Slupia river were the progeny of fish released from hatcheries and, most likely, were not progeny of stray fish from Sweden or Lithuania. Strong genetic differences were observed between the salmon populations from the three studied locations. Our recommendation is that future stocking activities that aim at restituting salmon populations in Poland include stocking material from the Lithuanian Neman river because of its closer geographic proximity.
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Qin, Shengfang; Wang, Xueyan; Li, Yunxing; Wei, Ping; Chen, Chun; Zeng, Lan
2016-02-01
To explore the genetics mechanism for the phenotypic variability in a patient carrying a rare ring chromosome 9. The karyotype of the patient was analyzed with cytogenetics method. Presence of sex chromosome was confirmed with fluorescence in situ hybridization. The SRY gene was subjected to PCR amplification and direct sequencing. Potential deletion and duplication were detected with array-based comparative genomic hybridization (array-CGH). The karyotype of the patient has comprised 6 types of cell lines containing a ring chromosome 9. The SRY gene sequence was normal. By array-CGH, the patient has carried a hemizygous deletion at 9p24.3-p23 (174 201-9 721 761) encompassing 30 genes from Online Mendelian Inheritance in Man. The phenotypic variability of the 9p deletion syndrome in conjunct with ring chromosome 9 may be attributable to multiple factors including loss of chromosomal material, insufficient dosage of genes, instability of ring chromosome, and pattern of inheritance.
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[Phenotypic and genetic analysis of a patient presented with Tietz/Waardenburg type II a syndrome].
Wang, Huanhuan; Tang, Lifang; Zhang, Jingmin; Hu, Qin; Chen, Yingwei; Xiao, Bing
2015-08-01
To determine the genetic cause for a patient featuring decreased pigmentation of the skin and iris, hearing loss and multiple congenital anomalies. Routine chromosomal banding was performed to analyze the karyotype of the patient and his parents. Single nucleotide polymorphism array (SNP array) was employed to identify cryptic chromosome aberrations, and quantitative real-time PCR was used to confirm the results. Karyotype analysis has revealed no obvious anomaly for the patient and his parents. SNP array analysis of the patient has demonstrated a 3.9 Mb deletion encompassing 3p13p14.1, which caused loss of entire MITF gene. The deletion was confirmed by quantitative real-time PCR. Clinical features of the patient have included severe bilateral hearing loss, decreased pigmentation of the skin and iris and multiple congenital anomalies. The patient, carrying a 3p13p14.1 deletion, has features of Tietz syndrome/Waardenburg syndrome type IIa. This case may provide additional data for the study of genotype-phenotype correlation of this disease.
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Brown, Allan F; Yousef, Gad G; Chebrolu, Kranthi K; Byrd, Robert W; Everhart, Koyt W; Thomas, Aswathy; Reid, Robert W; Parkin, Isobel A P; Sharpe, Andrew G; Oliver, Rebekah; Guzman, Ivette; Jackson, Eric W
2014-09-01
A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.
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Selecting Random Distributed Elements for HIFU using Genetic Algorithm
NASA Astrophysics Data System (ADS)
Zhou, Yufeng
2011-09-01
As an effective and noninvasive therapeutic modality for tumor treatment, high-intensity focused ultrasound (HIFU) has attracted attention from both physicians and patients. New generations of HIFU systems with the ability to electrically steer the HIFU focus using phased array transducers have been under development. The presence of side and grating lobes may cause undesired thermal accumulation at the interface of the coupling medium (i.e. water) and skin, or in the intervening tissue. Although sparse randomly distributed piston elements could reduce the amplitude of grating lobes, there are theoretically no grating lobes with the use of concave elements in the new phased array HIFU. A new HIFU transmission strategy is proposed in this study, firing a number of but not all elements for a certain period and then changing to another group for the next firing sequence. The advantages are: 1) the asymmetric position of active elements may reduce the side lobes, and 2) each element has some resting time during the entire HIFU ablation (up to several hours for some clinical applications) so that the decreasing efficiency of the transducer due to thermal accumulation is minimized. Genetic algorithm was used for selecting randomly distributed elements in a HIFU array. Amplitudes of the first side lobes at the focal plane were used as the fitness value in the optimization. Overall, it is suggested that the proposed new strategy could reduce the side lobe and the consequent side-effects, and the genetic algorithm is effective in selecting those randomly distributed elements in a HIFU array.
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Mulibrey nanism: Two novel mutations in a child identified by Array CGH and DNA sequencing.
Mozzillo, Enza; Cozzolino, Carla; Genesio, Rita; Melis, Daniela; Frisso, Giulia; Orrico, Ada; Lombardo, Barbara; Fattorusso, Valentina; Discepolo, Valentina; Della Casa, Roberto; Simonelli, Francesca; Nitsch, Lucio; Salvatore, Francesco; Franzese, Adriana
2016-08-01
In childhood, several rare genetic diseases have overlapping symptoms and signs, including those regarding growth alterations, thus the differential diagnosis is sometimes difficult. The proband, aged 3 years, was suspected to have Silver-Russel syndrome because of intrauterine growth retardation, postnatal growth retardation, typical facial dysmorphic features, macrocephaly, body asymmetry, and bilateral fifth finger clinodactyly. Other features were left atrial and ventricular enlargement and patent foramen ovale. Total X-ray skeleton showed hypoplasia of the twelfth rib bilaterally and of the coccyx, slender long bones with thick cortex, and narrow medullary channels. The genetic investigation did not confirm Silver-Russel syndrome. At the age of 5 the patient developed an additional sign: hepatomegaly. Array CGH revealed a 147 kb deletion (involving TRIM 37 and SKA2 genes) on one allele of chromosome 17, inherited from his mother. These results suggested Mulibrey nanism. The clinical features were found to fit this hypothesis. Sequencing of the TRIM 37 gene showed a single base change at a splicing locus, inherited from his father that provoked a truncated protein. The combined use of Array CGH and DNA sequencing confirmed diagnosis of Mulibrey nanism. The large deletion involving the SKA2 gene, along with the increased frequency of malignant tumours in mulibrey patients, suggests closed monitoring for cancer of our patient and his mother. Array CGH should be performed as first tier test in all infants with multiple anomalies. The clinician should reconsider the clinical features when the genetics suggests this. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
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Aziz Ebrahimi; Abdolkarim Zarei; Shaneka Lawson; Keith E. Woeste; M. J. M. Smulders
2016-01-01
Persian walnut (Juglans regia L.) is the world's most widely grown nut crop, but large-scale assessments and comparisons of the genetic diversity of the crop are notably lacking. To guide the conservation and utilization of Persian walnut genetic resources, genotypes (n = 189) from 25 different regions in 14 countries on...
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Molecular cytogenetic analysis of Xq critical regions in premature ovarian failure
2013-01-01
Background One of the frequent reasons for unsuccessful conception is premature ovarian failure/primary ovarian insufficiency (POF/POI) that is defined as the loss of functional follicles below the age of 40 years. Among the genetic causes the most common one involves the X chromosome, as in Turner syndrome, partial X deletion and X-autosome translocations. Here we report a case of a 27-year-old female patient referred to genetic counselling because of premature ovarian failure. The aim of this case study to perform molecular genetic and cytogenetic analyses in order to identify the exact genetic background of the pathogenic phenotype. Results For premature ovarian failure disease diagnostics we performed the Fragile mental retardation 1 gene analysis using Southern blot technique and Repeat Primed PCR in order to identify the relationship between the Fragile mental retardation 1 gene premutation status and the premature ovarion failure disease. At this early onset, the premature ovarian failure affected patient we detected one normal allele of Fragile mental retardation 1 gene and we couldn’t verify the methylated allele, therefore we performed the cytogenetic analyses using G-banding and fluorescent in situ hybridization methods and a high resolution molecular cytogenetic method, the array comparative genomic hybridization technique. For this patient applying the G-banding, we identified a large deletion on the X chromosome at the critical region (ChrX q21.31-q28) which is associated with the premature ovarian failure phenotype. In order to detect the exact breakpoints, we used a special cytogenetic array ISCA plus CGH array and we verified a 67.355 Mb size loss at the critical region which include total 795 genes. Conclusions We conclude for this case study that the karyotyping is definitely helpful in the evaluation of premature ovarian failure patients, to identify the non submicroscopic chromosomal rearrangement, and using the array CGH technique we can contribute to the most efficient detection and mapping of exact deletion breakpoints of the deleted Xq region. PMID:24359613
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Salari, Nader; Shohaimi, Shamarina; Najafi, Farid; Nallappan, Meenakshii; Karishnarajah, Isthrinayagy
2014-01-01
Among numerous artificial intelligence approaches, k-Nearest Neighbor algorithms, genetic algorithms, and artificial neural networks are considered as the most common and effective methods in classification problems in numerous studies. In the present study, the results of the implementation of a novel hybrid feature selection-classification model using the above mentioned methods are presented. The purpose is benefitting from the synergies obtained from combining these technologies for the development of classification models. Such a combination creates an opportunity to invest in the strength of each algorithm, and is an approach to make up for their deficiencies. To develop proposed model, with the aim of obtaining the best array of features, first, feature ranking techniques such as the Fisher's discriminant ratio and class separability criteria were used to prioritize features. Second, the obtained results that included arrays of the top-ranked features were used as the initial population of a genetic algorithm to produce optimum arrays of features. Third, using a modified k-Nearest Neighbor method as well as an improved method of backpropagation neural networks, the classification process was advanced based on optimum arrays of the features selected by genetic algorithms. The performance of the proposed model was compared with thirteen well-known classification models based on seven datasets. Furthermore, the statistical analysis was performed using the Friedman test followed by post-hoc tests. The experimental findings indicated that the novel proposed hybrid model resulted in significantly better classification performance compared with all 13 classification methods. Finally, the performance results of the proposed model was benchmarked against the best ones reported as the state-of-the-art classifiers in terms of classification accuracy for the same data sets. The substantial findings of the comprehensive comparative study revealed that performance of the proposed model in terms of classification accuracy is desirable, promising, and competitive to the existing state-of-the-art classification models. PMID:25419659
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A cMUT probe for ultrasound-guided focused ultrasound targeted therapy.
Gross, Dominique; Coutier, Caroline; Legros, Mathieu; Bouakaz, Ayache; Certon, Dominique
2015-06-01
Ultrasound-mediated targeted therapy represents a promising strategy in the arsenal of modern therapy. Capacitive micromachined ultrasonic transducer (cMUT) technology could overcome some difficulties encountered by traditional piezoelectric transducers. In this study, we report on the design, fabrication, and characterization of an ultrasound-guided focused ultrasound (USgFUS) cMUT probe dedicated to preclinical evaluation of targeted therapy (hyperthermia, thermosensitive liposomes activation, and sonoporation) at low frequency (1 MHz) with simultaneous ultrasonic imaging and guidance (15 to 20 MHz). The probe embeds two types of cMUT arrays to perform the modalities of targeted therapy and imaging respectively. The wafer-bonding process flow employed for the manufacturing of the cMUTs is reported. One of its main features is the possibility of implementing two different gap heights on the same wafer. All the design and characterization steps of the devices are described and discussed, starting from the array design up to the first in vitro measurements: optical (microscopy) and electrical (impedance) measurements, arrays' electroacoustic responses, focused pressure field mapping (maximum peak-to-peak pressure = 2.5 MPa), and the first B-scan image of a wire-target phantom.
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Held, Robert Thomas; Zderic, Vesna; Nguyen, Thuc Nghi; Vaezy, Shahram
2006-02-01
An ultrasound (US), image-guided high-intensity focused ultrasound (HIFU) device was developed for noninvasive ablation of uterine fibroids. The HIFU device was an annular phased array, with a focal depth range of 30-60 mm, a natural focus of 50 mm, and a resonant frequency of 3 MHz. The in-house control software was developed to operate the HIFU electronics drive system for inducing tissue coagulation at different distances from the array. A novel imaging algorithm was developed to minimize the HIFU-induced noise in the US images. The device was able to produce lesions in bovine serum albumin-embedded polyacrylamide gels and excised pig liver. The lesions could be seen on the US images as hyperechoic regions. Depths ranging from 30 to 60 mm were sonicated at acoustic intensities of 4100 and 6100 W/cm2 for 15 s each, with the latter producing average lesion volumes at least 63% larger than the former. Tissue sonication patterns that began distal to the transducer produced longer lesions than those that began proximally. The variation in lesion dimensions indicates the possible development of HIFU protocols that increase HIFU throughput and shorten tumor treatment times.
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A large array of high-performance artificial stars using airship-supported small mirrors
NASA Astrophysics Data System (ADS)
Content, Robert; Foxwell, Mark; Murray, Graham J.
2004-10-01
We propose a practical system that can provide a large number of high performance artificial stars, of the order of a few hundred, using an array of small mirrors on an airship supported platform illuminated from the ground by a laser. Our concept offers several advantages over other guide star schemes: Airborne mirror arrays can furnish tip-tilt information; they also permit a considerable reduction in the total ground-laser power required; high intensity guide stars with very small angular image size are possible; and finally they offer very low scattered parasite laser light. More basic & simpler launch-laser & AO technologies can therefore be employed, with potentially huge cost savings, with potentially significant improvement in the quality of the AO correction. The general platform scheme and suitable lift technologies are also discussed. A novel concept for achieving precise positioning is presented whereby the platform & the lifting vehicle are linked by a tether, the platform having a degree of independent control. Our proposal would employ as the lift vehicle an autonomous high altitude airship of the type currently under widespread development in the commercial sector, for use as hubs for telecommunication networks, mobile telephone relay stations, etc.
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Genomic networks of hybrid sterility.
Turner, Leslie M; White, Michael A; Tautz, Diethard; Payseur, Bret A
2014-02-01
Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities"). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad range of organisms and we advocate for widespread adoption of a network-centered approach in speciation genetics.
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Genomic Networks of Hybrid Sterility
Turner, Leslie M.; White, Michael A.; Tautz, Diethard; Payseur, Bret A.
2014-01-01
Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci (“Dobzhansky-Muller incompatibilities”). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven ‘hotspots,’ seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL—but not cis eQTL—were substantially lower when mapping was restricted to a ‘fertile’ subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad range of organisms and we advocate for widespread adoption of a network-centered approach in speciation genetics. PMID:24586194
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New CRISPR-Cas systems from uncultivated microbes
NASA Astrophysics Data System (ADS)
Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.
2017-02-01
CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.
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New CRISPR–Cas systems from uncultivated microbes
Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; ...
2016-12-22
We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNAmore » extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.« less
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New CRISPR–Cas systems from uncultivated microbes
DOE Office of Scientific and Technical Information (OSTI.GOV)
Burstein, David; Harrington, Lucas B.; Strutt, Steven C.
We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNAmore » extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.« less
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Panattoni, Laura; Brown, Paul M; Te Ao, Braden; Webster, Mark; Gladding, Patrick
2012-11-01
A recent clinical trial has demonstrated that patients with acute coronary syndromes (ACS) and the reduced function allele CYP2C19*2 (*2 allele), who are treated with thienopyridines, have an increased risk of adverse cardiac events with clopidogrel, but not with prasugrel. The frequency of the *2 allele varies by ethnicity and the Maoris, Asians and Pacific Islanders of New Zealand have a relatively high incidence. Our objective was to evaluate, from a New Zealand health system perspective, the cost effectiveness of treating all ACS patients with generic clopidogrel compared with prasugrel, and also compared with the genetically guided strategy that *2 allele carriers receive prasugrel and non-carriers receive clopidogrel. A decision-tree model consisting of five health states (myocardial infarction, stroke, bleeding, stent thrombosis and cardiovascular death) was developed. Clinical outcome data (two TRITON-TIMI 38 genetic sub-studies) comparing clopidogrel and prasugrel for both *2 allele carriers and non-carriers were combined with the prevalence of the heterozygosity for the *2 allele in New Zealand Europeans (15%), Maoris (24%), Asians (29%) and Pacific Islanders (45%) to determine the predicted adverse event rate for the New Zealand population. National hospital diagnosis-related group (DRG) discharge codes were used to determine alternative adverse event rates, along with the costs of hospitalizations during the 15 months after patients presented with an ACS. The primary outcome measure was the incremental cost per QALY (calculated using literature-reported weights). Monte Carlo simulations and alternative scenario analysis based on both clinical trial and national hospital incidence were used. Additional analysis considered the overall TRITON-TIMI 38 rates. Costs (in New Zealand dollars [$NZ], year 2009 values) and benefits were discounted at 3% per annum. Actual hospital-based adverse event rates were higher than those reported in the TRITON-TIMI 38 randomized controlled trial and the genetic sub-studies, especially for myocardial infarction and cardiovascular death, and for Maoris and Pacific Islanders. For both sources of adverse event rates, treating the population with prasugrel was associated with worse outcomes (QALYs) than clopidogrel. However, prasugrel became cost effective ($NZ31 751/QALY) when the overall TRITON-TIMI 38 rates were used. A genetic test to guide the selected use of prasugrel was cost effective ($NZ8702/QALY versus $NZ24 617/QALY) for hospital and clinical trial incidence, respectively. Based on the hospital rates, the genetically guided strategy was especially cost effective for Maoris ($NZ7312/QALY) and Pacific Islanders ($NZ7041/QALY). These results were robust to the sensitivity analysis, except the genetically guided strategy under the 15-month clinical trial event rate scenario ($NZ168 748/QALY) did not remain cost effective under a $NZ50 000 threshold. Use of a genetic test to guide thienopyridine treatment in patients with ACS is a potentially cost-effective treatment strategy, especially for Maoris and Pacific Islanders. This treatment strategy also has the potential to reduce ethnic health disparities that exist in New Zealand. However, the results comparing clopidogrel and prasugrel are sensitive to whether the genetic sub-studies or the overall TRITON-TIMI 38 rates are used. While the national hospital event rates may be more appropriate for the New Zealand population, many assumptions are required when they are used to adjust the genetic sub-studies rates.
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STS-116 Astronauts Curbeam and Fuglesang Perform Space Walk
NASA Technical Reports Server (NTRS)
2006-01-01
STS-116 astronaut and mission specialist, Robert Curbeam, along with the European Space Agency's (ESA) Christer Fuglesang (partially out of the frame), are anchored to the International Space Station's Canadarm2 foot restraints. The two were working on the port overhead solar array wing on the Station's P6 truss during the mission's fourth session of Extra Vehicular Activity (EVA). For 6 hours and 38 minutes, the space walkers used specially prepared, tape insulated tools to guide the array wing neatly inside its blanket box.
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A comparison study of different RF shields for an 8-element transceive small animal array at 9.4T.
Jin, Jin; Li, Yu; Liu, Feng; Weber, Ewald; Crozier, Stuart
2011-01-01
In this study, three types of radio-frequency shields are studied and compared in the context of ultra-high field small-animal magnetic resonance imaging. It has been demonstrated that the coil penetration depth and mutual coupling between the coils depend heavily on the type of shield employed. The results were used to guide the design of a 9.4T 8-element transceive small animal array, which provides high overall coil penetration.
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International Space Station (ISS)
2006-12-18
STS-116 astronaut and mission specialist, Robert Curbeam, along with the European Space Agency’s (ESA) Christer Fuglesang (partially out of the frame), are anchored to the International Space Station’s Canadarm2 foot restraints. The two were working on the port overhead solar array wing on the Station’s P6 truss during the mission’s fourth session of Extra Vehicular Activity (EVA). For 6 hours and 38 minutes, the space walkers used specially prepared, tape insulated tools to guide the array wing neatly inside its blanket box.
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Genetics and the unity of biology. Program
DOE Office of Scientific and Technical Information (OSTI.GOV)
Not Available
1988-12-31
International Congresses of Genetics, convened just once every five years, provide a rare opportunity for overview in the field of genetic engineering. The Congress, held August 20-27, 1988 in Toronto, Canada focused on the theme Genetics and the Unity of Biology, which was chosen because the concepts of modern genetics have provided biology with a unifying theoretical structure. This program guide contains a schedule of all Congress activities and a listing of all Symposia, Workshops and Poster Sessions held.
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Array comparative genome hybridization in patients with developmental delay: two example cases.
Hancarova, Miroslava; Drabova, Jana; Zmitkova, Zuzana; Vlckova, Marketa; Hedvicakova, Petra; Novotna, Drahuse; Vlckova, Zdenka; Vejvalkova, Sarka; Marikova, Tatana; Sedlacek, Zdenek
2012-02-15
Developmental delay is often a predictor of mental retardation (MR) or autism, two relatively frequent developmental disorders severely affecting intellectual and social functioning. The causes of these conditions remain unknown in most patients. They have a strong genetic component, but the specific genetic defects can only be identified in a fraction of patients. Recent developments in genomics supported the establishment of the causal link between copy number variants in the genomes of some patients and their affection. One of the techniques suitable for this analysis is array comparative genome hybridization, which can be used both for detailed mapping of chromosome rearrangements identified by classical cytogenetics and for the identification of novel submicroscopic gains or losses of genetic material. We illustrate the power of this approach in two patients. Patient 1 had a cytogenetically visible deletion of chromosome X and the molecular analysis was used to specify the gene content of the deletion and the prognosis of the child. Patient 2 had a seemingly normal karyotype and the analysis revealed a small recurrent deletion of chromosome 1 likely to be responsible for his phenotype. However, the genetic dissection of MR and autism is complicated by high heterogeneity of the genetic aberrations among patients and by broad variability of phenotypic effects of individual genetic defects. Copyright © 2010 Elsevier B.V. All rights reserved.
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Kelwick, Richard; Kopniczky, Margarita; Bower, Iain; Chi, Wenqiang; Chin, Matthew Ho Wai; Fan, Sisi; Pilcher, Jemma; Strutt, James; Webb, Alexander J; Jensen, Kirsten; Stan, Guy-Bart; Kitney, Richard; Freemont, Paul
2015-01-01
Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid phaCAB operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid phaCAB engineered Escherichia coli in comparison to E. coli engineered with the native phaCAB operon from Ralstonia eutropha H16. Additionally, we describe the utilization of non-recyclable waste as a low-cost carbon source for the production of P(3HB).
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Kelwick, Richard; Kopniczky, Margarita; Bower, Iain; Chi, Wenqiang; Chin, Matthew Ho Wai; Fan, Sisi; Pilcher, Jemma; Strutt, James; Webb, Alexander J.; Jensen, Kirsten; Stan, Guy-Bart; Kitney, Richard; Freemont, Paul
2015-01-01
Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid phaCAB operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid phaCAB engineered Escherichia coli in comparison to E. coli engineered with the native phaCAB operon from Ralstonia eutropha H16. Additionally, we describe the utilization of non-recyclable waste as a low-cost carbon source for the production of P(3HB). PMID:25699671
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High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT).
Howard, E L; Whittock, S P; Jakše, J; Carling, J; Matthews, P D; Probasco, G; Henning, J A; Darby, P; Cerenak, A; Javornik, B; Kilian, A; Koutoulis, A
2011-05-01
Implementation of molecular methods in hop (Humulus lupulus L.) breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. However, use of molecular marker technology is limited due to expense, time inefficiency, laborious methodology and dependence on DNA sequence information. Diversity arrays technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of quality polymorphic markers without reliance on DNA sequence information. This study is the first to utilise DArT for hop genotyping, identifying 730 polymorphic markers from 92 hop accessions. The marker quality was high and similar to the quality of DArT markers previously generated for other species; although percentage polymorphism and polymorphism information content (PIC) were lower than in previous studies deploying other marker systems in hop. Genetic relationships in hop illustrated by DArT in this study coincide with knowledge generated using alternate methods. Several statistical analyses separated the hop accessions into genetically differentiated North American and European groupings, with hybrids between the two groups clearly distinguishable. Levels of genetic diversity were similar in the North American and European groups, but higher in the hybrid group. The markers produced from this time and cost-efficient genotyping tool will be a valuable resource for numerous applications in hop breeding and genetics studies, such as mapping, marker-assisted selection, genetic identity testing, guidance in the maintenance of genetic diversity and the directed breeding of superior cultivars.
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ERIC Educational Resources Information Center
Portland Project Committee, OR.
This student guide is divided into two sections: "Mice and Men" and "Environmental Balance," and constitutes parts three and four of the first year of the Portland Project, a three-year, integrated high school science curriculum. Part One of the guide deals with topics such as cell, reproduction, embryology, genetics, genetic…
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Popovic, Milos
2011-03-08
Low-loss waveguide structures may comprise a multimode waveguide supporting a periodic light intensity pattern, and attachments disposed at the waveguide adjacent low-intensity regions of the light intensity pattern.
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Interstitial ablation and imaging of soft tissue using miniaturized ultrasound arrays
NASA Astrophysics Data System (ADS)
Makin, Inder R. S.; Gallagher, Laura A.; Mast, T. Douglas; Runk, Megan M.; Faidi, Waseem; Barthe, Peter G.; Slayton, Michael H.
2004-05-01
A potential alternative to extracorporeal, noninvasive HIFU therapy is minimally invasive, interstitial ultrasound ablation that can be performed laparoscopically or percutaneously. Research in this area at Guided Therapy Systems and Ethicon Endo-Surgery has included development of miniaturized (~3 mm diameter) linear ultrasound arrays capable of high power for bulk tissue ablation as well as broad bandwidth for imaging. An integrated control system allows therapy planning and automated treatment guided by real-time interstitial B-scan imaging. Image quality, challenging because of limited probe dimensions and channel count, is aided by signal processing techniques that improve image definition and contrast. Simulations of ultrasonic heat deposition, bio-heat transfer, and tissue modification provide understanding and guidance for development of treatment strategies. Results from in vitro and in vivo ablation experiments, together with corresponding simulations, will be described. Using methods of rotational scanning, this approach is shown to be capable of clinically relevant ablation rates and volumes.
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Seibert, Tyler M; Fan, Chun Chieh; Wang, Yunpeng; Zuber, Verena; Karunamuni, Roshan; Parsons, J Kellogg; Eeles, Rosalind A; Easton, Douglas F; Kote-Jarai, ZSofia; Al Olama, Ali Amin; Garcia, Sara Benlloch; Muir, Kenneth; Grönberg, Henrik; Wiklund, Fredrik; Aly, Markus; Schleutker, Johanna; Sipeky, Csilla; Tammela, Teuvo Lj; Nordestgaard, Børge G; Nielsen, Sune F; Weischer, Maren; Bisbjerg, Rasmus; Røder, M Andreas; Iversen, Peter; Key, Tim J; Travis, Ruth C; Neal, David E; Donovan, Jenny L; Hamdy, Freddie C; Pharoah, Paul; Pashayan, Nora; Khaw, Kay-Tee; Maier, Christiane; Vogel, Walther; Luedeke, Manuel; Herkommer, Kathleen; Kibel, Adam S; Cybulski, Cezary; Wokolorczyk, Dominika; Kluzniak, Wojciech; Cannon-Albright, Lisa; Brenner, Hermann; Cuk, Katarina; Saum, Kai-Uwe; Park, Jong Y; Sellers, Thomas A; Slavov, Chavdar; Kaneva, Radka; Mitev, Vanio; Batra, Jyotsna; Clements, Judith A; Spurdle, Amanda; Teixeira, Manuel R; Paulo, Paula; Maia, Sofia; Pandha, Hardev; Michael, Agnieszka; Kierzek, Andrzej; Karow, David S; Mills, Ian G; Andreassen, Ole A; Dale, Anders M
2018-01-10
To develop and validate a genetic tool to predict age of onset of aggressive prostate cancer (PCa) and to guide decisions of who to screen and at what age. Analysis of genotype, PCa status, and age to select single nucleotide polymorphisms (SNPs) associated with diagnosis. These polymorphisms were incorporated into a survival analysis to estimate their effects on age at diagnosis of aggressive PCa (that is, not eligible for surveillance according to National Comprehensive Cancer Network guidelines; any of Gleason score ≥7, stage T3-T4, PSA (prostate specific antigen) concentration ≥10 ng/L, nodal metastasis, distant metastasis). The resulting polygenic hazard score is an assessment of individual genetic risk. The final model was applied to an independent dataset containing genotype and PSA screening data. The hazard score was calculated for these men to test prediction of survival free from PCa. Multiple institutions that were members of international PRACTICAL consortium. All consortium participants of European ancestry with known age, PCa status, and quality assured custom (iCOGS) array genotype data. The development dataset comprised 31 747 men; the validation dataset comprised 6411 men. Prediction with hazard score of age of onset of aggressive cancer in validation set. In the independent validation set, the hazard score calculated from 54 single nucleotide polymorphisms was a highly significant predictor of age at diagnosis of aggressive cancer (z=11.2, P<10 -16 ). When men in the validation set with high scores (>98th centile) were compared with those with average scores (30th-70th centile), the hazard ratio for aggressive cancer was 2.9 (95% confidence interval 2.4 to 3.4). Inclusion of family history in a combined model did not improve prediction of onset of aggressive PCa (P=0.59), and polygenic hazard score performance remained high when family history was accounted for. Additionally, the positive predictive value of PSA screening for aggressive PCa was increased with increasing polygenic hazard score. Polygenic hazard scores can be used for personalised genetic risk estimates that can predict for age at onset of aggressive PCa. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
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USDA-ARS?s Scientific Manuscript database
Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such ...
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Sorting white blood cells in microfabricated arrays
NASA Astrophysics Data System (ADS)
Castelino, Judith Andrea Rose
Fractionating white cells in microfabricated arrays presents the potential for detecting cells with abnormal adhesive or deformation properties. A possible application is separating nucleated fetal red blood cells from maternal blood. Since fetal cells are nucleated, it is possible to extract genetic information about the fetus from them. Separating fetal cells from maternal blood would provide a low cost noninvasive prenatal diagnosis for genetic defects, which is not currently available. We present results showing that fetal cells penetrate further into our microfabricated arrays than adult cells, and that it is possible to enrich the fetal cell fraction using the arrays. We discuss modifications to the array which would result in further enrichment. Fetal cells are less adhesive and more deformable than adult white cells. To determine which properties limit penetration, we compared the penetration of granulocytes and lymphocytes in arrays with different etch depths, constriction size, constriction frequency, and with different amounts of metabolic activity. The penetration of lymphocytes and granulocytes into constrained and unconstrained arrays differed qualitatively. In constrained arrays, the cells were activated by repeated shearing, and the number of cells stuck as a function of distance fell superexponentially. In unconstrained arrays the number of cells stuck fell slower than an exponential. We attribute this result to different subpopulations of cells with different sticking parameters. We determined that penetration in unconstrained arrays was limited by metabolic processes, and that when metabolic activity was reduced penetration was limited by deformability. Fetal cells also contain a different form of hemoglobin with a higher oxygen affinity than adult hemoglobin. Deoxygenated cells are paramagnetic and are attracted to high magnetic field gradients. We describe a device which can separate cells using 10 μm magnetic wires to deflect the paramagnetic cells. We present preliminary results from a test system that separates paramagnetic beads from latex beads. The separation is limited by our ability to produce the high field gradients which are necessary to separate cells according to their hemoglobin content, and we present estimates of the magnetic gradients we achieved.
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NASA Technical Reports Server (NTRS)
Aboudi, Jacob; Pindera, Marek-Jerzy
1992-01-01
A user's guide for the program gmc.f is presented. The program is based on the generalized method of cells model (GMC) which is capable via a micromechanical analysis, of predicting the overall, inelastic behavior of unidirectional, multi-phase composites from the knowledge of the properties of the viscoplastic constituents. In particular, the program is sufficiently general to predict the response of unidirectional composites having variable fiber shapes and arrays.
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Future Field Programmable Gate Array (FPGA) Design Methodologies and Tool Flows
2008-07-01
a) that the results are accepted by users, vendors, … and (b) that they can quantitatively explain HPC rules of thumb such as: “OpenMP is easier...in productivity that were demonstrated by traditional software systems. Using advances in software productivity as a guide , we have identified three...of this study we developed a productivity model to guide our investigation (14). Models have limitations and the model we propose is no exception
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Improvement of illumination uniformity for LED flat panel light by using micro-secondary lens array.
Lee, Hsiao-Wen; Lin, Bor-Shyh
2012-11-05
LED flat panel light is an innovative lighting product in recent years. However, current flat panel light products still contain some drawbacks, such as narrow lighting areas and hot spots. In this study, a micro-secondary lens array technique was proposed and applied for the design of the light guide surface to improve the illumination uniformity. By using the micro-secondary lens array, the candela distribution of the LED flat panel light can be adjusted to similar to batwing distribution to improve the illumination uniformity. The experimental results show that the enhancement of the floor illumination uniformity is about 61%, and that of the wall illumination uniformity is about 20.5%.
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Ultrasound-guided chest biopsies.
Middleton, William D; Teefey, Sharlene A; Dahiya, Nirvikar
2006-12-01
Pulmonary nodules that are surrounded by aerated lung cannot be visualized with sonography. Therefore, percutaneous biopsy must be guided with computed tomography or fluoroscopy. Although this restriction only applies to central lung nodules, it has permeated referral patterns for other thoracic lesions and has retarded the growth of ultrasound-guided interventions. Nevertheless, sonography is an extremely flexible modality that can expeditiously guide many biopsy procedures in the thorax. Peripheral pulmonary nodules can be successfully biopsied with success rates exceeding 90% and complications rates of less than 5%. Orienting the probe parallel to the intercostal space facilitates biopsies of peripheral pulmonary nodules. Anterior mediastinal masses that extend to the parasternal region are often easily approachable provided the internal mammary vessels, costal cartilage, and deep great vessels are identified and avoided. Superior mediastinal masses can be sampled from a suprasternal or supraclavicular approach. Phased array probes or tightly curved arrays may provide improved access for biopsies in this location. Posterior mediastinal masses are more difficult to biopsy with ultrasound guidance because of the overlying paraspinal muscles. However, when posterior mediastinal masses extend into the posterior medial pleural region, they can be biopsied with ultrasound guidance. Because many lung cancers metastasize to the supraclavicular nodes, it is important to evaluate the supraclavicular region when determining the best approach to obtain a tissue diagnosis. When abnormal supraclavicular nodes are present, they often are the easiest and safest lesions to biopsy.
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Kluk, Michael Joseph; An, Yu; James, Philip; Coulter, David; Harris, David; Wu, Bai-Lin; Shen, Yiping
2011-05-01
The molecular testing options available for the diagnosis of genetic disorders are numerous and include a variety of different assay platforms. The consultative input of molecular pathologists and cytogeneticists, working closely with the ordering clinicians, is often important for definitive diagnosis. Herein, we describe two patients who had long histories of unexplained signs and symptoms with a high clinical suspicion of an underlying genetic etiology. Initial molecular testing in both cases was negative, but the application of high-resolution array comparative genomic hybridization technology lead to definitive diagnosis in both cases. We summarize the clinical findings and molecular testing in each case, discuss the differential diagnoses, and review the clinical and pathological findings of Mowat-Wilson syndrome. This report highlights the importance for those involved in molecular testing to know the nature of the underlying genetic abnormalities associated with the suspected diagnosis, to recognize the limitations of each testing platform, and to persistently pursue repeat testing using high-resolution technologies when indicated. This concept is applicable to both germline and somatic molecular genetic testing. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
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Standards of Practice: Applying Genetics and Genomics Resources to Oncology .
Kerber, Alice S; Ledbetter, Nancy J
2017-04-01
Knowledge about genetics and genomics and its application to oncology care is rapidly expanding and evolving. As a result, oncology nurses at all levels must develop and maintain their knowledge of genetics and genomics, as well as be aware of resources to guide practice. This article focuses on implementation of the standards described in the updated Genetics/Genomics Nursing: Scope and Standards of Practice by the basic practitioner. .
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High aspect ratio 10-nm-scale nanoaperture arrays with template-guided metal dewetting
Wang, Ying Min; Lu, Liangxing; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Zhang, Yong Wei; Yang, Joel K. W.
2015-01-01
We introduce an approach to fabricate ordered arrays of 10-nm-scale silica-filled apertures in a metal film without etching or liftoff. Using low temperature (<400°C) thermal dewetting of metal films guided by nano-patterned templates, apertures with aspect ratios up to 5:1 are demonstrated. Apertures form spontaneously during the thermal process without need for further processing. Although the phenomenon of dewetting has been well studied, this is the first demonstration of its use in the fabrication of nanoapertures in a spatially controllable manner. In particular, the achievement of 10-nm length-scale patterning at high aspect ratio with thermal dewetting is unprecedented. By varying the nanotemplate design, we show its strong influence over the positions and sizes of the nanoapertures. In addition, we construct a three-dimensional phase field model of metal dewetting on nano-patterned substrates. The simulation data obtained closely corroborates our experimental results and reveals new insights to template dewetting at the nanoscale. Taken together, this fabrication method and simulation model form a complete toolbox for 10-nm-scale patterning using template-guided dewetting that could be extended to a wide range of material systems and geometries. PMID:25858792
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High aspect ratio 10-nm-scale nanoaperture arrays with template-guided metal dewetting.
Wang, Ying Min; Lu, Liangxing; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Zhang, Yong Wei; Yang, Joel K W
2015-04-10
We introduce an approach to fabricate ordered arrays of 10-nm-scale silica-filled apertures in a metal film without etching or liftoff. Using low temperature (<400°C) thermal dewetting of metal films guided by nano-patterned templates, apertures with aspect ratios up to 5:1 are demonstrated. Apertures form spontaneously during the thermal process without need for further processing. Although the phenomenon of dewetting has been well studied, this is the first demonstration of its use in the fabrication of nanoapertures in a spatially controllable manner. In particular, the achievement of 10-nm length-scale patterning at high aspect ratio with thermal dewetting is unprecedented. By varying the nanotemplate design, we show its strong influence over the positions and sizes of the nanoapertures. In addition, we construct a three-dimensional phase field model of metal dewetting on nano-patterned substrates. The simulation data obtained closely corroborates our experimental results and reveals new insights to template dewetting at the nanoscale. Taken together, this fabrication method and simulation model form a complete toolbox for 10-nm-scale patterning using template-guided dewetting that could be extended to a wide range of material systems and geometries.
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Side-emitting illuminators using LED sources
NASA Astrophysics Data System (ADS)
Zhao, Feng; Van Derlofske, John F.
2003-11-01
This study investigates illuminators composed of light emitting diode (LED) array sources and side-emitting light guides to provide efficient general illumination. Specifically, new geometries are explored to increase the efficiency of current systems while maintaining desired light distribution. LED technology is already successfully applied in many illumination applications, such as traffic signals and liquid crystal display (LCD) backlighting. It provides energy-efficient, small-package, long-life, and color-adjustable illumination. However, the use of LEDs in general illumination is still in its early stages. Current side-emitting systems typically use a light guide with light sources at one end, an end-cap surface at the other end, and light releasing sidewalls. This geometry introduces efficiency loss that can be as high as 40%. The illuminators analyzed in this study use LED array sources along the longitude of a light guide to increase the system efficiency. These new geometries also provide the freedom of elongating the system without sacrificing system efficiency. In addition, alternative geometries can be used to create white light with monochromatic LED sources. As concluded by this study, the side-emitting illuminators using LED sources gives the possibility of an efficient, distribution-controllable linear lighting system.
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Prasad, Tushar; Colvin, Vicki L; Mittleman, Daniel M
2007-12-10
We measure the normal-incidence transmission coefficient of photonic crystal slabs with hexagonal arrays of air holes in silicon. The transmission spectra exhibit sharp resonant features with Fano line shapes. They are produced due to the coupling of the leaky photonic crystal modes, called guided resonances, to the continuum of free-space modes. We investigate the effects of several types of structural disorder on the spectra of these resonances. Our results indicate that guided resonances are very tolerant to disorder in the hole diameter and to interface roughness, but very sensitive to disorder in the lattice periodicity.
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Kreisel, F.; Kulkarni, S.; Kerns, R. T.; Hassan, A.; Deshmukh, H.; Nagarajan, R.; Frater, J. L.; Cashen, A.
2013-01-01
Despite recent attempts at sub-categorization, including gene expression profiling into prognostically different groups of “germinal center B-cell type” and “activated B-cell type”, diffuse large B-cell lymphoma (DLBCL) remains a biologically heterogenous tumor with no clear prognostic biomarkers to guide therapy. Whole genome, high resolution array comparative genomic hybridization (aCGH) was performed on 4 cases of chemoresistant DLBCL and 4 cases of chemo-responsive DLBCL to identify genetic differences which may correlate with response to R-CHOP therapy. Array CGH analysis identified 7 DNA copy number alteration (CNA) regions exclusive to the chemoresistant group, consisting of amplifications at 1p36.13, 1q42.3, 3p21.31, 7q11.23, and 16p13.3, and loss at 9p21.3, and 14p21.31. Copy number loss of the tumor suppressor genes CDKN2A (p16, p14) and CDKN2B (p15) at 9p21.3 was validated by fluorescence in situ hybridization and immunohistochemistry as independent techniques. In the chemo-sensitive group, 12 CNAs were detected consisting of segment gains on 1p36.11, 1p36.22, 2q11.2, 8q24.3, 12p13.33, and 22q13.2 and segment loss on 6p21.32. RUNX3, a tumor suppressor gene located on 1p36.11 and MTHFR, which encodes for the enzyme methylenetetrahydrofolate reductase, located on 1p36.22 are the only known genes in this group associated with lymphoma. Whole genome aCGH analysis has detected copy number alterations exclusive to either chemoresistant or chemo-responsive DLBCL that may represent consistent clonal changes predictive for prognosis and outcome of chemotherapy. PMID:21504712
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Experimental Validation of a Fast Forward Model for Guided Wave Tomography of Pipe Elbows.
Brath, Alex J; Simonetti, Francesco; Nagy, Peter B; Instanes, Geir
2017-05-01
Ultrasonic guided wave tomography (GWT) methods for the detection of corrosion and erosion damage in straight pipe sections are now well advanced. However, successful application of GWT to pipe bends has not yet been demonstrated due to the computational burden associated with the complex forward model required to simulate guided wave propagation through the bend. In a previous paper [Brath et al., IEEE Trans. Ultrason., Ferroelectr., Freq. Control, vol. 61, pp. 815-829, 2014], we have shown that the speed of the forward model can be increased by replacing the 3-D pipe bend with a 2-D rectangular domain in which guided wave propagation is formulated based on an artificially inhomogeneous and elliptically anisotropic (INELAN) acoustic model. This paper provides further experimental validation of the INLEAN model by studying the traveltime shifts caused by the introduction of shallow defects on the elbow of a pipe bend. Comparison between experiments and simulations confirms that a defect can be modeled as a phase velocity perturbation to the INLEAN velocity field with accuracy that is within the experimental error of the measurements. In addition, it is found that the sensitivity of traveltime measurements to the presence of damage decreases as the damage position moves from the interior side of the bend (intrados) to the exterior one (extrados). This effect is due to the nonuniform ray coverage obtainable when transmitting the guided wave signals with one ring array of sources on one side of the elbow and receiving with a second array on the other side.
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Systematic exploration of essential yeast gene function with temperature-sensitive mutants
Li, Zhijian; Vizeacoumar, Franco J; Bahr, Sondra; Li, Jingjing; Warringer, Jonas; Vizeacoumar, Frederick S; Min, Renqiang; VanderSluis, Benjamin; Bellay, Jeremy; DeVit, Michael; Fleming, James A; Stephens, Andrew; Haase, Julian; Lin, Zhen-Yuan; Baryshnikova, Anastasia; Lu, Hong; Yan, Zhun; Jin, Ke; Barker, Sarah; Datti, Alessandro; Giaever, Guri; Nislow, Corey; Bulawa, Chris; Myers, Chad L; Costanzo, Michael; Gingras, Anne-Claude; Zhang, Zhaolei; Blomberg, Anders; Bloom, Kerry; Andrews, Brenda; Boone, Charles
2012-01-01
Conditional temperature-sensitive (ts) mutations are valuable reagents for studying essential genes in the yeast Saccharomyces cerevisiae. We constructed 787 ts strains, covering 497 (~45%) of the 1,101 essential yeast genes, with ~30% of the genes represented by multiple alleles. All of the alleles are integrated into their native genomic locus in the S288C common reference strain and are linked to a kanMX selectable marker, allowing further genetic manipulation by synthetic genetic array (SGA)–based, high-throughput methods. We show two such manipulations: barcoding of 440 strains, which enables chemical-genetic suppression analysis, and the construction of arrays of strains carrying different fluorescent markers of subcellular structure, which enables quantitative analysis of phenotypes using high-content screening. Quantitative analysis of a GFP-tubulin marker identified roles for cohesin and condensin genes in spindle disassembly. This mutant collection should facilitate a wide range of systematic studies aimed at understanding the functions of essential genes. PMID:21441928
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Darcy, Diana C; Lewis, Eleanor T; Ormond, Kelly E; Clark, David J; Trafton, Jodie A
2011-11-02
Genetic testing is increasingly used as a tool throughout the health care system. In 2011 the number of clinically available genetic tests is approaching 2,000, and wide variation exists between these tests in their sensitivity, specificity, and clinical implications, as well as the potential for discrimination based on the results. As health care systems increasingly implement electronic medical record systems (EMRs) they must carefully consider how to use information from this wide spectrum of genetic tests, with whom to share information, and how to provide decision support for clinicians to properly interpret the information. Although some characteristics of genetic tests overlap with other medical test results, there are reasons to make genetic test results widely available to health care providers and counterbalancing reasons to restrict access to these test results to honor patient preferences, and avoid distracting or confusing clinicians with irrelevant but complex information. Electronic medical records can facilitate and provide reasonable restrictions on access to genetic test results and deliver education and decision support tools to guide appropriate interpretation and use. This paper will serve to review some of the key characteristics of genetic tests as they relate to design of access control and decision support of genetic test information in the EMR, emphasizing the clear need for health information technology (HIT) to be part of optimal implementation of genetic medicine, and the importance of understanding key characteristics of genetic tests when designing HIT applications.
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Kratchman, Louis B.; Schurzig, Daniel; McRackan, Theodore R.; Balachandran, Ramya; Noble, Jack H.; Webster, Robert J.; Labadie, Robert F.
2014-01-01
The current technique for cochlear implantation (CI) surgery requires a mastoidectomy to gain access to the cochlea for electrode array insertion. It has been shown that microstereotactic frames can enable an image-guided, minimally invasive approach to CI surgery called percutaneous cochlear implantation (PCI) that uses a single drill hole for electrode array insertion, avoiding a more invasive mastoidectomy. Current clinical methods for electrode array insertion are not compatible with PCI surgery because they require a mastoidectomy to access the cochlea; thus, we have developed a manually operated electrode array insertion tool that can be deployed through a PCI drill hole. The tool can be adjusted using a preoperative CT scan for accurate execution of the advance off-stylet (AOS) insertion technique and requires less skill to operate than is currently required to implant electrode arrays. We performed three cadaver insertion experiments using the AOS technique and determined that all insertions were successful using CT and microdissection. PMID:22851233
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AlGaAs phased array laser for optical communications
NASA Technical Reports Server (NTRS)
Carlson, N. W.
1989-01-01
Phased locked arrays of multiple AlGaAs diode laser emitters were investigated both in edge emitting and surface emitting configurations. CSP edge emitter structures, coupled by either evanescent waves or Y-guides, could not achieve the required powers (greater than or similar to 500 mW) while maintaining a diffraction limited, single lobed output beam. Indeed, although the diffraction limit was achieved in this type of device, it was at low powers and in the double lobed radiation pattern characteristic of out-of-phase coupling. Grating surface emitting (GSE) arrays were, therefore, investigated with more promising results. The incorporation of second order gratings in distribute Bragg reflector (DBR) structures allows surface emission, and can be configured to allow injection locking and lateral coupling to populate 2-D arrays that should be able to reach power levels commensurate with the needs of high performance, free space optical communications levels. Also, a new amplitude modulation scheme was developed for GSE array operation.
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Integrating surgery and genetic testing for the modern surgeon.
Caso, Raul; Beamer, Matthew; Lofthus, Alexander D; Sosin, Michael
2017-10-01
The field of cancer genetics is rapidly evolving and several genetic mutations have been identified in hereditary cancer syndromes. These mutations can be diagnosed via routine genetic testing allowing prompt intervention. This is especially true for certain variants of colorectal, breast, and thyroid cancers where genetic testing may guide surgical therapy. Ultimately, surgical intervention may drastically diminish disease manifestation or progression in individuals deemed as high-risk based on their genetic makeup. Understanding the concepts of gene-based testing and integrating into current surgical practice is crucial. This review addresses common genetic syndromes, tests, and interventions salient to the current surgeon.
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Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L.; Costanzo, Michael; Andrews, Brenda; Boone, Charles
2017-01-01
Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae. In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. PMID:28325812
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Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L; Costanzo, Michael; Andrews, Brenda; Boone, Charles
2017-05-05
Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. Copyright © 2017 Usaj et al.
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High Frequency Ultrasound Array Designed for Ultrasound Guided Breast Biopsy
Cummins, Thomas; Eliahoo, Payam; Shung, K. Kirk
2016-01-01
This paper describes the development of a miniaturized high frequency linear array that can be integrated within a core biopsy needle to improve tissue sampling accuracy during breast cancer biopsy procedures. The 64 element linear array has an element width of 14 μm, kerf width of 6 μm, element length of 1 mm and element thickness of 24 μm. The 2–2 array composite was fabricated using deep reactive ion etching of PMN-PT single crystal material. The array composite fabrication process as well as a novel high density electrical interconnect solution are presented and discussed. Array performance measurements show that the array had a center frequency and fractional bandwidth (−6 dB) of 59.1 MHz and 29.4%, respectively. Insertion loss and adjacent element cross talk at the center frequency were −41.0 dB and −23.7 dB, respectively. A B-mode image of a tungsten wire target phantom was captured using a synthetic aperture imaging system and the imaging test results demonstrate axial and lateral resolutions of 33.2 μm and 115.6 um, respectively. PMID:27046895
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2013-01-01
In this work, nanoimprint lithography combined with standard anodization etching is used to make perfectly organised triangular arrays of vertical cylindrical alumina nanopores onto standard <100>−oriented silicon wafers. Both the pore diameter and the period of alumina porous array are well controlled and can be tuned: the periods vary from 80 to 460 nm, and the diameters vary from 15 nm to any required diameter. These porous thin layers are then successfully used as templates for the guided epitaxial growth of organised mono-crystalline silicon nanowire arrays in a chemical vapour deposition chamber. We report the densities of silicon nanowires up to 9 × 109 cm−2 organised in highly regular arrays with excellent diameter distribution. All process steps are demonstrated on surfaces up to 2 × 2 cm2. Specific emphasis was made to select techniques compatible with microelectronic fabrication standards, adaptable to large surface samples and with a reasonable cost. Achievements made in the quality of the porous alumina array, therefore on the silicon nanowire array, widen the number of potential applications for this technology, such as optical detectors or biological sensors. PMID:23773702
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NASA Astrophysics Data System (ADS)
Yoo, Byungseok; Pines, Darryll J.
2018-05-01
This paper investigates the use of uniaxial comb-shaped Fe-Ga alloy (Galfenol) patches in the development of a Magnetostrictive Phased Array Sensor (MPAS) for the Guided Wave (GW) damage inspection technique. The MPAS consists of six highly-textured Galfenol patches with a <100> preferred orientation and a Hexagonal Magnetic Circuit Device (HMCD). The Galfenol patches individually aligned to distinct azimuthal directions were permanently attached to a thin aluminum plate specimen. The detachable HMCD encloses a biasing magnet and six sensing coils with unique directional sensing preferences, equivalent to the specific orientation of the discrete Galfenol patches. The preliminary experimental tests validated that the GW sensing performance and directional sensitivity of the Galfenol-based sensor were significantly improved by the magnetic shape anisotropy effect on the fabrication of uniaxial comb fingers to a Galfenol disc patch. We employed a series of uniaxial comb-shaped Galfenol patches to form an MPAS with a hexagonal sensor configuration, uniformly arranged within a diameter of 1". The Galfenol MPAS was utilized to identify structural damage simulated by loosening joint bolts used to fasten the plate specimen to a frame structure. We compared the damage detection results of the MPAS with those of a PZT Phased Array Sensor (PPAS) collocated to the back surface of the plate. The directional filtering characteristic of the Galfenol MPAS led to acquiring less complicated GW signals than the PPAS using omnidirectional PZT discs. However, due to the detection limit of the standard hexagonal patterned array, the two array sensors apparently identified only the loosened bolts located along one of the preferred orientations of the array configuration. The use of the fixed number of the Galfenol patches for the MPAS construction constrained the capability of sensing point multiplication of the HMCD by altering its rotational orientation, resulting in such damage detection limitation of the MPAS.
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PyRhO: A Multiscale Optogenetics Simulation Platform
Evans, Benjamin D.; Jarvis, Sarah; Schultz, Simon R.; Nikolic, Konstantin
2016-01-01
Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO. The purpose of developing PyRhO is three-fold: (i) to characterize new (and existing) opsins by automatically fitting a minimal set of experimental data to three-, four-, or six-state kinetic models, (ii) to simulate these models at the channel, neuron and network levels, and (iii) provide functional insights through model selection and virtual experiments in silico. The module is written in Python with an additional IPython/Jupyter notebook based GUI, allowing models to be fit, simulations to be run and results to be shared through simply interacting with a webpage. The seamless integration of model fitting algorithms with simulation environments (including NEURON and Brian2) for these virtual opsins will enable neuroscientists to gain a comprehensive understanding of their behavior and rapidly identify the most suitable variant for application in a particular biological system. This process may thereby guide not only experimental design and opsin choice but also alterations of the opsin genetic code in a neuro-engineering feed-back loop. In this way, we expect PyRhO will help to significantly advance optogenetics as a tool for transforming biological sciences. PMID:27148037
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PyRhO: A Multiscale Optogenetics Simulation Platform.
Evans, Benjamin D; Jarvis, Sarah; Schultz, Simon R; Nikolic, Konstantin
2016-01-01
Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO. The purpose of developing PyRhO is three-fold: (i) to characterize new (and existing) opsins by automatically fitting a minimal set of experimental data to three-, four-, or six-state kinetic models, (ii) to simulate these models at the channel, neuron and network levels, and (iii) provide functional insights through model selection and virtual experiments in silico. The module is written in Python with an additional IPython/Jupyter notebook based GUI, allowing models to be fit, simulations to be run and results to be shared through simply interacting with a webpage. The seamless integration of model fitting algorithms with simulation environments (including NEURON and Brian2) for these virtual opsins will enable neuroscientists to gain a comprehensive understanding of their behavior and rapidly identify the most suitable variant for application in a particular biological system. This process may thereby guide not only experimental design and opsin choice but also alterations of the opsin genetic code in a neuro-engineering feed-back loop. In this way, we expect PyRhO will help to significantly advance optogenetics as a tool for transforming biological sciences.
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[Dandy-walker syndrome and microdeletions on chromosome 7].
Liao, Can; Fu, Fang; Li, Ru; Pan, Min; Yang, Xin; Yi, Cui-xing; Li, Jian; Li, Dong-zhi
2012-02-01
To investigate genetic etiology of Dandy-Walker syndrome with array-based comparative genomic hybridization (array-CGH). Eight fetuses with Dandy-Walker malformations but normal karyotypes by conventional cytogenetic technique were selected. DNA samples were extracted and hybridized with Affymetrix cytogenetic 2.7 M arrays by following the manufacturer's standard protocol. The data were analyzed by special software packages. By using array-CGH technique, common deletions and duplication on chromosome 7p21.3 were identified in three cases, within which were central nervous system disease associated genes NDUFA4 and PHF14. Copy number variations (CNVs) of chromosome 7p21.3 region are associated with Dandy-Walker malformations which may be due to haploinsufficiency or overexpression of NDUFA4 and PHF14 genes.
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Mohapatra, Gayatry; Engler, David A.; Starbuck, Kristen D.; Kim, James C.; Bernay, Derek C.; Scangas, George A.; Rousseau, Audrey; Batchelor, Tracy T.; Betensky, Rebecca A.; Louis, David N.
2010-01-01
Molecular genetic analysis of cancer is rapidly evolving as a result of improvement in genomic technologies and the growing applicability of such analyses to clinical oncology. Array based comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA), particularly in solid tumors, and has been applied to the study of malignant gliomas. In the clinical setting, however, gliomas are often sampled by small biopsies and thus formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis, especially for rare types of gliomas. Moreover, the biological basis for the marked intratumoral heterogeneity in gliomas is most readily addressed in FFPE material. Therefore, for gliomas, the ability to use DNA from FFPE tissue is essential for both clinical and research applications. In this study, we have constructed a custom bacterial artificial chromosome (BAC) array and show excellent sensitivity and specificity for detecting CNAs in a panel of paired frozen and FFPE glioma samples. Our study demonstrates a high concordance rate between CNAs detected in FFPE compared to frozen DNA. We have also developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. This labeling technique was applied to a panel of biphasic anaplastic oligoastrocytomas (AOA) to identify genetic changes unique to each component. Together, results from these studies suggest that BAC and oligonucleotide aCGH are sensitive tools for detecting CNAs in FFPE DNA, and can enable genome-wide analysis of rare, small and/or histologically heterogeneous gliomas. PMID:21080181
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USDA-ARS?s Scientific Manuscript database
The long-term goal of our study is to understand the genetic and epigenetic mechanisms of breast cancer metastasis in human and to discover new possible genetic markers for use in clinical practice. We have used microarray technology (Human OneArray microarray, phylanxbiotech.com) to compare gene ex...
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USDA-ARS?s Scientific Manuscript database
Although apolipoprotein E (APOE) variants are associated with age related diseases, the underlying mechanism is unknown and DNA methylation may be a potential one. With methylation data, measured by the Infinium Human Methylation 450 array, from 993 participants (age ranging from 18 to 87 y) in the ...
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USDA-ARS?s Scientific Manuscript database
Cultivated carrot and its wild ancestor co-occur in most temperate regions of the world and can easily hybridize. The genetic basis of the process of domestication in carrot is not well recognized. Recent results of an investigation on genetic diversity structure of cultivated and wild carrot and si...
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Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana.
Wittenberg, Alexander H J; van der Lee, Theo; Cayla, Cyril; Kilian, Andrzej; Visser, Richard G F; Schouten, Henk J
2005-08-01
Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds of restriction site based polymorphisms between genotypes and does not require DNA sequence information or site-specific oligonucleotides. This paper demonstrates the potential of DArT for genetic mapping by validating the quality and molecular basis of the markers, using the model plant Arabidopsis thaliana. Restriction fragments from a genomic representation of the ecotype Landsberg erecta (Ler) were amplified by PCR, individualized by cloning and spotted onto glass slides. The arrays were then hybridized with labeled genomic representations of the ecotypes Columbia (Col) and Ler and of individuals from an F(2) population obtained from a Col x Ler cross. The scoring of markers with specialized software was highly reproducible and 107 markers could unambiguously be ordered on a genetic linkage map. The marker order on the genetic linkage map coincided with the order on the DNA sequence map. Sequencing of the Ler markers and alignment with the available Col genome sequence confirmed that the polymorphism in DArT markers is largely a result of restriction site polymorphisms.
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Adamczyk, Jagoda; Deregowska, Anna; Skoneczny, Marek; Skoneczna, Adrianna; Natkanska, Urszula; Kwiatkowska, Aleksandra; Rawska, Ewa; Potocki, Leszek; Kuna, Ewelina; Panek, Anita; Lewinska, Anna; Wnuk, Maciej
2016-09-01
The yeast strains of the Saccharomyces sensu stricto complex involved in beer production are a heterogeneous group whose genetic and genomic features are not adequately determined. Thus, the aim of the present study was to provide a genetic characterization of selected group of commercially available brewing yeasts both ale top-fermenting and lager bottom-fermenting strains. Molecular karyotyping revealed that the diversity of chromosome patterns and four strains with the most accented genetic variabilities were selected and subjected to genome-wide array-based comparative genomic hybridization (array-CGH) analysis. The differences in the gene copy number were found in five functional gene categories: (1) maltose metabolism and transport, (2) response to toxin, (3) siderophore transport, (4) cellular aldehyde metabolic process, and (5) L-iditol 2-dehydrogenase activity (p < 0.05). In the Saflager W-34/70 strain (Fermentis) with the most affected array-CGH profile, loss of aryl-alcohol dehydrogenase (AAD) gene dosage correlated with an imbalanced redox state, oxidative DNA damage and breaks, lower levels of nucleolar proteins Nop1 and Fob1, and diminished tolerance to fermentation-associated stress stimuli compared to other strains. We suggest that compromised stress response may not only promote oxidant-based changes in the nucleolus state that may affect fermentation performance but also provide novel directions for future strain improvement.
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Paulsson, Kajsa; Cazier, Jean-Baptiste; MacDougall, Finlay; Stevens, Jane; Stasevich, Irina; Vrcelj, Nikoletta; Chaplin, Tracy; Lillington, Debra M.; Lister, T. Andrew; Young, Bryan D.
2008-01-01
We present here a genome-wide map of abnormalities found in diagnostic samples from 45 adults and adolescents with acute lymphoblastic leukemia (ALL). A 500K SNP array analysis uncovered frequent genetic abnormalities, with cryptic deletions constituting half of the detected changes, implying that microdeletions are a characteristic feature of this malignancy. Importantly, the pattern of deletions resembled that recently reported in pediatric ALL, suggesting that adult, adolescent, and childhood cases may be more similar on the genetic level than previously thought. Thus, 70% of the cases displayed deletion of one or more of the CDKN2A, PAX5, IKZF1, ETV6, RB1, and EBF1 genes. Furthermore, several genes not previously implicated in the pathogenesis of ALL were identified as possible recurrent targets of deletion. In total, the SNP array analysis identified 367 genetic abnormalities not corresponding to known copy number polymorphisms, with all but two cases (96%) displaying at least one cryptic change. The resolution level of this SNP array study is the highest used to date to investigate a malignant hematologic disorder. Our findings provide insights into the leukemogenic process and may be clinically important in adult and adolescent ALL. Most importantly, we report that microdeletions of key genes appear to be a common, characteristic feature of ALL that is shared among different clinical, morphological, and cytogenetic subgroups. PMID:18458336
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1983-05-01
serve as inter- faces to provide a compatible hook-up. Recent advances in microprocessors are leaoing to the development of new techniques known as...killed. This sort of threat is new to warfare. Because of the lack of experience against such a threat, effective tactics have not been developed ...Recent developments have been on satellite-to-earth communications links, antijam capabilities, adaptive array antennas, and new equipment to exploit the
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ERIC Educational Resources Information Center
Graves, Ruth, Ed.
Based on the notion that reading is both fun and fundamental, this book contains a stimulating array of activities that parents can use to engage their children in reading from the toddler stage through primary school. The first section provides information on how to use the guide, and some tips for encouraging young readers. The second and major…
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Selection of appropriate treatment options for hand fractures.
Sammer, Douglas M; Husain, Tarik; Ramirez, Rey
2013-11-01
Selecting the appropriate treatment method for hand fractures is challenging due to the wide spectrum of presentation and the enormous array of surgical and nonoperative treatment options. Unfortunately, the scientific evidence to help guide decision making is not of high quality. Because of this, the surgeon must rely on a few basic principles to guide treatment. This article provides an overview of the scientific evidence, and discusses the principles and rationale used to treat hand fractures. Copyright © 2013 Elsevier Inc. All rights reserved.
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Optical trapping via guided resonance modes in a Slot-Suzuki-phase photonic crystal lattice.
Ma, Jing; Martínez, Luis Javier; Povinelli, Michelle L
2012-03-12
A novel photonic crystal lattice is proposed for trapping a two-dimensional array of particles. The lattice is created by introducing a rectangular slot in each unit cell of the Suzuki-Phase lattice to enhance the light confinement of guided resonance modes. Large quality factors on the order of 10⁵ are predicted in the lattice. A significant decrease of the optical power required for optical trapping can be achieved compared to our previous design.
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A Guide to the Microform Collections of the USMA (United States Military Academy) Library,
1983-01-01
array of material about the Manhattan Project and the atomic bombings of Hiroshima and Nagasaki; none of it was declassified until 1976. Foremost among...1946. The twenty-one page printed A Guide to the Manhattan Project : Official History and Documents, located on top of the metal cabinets in Room 212, is...organizational characteristics of the Manhattan Project . The seven succeeding books discussed the 49 various sub-projects of the effort, such as Book III
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Understanding Genetic Toxicity Through Data Mining: The ...
This paper demonstrates the usefulness of representing a chemical by its structural features and the use of these features to profile a battery of tests rather than relying on a single toxicity test of a given chemical. This paper presents data mining/profiling methods applied in a weight-of-evidence approach to assess potential for genetic toxicity, and to guide the development of intelligent testing strategies. This paper demonstrates the usefulness of representing a chemical by its structural features and the use of these features to profile a battery of tests rather than relying on a single toxicity test of a given chemical. This paper presents data mining/profiling methods applied in a weight-of-evidence approach to assess potential for genetic toxicity, and to guide the development of intelligent testing strategies.
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Novel applications of array comparative genomic hybridization in molecular diagnostics.
Cheung, Sau W; Bi, Weimin
2018-05-31
In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.
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MMIC devices for active phased array antennas
NASA Technical Reports Server (NTRS)
Mittra, R.
1986-01-01
The use of finlines for microwave monolithic integrated circuit application in the 20 to 40 GHz frequency range. Other wave guiding structures, are also examined from a comparative point of view and some sonclusions are drawn on the basis of the results.
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Todd B. Cross; Michael K. Schwartz; David E. Naugle; Brad C. Fedy; Jeffrey R. Row; Sara J. Oyler-McCance
2018-01-01
Genetic networks can characterize complex genetic relationships among groups of individuals, which can be used to rank nodes most important to the overall connectivity of the system. Ranking allows scarce resources to be guided toward nodes integral to connectivity. The greater sage-grouse (Centrocercus urophasianus) is a species of conservation concern that breeds on...
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Genetic and neurodevelopmental influences in autistic disorder.
Nicolson, Rob; Szatmari, Peter
2003-09-01
In the past, autism was considered to be largely psychogenic. However, research in the last 2 decades indicates that autism is largely caused by genetic factors that lead to abnormal brain development. This article reviews research into the genetic and neurodevelopmental factors underlying autism. We review the findings from genetic and brain-imaging studies of autism over the past 15 years and synthesize these findings as a guide for future research. Genome scans and association studies have suggested potential genomic regions and genes, respectively, that may be involved in the etiology of autism, and there have been some replications of these results. Similarly, the findings that brain volume is exaggerated in autism and corpus callosum size is reduced have also been independently replicated. Unfortunately, studies of other subcortical structures remain inconclusive or contradictory. Overwhelming evidence now supports a neurobiological basis for autism. However, further refinements will be needed to guide future studies, particularly to identify the most informative phenotypes to investigate. Additionally, studies examining the role of genetic factors in the brain abnormalities underlying autism will likely lead to further findings that will enhance our understanding of autism's causes.
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Heating performances of a IC in-blanket ring array
NASA Astrophysics Data System (ADS)
Bosia, G.; Ragona, R.
2015-12-01
An important limiting factor to the use of ICRF as candidate heating method in a commercial reactor is due to the evanescence of the fast wave in vacuum and in most of the SOL layer, imposing proximity of the launching structure to the plasma boundary and causing, at the highest power level, high RF standing and DC rectified voltages at the plasma periphery, with frequent voltage breakdowns and enhanced local wall loading. In a previous work [1] the concept for an Ion Cyclotron Heating & Current Drive array (and using a different wave guide technology, a Lower Hybrid array) based on the use of periodic ring structure, integrated in the reactor blanket first wall and operating at high input power and low power density, was introduced. Based on the above concept, the heating performance of such array operating on a commercial fusion reactor is estimated.
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Heating performances of a IC in-blanket ring array
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bosia, G., E-mail: gbosia@to.infn.it; Ragona, R.
2015-12-10
An important limiting factor to the use of ICRF as candidate heating method in a commercial reactor is due to the evanescence of the fast wave in vacuum and in most of the SOL layer, imposing proximity of the launching structure to the plasma boundary and causing, at the highest power level, high RF standing and DC rectified voltages at the plasma periphery, with frequent voltage breakdowns and enhanced local wall loading. In a previous work [1] the concept for an Ion Cyclotron Heating & Current Drive array (and using a different wave guide technology, a Lower Hybrid array) basedmore » on the use of periodic ring structure, integrated in the reactor blanket first wall and operating at high input power and low power density, was introduced. Based on the above concept, the heating performance of such array operating on a commercial fusion reactor is estimated.« less
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Design principles for wave plate metasurfaces using plasmonic L-shaped nanoantennas
NASA Astrophysics Data System (ADS)
Tahir, Asad A.; Schulz, Sebastian A.; De Leon, Israel; Boyd, Robert W.
2017-03-01
Plasmonic L-shaped antennas are an important building block of metasurfaces and have been used to fabricate ultra-thin wave plates. In this work we present principles that can be used to design wave plates at a wavelength of choice and for diverse application requirements using arrays of L-shaped plasmonic antennas. We derive these design principles by studying the behavior of the vast parameter space of these antenna arrays. We show that there are two distinct regimes: a weak inter-particle coupling and a strong inter-particle coupling regime. We describe the behavior of the antenna array in each regime with regards to wave plate functionality, without resorting to approximate theoretical models. Our work is the first to explain these design principles and serves as a guide for designing wave plates for specific application requirements using plasmonic L-shaped antenna arrays.
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Plasmonic nanopatch array for optical integrated circuit applications.
Qu, Shi-Wei; Nie, Zai-Ping
2013-11-08
Future plasmonic integrated circuits with the capability of extremely high-speed data processing at optical frequencies will be dominated by the efficient optical emission (excitation) from (of) plasmonic waveguides. Towards this goal, plasmonic nanoantennas, currently a hot topic in the field of plasmonics, have potential to bridge the mismatch between the wave vector of free-space photonics and that of the guided plasmonics. To manipulate light at will, plasmonic nanoantenna arrays will definitely be more efficient than isolated nanoantennas. In this article, the concepts of microwave antenna arrays are applied to efficiently convert plasmonic waves in the plasmonic waveguides into free-space optical waves or vice versa. The proposed plasmonic nanoantenna array, with nanopatch antennas and a coupled wedge plasmon waveguide, can also act as an efficient spectrometer to project different wavelengths into different directions, or as a spatial filter to absorb a specific wavelength at a specified incident angle.
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Wu, Jun
2018-03-01
The polarization-independent enhanced absorption effect of graphene in the near-infrared range is investigated. This is achieved by placing a graphene square array on top of a dielectric square array backed by a two-dimensional multilayer grating. Total optical absorption in graphene can be attributed to critical coupling, which is achieved through the combined effect of guided-mode resonance with the dielectric square array and the photonic band gap with the two-dimensional multilayer grating. To reveal the physical origin of such a phenomenon, the electromagnetic field distributions for both polarizations are illustrated. The designed graphene absorber exhibits near-unity polarization-independent absorption at resonance with an ultra-narrow spectrum. Moreover, the polarization-independent absorption can be tuned simply by changing the geometric parameters. The results may have promising potential for the design of graphene-based optoelectronic devices.
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Lu, Zhenghui; Zhou, Yuling; Zhang, Xiaozhou; Zhang, Guimin
2015-11-01
Bacillus subtilis is a generally recognized as safe (GRAS) strain that has been widely used in industries including fodder, food, and biological control. In addition, B. subtilis expression system also plays a significant role in the production of industrial enzymes. However, its application is limited by its low sporulation frequency and transformation efficiency. Immense studies have been done on interpreting the molecular mechanisms of sporulation and competence development, whereas only few of them were focused on improving sporulation frequency and transformation efficiency of B. subtilis by genetic modification. The main challenge is that sporulation and competence development, as the two major developmental events in the stationary phase of B. subtilis, are regulated by the complicated intracellular genetic regulatory systems. In addition, mutual regulatory mechanisms also exist in these two developmental events. With the development of genetic and metabolic engineering, constructing genetic regulatory networks is currently one of the most attractive research fields, together with the genetic information of cell growth, metabolism, and development, to guide the industrial application. In this review, the mechanisms of sporulation and competence development of B. subtilis, their interactions, and the genetic regulation of cell growth were interpreted. In addition, the roles of these regulatory networks in guiding basic and applied research of B. subtilis and its related species were discussed.
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Genetic testing in the workplace: the employer's coin toss.
French, Samantha
2002-09-05
A toss of the coin by the modern-day employer reveals two options regarding genetic testing in the workplace. The employer may choose to take advantage of increasingly precise, available, and affordable genetic testing in order to ascertain the genetic characteristics--and deficiencies--of its employees. This outcome exposes the employer to a vast array of potential litigation and liability relating to the Americans with Disabilities Act, the Fourth Amendment, Title VII of the Civil Rights Act, and state legislation designed to protect genetic privacy. Alternatively, the employer may neglect to indulge in this trend of genetic testing and may face liability for employer negligence, violations of federal legislation such as OSHA regulations, and increased costs associated with insuring the health of genetically endangered employees. In the rapidly developing universe of genetic intelligence, the employer is faced with a staggering dilemma.
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Portfolio Evaluation for Professional Competence: Credentialing in Genetics for Nurses.
ERIC Educational Resources Information Center
Cook, Sarah Sheets; Kase, Ron; Middelton, Lindsay; Monsen, Rita Black
2003-01-01
Describes the process used by the Credentialing Committee of the International Society of Nurses in Genetics to validate evaluation criteria for nursing portfolios using neural network programs. Illustrates how standards are translated into measurable competencies and provides a scoring guide. (SK)
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Ansermet, Francois; Lespinasse, James; Gimelli, Stefania; Béna, Frédérique; Paoloni-Giacobino, Ariane
2010-05-01
We report the case of a 34-year-old female resulting from a father-daughter sexual abuse and presenting a phenotype of mild intellectual disability with minor dysmorphic features. Karyotyping showed a normal 46, XX constitution. Array-based comparative genomic hybridization (array-CGH) revealed a heterozygote 320kb 6p22.3 microdeletion in the proband, encompassing only one known gene, and therefore unlikely to be the cause of the phenotype. However, the role of other genetic factors, such as a recessive condition, could not be ruled out as a putative cause for the phenotype. On the other hand, the role played by a heavily detrimental familial situation on the development and outcome, and possibly leading or contributing to a mild intellectual disability, should be taken into account.
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EHW Approach to Temperature Compensation of Electronics
NASA Technical Reports Server (NTRS)
Stoica, Adrian
2004-01-01
Efforts are under way to apply the concept of evolvable hardware (EHW) to compensate for variations, with temperature, in the operational characteristics of electronic circuits. To maintain the required functionality of a given circuit at a temperature above or below the nominal operating temperature for which the circuit was originally designed, a new circuit would be evolved; moreover, to obtain the required functionality over a very wide temperature range, there would be evolved a number of circuits, each of which would satisfy the performance requirements over a small part of the total temperature range. The basic concepts and some specific implementations of EHW were described in a number of previous NASA Tech Briefs articles, namely, "Reconfigurable Arrays of Transistors for Evolvable Hardware" (NPO-20078), Vol. 25, No. 2 (February 2001), page 36; Evolutionary Automated Synthesis of Electronic Circuits (NPO- 20535), Vol. 26, No. 7 (July 2002), page 37; "Designing Reconfigurable Antennas Through Hardware Evolution" (NPO-20666), Vol. 26, No. 7 (July 2002), page 38; "Morphing in Evolutionary Synthesis of Electronic Circuits" (NPO-20837), Vol. 26, No. 8 (August 2002), page 31; "Mixtrinsic Evolutionary Synthesis of Electronic Circuits" (NPO-20773) Vol. 26, No. 8 (August 2002), page 32; and "Synthesis of Fuzzy-Logic Circuits in Evolvable Hardware" (NPO-21095) Vol. 26, No. 11 (November 2002), page 38. To recapitulate from the cited prior articles: EHW is characterized as evolutionary in a quasi-genetic sense. The essence of EHW is to construct and test a sequence of populations of circuits that function as incrementally better solutions of a given design problem through the selective, repetitive connection and/or disconnection of capacitors, transistors, amplifiers, inverters, and/or other circuit building blocks. The connection and disconnection can be effected by use of field-programmable transistor arrays (FPTAs). The evolution is guided by a search-andoptimization algorithm (in particular, a genetic algorithm) that operates in the space of possible circuits to find a circuit that exhibits an acceptably close approximation of the desired functionality. The evolved circuits can be tested by mathematical modeling (that is, computational simulation) only, tested in real hardware, or tested in combinations of computational simulation and real hardware.
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The Role of Constitutional Copy Number Variants in Breast Cancer
Walker, Logan C.; Wiggins, George A.R.; Pearson, John F.
2015-01-01
Constitutional copy number variants (CNVs) include inherited and de novo deviations from a diploid state at a defined genomic region. These variants contribute significantly to genetic variation and disease in humans, including breast cancer susceptibility. Identification of genetic risk factors for breast cancer in recent years has been dominated by the use of genome-wide technologies, such as single nucleotide polymorphism (SNP)-arrays, with a significant focus on single nucleotide variants. To date, these large datasets have been underutilised for generating genome-wide CNV profiles despite offering a massive resource for assessing the contribution of these structural variants to breast cancer risk. Technical challenges remain in determining the location and distribution of CNVs across the human genome due to the accuracy of computational prediction algorithms and resolution of the array data. Moreover, better methods are required for interpreting the functional effect of newly discovered CNVs. In this review, we explore current and future application of SNP array technology to assess rare and common CNVs in association with breast cancer risk in humans. PMID:27600231
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Introductory Guide to the Statistics of Molecular Genetics
ERIC Educational Resources Information Center
Eley, Thalia C.; Rijsdijk, Fruhling
2005-01-01
Background: This introductory guide presents the main two analytical approaches used by molecular geneticists: linkage and association. Methods: Traditional linkage and association methods are described, along with more recent advances in methodologies such as those using a variance components approach. Results: New methods are being developed all…
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Career Education Resource Guide for Biology. Working Draft.
ERIC Educational Resources Information Center
Louisiana State Dept. of Education, Baton Rouge.
The resource guide integrates learning activities in biological science with an exploration of careers in biology or related fields. The materials are divided into seven units: tools of the scientist, basis for life, diversity (protists, plants, animals), structure and function, continuity (reproduction, development, and genetics), evolution, and…
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CRISPRDetect: A flexible algorithm to define CRISPR arrays.
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.
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1990-11-12
This feature prevents any significant unexpected and undesired size overhead introduced by the automatic inlining of a called subprogram. Any...PRESERVELAYOUT forces the 5.5.1 compiler to maintain the Ada source order of a given record type, thereby, preventing the compiler from performing this...Environment, Volme 2: Prgram nng Guide assignments to the copied array in Ada do not affect the Fortran version of the array. The dimensions and order of
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A broadband double-slot waveguide antenna
NASA Astrophysics Data System (ADS)
Kisliuk, M.; Axelrod, A.
1987-09-01
A double transverse slot broadband antenna based on the H-guide transverse-slot radiator design of Kisliuk and Axelrod (1985) is described. The double transverse slot antenna may be used in microwave and mm-wave applications (as a phased array element), in imaging systems, or as a stand-alone linearly polarized antenna. The equations for calculating the radiation efficiency and the input impedance and the experimental and theoretical curves for radiation efficiency of the double-slot antenna are presented along with diagrams of the antenna and the equivalent circuit of an individual slot in a slot array.
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Hill, Theresa A.; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W.; Van Deynze, Allen
2013-01-01
The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum. PMID:23409153
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Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen
2013-01-01
The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.
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Fox, Ervin R.; Young, J. Hunter; Li, Yali; Dreisbach, Albert W.; Keating, Brendan J.; Musani, Solomon K.; Liu, Kiang; Morrison, Alanna C.; Ganesh, Santhi; Kutlar, Abdullah; Ramachandran, Vasan S.; Polak, Josef F.; Fabsitz, Richard R.; Dries, Daniel L.; Farlow, Deborah N.; Redline, Susan; Adeyemo, Adebowale; Hirschorn, Joel N.; Sun, Yan V.; Wyatt, Sharon B.; Penman, Alan D.; Palmas, Walter; Rotter, Jerome I.; Townsend, Raymond R.; Doumatey, Ayo P.; Tayo, Bamidele O.; Mosley, Thomas H.; Lyon, Helen N.; Kang, Sun J.; Rotimi, Charles N.; Cooper, Richard S.; Franceschini, Nora; Curb, J. David; Martin, Lisa W.; Eaton, Charles B.; Kardia, Sharon L.R.; Taylor, Herman A.; Caulfield, Mark J.; Ehret, Georg B.; Johnson, Toby; Chakravarti, Aravinda; Zhu, Xiaofeng; Levy, Daniel; Munroe, Patricia B.; Rice, Kenneth M.; Bochud, Murielle; Johnson, Andrew D.; Chasman, Daniel I.; Smith, Albert V.; Tobin, Martin D.; Verwoert, Germaine C.; Hwang, Shih-Jen; Pihur, Vasyl; Vollenweider, Peter; O'Reilly, Paul F.; Amin, Najaf; Bragg-Gresham, Jennifer L.; Teumer, Alexander; Glazer, Nicole L.; Launer, Lenore; Zhao, Jing Hua; Aulchenko, Yurii; Heath, Simon; Sõber, Siim; Parsa, Afshin; Luan, Jian'an; Arora, Pankaj; Dehghan, Abbas; Zhang, Feng; Lucas, Gavin; Hicks, Andrew A.; Jackson, Anne U.; Peden, John F.; Tanaka, Toshiko; Wild, Sarah H.; Rudan, Igor; Igl, Wilmar; Milaneschi, Yuri; Parker, Alex N.; Fava, Cristiano; Chambers, John C.; Kumari, Meena; JinGo, Min; van der Harst, Pim; Kao, Wen Hong Linda; Sjögren, Marketa; Vinay, D.G.; Alexander, Myriam; Tabara, Yasuharu; Shaw-Hawkins, Sue; Whincup, Peter H.; Liu, Yongmei; Shi, Gang; Kuusisto, Johanna; Seielstad, Mark; Sim, Xueling; Nguyen, Khanh-Dung Hoang; Lehtimäki, Terho; Matullo, Giuseppe; Wu, Ying; Gaunt, Tom R.; Charlotte Onland-Moret, N.; Cooper, Matthew N.; Platou, Carl G.P.; Org, Elin; Hardy, Rebecca; Dahgam, Santosh; Palmen, Jutta; Vitart, Veronique; Braund, Peter S.; Kuznetsova, Tatiana; Uiterwaal, Cuno S.P.M.; Campbell, Harry; Ludwig, Barbara; Tomaszewski, Maciej; Tzoulaki, Ioanna; Palmer, Nicholette D.; Aspelund, Thor; Garcia, Melissa; Chang, Yen-Pei C.; O'Connell, Jeffrey R.; Steinle, Nanette I.; Grobbee, Diederick E.; Arking, Dan E.; Hernandez, Dena; Najjar, Samer; McArdle, Wendy L.; Hadley, David; Brown, Morris J.; Connell, John M.; Hingorani, Aroon D.; Day, Ian N.M.; Lawlor, Debbie A.; Beilby, John P.; Lawrence, Robert W.; Clarke, Robert; Collins, Rory; Hopewell, Jemma C.; Ongen, Halit; Bis, Joshua C.; Kähönen, Mika; Viikari, Jorma; Adair, Linda S.; Lee, Nanette R.; Chen, Ming-Huei; Olden, Matthias; Pattaro, Cristian; Hoffman Bolton, Judith A.; Köttgen, Anna; Bergmann, Sven; Mooser, Vincent; Chaturvedi, Nish; Frayling, Timothy M.; Islam, Muhammad; Jafar, Tazeen H.; Erdmann, Jeanette; Kulkarni, Smita R.; Bornstein, Stefan R.; Grässler, Jürgen; Groop, Leif; Voight, Benjamin F.; Kettunen, Johannes; Howard, Philip; Taylor, Andrew; Guarrera, Simonetta; Ricceri, Fulvio; Emilsson, Valur; Plump, Andrew; Barroso, Inês; Khaw, Kay-Tee; Weder, Alan B.; Hunt, Steven C.; Bergman, Richard N.; Collins, Francis S.; Bonnycastle, Lori L.; Scott, Laura J.; Stringham, Heather M.; Peltonen, Leena; Perola, Markus; Vartiainen, Erkki; Brand, Stefan-Martin; Staessen, Jan A.; Wang, Thomas J.; Burton, Paul R.; SolerArtigas, Maria; Dong, Yanbin; Snieder, Harold; Wang, Xiaoling; Zhu, Haidong; Lohman, Kurt K.; Rudock, Megan E.; Heckbert, Susan R.; Smith, Nicholas L.; Wiggins, Kerri L.; Shriner, Daniel; Veldre, Gudrun; Viigimaa, Margus; Kinra, Sanjay; Prabhakaran, Dorairajan; Tripathy, Vikal; Langefeld, Carl D.; Rosengren, Annika; Thelle, Dag S.; MariaCorsi, Anna; Singleton, Andrew; Forrester, Terrence; Hilton, Gina; McKenzie, Colin A.; Salako, Tunde; Iwai, Naoharu; Kita, Yoshikuni; Ogihara, Toshio; Ohkubo, Takayoshi; Okamura, Tomonori; Ueshima, Hirotsugu; Umemura, Satoshi; Eyheramendy, Susana; Meitinger, Thomas; Wichmann, H.-Erich; Cho, Yoon Shin; Kim, Hyung-Lae; Lee, Jong-Young; Scott, James; Sehmi, Joban S.; Zhang, Weihua; Hedblad, Bo; Nilsson, Peter; Smith, George Davey; Wong, Andrew; Narisu, Narisu; Stančáková, Alena; Raffel, Leslie J.; Yao, Jie; Kathiresan, Sekar; O'Donnell, Chris; Schwartz, Steven M.; Arfan Ikram, M.; Longstreth, Will T.; Seshadri, Sudha; Shrine, Nick R.G.; Wain, Louise V.; Morken, Mario A.; Swift, Amy J.; Laitinen, Jaana; Prokopenko, Inga; Zitting, Paavo; Cooper, Jackie A.; Humphries, Steve E.; Danesh, John; Rasheed, Asif; Goel, Anuj; Hamsten, Anders; Watkins, Hugh; Bakker, Stephan J.L.; van Gilst, Wiek H.; Janipalli, Charles S.; Radha Mani, K.; Yajnik, Chittaranjan S.; Hofman, Albert; Mattace-Raso, Francesco U.S.; Oostra, Ben A.; Demirkan, Ayse; Isaacs, Aaron; Rivadeneira, Fernando; Lakatta, Edward G.; Orru, Marco; Scuteri, Angelo; Ala-Korpela, Mika; Kangas, Antti J.; Lyytikäinen, Leo-Pekka; Soininen, Pasi; Tukiainen, Taru; Würz, Peter; Twee-Hee Ong, Rick; Dörr, Marcus; Kroemer, Heyo K.; Völker, Uwe; Völzke, Henry; Galan, Pilar; Hercberg, Serge; Lathrop, Mark; Zelenika, Diana; Deloukas, Panos; Mangino, Massimo; Spector, Tim D.; Zhai, Guangju; Meschia, James F.; Nalls, Michael A.; Sharma, Pankaj; Terzic, Janos; Kranthi Kumar, M.J.; Denniff, Matthew; Zukowska-Szczechowska, Ewa; Wagenknecht, Lynne E.; Fowkes, Gerald R.; Charchar, Fadi J.; Schwarz, Peter E.H.; Hayward, Caroline; Guo, Xiuqing; Bots, Michiel L.; Brand, Eva; Samani, Nilesh J.; Polasek, Ozren; Talmud, Philippa J.; Nyberg, Fredrik; Kuh, Diana; Laan, Maris; Hveem, Kristian; Palmer, Lyle J.; van der Schouw, Yvonne T.; Casas, Juan P.; Mohlke, Karen L.; Vineis, Paolo; Raitakari, Olli; Wong, Tien Y.; Shyong Tai, E.; Laakso, Markku; Rao, Dabeeru C.; Harris, Tamara B.; Morris, Richard W.; Dominiczak, Anna F.; Kivimaki, Mika; Marmot, Michael G.; Miki, Tetsuro; Saleheen, Danish; Chandak, Giriraj R.; Coresh, Josef; Navis, Gerjan; Salomaa, Veikko; Han, Bok-Ghee; Kooner, Jaspal S.; Melander, Olle; Ridker, Paul M.; Bandinelli, Stefania; Gyllensten, Ulf B.; Wright, Alan F.; Wilson, James F.; Ferrucci, Luigi; Farrall, Martin; Tuomilehto, Jaakko; Pramstaller, Peter P.; Elosua, Roberto; Soranzo, Nicole; Sijbrands, Eric J.G.; Altshuler, David; Loos, Ruth J.F.; Shuldiner, Alan R.; Gieger, Christian; Meneton, Pierre; Uitterlinden, Andre G.; Wareham, Nicholas J.; Gudnason, Vilmundur; Rettig, Rainer; Uda, Manuela; Strachan, David P.; Witteman, Jacqueline C.M.; Hartikainen, Anna-Liisa; Beckmann, Jacques S.; Boerwinkle, Eric; Boehnke, Michael; Larson, Martin G.; Järvelin, Marjo-Riitta; Psaty, Bruce M.; Abecasis, Gonçalo R.; Elliott, Paul; van Duijn , Cornelia M.; Newton-Cheh, Christopher
2011-01-01
The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity. PMID:21378095
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Fox, Ervin R; Young, J Hunter; Li, Yali; Dreisbach, Albert W; Keating, Brendan J; Musani, Solomon K; Liu, Kiang; Morrison, Alanna C; Ganesh, Santhi; Kutlar, Abdullah; Ramachandran, Vasan S; Polak, Josef F; Fabsitz, Richard R; Dries, Daniel L; Farlow, Deborah N; Redline, Susan; Adeyemo, Adebowale; Hirschorn, Joel N; Sun, Yan V; Wyatt, Sharon B; Penman, Alan D; Palmas, Walter; Rotter, Jerome I; Townsend, Raymond R; Doumatey, Ayo P; Tayo, Bamidele O; Mosley, Thomas H; Lyon, Helen N; Kang, Sun J; Rotimi, Charles N; Cooper, Richard S; Franceschini, Nora; Curb, J David; Martin, Lisa W; Eaton, Charles B; Kardia, Sharon L R; Taylor, Herman A; Caulfield, Mark J; Ehret, Georg B; Johnson, Toby; Chakravarti, Aravinda; Zhu, Xiaofeng; Levy, Daniel
2011-06-01
The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10(-8)) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10(-8)). The top IBC association for SBP was rs2012318 (P= 6.4 × 10(-6)) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10(-6)) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity.
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Arrays of microscopic organic LEDs for high-resolution optogenetics
Steude, Anja; Witts, Emily C.; Miles, Gareth B.; Gather, Malte C.
2016-01-01
Optogenetics is a paradigm-changing new method to study and manipulate the behavior of cells with light. Following major advances of the used genetic constructs over the last decade, the light sources required for optogenetic control are now receiving increased attention. We report a novel optogenetic illumination platform based on high-density arrays of microscopic organic light-emitting diodes (OLEDs). Because of the small dimensions of each array element (6 × 9 μm2) and the use of ultrathin device encapsulation, these arrays enable illumination of cells with unprecedented spatiotemporal resolution. We show that adherent eukaryotic cells readily proliferate on these arrays, and we demonstrate specific light-induced control of the ionic current across the membrane of individual live cells expressing different optogenetic constructs. Our work paves the way for the use of OLEDs for cell-specific optogenetic control in cultured neuronal networks and for acute brain slices, or as implants in vivo. PMID:27386540
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A Guiding Evolutionary Algorithm with Greedy Strategy for Global Optimization Problems
Cao, Leilei; Xu, Lihong; Goodman, Erik D.
2016-01-01
A Guiding Evolutionary Algorithm (GEA) with greedy strategy for global optimization problems is proposed. Inspired by Particle Swarm Optimization, the Genetic Algorithm, and the Bat Algorithm, the GEA was designed to retain some advantages of each method while avoiding some disadvantages. In contrast to the usual Genetic Algorithm, each individual in GEA is crossed with the current global best one instead of a randomly selected individual. The current best individual served as a guide to attract offspring to its region of genotype space. Mutation was added to offspring according to a dynamic mutation probability. To increase the capability of exploitation, a local search mechanism was applied to new individuals according to a dynamic probability of local search. Experimental results show that GEA outperformed the other three typical global optimization algorithms with which it was compared. PMID:27293421
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A Guiding Evolutionary Algorithm with Greedy Strategy for Global Optimization Problems.
Cao, Leilei; Xu, Lihong; Goodman, Erik D
2016-01-01
A Guiding Evolutionary Algorithm (GEA) with greedy strategy for global optimization problems is proposed. Inspired by Particle Swarm Optimization, the Genetic Algorithm, and the Bat Algorithm, the GEA was designed to retain some advantages of each method while avoiding some disadvantages. In contrast to the usual Genetic Algorithm, each individual in GEA is crossed with the current global best one instead of a randomly selected individual. The current best individual served as a guide to attract offspring to its region of genotype space. Mutation was added to offspring according to a dynamic mutation probability. To increase the capability of exploitation, a local search mechanism was applied to new individuals according to a dynamic probability of local search. Experimental results show that GEA outperformed the other three typical global optimization algorithms with which it was compared.
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NASA Astrophysics Data System (ADS)
Ren, Baiyang
Composite materials, especially carbon fiber reinforced polymers (CFRP), have been widely used in the aircraft industry because of their high specific strength and stiffness, resistance to corrosion and good fatigue life. Due to their highly anisotropic material properties and laminated structures, joining methods like bolting and riveting are no longer appropriate for joining CFRP since they initiate defects during the assembly and severely compromise the integrity of the structure; thus new techniques for joining CFRP are highly demanded. Adhesive bonding is a promising method because it relieves stress concentration, reduces weight and provides smooth surfaces. Additionally, it is a low-cost alternative to the co-cured method which is currently used to manufacture components of aircraft fuselage. Adhesive defects, disbonds at the interface between adherend and adhesive layer, are focused on in this thesis because they can be initialized by either poor surface preparation during the manufacturing or fatigue loads during service. Aircraft need structural health monitoring (SHM) systems to increase safety and reduce loss, and adhesive bonds usually represent the hotspots of the assembled structure. There are many nondestructive evaluation (NDE) methods for bond inspection. However, these methods cannot be readily integrated into an SHM system because of the bulk size and weight of the equipment and requirement of accessibility to one side of the bonded joint. The first objective of this work is to develop instruments, actuators, sensors and a data acquisition system for SHM of bond lines using ultrasonic guided waves which are well known to be able to cover large volume of the structure and inaccessible regions. Different from widely used guided wave sensors like PZT disks, the new actuators, piezoelectric fiber composite (PFC) phased array transducers0 (PAT), can control the modal content of the excited waves and the new sensors, polyvinylidene fluoride (PVDF) arrays, which can extract modal information from the received waves. Also, the PATs and array sensors have broad frequency bandwidth and can easily excite and receive high order guided wave modes which are not possible using PZT disks. Currently, many guided wave SHM techniques employ the fundamental guided wave modes below the first cut-off frequency because of their low dispersion in this frequency range. Such a practice ignores the possibility of using higher order modes which sometimes have much better sensitivity to defects. A frequency domain finite element model is created in this work to study the behavior of the interaction between guided waves and a disbond. The sensitivities of modes are classified into three levels, namely, good sensitivity, intermediate sensitivity and no sensitivity. The novel damage indicators, wave modal amplitude and wave modal composition, are proposed to increase the sensitivity to disbonds. The effects of environmental operational conditions (EOC) are presenting great challenges to reliable SHM practice because they may influence the wave amplitude and time of flight. The use of fundamental modes shows poor sensitivity to the disbond; but the use of higher order modes shows good sensitivity. The experiments demonstrate that the new damage indicators have excellent sensitivity to disbonds even with elevated temperatures and have the capability to characterize the size of a disbond. Additionally, the detection of other types of defects like notches on aluminum plates and disbonds in adhesively bonded aluminum plate are also demonstrated using the proposed damage indicators. The use of the new damage indicators for SHM applications relies on the capability of resolving the modal content of wave signals which is enabled only by using PFC PATs and polyvinylidene fluoride (PVDF) array sensors.
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Exome Array Analysis of Nuclear Lens Opacity.
Loomis, Stephanie J; Klein, Alison P; Lee, Kristine E; Chen, Fei; Bomotti, Samantha; Truitt, Barbara; Iyengar, Sudha K; Klein, Ronald; Klein, Barbara E K; Duggal, Priya
2018-06-01
Nuclear cataract is the most common subtype of age-related cataract, the leading cause of blindness worldwide. It results from advanced nuclear sclerosis, or opacity in the center of the optic lens, and is affected by both genetic and environmental risk factors, including smoking. We sought to understand the genetic factors associated with nuclear sclerosis through interrogation of rare and low frequency coding variants using exome array data. We analyzed Illumina Human Exome Array data for 1,488 participants of European ancestry in the Beaver Dam Eye Study who were without cataract surgery for association with nuclear sclerosis grade, controlling for age and sex. We performed single-variant regression analysis for 32,138 variants with minor allele frequency (MAF) ≥0.003. In addition, gene-based analysis of 11,844 genes containing at least two variants with MAF < 0.05 was performed using a gene-based unified burden and non-burden sequence kernel association test (SKAT-O). Additionally, both single-variant and gene-based analyses were analyzed stratified by smoking status. No single-variant test was statistically significant after Bonferroni correction (p < 1.6 × 10 -6 ; top single nucleotide polymorphism (SNP): rs144458991, p = 2.83 × 10 -5 ). Gene-based tests were suggestively associated with the gene RNF149 overall (p = 8.29 × 10 -6 ) and among never smokers (N = 790, p = 2.67 × 10 -6 ). This study did not find a significant genetic association with nuclear sclerosis, the possible association with the RNF149 gene highlights a potential candidate gene for future studies that aim to understand the genetic architecture of nuclear sclerosis.
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Bonifaz-Peña, Vania; Contreras, Alejandra V.; Struchiner, Claudio Jose; Roela, Rosimeire A.; Furuya-Mazzotti, Tatiane K.; Chammas, Roger; Rangel-Escareño, Claudia; Uribe-Figueroa, Laura; Gómez-Vázquez, María José; McLeod, Howard L.; Hidalgo-Miranda, Alfredo
2014-01-01
Studies of pharmacogenomics-related traits are increasingly being performed to identify loci that affect either drug response or susceptibility to adverse drug reactions. However, the effect of the polymorphisms can differ in magnitude or be absent depending on the population being assessed. We used the Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus array to characterize the distribution of polymorphisms of pharmacogenetics and pharmacogenomics (PGx) relevance in two samples from the most populous Latin American countries, Brazil and Mexico. The sample from Brazil included 268 individuals from the southeastern state of Rio de Janeiro, and was stratified into census categories. The sample from Mexico comprised 45 Native American Zapotecas and 224 self-identified Mestizo individuals from 5 states located in geographically distant regions in Mexico. We evaluated the admixture proportions in the Brazilian and Mexican samples using a panel of Ancestry Informative Markers extracted from the DMET array, which was validated with genome-wide data. A substantial variation in ancestral proportions across census categories in Brazil, and geographic regions in Mexico was identified. We evaluated the extent of genetic differentiation (measured as FST values) of the genetic markers of the DMET Plus array between the relevant parental populations. Although the average levels of genetic differentiation are low, there is a long tail of markers showing large frequency differences, including markers located in genes belonging to the Cytochrome P450, Solute Carrier (SLC) and UDP-glucuronyltransferase (UGT) families as well as other genes of PGx relevance such as ABCC8, ADH1A, CHST3, PON1, PPARD, PPARG, and VKORC1. We show how differences in admixture history may have an important impact in the distribution of allele and genotype frequencies at the population level. PMID:25419701
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NASA Astrophysics Data System (ADS)
Williams, Westin B.; Michaels, Thomas E.; Michaels, Jennifer E.
2018-04-01
Composite materials used for aerospace applications are highly susceptible to impacts, which can result in barely visible delaminations. Reliable and fast detection of such damage is needed before structural failures occur. One approach is to use ultrasonic guided waves generated from a sparse array consisting of permanently mounted or embedded transducers for performing structural health monitoring. This array can detect introduction of damage after baseline subtraction, and also provide localization and characterization information via the minimum variance imaging algorithm. Imaging performance can vary considerably depending upon where damage is located with respect to the array; however, prior work has shown that knowledge of expected scattering can improve imaging consistency for artificial damage at various locations. In this study, anisotropic material attenuation and wave speed are estimated as a function of propagation angle using wavefield data recorded along radial lines at multiple angles with respect to an omnidirectional guided wave source. Additionally, full wavefield data are recorded before and after the introduction of artificial and impact damage so that wavefield baseline subtraction may be applied. 3-D filtering techniques are then used to reduce noise and isolate scattered waves. A model for estimating scattering of a circular defect is developed and scattering estimates for both artificial and impact damage are presented and compared.
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Riffe, Matthew J; Yutzy, Stephen R; Jiang, Yun; Twieg, Michael D; Blumenthal, Colin J; Hsu, Daniel P; Pan, Li; Gilson, Wesley D; Sunshine, Jeffrey L; Flask, Christopher A; Duerk, Jeffrey L; Nakamoto, Dean; Gulani, Vikas; Griswold, Mark A
2014-06-01
A prototype wireless guidance device using single sideband amplitude modulation (SSB) is presented for a 1.5T magnetic resonance imaging system. The device contained three fiducial markers each mounted to an independent receiver coil equipped with wireless SSB technology. Acquiring orthogonal projections of these markers determined the position and orientation of the device, which was used to define the scan plane for a subsequent image acquisition. Device localization and scan plane update required approximately 30 ms, so it could be interleaved with high temporal resolution imaging. Since the wireless device is used for localization and does not require full imaging capability, the design of the SSB wireless system was simplified by allowing an asynchronous clock between the transmitter and receiver. When coupled to a high readout bandwidth, the error caused by the lack of a shared frequency reference was quantified to be less than one pixel (0.78 mm) in the projection acquisitions. Image guidance with the prototype was demonstrated with a phantom where a needle was successfully guided to a target and contrast was delivered. The feasibility of active tracking with a wireless detector array is demonstrated. Wireless arrays could be incorporated into devices to assist in image-guided procedures. Copyright © 2013 Wiley Periodicals, Inc.
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A multi-element high intensity focused ultrasound transducer: Design, fabrication, and testing
NASA Astrophysics Data System (ADS)
Vaezy, Shahram; Held, Robert; Miller, Blake; Fleury, Gerard
2004-05-01
The goal of this project is to develop an intra-cavity image-guided high intensity focused ultrasound (HIFU) device using piezocomposite technology and commercially available ultrasound imaging. The HIFU array, manufactured by Imasonic Corporation, is an 11-element annular phased array, with a focal length range of 30-60 mm, and operating frequency of 3 MHz (bandwidth of 1 MHz). The imaging probe (C9-5, Philips) is configured such that the focal axis of the HIFU beam was within the image plane. The array includes six complete central rings and five side-truncated peripheral rings, all with the natural radius of curvature of 50 mm. Impedance of all elements is approximately 50 ohms (10% accuracy for real and imaginary parts). Cross coupling between adjacent elements is less than, -40 dB. High power measurements showed more than 75% efficiency, at surface intensity of 2.66 W/cm2. Schlieren imaging showed effective focusing at all focal lengths (30-60 mm). The image-guided HIFU device requires water or hydrogel coupling, and possibly water cooling. The results of the full characterization for lesion formation in tissue-mimicking phantoms and biological tissues will be presented. Possible applications include uterine fibroids, abnormal uterine bleeding, and intraoperative hemostasis of occult hemorrhage.
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Device localization and dynamic scan plane selection using a wireless MRI detector array
Riffe, Matthew J.; Yutzy, Stephen R.; Jiang, Yun; Twieg, Michael D.; Blumenthal, Colin J.; Hsu, Daniel P.; Pan, Li; Gilson, Wesley D.; Sunshine, Jeffrey L.; Flask, Christopher A.; Duerk, Jeffrey L.; Nakamoto, Dean; Gulani, Vikas; Griswold, Mark A.
2013-01-01
Purpose A prototype wireless guidance device using single sideband amplitude modulation (SSB) is presented for a 1.5T MRI system. Methods The device contained three fiducial markers each mounted to an independent receiver coil equipped with wireless SSB technology. Acquiring orthogonal projections of these markers determined the position and orientation of the device, which was used to define the scan plane for a subsequent image acquisition. Device localization and scan plane update required approximately 30 ms, so it could be interleaved with high temporal resolution imaging. Since the wireless device is used for localization and doesn’t require full imaging capability, the design of the SSB wireless system was simplified by allowing an asynchronous clock between the transmitter and receiver. Results When coupled to a high readout bandwidth, the error caused by the lack of a shared frequency reference was quantified to be less than one pixel (0.78 mm) in the projection acquisitions. Image-guidance with the prototype was demonstrated with a phantom where a needle was successfully guided to a target and contrast was delivered. Conclusion The feasibility of active tracking with a wireless detector array is demonstrated. Wireless arrays could be incorporated into devices to assist in image-guided procedures. PMID:23900921
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WE-H-209-00: Carson/Zagzebski Distinguished Lectureship: Image Guided Ultrasound Therapy
DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
Focused ultrasound has been shown to be the only method that allows noninvasive thermal coagulation of tissues and recently this potential has been explored for image-guided drug delivery. In this presentation, the advances in ultrasound phased array technology for energy delivery, exposure monitoring and control will be discussed. Experimental results from novel multi-frequency transmit/receive arrays will be presented. In addition, the feasibility of fully electronically focused and steered high power arrays with many thousands of transducer elements will be discussed. Finally, some of the recent clinical and preclinical results for the treatment of brain disease will be reviewed. Learning Objectives:more » Introduce FUS therapy principles and modern techniques Discuss use of FUS for drug delivery Cover the technology required to deliver FUS and monitor therapy Present clinical examples of the uses of these techniques This research was supported by funding from The Canada Research Chair Program, Grants from CIHR and NIH (no. EB003268).; K. Hynynen, Canada Foundation for Innovation; Canadian Institutes of Health Research; Focused Ultrasound Surgery Foundation; Canada Research Chair Program; Natural Sciences and Engineering Research Council of Canada; Ontario Research Fund; National Institutes of Health; Canadian Cancer Society Research Institute; The Weston Brain Institute; Harmonic Medical; Focused Ultrasound Instruments.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Hu, Y.; Chen, D; Park, S
High-density arrays of highly ordered ferritin nanocages are fabricated through the guided assembly of thiol-modified ferritin on prepatterned gold nanodots, which are prepared by block copolymer micelle lithography. One and only one ferritin nanocage is anchored to each gold nanodot, as confirmed by scanning electron and scanning force microscopy.
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Enhanced Ultrafast Nonlinear Optics With Microstructure Fibers And Photonic Crystals
2004-07-01
NANOHOLES FREQUENCY-TUNABLE ANTI-STOKES LINE EMISSION BY EIGENMODES OF A BIREFRINGENT MICROSTRUCTURE FIBER GENERATION OF FEMTOSECOND ANTI-STOKES PULSES...laser technologies, and ultrafast photonics. ANTI-STOKES GENERATION IN GUIDED MODES OF PHOTONIC-CRYSTAL FIBERS MODIFIED WITH AN ARRAY OF NANOHOLES
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SNPConvert: SNP Array Standardization and Integration in Livestock Species.
Nicolazzi, Ezequiel Luis; Marras, Gabriele; Stella, Alessandra
2016-06-09
One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git.
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Genetic Testing in the Multidisciplinary Management of Melanoma.
Rashid, Omar M; Zager, Jonathan S
2015-10-01
Melanoma is increasing in incidence and represents an aggressive type of cancer. Efforts have focused on identifying genetic factors in melanoma carcinogenesis to guide prevention, screening, early detection, and targeted therapy. This article reviews the hereditary risk factors associated with melanoma and the known molecular pathways and genetic mutations associated with this disease. This article also explores the controversies associated with genetic testing and the latest advances in identifying genetic targets in melanoma, which offer promise for future application in the multidisciplinary management of melanoma. Copyright © 2015 Elsevier Inc. All rights reserved.
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Genetics Home Reference: lattice corneal dystrophy type II
... lattice corneal dystrophy type II can have a facial expression that appears sad. Related Information What does it ... links) Children's Craniofacial Association: A Guide to Understanding Facial ... pathogenic mechanisms in gelsolin-related amyloidosis: in vitro expression reveals an abnormal gelsolin fragment. Hum Mol Genet. ...
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Troggio, Michela; Šurbanovski, Nada; Bianco, Luca; Moretto, Marco; Giongo, Lara; Banchi, Elisa; Viola, Roberto; Fernández, Felicdad Fernández; Costa, Fabrizio; Velasco, Riccardo; Cestaro, Alessandro; Sargent, Daniel James
2013-01-01
High throughput arrays for the simultaneous genotyping of thousands of single-nucleotide polymorphisms (SNPs) have made the rapid genetic characterisation of plant genomes and the development of saturated linkage maps a realistic prospect for many plant species of agronomic importance. However, the correct calling of SNP genotypes in divergent polyploid genomes using array technology can be problematic due to paralogy, and to divergence in probe sequences causing changes in probe binding efficiencies. An Illumina Infinium II whole-genome genotyping array was recently developed for the cultivated apple and used to develop a molecular linkage map for an apple rootstock progeny (M432), but a large proportion of segregating SNPs were not mapped in the progeny, due to unexpected genotype clustering patterns. To investigate the causes of this unexpected clustering we performed BLAST analysis of all probe sequences against the ‘Golden Delicious’ genome sequence and discovered evidence for paralogous annealing sites and probe sequence divergence for a high proportion of probes contained on the array. Following visual re-evaluation of the genotyping data generated for 8,788 SNPs for the M432 progeny using the array, we manually re-scored genotypes at 818 loci and mapped a further 797 markers to the M432 linkage map. The newly mapped markers included the majority of those that could not be mapped previously, as well as loci that were previously scored as monomorphic, but which segregated due to divergence leading to heterozygosity in probe annealing sites. An evaluation of the 8,788 probes in a diverse collection of Malus germplasm showed that more than half the probes returned genotype clustering patterns that were difficult or impossible to interpret reliably, highlighting implications for the use of the array in genome-wide association studies. PMID:23826289
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Guide to good practices for operations and administration updates through required reading
DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
1998-12-01
This Guide to Good Practices is written to enhance understanding of, and provide direction for, Required Reading, Chapter XIV of Department of Energy (DOE) Order 5480.19, Conduct of Operations Requirements for DOE Facilities. The practices in this guide should be considered when planning or reviewing programs for updating personnel with operations and administration information through required reading. Contractors are advised to adopt procedures that meet the intent of DOE Order 5480.19. Required Reading is an element of an effective Conduct of Operations program. The complexity and array of activities performed in DOE facilities dictate the necessity for a coordinated requiredmore » reading program to promote safe and efficient operations.« less
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Historical development of worldwide guided missiles
NASA Technical Reports Server (NTRS)
Spearman, M. L.
1983-01-01
The development of missiles from early history to present time is put in perspective. The influence of World War II in accelerating the development of guided missiles, particularly through German scientists, is discussed. The dispersion of German scientists to other countries and the coupling of their work with native talent to develop guide missiles is traced. Particular emphasis is placed on the evolution of the missile in the U.S. and the U.S.S.R. Since the Soviets possess what is probably the world's most complete array of dedicated missile system types, their known inventory is reviewed. Some philosophical observations of missile design trends and missile purposes are made as related to the interests of various countries.
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Diergaarde, Brenda; Bowen, Deborah J; Ludman, Evette J; Culver, Julie O; Press, Nancy; Burke, Wylie
2007-03-15
Genetic information is used increasingly in health care. Some experts have argued that genetic information is qualitatively different from other medical information and, therefore, raises unique social issues. This view, called "genetic exceptionalism," has importantly influenced recent policy efforts. Others have argued that genetic information is like other medical information and that treating it differently may actually result in unintended disparities. Little is known about how the general public views genetic information. To identify opinions about implications of genetic and other medical information among the general population, we conducted a series of focus groups in Seattle, WA. Participants were women and men between ages 18 and 74, living within 30 miles of Seattle and members of the Group Health Cooperative. A structured discussion guide was used to ensure coverage of all predetermined topics. Sessions lasted approximately 2 hr; were audio taped and transcribed. The transcripts formed the basis of the current analysis. Key findings included the theme that genetic information was much like other medical information and that all sensitive medical information should be well protected. Personal choice (i.e., the right to choose whether to know health risk information and to control who else knows) was reported to be of crucial importance. Participants had an understanding of the tensions involved in protecting privacy versus sharing medical information to help another person. These data may guide future research and policy concerning the use and protection of medical information, including genetic information. (c) 2007 Wiley-Liss, Inc.
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Yamamoto, Toshio; Nagasaki, Hideki; Yonemaru, Jun-ichi; Ebana, Kaworu; Nakajima, Maiko; Shibaya, Taeko; Yano, Masahiro
2010-04-27
To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition. The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7 x the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67,051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.
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2012-01-01
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 information due to genotyping errors are widely recognized as limiting factors in genetic studies. We have conducted the first formal analysis of the effect of novel variants on genotyping arrays, and we have shown that these variants account for a large portion of miscalled and uncalled genotypes. Genetic studies will benefit from substantial improvements in the accuracy of their results by incorporating VINOs in their analyses. PMID:22260749
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Advances in autism genetics: on the threshold of a new neurobiology
Abrahams, Brett S.; Geschwind, Daniel H.
2009-01-01
Autism is a heterogeneous syndrome defined by impairments in three core domains: social interaction, language and range of interests. Recent work has led to the identification of several autism susceptibility genes and an increased appreciation of the contribution of de novo and inherited copy number variation. Promising strategies are also being applied to identify common genetic risk variants. Systems biology approaches, including array-based expression profiling, are poised to provide additional insights into this group of disorders, in which heterogeneity, both genetic and phenotypic, is emerging as a dominant theme. PMID:18414403
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Levin, M
1999-01-01
Screening for genetic disorders, particularly Tay-Sachs Disease, has been traditionally welcome by the Jewish community. I review the history of genetic screening among Jews and the views from the Jewish tradition on the subject, and then discuss ethical challenges of screening and the impact of historical memories upon future acceptance of screening programs. Some rational principles to guide future design of genetic screening programs among Jews are proposed.
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Pengelly, Reuben J; Tapper, William; Gibson, Jane; Knut, Marcin; Tearle, Rick; Collins, Andrew; Ennis, Sarah
2015-09-03
An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution. We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure. WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.
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Inconspicuous echolocation in hoary bats (Lasiurus cinereus)
Aaron J. Corcoran; Theodore J. Weller
2018-01-01
Echolocation allows bats to occupy diverse nocturnal niches. Bats almost always use echolocation, even when other sensory stimuli are available to guide navigation. Here, using arrays of calibrated infrared cameras and ultrasonic microphones, we demonstrate that hoary bats (Lasiurus cinereus) use previously unknown echolocation behaviours that...
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Coherent beam combining in atmospheric channels using gated backscatter.
Naeh, Itay; Katzir, Abraham
2016-02-01
This paper introduces the concept of atmospheric channels and describes a possible approach for the coherent beam combining of lasers of an optical phased array (OPA) in a turbulent atmosphere. By using the recently introduced sparse spectrum harmonic augmentation method, a comprehensive simulative investigation was performed and the exceptional properties of the atmospheric channels were numerically demonstrated. Among the interesting properties are the ability to guide light in a confined manner in a refractive channel, the ability to gather different sources to the same channel, and the ability to maintain a constant relative phase within the channel between several sources. The newly introduced guiding properties combined with a suggested method for channel probing and phase measurement by aerosol backscattered radiation allows coherence improvement of the phased array's elements and energy refocusing at the location of the channel in order to increase power in the bucket without feedback from the target. The method relies on the electronic focusing, electronic scanning, and time gating of the OPA, combined with elements of the relative phase measurements.
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Preschoolers' speed of locating a target symbol under different color conditions.
Wilkinson, Krista M; Carlin, Michael; Jagaroo, Vinoth
2006-06-01
A pressing decision in AAC concerns the organization of aided visual symbols. One recent proposal suggested that basic principles of visual processing may be important determinants of how easily a symbol is found in an array, and that this, in turn will influence more functional outcomes like symbol identification or use. This study examined the role of color on accuracy and speed of symbol location by 16 preschool children without disabilities. Participants searched for a target stimulus in an array of eight stimuli. In the same-color condition, the eight stimuli were all red; in the guided search condition, four of the stimuli were red and four were yellow; in the unique-color condition, all stimuli were unique colors. Accuracy was higher and reaction time was faster when stimuli were unique colors than when they were all one color. Reaction time and accuracy did not differ under the guided search and the color-unique conditions. The implications for AAC are discussed.
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Scintillating fiber-based photon beam profiler for the Jefferson Lab tagged photon beam line
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zorn, C.; Barbosa, F.J.; Freyberger, A.
2000-10-01
A scintillating fiber hodoscope has been built for use as a photon beam profiler in the bremsstrahlung tagged photon beam in Hall B of the Thomas Jefferson National Accelerator Facility (Jefferson Lab). The device consists of a linear array of 64 2-2 mm2 scintillating fibers glued to a corresponding set of light guide fibers. Both fiber types use double-clad technology for maximum intensity. The light guide fibers are gently bent into a square array of holes and air-gap coupled to four compact position-sensitive photomultipliers (16 channel Hamamatsu R5900-M16). Custom electronics amplifies and converts the analog outputs to ECL pulses whichmore » are counted by VME-based scalars. The device consisting of the fibers, photomultipliers, and electronics is sealed within a light-tight aluminum box. Two modules make up a beam imaging 2-D system. The system has been tested successfully during an experimental run« less
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Wu, Han; Chen, Xinlian; Gao, Xinghua; Zhang, Mengying; Wu, Jinbo; Wen, Weijia
2018-04-03
High-throughput measurements can be achieved using droplet-based assays. In this study, we exploited the principles of wetting behavior and capillarity to guide liquids sliding along a solid surface with hybrid wettability. Oil-covered droplet arrays with uniformly sized and regularly shaped picoliter droplets were successfully generated on hydrophilic-in-hydrophobic patterned substrates. More than ten thousand 31-pL droplets were generated in 5 s without any sophisticated instruments. Covering the droplet arrays with oil during generation not only isolated the droplets from each other but also effectively prevented droplet evaporation. The oil-covered droplet arrays could be stored for more than 2 days with less than 35% volume loss. Single microspheres, microbial cells, or mammalian cells were successfully captured in the droplets. We demonstrate that Escherichia coli could be encapsulated at a certain number (1-4) and cultured for 3 days in droplets. Cell population and morphology were dynamically tracked within individual droplets. Our droplet array generation method enables high-throughput processing and is facile, efficient, and low-cost; in addition, the prepared droplet arrays have enormous potential for applications in chemical and biological assays.
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Quadrupole ion traps and trap arrays: geometry, material, scale, performance.
Ouyang, Z; Gao, L; Fico, M; Chappell, W J; Noll, R J; Cooks, R G
2007-01-01
Quadrupole ion traps are reviewed, emphasizing recent developments, especially the investigation of new geometries, guided by multiple particle simulations such as the ITSIM program. These geometries include linear ion traps (LITs) and the simplified rectilinear ion trap (RIT). Various methods of fabrication are described, including the use of rapid prototyping apparatus (RPA), in which 3D objects are generated through point-by-point laser polymerization. Fabrication in silicon using multilayer semi-conductor fabrication techniques has been used to construct arrays of micro-traps. The performance of instruments containing individual traps as well as arrays of traps of various sizes and geometries is reviewed. Two types of array are differentiated. In the first type, trap arrays constitute fully multiplexed mass spectrometers in which multiple samples are examined using multiple sources, analyzers and detectors, to achieve high throughput analysis. In the second, an array of individual traps acts collectively as a composite trap to increase trapping capacity and performance for a single sample. Much progress has been made in building miniaturized mass spectrometers; a specific example is a 10 kg hand-held tandem mass spectrometer based on the RIT mass analyzer. The performance of this instrument in air and water analysis, using membrane sampling, is described.
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NASA Astrophysics Data System (ADS)
Gleghorn, Jason P.; Smith, James P.; Kirby, Brian J.
2013-09-01
Microfluidic obstacle arrays have been used in numerous applications, and their ability to sort particles or capture rare cells from complex samples has broad and impactful applications in biology and medicine. We have investigated the transport and collision dynamics of particles in periodic obstacle arrays to guide the design of convective, rather than diffusive, transport-based immunocapture microdevices. Ballistic and full computational fluid dynamics simulations are used to understand the collision modes that evolve in cylindrical obstacle arrays with various geometries. We identify previously unrecognized collision mode structures and differential size-based collision frequencies that emerge from these arrays. Previous descriptions of transverse displacements that assume unidirectional flow in these obstacle arrays cannot capture mode transitions properly as these descriptions fail to capture the dependence of the mode transitions on column spacing and the attendant change in the flow field. Using these analytical and computational simulations, we elucidate design parameters that induce high collision rates for all particles larger than a threshold size or selectively increase collision frequencies for a narrow range of particle sizes within a polydisperse population. Furthermore, we investigate how the particle Péclet number affects collision dynamics and mode transitions and demonstrate that experimental observations from various obstacle array geometries are well described by our computational model.
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Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile
Boudry, Pierre; Semenova, Ekaterina; Monot, Marc; Datsenko, Kirill A.; Lopatina, Anna; Sekulovic, Ognjen; Ospina-Bedoya, Maicol; Fortier, Louis-Charles; Severinov, Konstantin; Dupuy, Bruno
2015-01-01
ABSTRACT Clostridium difficile is the cause of most frequently occurring nosocomial diarrhea worldwide. As an enteropathogen, C. difficile must be exposed to multiple exogenous genetic elements in bacteriophage-rich gut communities. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems allow bacteria to adapt to foreign genetic invaders. Our recent data revealed active expression and processing of CRISPR RNAs from multiple type I-B CRISPR arrays in C. difficile reference strain 630. Here, we demonstrate active expression of CRISPR arrays in strain R20291, an epidemic C. difficile strain. Through genome sequencing and host range analysis of several new C. difficile phages and plasmid conjugation experiments, we provide evidence of defensive function of the CRISPR-Cas system in both C. difficile strains. We further demonstrate that C. difficile Cas proteins are capable of interference in a heterologous host, Escherichia coli. These data set the stage for mechanistic and physiological analyses of CRISPR-Cas-mediated interactions of important global human pathogen with its genetic parasites. PMID:26330515
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A high-throughput method for GMO multi-detection using a microfluidic dynamic array.
Brod, Fábio Cristiano Angonesi; van Dijk, Jeroen P; Voorhuijzen, Marleen M; Dinon, Andréia Zilio; Guimarães, Luis Henrique S; Scholtens, Ingrid M J; Arisi, Ana Carolina Maisonnave; Kok, Esther J
2014-02-01
The ever-increasing production of genetically modified crops generates a demand for high-throughput DNA-based methods for the enforcement of genetically modified organisms (GMO) labelling requirements. The application of standard real-time PCR will become increasingly costly with the growth of the number of GMOs that is potentially present in an individual sample. The present work presents the results of an innovative approach in genetically modified crops analysis by DNA based methods, which is the use of a microfluidic dynamic array as a high throughput multi-detection system. In order to evaluate the system, six test samples with an increasing degree of complexity were prepared, preamplified and subsequently analysed in the Fluidigm system. Twenty-eight assays targeting different DNA elements, GM events and species-specific reference genes were used in the experiment. The large majority of the assays tested presented expected results. The power of low level detection was assessed and elements present at concentrations as low as 0.06 % were successfully detected. The approach proposed in this work presents the Fluidigm system as a suitable and promising platform for GMO multi-detection.
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Genetics Home Reference: cri-du-chat syndrome
... Pinkel D. High-resolution mapping of genotype-phenotype relationships in cri du chat syndrome using array comparative ... for Links Data Files & API Site Map Subscribe Customer Support USA.gov Copyright Privacy Accessibility FOIA Viewers & ...
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Evolution of Analog Circuits on Field Programmable Transistor Arrays
NASA Technical Reports Server (NTRS)
Stoica, A.; Keymeulen, D.; Zebulum, R.; Thakoor, A.; Daud, T.; Klimeck, G.; Jin, Y.; Tawel, R.; Duong, V.
2000-01-01
Evolvable Hardware (EHW) refers to HW design and self-reconfiguration using evolutionary/genetic mechanisms. The paper presents an overview of some key concepts of EHW, describing also a set of selected applications.
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Genetics Home Reference: mycosis fungoides
... Cigudosa JC, Barranco C, Serrano S, Dummer R, Tensen CP, Solé F, Pujol RM, Espinet B. Oligonucleotide array- ... K, Knijnenburg J, Boer JM, Willemze R, Tensen CP. Oncogenomic analysis of mycosis fungoides reveals major differences ...
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Interaction between scene-based and array-based contextual cueing.
Rosenbaum, Gail M; Jiang, Yuhong V
2013-07-01
Contextual cueing refers to the cueing of spatial attention by repeated spatial context. Previous studies have demonstrated distinctive properties of contextual cueing by background scenes and by an array of search items. Whereas scene-based contextual cueing reflects explicit learning of the scene-target association, array-based contextual cueing is supported primarily by implicit learning. In this study, we investigated the interaction between scene-based and array-based contextual cueing. Participants searched for a target that was predicted by both the background scene and the locations of distractor items. We tested three possible patterns of interaction: (1) The scene and the array could be learned independently, in which case cueing should be expressed even when only one cue was preserved; (2) the scene and array could be learned jointly, in which case cueing should occur only when both cues were preserved; (3) overshadowing might occur, in which case learning of the stronger cue should preclude learning of the weaker cue. In several experiments, we manipulated the nature of the contextual cues present during training and testing. We also tested explicit awareness of scenes, scene-target associations, and arrays. The results supported the overshadowing account: Specifically, scene-based contextual cueing precluded array-based contextual cueing when both were predictive of the location of a search target. We suggest that explicit, endogenous cues dominate over implicit cues in guiding spatial attention.
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Leng, Yuankui
2017-01-01
Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and “point of care” platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields. PMID:26021602
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Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly
DOE Office of Scientific and Technical Information (OSTI.GOV)
Torella, JP; Boehm, CR; Lienert, F
2013-12-28
In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminatormore » parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.« less
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User's guide to the Octopus computer network (the SHOC manual)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schneider, C.; Thompson, D.; Whitten, G.
1977-07-18
This guide explains how to enter, run, and debug programs on the Octopus network. It briefly describes the network's operation, and directs the reader to other documents for further information. It stresses those service programs that will be most useful in the long run; ''quick'' methods that have little flexibility are not discussed. The Octopus timesharing network gives the user access to four CDC 7600 computers, two CDC STAR computers, and a broad array of peripheral equipment, from any of 800 or so remote terminals. 16 figures, 7 tables.
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User's guide to the Octopus computer network (the SHOC manual)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schneider, C.; Thompson, D.; Whitten, G.
1976-10-07
This guide explains how to enter, run, and debug programs on the Octopus network. It briefly describes the network's operation, and directs the reader to other documents for further information. It stresses those service programs that will be most useful in the long run; ''quick'' methods that have little flexibility are not discussed. The Octopus timesharing network gives the user access to four CDC 7600 computers, two CDC STAR computers, and a broad array of peripheral equipment, from any of 800 or so remote terminals. 8 figures, 4 tables.
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User's guide to the Octopus computer network (the SHOC manual)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schneider, C.; Thompson, D.; Whitten, G.
1975-06-02
This guide explains how to enter, run, and debug programs on the Octopus network. It briefly describes the network's operation, and directs the reader to other documents for further information. It stresses those service programs that will be most useful in the long run; ''quick'' methods that have little flexibility are not discussed. The Octopus timesharing network gives the user access to four CDC 7600 computers and a broad array of peripheral equipment, from any of 800 remote terminals. Octopus will soon include the Laboratory's STAR-100 computers. 9 figures, 5 tables. (auth)
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USDA-ARS?s Scientific Manuscript database
Moniliophthora roreri is the fungal pathogen that causes frosty pod rot (FPR) disease of Theobroma cacao L., the source of chocolate. FPR occurs in most of the cacao producing countries in the Western Hemisphere, causing yield losses up to 80%. Genetic diversity within the FPR pathogen population ma...
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Bubble Transport through Micropillar Arrays
NASA Astrophysics Data System (ADS)
Lee, Kenneth; Savas, Omer
2012-11-01
In current energy research, artificial photosynthetic devices are being designed to split water and harvest hydrogen gas using energy from the sun. In one such design, hydrogen gas bubbles evolve on the catalytic surfaces of arrayed micropillars. If these bubbles are not promptly removed from the surface, they can adversely affect gas evolution rates, water flow rates, sunlight capture, and heat management of the system. Therefore, an efficient method of collecting the evolved gas bubbles is crucial. Preliminary flow visualization has been conducted of bubbles advecting through dense arrays of pillars. Bubbles moving through square and hexagonal arrays are tracked, and the results are qualitatively described. Initial attempts to correlate bubble motion with relevant lengthscales and forces are also presented. These observations suggest how bubble transport within such pillar arrays can be managed, as well as guide subsequent experiments that investigate bubble evolution and collection. This material is based upon work performed by the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy under Award Number DE-SC0004993.
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Definition study for photovoltaic residential prototype system
NASA Technical Reports Server (NTRS)
Imamura, M. S.; Hulstrom, R. L.; Cookson, C.; Waldman, B. H.; Lane, R. A.
1976-01-01
A parametric sensitivity study and definition of the conceptual design is presented. A computer program containing the solar irradiance, solar array, and energy balance models was developed to determine the sensitivities of solar insolation and the corresponding solar array output at five sites selected for this study as well as the performance of several solar array/battery systems. A baseline electrical configuration was chosen, and three design options were recommended. The study indicates that the most sensitive parameters are the solar insolation and the inverter efficiency. The baseline PST selected is comprised of a 133 sg m solar array, 250 ampere hour battery, one to three inverters, and a full shunt regulator to limit the upper solar array voltage. A minicomputer controlled system is recommended to provide the overall control, display, and data acquisition requirements. Architectural renderings of two photovoltaic residential concepts, one above ground and the other underground, are presented. The institutional problems were defined in the areas of legal liabilities during and after installation of the PST, labor practices, building restrictions and architectural guides, and land use.
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Johnson, Julie A.; Cavallari, Larisa H.
2014-01-01
The cytochrome P450 (CYP) 2C9 and vitamin K epoxide reductase complex 1 (VKORC1) genotypes have been strongly and consistently associated with warfarin dose requirements, and dosing algorithms incorporating genetic and clinical information have been shown to be predictive of stable warfarin dose. However, clinical trials evaluating genotype-guided warfarin dosing produced mixed results, calling into question the utility of this approach. Recent trials used surrogate markers as endpoints rather than clinical endpoints, further complicating translation of the data to clinical practice. The present data do not support genetic testing to guide warfarin dosing, but in the setting where genotype data are available, use of such data in those of European ancestry is reasonable. Outcomes data are expected from an on-going trial, observational studies continue, and more work is needed to define dosing algorithms that incorporate appropriate variants in minority populations; all these will further shape guidelines and recommendations on the clinical utility of genotype-guided warfarin dosing. PMID:25282448
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Sorrentino, F S; Gallenga, C E; Bonifazzi, C; Perri, P
2016-01-01
Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by a complex association between tremendous genotypic multiplicity and great phenotypic heterogeneity. The severity of the clinical manifestation depends on penetrance and expressivity of the disease-gene. Also, various interactions between gene expression and environmental factors have been hypothesized. More than 250 genes with ~4500 causative mutations have been reported to be involved in different RP-related mechanisms. Nowadays, not more than the 50% of RPs are attributable to identified genes, whereas the rest of molecular defects are still undetectable, especially in populations where few genetic screenings have been performed. Therefore, new genetic strategies can be a remarkably useful tool to aid clinical diagnosis, potentially modifying treatment options, and family counseling. Genome-wide analytical techniques (array comparative genomic hybridization and single-nucleotide polymorphism genotyping) and DNA sequencing strategies (arrayed primer extension, Sanger sequencing, and ultra high-throughput sequencing) are successfully used to early make molecular diagnosis detecting single or multiple mutations in the huge heterogeneity of RPs. To date, further research needs to be carried out to better investigate the genotype/phenotype correlation, putting together genetic and clinical findings to provide detailed information concerning the risk of RP development and novel effective treatments. PMID:27564722
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Increased genomic prediction accuracy in wheat breeding using a large Australian panel.
Norman, Adam; Taylor, Julian; Tanaka, Emi; Telfer, Paul; Edwards, James; Martinant, Jean-Pierre; Kuchel, Haydn
2017-12-01
Genomic prediction accuracy within a large panel was found to be substantially higher than that previously observed in smaller populations, and also higher than QTL-based prediction. In recent years, genomic selection for wheat breeding has been widely studied, but this has typically been restricted to population sizes under 1000 individuals. To assess its efficacy in germplasm representative of commercial breeding programmes, we used a panel of 10,375 Australian wheat breeding lines to investigate the accuracy of genomic prediction for grain yield, physical grain quality and other physiological traits. To achieve this, the complete panel was phenotyped in a dedicated field trial and genotyped using a custom Axiom TM Affymetrix SNP array. A high-quality consensus map was also constructed, allowing the linkage disequilibrium present in the germplasm to be investigated. Using the complete SNP array, genomic prediction accuracies were found to be substantially higher than those previously observed in smaller populations and also more accurate compared to prediction approaches using a finite number of selected quantitative trait loci. Multi-trait genetic correlations were also assessed at an additive and residual genetic level, identifying a negative genetic correlation between grain yield and protein as well as a positive genetic correlation between grain size and test weight.
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A Guide to Selected National Genetic Voluntary Organizations.
ERIC Educational Resources Information Center
National Center for Education in Maternal and Child Health, Washington, DC.
The directory lists mutual support groups concerned with the medical and psychosocial impacts of genetic disorders and birth defects on affected individuals and families. Each organization included is dedicated to the ongoing emotional, practical, and financial needs of these populations. Entries are categorized by disorder, including: general,…
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A Guide to Selected National Genetic Voluntary Organizations.
ERIC Educational Resources Information Center
National Center for Education in Maternal and Child Health, Washington, DC.
The directory lists approximately 120 mutual support groups concerned with the medical and psychological impacts of genetic disorders and birth defects on individuals and their families. The groups are dedicated to serving the ongoing emotional, practical, and financial needs of these populations. The entries are arranged alphabetically and…
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Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.
Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A P; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N
2016-02-01
Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. Copyright © 2016 by the Genetics Society of America.
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Transvaginal 3D Image-Guided High Intensity Focused Ultrasound Array
NASA Astrophysics Data System (ADS)
Held, Robert; Nguyen, Thuc Nghi; Vaezy, Shahram
2005-03-01
The goal of this project is to develop a transvaginal image-guided High Intensity Focused Ultrasound (HIFU) device using piezocomposite HIFU array technology, and commercially-available ultrasound imaging. Potential applications include treatment of uterine fibroids and abnormal uterine bleeding. The HIFU transducer was an annular phased array, with a focal length range of 30-60 mm, an elliptically-shaped aperture of 35×60 mm, and an operating frequency of 3 MHz. A pillow-shaped bag with water circulation will be used for coupling the HIFU energy into the tissue. An intra-cavity imaging probe (C9-5, Philips) was integrated with the HIFU array such that the focal axis of the HIFU transducer was within the image plane. The entire device will be covered by a gel-filled condom when inserted in the vaginal cavity. To control it, software packages were developed in the LabView programming environment. An imaging algorithm processed the ultrasound image to remove noise patterns due to the HIFU signal. The device will be equipped with a three-dimensional tracking system, using a six-degrees-of-freedom articulating arm. Necrotic lesions were produced in a tissue-mimicking phantom and a turkey breast sample for all focal lengths. Various HIFU doses allow various necrotic lesion shapes, including thin ellipsoidal, spherical, wide cylindrical, and teardrop-shaped. Software control of the device allows multiple foci to be activated sequentially for desired lesion patterns. Ultrasound imaging synchronization can be achieved using hardware signals obtained from the imaging system, or software signals determined empirically for various imaging probes. The image-guided HIFU device will provide a valuable tool in visualization of uterine fibroid tumors for the purposes of planning and subsequent HIFU treatment of the tumor, all in a 3D environment. The control system allows for various lesions of different shapes to be optimally positioned in the tumor to cover the entire tumor volume. Real-time ultrasound imaging for guidance and monitoring of HIFU treatment provides an effective method for outpatient-based procedures.
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Cicada-inspired cell-instructive nanopatterned arrays
NASA Astrophysics Data System (ADS)
Diu, Ting; Faruqui, Nilofar; Sjöström, Terje; Lamarre, Baptiste; Jenkinson, Howard F.; Su, Bo; Ryadnov, Maxim G.
2014-11-01
Biocompatible surfaces hold key to a variety of biomedical problems that are directly related to the competition between host-tissue cell integration and bacterial colonisation. A saving solution to this is seen in the ability of cells to uniquely respond to physical cues on such surfaces thus prompting the search for cell-instructive nanoscale patterns. Here we introduce a generic rationale engineered into biocompatible, titanium, substrates to differentiate cell responses. The rationale is inspired by cicada wing surfaces that display bactericidal nanopillar patterns. The surfaces engineered in this study are titania (TiO2) nanowire arrays that are selectively bactericidal against motile bacteria, while capable of guiding mammalian cell proliferation according to the type of the array. The concept holds promise for clinically relevant materials capable of differential physico-mechanical responses to cellular adhesion.
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Cicada-inspired cell-instructive nanopatterned arrays.
Diu, Ting; Faruqui, Nilofar; Sjöström, Terje; Lamarre, Baptiste; Jenkinson, Howard F; Su, Bo; Ryadnov, Maxim G
2014-11-20
Biocompatible surfaces hold key to a variety of biomedical problems that are directly related to the competition between host-tissue cell integration and bacterial colonisation. A saving solution to this is seen in the ability of cells to uniquely respond to physical cues on such surfaces thus prompting the search for cell-instructive nanoscale patterns. Here we introduce a generic rationale engineered into biocompatible, titanium, substrates to differentiate cell responses. The rationale is inspired by cicada wing surfaces that display bactericidal nanopillar patterns. The surfaces engineered in this study are titania (TiO2) nanowire arrays that are selectively bactericidal against motile bacteria, while capable of guiding mammalian cell proliferation according to the type of the array. The concept holds promise for clinically relevant materials capable of differential physico-mechanical responses to cellular adhesion.
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FIBER AND INTEGRATED OPTICS: Bandgap modes in a coupled waveguide array
NASA Astrophysics Data System (ADS)
Usievich, B. A.; Nurligareev, D. Kh; Svetikov, V. V.; Sychugov, V. A.
2009-08-01
This work examines a waveguide array that consists of ten Nb2O5/SiO2 double layers and supports a 0.63-μm surface wave. The deposition of a Nb2O5 capping layer on top of the waveguide array enables a marked increase in the wave field intensity on its surface. The efficiency of surface-wave excitation in the Kretschmann configuration can be optimised by adjusting the number of double layers. We analyse the behaviour of the Bragg mode in relation to the thickness of the layer exposed to air and the transition of this mode from the second allowed band to the first through the bandgap of the system. In addition, the conventional leaky mode converts to a surface mode and then to a guided mode.
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Lin, Chenxi; Povinelli, Michelle L
2009-10-26
In this paper, we use the transfer matrix method to calculate the optical absorptance of vertically-aligned silicon nanowire (SiNW) arrays. For fixed filling ratio, significant optical absorption enhancement occurs when the lattice constant is increased from 100 nm to 600 nm. The enhancement arises from an increase in field concentration within the nanowire as well as excitation of guided resonance modes. We quantify the absorption enhancement in terms of ultimate efficiency. Results show that an optimized SiNW array with lattice constant of 600 nm and wire diameter of 540 nm has a 72.4% higher ultimate efficiency than a Si thin film of equal thickness. The enhancement effect can be maintained over a large range of incidence angles.
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Imagining physically impossible self-rotations: geometry is more important than gravity.
Creem, S H; Wraga, M; Proffitt, D R
2001-08-01
Previous studies found that it is easier for observers to spatially update displays during imagined self-rotation versus array rotation. The present study examined whether either the physics of gravity or the geometric relationship between the viewer and array guided this self-rotation advantage. Experiments 1-3 preserved a real or imagined orthogonal relationship between the viewer and the array, requiring a rotation in the observer's transverse plane. Despite imagined self-rotations that defied gravity, a viewer advantage remained. Without this orthogonal relationship (Experiment 4), the viewer advantage was lost. We suggest that efficient transformation of the egocentric reference frame relies on the representation of body-environment relations that allow rotation around the observer's principal axis. This efficiency persists across different and conflicting physical and imagined postures.
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Imagining physically impossible self-rotations: geometry is more important than gravity
NASA Technical Reports Server (NTRS)
Creem, S. H.; Wraga, M.; Proffitt, D. R.; Kaiser, M. K. (Principal Investigator)
2001-01-01
Previous studies found that it is easier for observers to spatially update displays during imagined self-rotation versus array rotation. The present study examined whether either the physics of gravity or the geometric relationship between the viewer and array guided this self-rotation advantage. Experiments 1-3 preserved a real or imagined orthogonal relationship between the viewer and the array, requiring a rotation in the observer's transverse plane. Despite imagined self-rotations that defied gravity, a viewer advantage remained. Without this orthogonal relationship (Experiment 4), the viewer advantage was lost. We suggest that efficient transformation of the egocentric reference frame relies on the representation of body-environment relations that allow rotation around the observer's principal axis. This efficiency persists across different and conflicting physical and imagined postures.
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Genetic heterogeneity in autism: From single gene to a pathway perspective.
An, Joon Yong; Claudianos, Charles
2016-09-01
The extreme genetic heterogeneity of autism spectrum disorder (ASD) represents a major challenge. Recent advances in genetic screening and systems biology approaches have extended our knowledge of the genetic etiology of ASD. In this review, we discuss the paradigm shift from a single gene causation model to pathway perturbation model as a guide to better understand the pathophysiology of ASD. We discuss recent genetic findings obtained through next-generation sequencing (NGS) and examine various integrative analyses using systems biology and complex networks approaches that identify convergent patterns of genetic elements associated with ASD. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Sanner, Jennifer E; Yu, Erica; Udtha, Malini; Williams, Pamela Holtzclaw
2013-12-01
Biobanks function as vital components in genetic research, which often requires large disease-based or population-based biospecimens and clinical data to study complex or rare diseases. Genetic biobanks aim to provide resources for translational research focusing on rapidly moving scientific findings from the laboratory into health care practice. The nursing profession must evolve as genetic biobanking practices advance. Nursing involvement in genetic biobanking practices comes with a distinct set of educational, ethical, and practice competencies. In response to these growing competency standards, nursing science developed a conceptual framework and continues to study ethical considerations to guide genetic biobanking initiatives. Copyright © 2013 Elsevier Inc. All rights reserved.
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High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster).
Plomion, C; Bartholomé, J; Lesur, I; Boury, C; Rodríguez-Quilón, I; Lagraulet, H; Ehrenmann, F; Bouffier, L; Gion, J M; Grivet, D; de Miguel, M; de María, N; Cervera, M T; Bagnoli, F; Isik, F; Vendramin, G G; González-Martínez, S C
2016-03-01
Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies. © 2015 John Wiley & Sons Ltd.
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Information Literacy in the 21st Century Multicultural Classroom: Using Sociocultural Literacy
ERIC Educational Resources Information Center
Blas, Elise A.
2014-01-01
Sociocultural literacy guides an instructor's pedagogy in the multicultural university classroom. By employing sociocultural literacy in the information literacy classroom, the instruction librarian can better teach students from all cultures including international students, first generation students, or students from a wide array of…
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Universal Design in Higher Education: From Principles to Practice
ERIC Educational Resources Information Center
Burgstahler, Sheryl E., Ed.; Cory, Rebecca C., Ed.
2008-01-01
"Universal Design in Higher Education" looks at the design of physical and technological environments at institutions of higher education; at issues pertaining to curriculum and instruction; and at the full array of student services. "Universal Design in Higher Education" is a comprehensive guide for researchers and…
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DORCA 2 computer program. Volume 2: Programmer's manual
NASA Technical Reports Server (NTRS)
Gold, B. J.
1972-01-01
A guide for coding the Dynamic Operational Requirements and Cost Analysis Program (DORCA 2) is presented. The manual provides a detailed operation of every subroutine, the layout in core of the major matrices and arrays, and the meaning of all program values. Flow charts are included.
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An overview of STRUCTURE: applications, parameter settings, and supporting software
Porras-Hurtado, Liliana; Ruiz, Yarimar; Santos, Carla; Phillips, Christopher; Carracedo, Ángel; Lareu, Maria V.
2013-01-01
Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE. Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS. Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data. PMID:23755071
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Elimination of the cryptic plasmid in Leuconostoc citreum by CRISPR/Cas9 system.
Jang, Ye-Ji; Seo, Seung-Oh; Kim, Seul-Ah; Li, Ling; Kim, Tae-Jip; Kim, Sun Chang; Jin, Yong-Su; Han, Nam Soo
2017-06-10
Leuconostoc spp. are important lactic acid bacteria for the fermentation of foods. In particular, L. citreum strains isolated from various foods have been used as host strains for genetic and metabolic engineering studies. In order to develop a food-grade genetic engineering system, L. citreum CB2567 was isolated from Kimchi. However, the isolated bacterium contained a cryptic plasmid which was difficult to eliminate. As the existence of the plasmid might hinder strain engineering, we eliminated the plasmid using an RNA-guided DNA endonuclease CRISPR/Cas9 system. We demonstrated that a plasmid-free L. citreum CB2567 host strain could be efficiently constructed through a two-step procedure: 1) transformation of the "killer" plasmid expressing Cas9 endonuclease and a guide RNA (gRNA) targeting for a specific sequence in the cryptic plasmid, and 2) serial subculture without antibiotics for curing the killer plasmid. When the crude extract of L. citreum expressing Cas9 and the guide RNA was incubated with a PCR fragment containing the specific sequence recognized by the guide RNA, the PCR fragment was cleaved. Also, the cryptic plasmid pCB42 was successfully eliminated from the host strain after transforming the plasmid harboring Cas9 and the guide RNA. The Cas9 and gRNA expression plasmid used in this study can be applied for genome engineering purposes by additionally introducing an editing DNA template to repair the double strand DNA breakage caused by Cas9 in the genome of L. citreum. This study demonstrates the feasibility of developing CRISPR/Cas9-based genetic engineering tools to develop a safe host strain and construct food-grade lactic acid bacteria without residual antibiotic markers. Copyright © 2017 Elsevier B.V. All rights reserved.
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Metabolic thrift and the genetic basis of human obesity
O’Rourke, Robert W.
2014-01-01
Evolution has molded metabolic thrift within humans, a genetic heritage that, when thrust into our modern “obesogenic” environment, creates the current obesity crisis. Modern genetic analysis has identified genetic and epigenetic contributors to obesity, an understanding of which will guide the development of environmental, pharmacologic, and genetic therapeutic interventions. “The voyage was so long, food and water ran out. One hundred of the paddlers died; forty men remained. The voyagers finally reached Fitinui, then Aotona.”-From “The Story of Aka”, in The Native Culture in the Marquesas by E. S. Craighill Handy PMID:24368636
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Bernstein, Jacob G.; Allen, Brian D.; Guerra, Alexander A.; Boyden, Edward S.
2016-01-01
Optogenetics enables light to be used to control the activity of genetically targeted cells in the living brain. Optical fibers can be used to deliver light to deep targets, and LEDs can be spatially arranged to enable patterned light delivery. In combination, arrays of LED-coupled optical fibers can enable patterned light delivery to deep targets in the brain. Here we describe the process flow for making LED arrays and LED-coupled optical fiber arrays, explaining key optical, electrical, thermal, and mechanical design principles to enable the manufacturing, assembly, and testing of such multi-site targetable optical devices. We also explore accessory strategies such as surgical automation approaches as well as innovations to enable low-noise concurrent electrophysiology. PMID:26798482
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Detecting Spatial Patterns in Biological Array Experiments
ROOT, DAVID E.; KELLEY, BRIAN P.; STOCKWELL, BRENT R.
2005-01-01
Chemical genetic screening and DNA and protein microarrays are among a number of increasingly important and widely used biological research tools that involve large numbers of parallel experiments arranged in a spatial array. It is often difficult to ensure that uniform experimental conditions are present throughout the entire array, and as a result, one often observes systematic spatially correlated errors, especially when array experiments are performed using robots. Here, the authors apply techniques based on the discrete Fourier transform to identify and quantify spatially correlated errors superimposed on a spatially random background. They demonstrate that these techniques are effective in identifying common spatially systematic errors in high-throughput 384-well microplate assay data. In addition, the authors employ a statistical test to allow for automatic detection of such errors. Software tools for using this approach are provided. PMID:14567791
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Array CGH analysis of a cohort of Russian patients with intellectual disability.
Kashevarova, Anna A; Nazarenko, Lyudmila P; Skryabin, Nikolay A; Salyukova, Olga A; Chechetkina, Nataliya N; Tolmacheva, Ekaterina N; Sazhenova, Elena A; Magini, Pamela; Graziano, Claudio; Romeo, Giovanni; Kučinskas, Vaidutis; Lebedev, Igor N
2014-02-15
The use of array comparative genomic hybridization (array CGH) as a diagnostic tool in molecular genetics has facilitated the identification of many new microdeletion/microduplication syndromes (MMSs). Furthermore, this method has allowed for the identification of copy number variations (CNVs) whose pathogenic role has yet to be uncovered. Here, we report on our application of array CGH for the identification of pathogenic CNVs in 79 Russian children with intellectual disability (ID). Twenty-six pathogenic or likely pathogenic changes in copy number were detected in 22 patients (28%): 8 CNVs corresponded to known MMSs, and 17 were not associated with previously described syndromes. In this report, we describe our findings and comment on genes potentially associated with ID that are located within the CNV regions. Copyright © 2013 Elsevier B.V. All rights reserved.
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NGS2: a focal plane array upgrade for the GeMS multiple tip-tilt wavefront sensor
NASA Astrophysics Data System (ADS)
Rigaut, François; Price, Ian; d'Orgeville, Céline; Bennet, Francis; Herrald, Nick; Paulin, Nicolas; Uhlendorf, Kristina; Garrel, Vincent; Sivo, Gaetano; Montes, Vanessa; Trujillo, Chad
2016-07-01
NGS2 is an upgrade for the multi-natural guide star tip-tilt & plate scale wavefront sensor for GeMS (Gemini Multi-Conjugate Adaptive Optics system). It uses a single Nüvü HNü-512 Electron-Multiplied CCD array that spans the entire GeMS wavefront sensor focal plane. Multiple small regions-of-interest are used to enable frame rates up to 800Hz. This set up will improve the optical throughput with respect to the current wavefront sensor, as well as streamline acquisition and allow for distortion compensation.
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Array-based detection of genetic alterations associated with disease
Pinkel, Daniel; Albertson, Donna G.; Gray, Joe W.
2017-09-05
The present invention relates to DNA sequences from regions of copy number change on chromosome 20. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases.
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Array-based detection of genetic alterations associated with disease
Pinkel, Daniel; Albertson, Donna G.; Gray, Joe W.
2007-09-11
The present invention relates to DNA sequences from regions of copy number change on chromosome 20. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases.
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Brandt-Rauf, Sherry I; Brandt-Rauf, Elka; Gershon, Robyn; Brandt-Rauf, Paul W
2011-01-01
Genetic testing in the workplace holds the promise of improving worker health but also raises ethical, legal, and social issues. In considering such testing, it is critical to understand the perspectives of workers, who are most directly affected by it, and occupational health professionals, who are often directly involved in its implementation. Therefore, a series of focus groups of unionized workers (n=25) and occupational medicine physicians (n=23) was conducted. The results demonstrated strikingly different perspectives of workers and physicians in several key areas, including the goals and appropriateness of genetic testing, and methods to minimize its risks. In general, workers were guided by a profound mistrust of the employer, physician, and government, while physicians were guided primarily by scientific and medical concerns, and, in many cases, by the business concerns distrusted by the workers.
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Sensory Transduction in Caenorhabditis elegans
NASA Astrophysics Data System (ADS)
Brown, Austin L.; Ramot, Daniel; Goodman, Miriam B.
The roundworm Caenorhabditis elegans has a well-defined and comparatively simple repertoire of sensory-guided behaviors, all of which rely on its ability to detect chemical, mechanical or thermal stimuli. In this chapter, we review what is known about the ion channels that mediate sensation in this remarkable model organism. Genetic screens for mutants defective in sensory-guided behaviors have identified genes encoding channel proteins, which are likely transducers of chemical, thermal, and mechanical stimuli. Such classical genetic approaches are now being coupled with molecular genetics and in vivo cellular physiology to elucidate how these channels are activated in specific sensory neurons. The ion channel superfamilies implicated in sensory transduction in C. elegans - CNG, TRP, and DEG/ENaC - are conserved across phyla and also appear to contribute to sensory transduction in other organisms, including vertebrates. What we learn about the role of these ion channels in C. elegans sensation is likely to illuminate analogous processes in other animals, including humans.
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Li, Y.-G.; Ellsworth, W.L.; Thurber, C.H.; Malin, P.E.; Aki, K.
1997-01-01
Fault-zone guided waves were successfully excited by near-surface explosions in the San Andreas fault zone both at Parkfield and Cienega Valley, central California. The guided waves were observed on linear, three-component seismic arrays deployed across the fault trace. These waves were not excited by explosions located outside the fault zone. The amplitude spectra of guided waves show a maximum peak at 2 Hz at Parkfield and 3 Hz at Cienega Valley. The guided wave amplitude decays sharply with observation distance from the fault trace. The explosion-excited fault-zone guided waves are similar to those generated by earthquakes at Parkfield but have lower frequencies and travel more slowly. These observations suggest that the fault-zone wave guide has lower seismic velocities as it approaches the surface at Parkfield. We have modeled the waveforms as S waves trapped in a low-velocity wave guide sandwiched between high-velocity wall rocks, resulting in Love-type fault-zone guided waves. While the results are nonunique, the Parkfield data are adequately fit by a shallow wave guide 170 m wide with an S velocity 0.85 km/sec and an apparent Q ??? 30 to 40. At Cienega Valley, the fault-zone wave guide appears to be about 120 m wide with an S velocity 0.7 km/sec and a Q ??? 30.
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Friend, Milton; Franson, J. Christian; Friend, Milton; Gibbs, Samantha E.J.; Wild, Margaret A.
2015-01-01
This is the third iteration of the National Wildlife Health Center's (NWHC) field guide developed primarily to assist field managers and biologists address diseases they encounter. By itself, the first iteration, “Field Guide of Wildlife Diseases: General Field Procedures and Diseases of Migratory Birds,” was simply another addition to an increasing array of North American field guides and other publications focusing on disease in free-ranging wildlife populations. Collectively, those publications were reflecting the ongoing transition in the convergence of wildlife management and wildlife disease as foundational components within the structure of wildlife conservation as a social enterprise serving the stewardship of our wildlife resources. For context, it is useful to consider those publications relative to a timeline of milestones involving the evolution of wildlife conservation in North America.
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Histone modifications influence mediator interactions with chromatin
Zhu, Xuefeng; Zhang, Yongqiang; Bjornsdottir, Gudrun; Liu, Zhongle; Quan, Amy; Costanzo, Michael; Dávila López, Marcela; Westholm, Jakub Orzechowski; Ronne, Hans; Boone, Charles; Gustafsson, Claes M.; Myers, Lawrence C.
2011-01-01
The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator—histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. PMID:21742760
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Molecular Pathology: A Requirement for Precision Medicine in Cancer.
Dietel, Manfred
2016-01-01
The increasing importance of targeting drugs and check-point inhibitors in the treatment of several tumor entities (breast, colon, lung, malignant melanoma, lymphoma, etc.) and the necessity of a companion diagnostic (HER2, (pan)RAS, EGFR, ALK, BRAF, ROS1, MET, PD-L1, etc.) is leading to new challenges for surgical pathology. Since almost all the biomarkers to be specifically detected are tissue based, a precise and reliable diagnostic is absolutely crucial. To meet this challenge surgical pathology has adapted a number of molecular methods (semi-quantitative immunohistochemistry, fluorescence in situ hybridization, PCR and its multiple variants, (pyro/Sanger) sequencing, next generation sequencing (amplicon, whole exome, whole genome), DNA arrays, methylation analyses, etc.) to be applicable for formalin-fixed paraffin-embedded tissue. Reading a patient's tissue as 'deeply' as possible and obtaining information on the morphological, genetic, proteomic and epigenetic background are the tasks of pathologists and molecular biologists and provide the clinicians with information relevant for precision medicine. Intensified cooperation between clinicians and pathologists will provide the basis of improved clinical drug selection and guide development of new cancer gene therapies and molecularly targeted drugs by research units and the pharmaceutical industry. © 2016 S. Karger GmbH, Freiburg.
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Hitchhiker's guide to multi-dimensional plant pathology.
Saunders, Diane G O
2015-02-01
Filamentous pathogens pose a substantial threat to global food security. One central question in plant pathology is how pathogens cause infection and manage to evade or suppress plant immunity to promote disease. With many technological advances over the past decade, including DNA sequencing technology, an array of new tools has become embedded within the toolbox of next-generation plant pathologists. By employing a multidisciplinary approach plant pathologists can fully leverage these technical advances to answer key questions in plant pathology, aimed at achieving global food security. This review discusses the impact of: cell biology and genetics on progressing our understanding of infection structure formation on the leaf surface; biochemical and molecular analysis to study how pathogens subdue plant immunity and manipulate plant processes through effectors; genomics and DNA sequencing technologies on all areas of plant pathology; and new forms of collaboration on accelerating exploitation of big data. As we embark on the next phase in plant pathology, the integration of systems biology promises to provide a holistic perspective of plant–pathogen interactions from big data and only once we fully appreciate these complexities can we design truly sustainable solutions to preserve our resources.
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Elad, Tal; Lee, Jin Hyung; Belkin, Shimshon; Gu, Man Bock
2008-01-01
Summary The coming of age of whole‐cell biosensors, combined with the continuing advances in array technologies, has prepared the ground for the next step in the evolution of both disciplines – the whole‐cell array. In the present review, we highlight the state‐of‐the‐art in the different disciplines essential for a functional bacterial array. These include the genetic engineering of the biological components, their immobilization in different polymers, technologies for live cell deposition and patterning on different types of solid surfaces, and cellular viability maintenance. Also reviewed are the types of signals emitted by the reporter cell arrays, some of the transduction methodologies for reading these signals and the mathematical approaches proposed for their analysis. Finally, we review some of the potential applications for bacterial cell arrays, and list the future needs for their maturation: a richer arsenal of high‐performance reporter strains, better methodologies for their incorporation into hardware platforms, design of appropriate detection circuits, the continuing development of dedicated algorithms for multiplex signal analysis and – most importantly – enhanced long‐term maintenance of viability and activity on the fabricated biochips. PMID:21261831
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Optimized Hyper Beamforming of Linear Antenna Arrays Using Collective Animal Behaviour
Ram, Gopi; Mandal, Durbadal; Kar, Rajib; Ghoshal, Sakti Prasad
2013-01-01
A novel optimization technique which is developed on mimicking the collective animal behaviour (CAB) is applied for the optimal design of hyper beamforming of linear antenna arrays. Hyper beamforming is based on sum and difference beam patterns of the array, each raised to the power of a hyperbeam exponent parameter. The optimized hyperbeam is achieved by optimization of current excitation weights and uniform interelement spacing. As compared to conventional hyper beamforming of linear antenna array, real coded genetic algorithm (RGA), particle swarm optimization (PSO), and differential evolution (DE) applied to the hyper beam of the same array can achieve reduction in sidelobe level (SLL) and same or less first null beam width (FNBW), keeping the same value of hyperbeam exponent. Again, further reductions of sidelobe level (SLL) and first null beam width (FNBW) have been achieved by the proposed collective animal behaviour (CAB) algorithm. CAB finds near global optimal solution unlike RGA, PSO, and DE in the present problem. The above comparative optimization is illustrated through 10-, 14-, and 20-element linear antenna arrays to establish the optimization efficacy of CAB. PMID:23970843
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Wang, Jiao; Chu, Shanshan; Zhang, Huairen; Zhu, Ying; Cheng, Hao; Yu, Deyue
2016-01-01
Domestication of soybeans occurred under the intense human-directed selections aimed at developing high-yielding lines. Tracing the domestication history and identifying the genes underlying soybean domestication require further exploration. Here, we developed a high-throughput NJAU 355 K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight. Genome-wide scanning for evidence of artificial selection revealed signs of selective sweeps involving genes controlling domestication-related agronomic traits including seed weight. To further identify genomic regions related to seed weight, a genome-wide association study (GWAS) was conducted across multiple environments in wild and cultivated soybeans. As a result, a strong linkage disequilibrium region on chromosome 20 was found to be significantly correlated with seed weight in cultivated soybeans. Collectively, these findings should provide an important basis for genomic-enabled breeding and advance the study of functional genomics in soybean. PMID:26856884
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Wang, Jiao; Chu, Shanshan; Zhang, Huairen; Zhu, Ying; Cheng, Hao; Yu, Deyue
2016-02-09
Domestication of soybeans occurred under the intense human-directed selections aimed at developing high-yielding lines. Tracing the domestication history and identifying the genes underlying soybean domestication require further exploration. Here, we developed a high-throughput NJAU 355 K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight. Genome-wide scanning for evidence of artificial selection revealed signs of selective sweeps involving genes controlling domestication-related agronomic traits including seed weight. To further identify genomic regions related to seed weight, a genome-wide association study (GWAS) was conducted across multiple environments in wild and cultivated soybeans. As a result, a strong linkage disequilibrium region on chromosome 20 was found to be significantly correlated with seed weight in cultivated soybeans. Collectively, these findings should provide an important basis for genomic-enabled breeding and advance the study of functional genomics in soybean.
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NASA Astrophysics Data System (ADS)
Tebbutt, J. A.; Vahdati, M.; Carolan, D.; Dear, J. P.
2017-07-01
Previous research has proposed that an array of Helmholtz resonators may be an effective method for suppressing the propagation of pressure and sound waves, generated by a high-speed train entering and moving in a tunnel. The array can be used to counteract environmental noise from tunnel portals and also the emergence of a shock wave in the tunnel. The implementation of an array of Helmholtz resonators in current and future high-speed train-tunnel systems is studied. Wave propagation in the tunnel is modelled using a quasi-one-dimensional formulation, accounting for non-linear effects, wall friction and the diffusivity of sound. A multi-objective genetic algorithm is then used to optimise the design of the array, subject to the geometric constraints of a demonstrative tunnel system and the incident wavefront in order to attenuate the propagation of pressure waves. It is shown that an array of Helmholtz resonators can be an effective countermeasure for various tunnel lengths. In addition, the array can be designed to function effectively over a wide operating envelope, ensuring it will still function effectively as train speeds increase into the future.
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Jiménez, Cristina; Jara-Acevedo, María; Corchete, Luis A; Castillo, David; Ordóñez, Gonzalo R; Sarasquete, María E; Puig, Noemí; Martínez-López, Joaquín; Prieto-Conde, María I; García-Álvarez, María; Chillón, María C; Balanzategui, Ana; Alcoceba, Miguel; Oriol, Albert; Rosiñol, Laura; Palomera, Luis; Teruel, Ana I; Lahuerta, Juan J; Bladé, Joan; Mateos, María V; Orfão, Alberto; San Miguel, Jesús F; González, Marcos; Gutiérrez, Norma C; García-Sanz, Ramón
2017-01-01
Identification and characterization of genetic alterations are essential for diagnosis of multiple myeloma and may guide therapeutic decisions. Currently, genomic analysis of myeloma to cover the diverse range of alterations with prognostic impact requires fluorescence in situ hybridization (FISH), single nucleotide polymorphism arrays, and sequencing techniques, which are costly and labor intensive and require large numbers of plasma cells. To overcome these limitations, we designed a targeted-capture next-generation sequencing approach for one-step identification of IGH translocations, V(D)J clonal rearrangements, the IgH isotype, and somatic mutations to rapidly identify risk groups and specific targetable molecular lesions. Forty-eight newly diagnosed myeloma patients were tested with the panel, which included IGH and six genes that are recurrently mutated in myeloma: NRAS, KRAS, HRAS, TP53, MYC, and BRAF. We identified 14 of 17 IGH translocations previously detected by FISH and three confirmed translocations not detected by FISH, with the additional advantage of breakpoint identification, which can be used as a target for evaluating minimal residual disease. IgH subclass and V(D)J rearrangements were identified in 77% and 65% of patients, respectively. Mutation analysis revealed the presence of missense protein-coding alterations in at least one of the evaluating genes in 16 of 48 patients (33%). This method may represent a time- and cost-effective diagnostic method for the molecular characterization of multiple myeloma. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
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Díez-Villaseñor, César; Guzmán, Noemí M.; Almendros, Cristóbal; García-Martínez, Jesús; Mojica, Francisco J.M.
2013-01-01
Prokaryotes immunize themselves against transmissible genetic elements by the integration (acquisition) in clustered regularly interspaced short palindromic repeats (CRISPR) loci of spacers homologous to invader nucleic acids, defined as protospacers. Following acquisition, mono-spacer CRISPR RNAs (termed crRNAs) guide CRISPR-associated (Cas) proteins to degrade (interference) protospacers flanked by an adjacent motif in extrachomosomal DNA. During acquisition, selection of spacer-precursors adjoining the protospacer motif and proper orientation of the integrated fragment with respect to the leader (sequence leading transcription of the flanking CRISPR array) grant efficient interference by at least some CRISPR-Cas systems. This adaptive stage of the CRISPR action is poorly characterized, mainly due to the lack of appropriate genetic strategies to address its study and, at least in Escherichia coli, the need of Cas overproduction for insertion detection. In this work, we describe the development and application in Escherichia coli strains of an interference-independent assay based on engineered selectable CRISPR-spacer integration reporter plasmids. By using this tool without the constraint of interference or cas overexpression, we confirmed fundamental aspects of this process such as the critical requirement of Cas1 and Cas2 and the identity of the CTT protospacer motif for the E. coli K12 system. In addition, we defined the CWT motif for a non-K12 CRISPR-Cas variant, and obtained data supporting the implication of the leader in spacer orientation, the preferred acquisition from plasmids harboring cas genes and the occurrence of a sequential cleavage at the insertion site by a ruler mechanism. PMID:23445770
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Díez-Villaseñor, César; Guzmán, Noemí M; Almendros, Cristóbal; García-Martínez, Jesús; Mojica, Francisco J M
2013-05-01
Prokaryotes immunize themselves against transmissible genetic elements by the integration (acquisition) in clustered regularly interspaced short palindromic repeats (CRISPR) loci of spacers homologous to invader nucleic acids, defined as protospacers. Following acquisition, mono-spacer CRISPR RNAs (termed crRNAs) guide CRISPR-associated (Cas) proteins to degrade (interference) protospacers flanked by an adjacent motif in extrachomosomal DNA. During acquisition, selection of spacer-precursors adjoining the protospacer motif and proper orientation of the integrated fragment with respect to the leader (sequence leading transcription of the flanking CRISPR array) grant efficient interference by at least some CRISPR-Cas systems. This adaptive stage of the CRISPR action is poorly characterized, mainly due to the lack of appropriate genetic strategies to address its study and, at least in Escherichia coli, the need of Cas overproduction for insertion detection. In this work, we describe the development and application in Escherichia coli strains of an interference-independent assay based on engineered selectable CRISPR-spacer integration reporter plasmids. By using this tool without the constraint of interference or cas overexpression, we confirmed fundamental aspects of this process such as the critical requirement of Cas1 and Cas2 and the identity of the CTT protospacer motif for the E. coli K12 system. In addition, we defined the CWT motif for a non-K12 CRISPR-Cas variant, and obtained data supporting the implication of the leader in spacer orientation, the preferred acquisition from plasmids harboring cas genes and the occurrence of a sequential cleavage at the insertion site by a ruler mechanism.
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NASA Astrophysics Data System (ADS)
Pérez Urquiza, M.; Acatzi Silva, A. I.
2014-02-01
Three certified reference materials produced from powdered seeds to measure the copy number ratio sequences of p35S/hmgA in maize containing MON 810 event, p35S/Le1 in soybeans containing GTS 40-3-2 event and DREB1A/acc1 in wheat were produced according to the ISO Guides 34 and 35. In this paper, we report digital polymerase chain reaction (dPCR) protocols, performance parameters and results of copy number ratio content of genetically modified organisms (GMOs) in these materials using two new dPCR systems to detect and quantify molecular deoxyribonucleic acid: the BioMark® (Fluidigm) and the OpenArray® (Life Technologies) systems. These technologies were implemented at the National Institute of Metrology in Mexico (CENAM) and in the Reference Center for GMO Detection from the Ministry of Agriculture (CNRDOGM), respectively. The main advantage of this technique against the more-used quantitative polymerase chain reaction (qPCR) is that it generates an absolute number of target molecules in the sample, without reference to standards or an endogenous control, which is very useful when not much information is available for new developments or there are no standard reference materials in the market as in the wheat case presented, or when it was not possible to test the purity of seeds as in the maize case presented here. Both systems reported enhanced productivity, increased reliability and reduced instrument footprint. In this paper, the performance parameters and uncertainty of measurement obtained with both systems are presented and compared.
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Truss Optimization for a Manned Nuclear Electric Space Vehicle using Genetic Algorithms
NASA Technical Reports Server (NTRS)
Benford, Andrew; Tinker, Michael L.
2004-01-01
The purpose of this paper is to utilize the genetic algorithm (GA) optimization method for structural design of a nuclear propulsion vehicle. Genetic algorithms provide a guided, random search technique that mirrors biological adaptation. To verify the GA capabilities, other traditional optimization methods were used to generate results for comparison to the GA results, first for simple two-dimensional structures, and then for full-scale three-dimensional truss designs.
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HIGH-SPEED IMAGING AND WAVEFRONT SENSING WITH AN INFRARED AVALANCHE PHOTODIODE ARRAY
DOE Office of Scientific and Technical Information (OSTI.GOV)
Baranec, Christoph; Atkinson, Dani; Hall, Donald
2015-08-10
Infrared avalanche photodiode (APD) arrays represent a panacea for many branches of astronomy by enabling extremely low-noise, high-speed, and even photon-counting measurements at near-infrared wavelengths. We recently demonstrated the use of an early engineering-grade infrared APD array that achieves a correlated double sampling read noise of 0.73 e{sup −} in the lab, and a total noise of 2.52 e{sup −} on sky, and supports simultaneous high-speed imaging and tip-tilt wavefront sensing with the Robo-AO visible-light laser adaptive optics (AO) system at the Palomar Observatory 1.5 m telescope. Here we report on the improved image quality simultaneously achieved at visible andmore » infrared wavelengths by using the array as part of an image stabilization control loop with AO-sharpened guide stars. We also discuss a newly enabled survey of nearby late M-dwarf multiplicity, as well as future uses of this technology in other AO and high-contrast imaging applications.« less
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Threat captures attention but does not affect learning of contextual regularities.
Yamaguchi, Motonori; Harwood, Sarah L
2017-04-01
Some of the stimulus features that guide visual attention are abstract properties of objects such as potential threat to one's survival, whereas others are complex configurations such as visual contexts that are learned through past experiences. The present study investigated the two functions that guide visual attention, threat detection and learning of contextual regularities, in visual search. Search arrays contained images of threat and non-threat objects, and their locations were fixed on some trials but random on other trials. Although they were irrelevant to the visual search task, threat objects facilitated attention capture and impaired attention disengagement. Search time improved for fixed configurations more than for random configurations, reflecting learning of visual contexts. Nevertheless, threat detection had little influence on learning of the contextual regularities. The results suggest that factors guiding visual attention are different from factors that influence learning to guide visual attention.
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Classroom Technology Use and Middle School Mathematics Students' Self-Efficacy
ERIC Educational Resources Information Center
King, Jeriann Cline
2014-01-01
Educators face decisions when incorporating an expanding array of technological resources in mathematics education and interventions. Guided by Bandura's theory of self-efficacy, which holds that self-efficacy augments personal accomplishments, this quantitative study explored the relationship of Web 2.0 technology use and the development of…
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ERIC Educational Resources Information Center
Minetola, Janice; Serr, Konnie; Nelson, Laureen
2012-01-01
Teachers have the opportunity to capitalize on a vast array of real-world, two- and three-dimensional objects as they guide students in developing a conceptual understanding of geometric shapes. An important component of the NCTM Standards is to use teaching methodologies that engage children in making real-world connections to the mathematics…
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Using Asynchronous AV Communication Tools to Increase Academic Self-Efficacy
ERIC Educational Resources Information Center
Girasoli, Anthony J.; Hannafin, Robert D.
2008-01-01
Technology-enhanced learning environments (TELEs) deliver instructional content and provide an array of scaffolding features designed to support independent student learning. TELEs also support teacher efforts to guide student inquiry within these sometimes complex environments. Self-efficacy, defined by Bandura [Bandura, A. (1994). Self-efficacy.…
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Louisiana Folklife: A Guide to the State.
ERIC Educational Resources Information Center
Spitzer, Nicholas R., Ed.
Louisiana is composed of a vast array of traditional cultures and activities. This resource directory to Louisiana folk arts and folk communities aims to promote better understanding and preservation of the cultural settings and meanings of those things already well known and to explicate the lesser-known activities that comprise living folk…
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[Prenatal genetic diagnosis for a fetus with atypical neurofibromatosis type 1 microdeletion].
Lin, Shaobin; Wu, Jianzhu; Zhang, Zhiqiang; Ji, Yuanjun; Fang, Qun; Chen, Baojiang; Luo, Yanmin
2016-04-01
To analyze the correlation between atypical neurofibromatosis type 1(NF1) microdeletion and fetal phenotype. Fetal blood sampling was carried out for a woman bearing a fetus with talipes equinovarus. G-banded karyotyping and single nucleotide polymorphism array (SNP-array) were performed on the fetal blood sample. Fluorescence in situ hybridization (FISH) was used to confirm the result of SNP array analysis. FISH assay was also carried out on peripheral blood specimens from the parents to ascertain the origin of mutation. The karyotype of fetus was found to be 46, XY by G-banding analysis. However, a 3.132 Mb microdeletion was detected in chromosome region 17q11.2 by SNP array, which overlaped with the region of NF1 microdeletion syndrome. Analyzing of the specimens from the fetus and its parents with FISH has confirmed it to be a de novo deletion. Talipes equinovarus may be an abnormal sonographic feature of fetus with atypical NF1 microdeletion which can be accurately diagnosed with SNP array.
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Kadam, Anagha; Janto, Benjamin; Eutsey, Rory; Earl, Joshua P; Powell, Evan; Dahlgren, Margaret E; Hu, Fen Z; Ehrlich, Garth D; Hiller, N Luisa
2015-02-02
There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome. Copyright © 2015 John Wiley & Sons, Inc.
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Philibert, Robert A; Terry, Nicolas; Erwin, Cheryl; Philibert, Winter J; Beach, Steven Rh; Brody, Gene H
2014-01-01
Genome-wide methylation arrays are increasingly used tools in studies of complex medical disorders. Because of their expense and potential utility to the scientific community, current federal policy dictates that data from these arrays, like those from genome-wide genotyping arrays, be deposited in publicly available databases. Unlike the genotyping information, access to the expression data is not restricted. An underlying supposition in the current nonrestricted access to methylation data is the belief that protected health and personal identifying information cannot be simultaneously extracted from these arrays. In this communication, we analyze methylation data from the Illumina HumanMethylation450 array and show that genotype at 1,069 highly informative loci, and both alcohol and smoking consumption information, can be derived from the array data. We conclude that both potentially personally identifying information and substance-use histories can be simultaneously derived from methylation array data. Because access to genetic information about a database subject or one of their relatives is critical to the de-identification process, this risk of de-identification is limited at the current time. We propose that access to genome-wide methylation data be restricted to institutionally approved investigators who accede to data use agreements prohibiting re-identification.
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Template-guided self-assembly of discrete optoplasmonic molecules and extended optoplasmonic arrays
Reinhard, Björn M.; Ahn, Wonmi; Hong, Yan; ...
2015-10-06
The integration of metallic and dielectric building blocks into optoplasmonic structures creates new electromagnetic systems in which plasmonic and photonic modes can interact in the near-, intermediate- and farfield. The morphology-dependent electromagnetic coupling between the different building blocks in these hybrid structures provides a multitude of opportunities for controlling electromagnetic fields in both spatial and frequency domain as well as for engineering the phase landscape and the local density of optical states. Control over any of these properties requires, however, rational fabrication approaches for well-defined metal-dielectric hybrid structures. Template-guided self-assembly is a versatile fabrication method capable of integrating metallic andmore » dielectric components into discrete optoplasmonic structures, arrays, or metasurfaces. The structural flexibility provided by the approach is illustrated by two representative implementations of optoplasmonic materials discussed in this review. In optoplasmonic atoms or molecules optical microcavities (OMs) serve as whispering gallery mode resonators that provide a discrete photonic mode spectrum to interact with plasmonic nanostructures contained in the evanescent fields of the OMs. In extended hetero-nanoparticle arrays in-plane scattered light induces geometry-dependent photonic resonances that mix with the localized surface plasmon resonances of the metal nanoparticles. As a result, we characterize the fundamental electromagnetic working principles underlying both optoplasmonic approaches and review the fabrication strategies implemented to realize them.« less
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Template-guided self-assembly of discrete optoplasmonic molecules and extended optoplasmonic arrays
DOE Office of Scientific and Technical Information (OSTI.GOV)
Reinhard, Björn M.; Ahn, Wonmi; Hong, Yan
The integration of metallic and dielectric building blocks into optoplasmonic structures creates new electromagnetic systems in which plasmonic and photonic modes can interact in the near-, intermediate- and farfield. The morphology-dependent electromagnetic coupling between the different building blocks in these hybrid structures provides a multitude of opportunities for controlling electromagnetic fields in both spatial and frequency domain as well as for engineering the phase landscape and the local density of optical states. Control over any of these properties requires, however, rational fabrication approaches for well-defined metal-dielectric hybrid structures. Template-guided self-assembly is a versatile fabrication method capable of integrating metallic andmore » dielectric components into discrete optoplasmonic structures, arrays, or metasurfaces. The structural flexibility provided by the approach is illustrated by two representative implementations of optoplasmonic materials discussed in this review. In optoplasmonic atoms or molecules optical microcavities (OMs) serve as whispering gallery mode resonators that provide a discrete photonic mode spectrum to interact with plasmonic nanostructures contained in the evanescent fields of the OMs. In extended hetero-nanoparticle arrays in-plane scattered light induces geometry-dependent photonic resonances that mix with the localized surface plasmon resonances of the metal nanoparticles. As a result, we characterize the fundamental electromagnetic working principles underlying both optoplasmonic approaches and review the fabrication strategies implemented to realize them.« less
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Influence of resonant transducer variations on long range guided wave monitoring of rail track
NASA Astrophysics Data System (ADS)
Loveday, Philip W.; Long, Craig S.
2016-02-01
The ability of certain guided wave modes to propagate long distances in continuously welded rail track is exploited in permanently installed monitoring systems. Previous work demonstrated that reflections from thermite welds could be measured at distances of the order of 1 km from a transducer array. The availability of numerous thermite welds is useful during the development of a monitoring system as real defects are not available. Measurements of reflections from welds were performed over an eleven month period with two permanently installed transducers. Phased array processing was performed and the true location of a weld is indicated by a strong reflection but there is generally also a smaller, spurious replica reflection, at the same distance but in the incorrect direction. In addition, the relative reflection from different welds appears to change over time. The influence of differences between the two resonant transducers was investigated using a model. It was found that estimating the attenuation in either direction and scaling the reflections in either direction decreased the variability in the reflection measurements. Transducer interaction effects, where the transducer closer to the weld records a greater reflection than the second transducer were observed and can be used to determine the direction of a weld. This feature was used to demonstrate a simple alternative to phased array processing that can be used with resonant transducers.
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Kilappa, Vantte; Moilanen, Petro; Salmi, Ari; Haeggström, Edward; Zhao, Zuomin; Myllylä, Risto; Timonen, Jussi
2015-03-01
The fundamental flexural guided wave (FFGW) enables ultrasonic assessment of cortical bone thickness. In vivo, it is challenging to detect this mode, as its power ratio with respect to disturbing ultrasound is reduced by soft tissue covering the bone. A phase-delayed ultrasound source is proposed to tailor the FFGW excitation in order to improve its power ratio. This situation is analyzed by 2D finite-element simulations. The soft tissue coating (7-mm thick) was simulated as a fluid covering an elastic plate (bone, 2-6 mm thick). A six-element array of emitters on top of the coating was excited by 50-kHz tone bursts so that each emitter was appropriately delayed from the previous one. Response was recorded by an array of receivers on top of the coating, 20-50 mm away from the closest emitter. Simulations predicted that such tailored/phase-delayed excitations should improve the power ratio of FFGW by 23 ± 5 dB, independent of the number of emitters (N). On the other hand, the FFGW magnitude should increase by 5.8 ± 0.5 dB for each doubling of N. This suggests that mode tailoring based on phase-delayed excitation may play a key role in the development of an in vivo FFGW assessment.
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NASA Astrophysics Data System (ADS)
Xie, Hongxing; Huang, Jiamin; Ye, Yun; Chen, Enguo; Xu, Sheng
2017-10-01
Light Guide Plate (LGP) plays an irreplaceable role in Liquid Crystal Display (LCD) backlight. LGP with quantum-dot (QD) shows promise in the development of next-generation displays because of QDs' beneficial characteristics. In this paper, we present a novel QD LGP for LCD backlight based on QD scattering microstructure array (SMA), in which the QD net dots are located discretely and arranged in arrays on the bottom surface of LGP. The paper first introduces the QD backlight briefly, then discusses the preparation and fabrication process of the proposed prototype, and finally presents a systematic photometric approach to reveal the remarkable advantages of QD backlight. The white-balance is achieved by adjusting the proportion of the QDs in the mixture and optimizing the R-QD / G-QD ratio. The apparent morphology of QD SMA is characterized by OLYMPUS laser microscope, while the optical properties of QD backlight are investigated by F-4600 fluorescence spectrophotometer and SRC-200M spectrum color luminance meter, respectively. Experimental results show that the white balance can be achieved when the QDs account for a certain proportion about 7% within the mixture, and the ratio of R-QD / G-QD is optimized to about 1:12. The proposed system offers an alternative and feasible method for fabricating QD backlight, which may have great application prospects in the future.
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Air data system optimization using a genetic algorithm
NASA Technical Reports Server (NTRS)
Deshpande, Samir M.; Kumar, Renjith R.; Seywald, Hans; Siemers, Paul M., III
1992-01-01
An optimization method for flush-orifice air data system design has been developed using the Genetic Algorithm approach. The optimization of the orifice array minimizes the effect of normally distributed random noise in the pressure readings on the calculation of air data parameters, namely, angle of attack, sideslip angle and freestream dynamic pressure. The optimization method is applied to the design of Pressure Distribution/Air Data System experiment (PD/ADS) proposed for inclusion in the Aeroassist Flight Experiment (AFE). Results obtained by the Genetic Algorithm method are compared to the results obtained by conventional gradient search method.
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USDA-ARS?s Scientific Manuscript database
The nutritional and economic value of soybean [Glycine max (L.) Merrill] is effectively a function of its seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide future soybean ...
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Design of sparse Halbach magnet arrays for portable MRI using a genetic algorithm.
Cooley, Clarissa Zimmerman; Haskell, Melissa W; Cauley, Stephen F; Sappo, Charlotte; Lapierre, Cristen D; Ha, Christopher G; Stockmann, Jason P; Wald, Lawrence L
2018-01-01
Permanent magnet arrays offer several attributes attractive for the development of a low-cost portable MRI scanner for brain imaging. They offer the potential for a relatively lightweight, low to mid-field system with no cryogenics, a small fringe field, and no electrical power requirements or heat dissipation needs. The cylindrical Halbach array, however, requires external shimming or mechanical adjustments to produce B 0 fields with standard MRI homogeneity levels (e.g., 0.1 ppm over FOV), particularly when constrained or truncated geometries are needed, such as a head-only magnet where the magnet length is constrained by the shoulders. For portable scanners using rotation of the magnet for spatial encoding with generalized projections, the spatial pattern of the field is important since it acts as the encoding field. In either a static or rotating magnet, it will be important to be able to optimize the field pattern of cylindrical Halbach arrays in a way that retains construction simplicity. To achieve this, we present a method for designing an optimized cylindrical Halbach magnet using the genetic algorithm to achieve either homogeneity (for standard MRI applications) or a favorable spatial encoding field pattern (for rotational spatial encoding applications). We compare the chosen designs against a standard, fully populated sparse Halbach design, and evaluate optimized spatial encoding fields using point-spread-function and image simulations. We validate the calculations by comparing to the measured field of a constructed magnet. The experimentally implemented design produced fields in good agreement with the predicted fields, and the genetic algorithm was successful in improving the chosen metrics. For the uniform target field, an order of magnitude homogeneity improvement was achieved compared to the un-optimized, fully populated design. For the rotational encoding design the resolution uniformity is improved by 95% compared to a uniformly populated design.
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Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.
Hinze, Lori L; Hulse-Kemp, Amanda M; Wilson, Iain W; Zhu, Qian-Hao; Llewellyn, Danny J; Taylor, Jen M; Spriggs, Andrew; Fang, David D; Ulloa, Mauricio; Burke, John J; Giband, Marc; Lacape, Jean-Marc; Van Deynze, Allen; Udall, Joshua A; Scheffler, Jodi A; Hague, Steve; Wendel, Jonathan F; Pepper, Alan E; Frelichowski, James; Lawley, Cindy T; Jones, Don C; Percy, Richard G; Stelly, David M
2017-02-03
Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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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 this study. Utilizing different linkage disequilibrium patterns observed between European and African ancestries, we narrowed the suggestive region containing causative variants for all four loci. PMID:27867202
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ERIC Educational Resources Information Center
Leffert, Kenneth L.; And Others
This instructor guide and the corresponding student reference contain 10 lessons to enhance an Agricultural Science I course for grade 9. The lessons cover the following topics: introduction, psychology and handling, conformation and selection, genetics and reproduction, herd health, hoof care, nutrition, equipment and facilities, handling horses,…
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Xu, Li-Xin; Holland, Heidrun; Kirsten, Holger; Ahnert, Peter; Krupp, Wolfgang; Bauer, Manfred; Schober, Ralf; Mueller, Wolf; Fritzsch, Dominik; Meixensberger, Jürgen; Koschny, Ronald
2015-04-01
According to the World Health Organization gangliogliomas are classified as well-differentiated and slowly growing neuroepithelial tumors, composed of neoplastic mature ganglion and glial cells. It is the most frequent tumor entity observed in patients with long-term epilepsy. Comprehensive cytogenetic and molecular cytogenetic data including high-resolution genomic profiling (single nucleotide polymorphism (SNP)-array) of gangliogliomas are scarce but necessary for a better oncological understanding of this tumor entity. For a detailed characterization at the single cell and cell population levels, we analyzed genomic alterations of three gangliogliomas using trypsin-Giemsa banding (GTG-banding) and by spectral karyotyping (SKY) in combination with SNP-array and gene expression array experiments. By GTG and SKY, we could confirm frequently detected chromosomal aberrations (losses within chromosomes 10, 13 and 22; gains within chromosomes 5, 7, 8 and 12), and identify so far unknown genetic aberrations like the unbalanced non-reciprocal translocation t(1;18)(q21;q21). Interestingly, we report on the second so far detected ganglioglioma with ring chromosome 1. Analyses of SNP-array data from two of the tumors and respective germline DNA (peripheral blood) identified few small gains and losses and a number of copy-neutral regions with loss of heterozygosity (LOH) in germline and in tumor tissue. In comparison to germline DNA, tumor tissues did not show substantial regions with significant loss or gain or with newly developed LOH. Gene expression analyses of tumor-specific genes revealed similarities in the profile of the analyzed samples regarding different relevant pathways. Taken together, we describe overlapping but also distinct and novel genetic aberrations of three gangliogliomas. © 2014 Japanese Society of Neuropathology.
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Wang, Yao; Cui, Yazhou; Zhou, Xiaoyan; Han, Jinxiang
2015-01-01
Objective Osteogenesis imperfecta (OI) is a rare inherited skeletal disease, characterized by bone fragility and low bone density. The mutations in this disorder have been widely reported to be on various exonal hotspots of the candidate genes, including COL1A1, COL1A2, CRTAP, LEPRE1, and FKBP10, thus creating a great demand for precise genetic tests. However, large genome sizes make the process daunting and the analyses, inefficient and expensive. Therefore, we aimed at developing a fast, accurate, efficient, and cheaper sequencing platform for OI diagnosis; and to this end, use of an advanced array-based technique was proposed. Method A CustomSeq Affymetrix Resequencing Array was established for high-throughput sequencing of five genes simultaneously. Genomic DNA extraction from 13 OI patients and 85 normal controls and amplification using long-range PCR (LR-PCR) were followed by DNA fragmentation and chip hybridization, according to standard Affymetrix protocols. Hybridization signals were determined using GeneChip Sequence Analysis Software (GSEQ). To examine the feasibility, the outcome from new resequencing approach was validated by conventional capillary sequencing method. Result Overall call rates using resequencing array was 96–98% and the agreement between microarray and capillary sequencing was 99.99%. 11 out of 13 OI patients with pathogenic mutations were successfully detected by the chip analysis without adjustment, and one mutation could also be identified using manual visual inspection. Conclusion A high-throughput resequencing array was developed that detects the disease-associated mutations in OI, providing a potential tool to facilitate large-scale genetic screening for OI patients. Through this method, a novel mutation was also found. PMID:25742658
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Genetics Home Reference: distal 18q deletion syndrome
... Veltman JA, van Ravenswaaij-Arts CM. Genotype-phenotype mapping of chromosome 18q deletions by high-resolution array ... L, Pihko H. 18q deletions: clinical, molecular, and brain MRI findings of 14 individuals. Am J Med ...
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The new technology using plant genetics to produce chemicals, pharmaceuticals, and therapeuitics in a wide array of new plant forms requires sufficient testing to ensure that these new plant introductions are benign in the environment. A recent effort to provide necessary guidan...
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Yelk, Joseph; Sukharev, Maxim; Seideman, Tamar
2008-08-14
An optimal control approach based on multiple parameter genetic algorithms is applied to the design of plasmonic nanoconstructs with predetermined optical properties and functionalities. We first develop nanoscale metallic lenses that focus an incident plane wave onto a prespecified, spatially confined spot. Our results illustrate the mechanism of energy flow through wires and cavities. Next we design a periodic array of silver particles to modify the polarization of an incident, linearly polarized plane wave in a desired fashion while localizing the light in space. The results provide insight into the structural features that determine the birefringence properties of metal nanoparticles and their arrays. Of the variety of potential applications that may be envisioned, we note the design of nanoscale light sources with controllable coherence and polarization properties that could serve for coherent control of molecular, electronic, or electromechanical dynamics in the nanoscale.
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Target Discovery for Precision Medicine Using High-Throughput Genome Engineering.
Guo, Xinyi; Chitale, Poonam; Sanjana, Neville E
2017-01-01
Over the past few years, programmable RNA-guided nucleases such as the CRISPR/Cas9 system have ushered in a new era of precision genome editing in diverse model systems and in human cells. Functional screens using large libraries of RNA guides can interrogate a large hypothesis space to pinpoint particular genes and genetic elements involved in fundamental biological processes and disease-relevant phenotypes. Here, we review recent high-throughput CRISPR screens (e.g. loss-of-function, gain-of-function, and targeting noncoding elements) and highlight their potential for uncovering novel therapeutic targets, such as those involved in cancer resistance to small molecular drugs and immunotherapies, tumor evolution, infectious disease, inborn genetic disorders, and other therapeutic challenges.
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NASA Astrophysics Data System (ADS)
Bamiedakis, N.; McKendry, J. J. D.; Xie, E.; Gu, E.; Dawson, M. D.; Penty, R. V.; White, I. H.
2018-02-01
In recent years, light emitting diodes (LEDs) have gained renewed interest for use in visible light communication links (VLC) owing to their potential use as both high-quality power-efficient illumination sources as well as low-cost optical transmitters in free-space and guided-wave links. Applications that can benefit from their use include optical wireless systems (LiFi and Internet of Things), in-home and automotive networks, optical USBs and short-reach low-cost optical interconnects. However, VLC links suffer from the limited LED bandwidth (typically 100 MHz). As a result, a combination of novel LED devices, advanced modulation formats and multiplexing methods are employed to overcome this limitation and achieve high-speed (>1 Gb/s) data transmission over such links. In this work, we present recent advances in the formation of high-aggregate-capacity low cost guided wave VLC links using stacked polymer multimode waveguides and matching micro-pixelated LED (μLED) arrays. μLEDs have been shown to exhibit larger bandwidths (>200 MHz) than conventional broad-area LEDs and can be formed in large array configurations, while multimode polymer waveguides enable the formation of low-cost optical links onto standard PCBs. Here, three- and four-layered stacks of multimode waveguides, as well as matching GaN μLED arrays, are fabricated in order to generate high-density yet low-cost optical interconnects. Different waveguide topologies are implemented and are investigated in terms of loss and crosstalk performance. The initial results presented herein demonstrate good intrinsic crosstalk performance and indicate the potential to achieve >= 0.5 Tb/s/mm2 aggregate interconnection capacity using this low-cost technology.
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Abstract number and arithmetic in preschool children.
Barth, Hilary; La Mont, Kristen; Lipton, Jennifer; Spelke, Elizabeth S
2005-09-27
Educated humans use language to express abstract number, applying the same number words to seven apples, whistles, or sins. Is language or education the source of numerical abstraction? Claims to the contrary must present evidence for numerical knowledge that applies to disparate entities, in people who have received no formal mathematics instruction and cannot express such knowledge in words. Here we show that preschool children can compare and add large sets of elements without counting, both within a single visual-spatial modality (arrays of dots) and across two modalities and formats (dot arrays and tone sequences). In two experiments, children viewed animations and either compared one visible array of dots to a second array or added two successive dot arrays and compared the sum to a third array. In further experiments, a dot array was replaced by a sequence of sounds, so that participants had to integrate quantity information presented aurally and visually. Children performed all tasks successfully, without resorting to guessing strategies or responding to continuous variables. Their accuracy varied with the ratio of the two quantities: a signature of large, approximate number representations in adult humans and animals. Addition was as accurate as comparison, even though children showed no relevant knowledge when presented with symbolic versions of the addition tasks. Abstract knowledge of number and addition therefore precedes, and may guide, language-based instruction in mathematics.
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Joint estimation of 2D-DOA and frequency based on space-time matrix and conformal array.
Wan, Liang-Tian; Liu, Lu-Tao; Si, Wei-Jian; Tian, Zuo-Xi
2013-01-01
Each element in the conformal array has a different pattern, which leads to the performance deterioration of the conventional high resolution direction-of-arrival (DOA) algorithms. In this paper, a joint frequency and two-dimension DOA (2D-DOA) estimation algorithm for conformal array are proposed. The delay correlation function is used to suppress noise. Both spatial and time sampling are utilized to construct the spatial-time matrix. The frequency and 2D-DOA estimation are accomplished based on parallel factor (PARAFAC) analysis without spectral peak searching and parameter pairing. The proposed algorithm needs only four guiding elements with precise positions to estimate frequency and 2D-DOA. Other instrumental elements can be arranged flexibly on the surface of the carrier. Simulation results demonstrate the effectiveness of the proposed algorithm.
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Self-assembled pit arrays as templates for the integration of Au nanocrystals in oxide surfaces.
Konstantinović, Z; Sandiumenge, F; Santiso, J; Balcells, Ll; Martínez, B
2013-02-07
We report on the fabrication of long-range ordered arrays of Au nanocrystals (sub-50 nm range) on top of manganite (La(2/3)Sr(1/3)MnO(3)) thin films achieving area densities around 2 × 10(10) gold nanocrystals per cm(2), well above the densities achievable by using conventional nanofabrication techniques. The gold-manganite interface exhibits excellent conduction properties. Long-range order is achieved by a guided self-assembling process of Au nanocrystals on self-organized pit-arrays acting as a template for the nucleation of gold nanocrystals. Self-organization of pits on the manganite film surface promoted by the underlying stepped SrTiO(3) substrate is achieved by a fine tuning of the growth kinetic pathway, taking advantage of the unusual misfit strain relaxation behaviour of manganite films.
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Refractive index dispersion sensing using an array of photonic crystal resonant reflectors
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hermannsson, Pétur G.; Vannahme, Christoph; Smith, Cameron L. C.
2015-08-10
Refractive index sensing plays a key role in various environmental and biological sensing applications. Here, a method is presented for measuring the absolute refractive index dispersion of liquids using an array of photonic crystal resonant reflectors of varying periods. It is shown that by covering the array with a sample liquid and measuring the resonance wavelength associated with transverse electric polarized quasi guided modes as a function of period, the refractive index dispersion of the liquid can be accurately obtained using an analytical expression. This method is compact, can perform measurements at arbitrary number of wavelengths, and requires only amore » minute sample volume. The ability to sense a material's dispersion profile offers an added dimension of information that may be of benefit to optofluidic lab-on-a-chip applications.« less
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NASA Astrophysics Data System (ADS)
Bhattacharya, P.; Hazari, A.; Jahangir, S.
2018-02-01
GaN-based nanowire heterostructure arrays epitaxially grown on (001)Si substrates have unique properties and present the potential to realize useful devices. The active light-emitting region in the nanowire heterostructures are usually InGaN disks, whose composition can be varied to tune the emission wavelength. We have demonstrated light emitting diodes and edgeemitting diode lasers with power outputs 10mW with emission in the 600-1300nm wavelength range. These light sources are therefore useful for a variety of applications, including silicon photonics. Molecular beam epitaxial growth of the nanowire heterostructure arrays on (001)Si substrates and the characteristics of 1.3μm nanowire array edge emitting lasers, guided wave photodiodes and a monolithic photonic integrated circuit designed for 1.3μm operation are described.
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Simčič, Mojca; Smetko, Anamarija; Sölkner, Johann; Seichter, Doris; Gorjanc, Gregor; Kompan, Dragomir; Medugorac, Ivica
2015-01-01
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest. PMID:25923207
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Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data
Oetjens, Matthew T.; Brown-Gentry, Kristin; Goodloe, Robert; Dilks, Holli H.; Crawford, Dana C.
2016-01-01
Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES), population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n = 14,998) were extracted from biospecimens from consented NHANES participants between 1991–1994 (NHANES III, phase 2) and 1999–2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We as the Epidemiologic Architecture for Genes Linked to Environment study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999–2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants, although less so for ethnicity. Overall, the strategies outlined here for a large epidemiologic study can be applied to other datasets accessible for genotype–phenotype studies but are sans genome-wide data. PMID:27200085
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Vasson, Aurélie; Leroux, Céline; Orhant, Lucie; Boimard, Mathieu; Toussaint, Aurélie; Leroy, Chrystel; Commere, Virginie; Ghiotti, Tiffany; Deburgrave, Nathalie; Saillour, Yoann; Atlan, Isabelle; Fouveaut, Corinne; Beldjord, Cherif; Valleix, Sophie; Leturcq, France; Dodé, Catherine; Bienvenu, Thierry; Chelly, Jamel; Cossée, Mireille
2013-01-01
The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed high-density oligonucleotide-based arrays allowed the development of a powerful tool for detection of alterations at the level of exons and made it possible to provide flexibility through the possibility of modeling chips. The aim of our study was to test custom-designed oligonucleotide CGH array in a diagnostic laboratory setting that analyses several genes involved in various genetic diseases, and to compare it with conventional strategies. To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints. All of these points, associated with the possibility of a simultaneous analysis of several genes and scalability ‘homemade' make it a valuable tool as a new diagnostic approach of CNMs. PMID:23340513
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Hough, Soren H; Ajetunmobi, Ayokunmi; Brody, Leigh; Humphryes-Kirilov, Neil; Perello, Edward
2016-11-01
Desktop Genetics is a bioinformatics company building a gene-editing platform for personalized medicine. The company works with scientists around the world to design and execute state-of-the-art clustered regularly interspaced short palindromic repeats (CRISPR) experiments. Desktop Genetics feeds the lessons learned about experimental intent, single-guide RNA design and data from international genomics projects into a novel CRISPR artificial intelligence system. We believe that machine learning techniques can transform this information into a cognitive therapeutic development tool that will revolutionize medicine.
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Yusuf, Leeban; Anderson, Ainan I J; Pirooznia, Mehdi; Arnellos, Dimitrios; Vilshansky, Gregory; Ercal, Gunes; Lu, Yontao; Webster, Teresa; Baird, Michael L; Esposito, Umberto
2017-01-01
Abstract The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)—an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM’s autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies. PMID:29165562
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Photon collider: a four-channel autoguider solution
NASA Astrophysics Data System (ADS)
Hygelund, John C.; Haynes, Rachel; Burleson, Ben; Fulton, Benjamin J.
2010-07-01
The "Photon Collider" uses a compact array of four off axis autoguider cameras positioned with independent filtering and focus. The photon collider is two way symmetric and robustly mounted with the off axis light crossing the science field which allows the compact single frame construction to have extremely small relative deflections between guide and science CCDs. The photon collider provides four independent guiding signals with a total of 15 square arc minutes of sky coverage. These signals allow for simultaneous altitude, azimuth, field rotation and focus guiding. Guide cameras read out without exposure overhead increasing the tracking cadence. The independent focus allows the photon collider to maintain in focus guide stars when the main science camera is taking defocused exposures as well as track for telescope focus changes. Independent filters allow auto guiding in the science camera wavelength bandpass. The four cameras are controlled with a custom web services interface from a single Linux based industrial PC, and the autoguider mechanism and telemetry is built around a uCLinux based Analog Devices BlackFin embedded microprocessor. Off axis light is corrected with a custom meniscus correcting lens. Guide CCDs are cooled with ethylene glycol with an advanced leak detection system. The photon collider was built for use on Las Cumbres Observatory's 2 meter Faulks telescopes and currently used to guide the alt-az mount.
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2017-01-01
Ribosomal RNAs (rRNAs) are transcribed from two multicopy DNA arrays: the 5S ribosomal DNA (rDNA) array residing in a single human autosome and the 45S rDNA array residing in five human autosomes. The arrays are among the most variable segments of the genome, exhibit concerted copy number variation (cCNV), encode essential components of the ribosome, and modulate global gene expression. Here we combined whole genome data from >700 tumors and paired normal tissues to provide a portrait of rDNA variation in human tissues and cancers of diverse mutational signatures, including stomach and lung adenocarcinomas, ovarian cancers, and others of the TCGA panel. We show that cancers undergo coupled 5S rDNA array expansion and 45S rDNA loss that is accompanied by increased estimates of proliferation rate and nucleolar activity. These somatic changes in rDNA CN occur in a background of over 10-fold naturally occurring rDNA CN variation across individuals and cCNV of 5S-45S arrays in some but not all tissues. Analysis of genetic context revealed associations between cancer rDNA CN amplification or loss and the presence of specific somatic alterations, including somatic SNPs and copy number gain/losses in protein coding genes across the cancer genome. For instance, somatic inactivation of the tumor suppressor gene TP53 emerged with a strong association with coupled 5S expansion / 45S loss in several cancers. Our results uncover frequent and contrasting changes in the 5S and 45S rDNA along rapidly proliferating cell lineages with high nucleolar activity. We suggest that 5S rDNA amplification facilitates increased proliferation, nucleolar activity, and ribosomal synthesis in cancer, whereas 45S rDNA loss emerges as a byproduct of transcription-replication conflict in rapidly replicating tumor cells. The observations raise the prospects of using the rDNA arrays as re-emerging targets for the design of novel strategies in cancer therapy. PMID:28880866
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Clinical applications of preimplantation genetic testing.
Brezina, Paul R; Kutteh, William H
2015-02-19
Genetic diagnostic technologies are rapidly changing the way medicine is practiced. Preimplantation genetic testing is a well established application of genetic testing within the context of in vitro fertilization cycles. It involves obtaining a cell(s) from a developing embryo in culture, which is then subjected to genetic diagnostic analysis; the resulting information is used to guide which embryos are transferred into the uterus. The potential applications and use of this technology have increased in recent years. Experts agree that preimplantation genetic diagnosis is clinically appropriate for many known genetic disorders. However, some applications of such testing, such as preimplantation genetic screening for aneuploidy, remain controversial. Clinical data suggest that preimplantation genetic screening may be useful, but further studies are needed to quantify the size of the effect and who would benefit most. © BMJ Publishing Group Ltd 2015.
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Chang, Tzu-Hsuan; Xiong, Shisheng; Liu, Chi-Chun; Liu, Dong; Nealey, Paul F; Ma, Zhenqiang
2017-09-01
The direct self-assembly of cylinder-forming poly(styrene-block-methyl-methacrylate) (PS-b-PMMA) block copolymer is successfully assembled into two orientations, according to the underlying guiding pattern in different areas. Lying-down and perpendicular cylinders are formed, respectively, depending on the design of chemical pattern: sparse line/space pattern or hexagonal dot array. The first chemical pattern composed of prepatterned cross-linked polystyrene (XPS) line/space structure has a period (L S ) equal to twice the intercylinder period of the block copolymer (L 0 ). The PS-b-PMMA thin film on the prepared chemical template after thermal annealing forms a lying-down cylinder morphology when the width of the PS strips is less than the width of PS block in the PS-b-PMMA block copolymer. The morphology is only applicable at the discrete thickness of the PS-b-PMMA film. In addition to forming the lying-down cylinders directly on the XPS guiding pattern, the cylinder-forming block copolymer can also be assembled in a perpendicular way on the second guiding pattern (the hexagonal dot array). The block copolymer films are registered into two orientations in a single directed self-assembly process. The features of the assembled patterns are successfully transferred down to the silicon oxide substrate. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Backscattering analysis of high frequency ultrasonic imaging for ultrasound-guided breast biopsy
NASA Astrophysics Data System (ADS)
Cummins, Thomas; Akiyama, Takahiro; Lee, Changyang; Martin, Sue E.; Shung, K. Kirk
2017-03-01
A new ultrasound-guided breast biopsy technique is proposed. The technique utilizes conventional ultrasound guidance coupled with a high frequency embedded ultrasound array located within the biopsy needle to improve the accuracy in breast cancer diagnosis.1 The array within the needle is intended to be used to detect micro- calcifications indicative of early breast cancers such as ductal carcinoma in situ (DCIS). Backscattering analysis has the potential to characterize tissues to improve localization of lesions. This paper describes initial results of the application of backscattering analysis of breast biopsy tissue specimens and shows the usefulness of high frequency ultrasound for the new biopsy related technique. Ultrasound echoes of ex-vivo breast biopsy tissue specimens were acquired by using a single-element transducer with a bandwidth from 41 MHz to 88 MHz utilizing a UBM methodology, and the backscattering coefficients were calculated. These values as well as B-mode image data were mapped in 2D and matched with each pathology image for the identification of tissue type for the comparison to the pathology images corresponding to each plane. Microcalcifications were significantly distinguished from normal tissue. Adenocarcinoma was also successfully differentiated from adipose tissue. These results indicate that backscattering analysis is able to quantitatively distinguish tissues into normal and abnormal, which should help radiologists locate abnormal areas during the proposed ultrasound-guided breast biopsy with high frequency ultrasound.
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Exploration of the horizontally staggered light guides for high concentration CPV applications.
Selimoglu, Ozgur; Turan, Rasit
2012-08-13
The material and processing costs are still the major drawbacks of the c-Si based photovoltaic (PV) technology. The wafer cost comprises up to 35-40% of the total module cost. New approaches and system designs are needed in order to reduce the share of the wafer cost in photovoltaic energy systems. Here we explore the horizontally staggered light guide solar optics for use in Concentrated Photovoltaic (CPV) applications. This optical system comprises a lens array system coupled to a horizontal light guide which directs the incoming light beam to its edge. We have designed and simulated this system using a commercial ray tracing software (Zemax). The system is more compact, thinner and more robust compared to the conventional CPV systems. Concentration levels as high as 1000x can easily be reached when the system is properly designed. With such a high concentration level, a good acceptance angle of + -1 degree is still be conserved. The analysis of the system reveals that the total optical efficiency of the system could be as high as %94.4 without any anti-reflection (AR) coating. Optical losses can be reduced by just accommodating a single layer AR coating on the initial lens array leading to a %96.5 optical efficiency. Thermal behavior of high concentration linear concentrator is also discussed and compared with a conventional point focus CPV system.
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Rata, Mihaela; Birlea, Vlad; Murillo, Adriana; Paquet, Christian; Cotton, François; Salomir, Rares
2015-01-01
MR-guided high-intensity contact ultrasound (HICU) was suggested as an alternative therapy for esophageal and rectal cancer. To offer high-quality MR guidance, two prototypes of receive-only opposed-solenoid coil were integrated with 64-element cylindrical phased-array ultrasound transducers (rectal/esophageal). The design of integrated coils took into account the transducer geometry (360° acoustic window within endoluminal space). The rectal coil was sealed on a plastic support and placed reversibly on the transducer head. The esophageal coil was fully embedded within the transducer head, resulting in one indivisible device. Comparison of integrated versus external coils was performed on a clinical 1.5T scanner. The integrated coils showed higher sensitivity compared with the standard extracorporeal coil with factors of up to 7.5 (rectal applicator) and 3.3 (esophageal applicator). High-resolution MR images for both anatomy (voxel 0.4 × 0.4 × 5 mm(3)) and thermometry (voxel 0.75 × 0.75 × 8 mm(3), 2 s/image) were acquired in vivo with the rectal endoscopic device. The temperature feedback loop accurately controlled multiple control points over the region of interest. This study showed significant improvement of MR data quality using endoluminal integrated coils versus standard external coil. Inframillimeter spatial resolution and accurate feedback control of MR-guided HICU thermotherapy were achieved. © 2014 Wiley Periodicals, Inc.
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Spin wave filtering and guiding in Permalloy/iron nanowires
NASA Astrophysics Data System (ADS)
Silvani, R.; Kostylev, M.; Adeyeye, A. O.; Gubbiotti, G.
2018-03-01
We have investigated the spin wave filtering and guiding properties of periodic array of single (Permalloy and Fe) and bi-layer (Py/Fe) nanowires (NWs) by means of Brillouin light scattering measurements and micromagnetic simulations. For all the nanowire arrays, the thickness of the layers is 10 nm while all NWs have the same width of 340 nm and edge-to-edge separation of 100 nm. Spin wave dispersion has been measured in the Damon-Eshbach configuration for wave vector either parallel or perpendicular to the nanowire length. This study reveals the filtering property of the spin waves when the wave vector is perpendicular to the NW length, with frequency ranges where the spin wave propagation is permitted separated by frequency band gaps, and the guiding property of NW when the wave vector is oriented parallel to the NW, with spin wave modes propagating in parallel channels in the central and edge regions of the NW. The measured dispersions were well reproduced by micromagnetic simulations, which also deliver the spatial profiles for the modes at zero wave vector. To reproduce the dispersion of the modes localized close to the NW edges, uniaxial anisotropy has been introduced. In the case of Permalloy/iron NWs, the obtained results have been compared with those for a 20 nm thick effective NW having average magnetic properties of the two materials.
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Whatever you do, don't look at the...: Evaluating guidance by an exclusionary attentional template.
Beck, Valerie M; Luck, Steven J; Hollingworth, Andrew
2018-04-01
People can use a target template consisting of one or more features to guide attention and gaze to matching objects in a search array. But can we also use feature information to guide attention away from known irrelevant items? Some studies found a benefit from foreknowledge of a distractor feature, whereas others found a cost. Importantly, previous work has largely relied on end-of-trial manual responses; it is unclear how feature-guided avoidance might unfold as candidate objects are inspected. In the current experiments, participants were cued with a distractor feature to avoid, then performed a visual search task while eye movements were recorded. Participants initially fixated a to-be-avoided object more frequently than predicted by chance, but they also demonstrated avoidance of cue-matching objects later in the trial. When provided more time between cue stimulus and search array, participants continued to be initially captured by a cued-color item. Furthermore, avoidance of cue-matching objects later in the trial was not contingent on initial capture by a cue-matching object. These results suggest that the conflicting findings in previous negative-cue experiments may be explained by a mixture of two independent processes: initial attentional capture by memory-matching items and later avoidance of known irrelevant items. (PsycINFO Database Record (c) 2018 APA, all rights reserved).
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Evidence for negative feature guidance in visual search is explained by spatial recoding.
Beck, Valerie M; Hollingworth, Andrew
2015-10-01
Theories of attention and visual search explain how attention is guided toward objects with known target features. But can attention be directed away from objects with a feature known to be associated only with distractors? Most studies have found that the demand to maintain the to-be-avoided feature in visual working memory biases attention toward matching objects rather than away from them. In contrast, Arita, Carlisle, and Woodman (2012) claimed that attention can be configured to selectively avoid objects that match a cued distractor color, and they reported evidence that this type of negative cue generates search benefits. However, the colors of the search array items in Arita et al. (2012) were segregated by hemifield (e.g., blue items on the left, red on the right), which allowed for a strategy of translating the feature-cue information into a simple spatial template (e.g., avoid right, or attend left). In the present study, we replicated the negative cue benefit using the Arita et al. (2012), method (albeit within a subset of participants who reliably used the color cues to guide attention). Then, we eliminated the benefit by using search arrays that could not be grouped by hemifield. Our results suggest that feature-guided avoidance is implemented only indirectly, in this case by translating feature-cue information into a spatial template. (c) 2015 APA, all rights reserved).
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NASA Astrophysics Data System (ADS)
Palermo, Antonio; Krödel, Sebastian; Matlack, Kathryn H.; Zaccherini, Rachele; Dertimanis, Vasilis K.; Chatzi, Eleni N.; Marzani, Alessandro; Daraio, Chiara
2018-05-01
We investigate the interaction of guided surface acoustic modes (GSAMs) in unconsolidated granular media with a metasurface, consisting of an array of vertical oscillators. We experimentally observe the hybridization of the lowest-order GSAM at the metasurface resonance, and note the absence of mode delocalization found in homogeneous media. Our numerical studies reveal how the stiffness gradient induced by gravity in granular media causes a down-conversion of all the higher-order GSAMs, which preserves the acoustic energy confinement. We anticipate these findings to have implications in the design of seismic-wave protection devices in stratified soils.
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An efficient system for selectively altering genetic information within mRNAs
Montiel-González, Maria Fernanda; Vallecillo-Viejo, Isabel C.; Rosenthal, Joshua J. C.
2016-01-01
Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a UAG premature termination codon (PTC) to tryptophan (UGG) was improved from ∼11 % to ∼70 %. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool. PMID:27557710