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Sample records for array-based fmr1 sequencing

  1. Array-based FMR1 sequencing and deletion analysis in patients with a fragile X syndrome-like phenotype.

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    Stephen C Collins

    2010-03-01

    Full Text Available Fragile X syndrome (FXS is caused by loss of function mutations in the FMR1 gene. Trinucleotide CGG-repeat expansions, resulting in FMR1 gene silencing, are the most common mutations observed at this locus. Even though the repeat expansion mutation is a functional null mutation, few conventional mutations have been identified at this locus, largely due to the clinical laboratory focus on the repeat tract.To more thoroughly evaluate the frequency of conventional mutations in FXS-like patients, we used an array-based method to sequence FMR1 in 51 unrelated males exhibiting several features characteristic of FXS but with normal CGG-repeat tracts of FMR1. One patient was identified with a deletion in FMR1, but none of the patients were found to have other conventional mutations.These data suggest that missense mutations in FMR1 are not a common cause of the FXS phenotype in patients who have normal-length CGG-repeat tracts. However, screening for small deletions of FMR1 may be of clinically utility.

  2. Array-based FMR1 sequencing and deletion analysis in patients with a fragile X syndrome-like phenotype

    NARCIS (Netherlands)

    S.C. Collins (Stephen); B. Coffee (Brad); P.J. Benke (Paul); E.M. Berry-Kravis (Elizabeth); F. Gilbert (Fred); B.A. Oostra (Ben); D. Halley (Dicky); M.E. Zwick (Michael); D.J. Cutler (David); S.T. Warren (Stephen)

    2010-01-01

    textabstractBackground: Fragile X syndrome (FXS) is caused by loss of function mutations in the FMR1 gene. Trinucleotide CGG-repeat expansions, resulting in FMR1 gene silencing, are the most common mutations observed at this locus. Even though the repeat expansion mutation is a functional null

  3. Intragenic FMR1 disease-causing variants: a significant mutational mechanism leading to Fragile-X syndrome

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    Quartier, Angélique; Poquet, Hélène; Gilbert-Dussardier, Brigitte; Rossi, Massimiliano; Casteleyn, Anne-Sophie; Portes, Vincent des; Feger, Claire; Nourisson, Elsa; Kuentz, Paul; Redin, Claire; Thevenon, Julien; Mosca-Boidron, Anne-Laure; Callier, Patrick; Muller, Jean; Lesca, Gaetan; Huet, Frédéric; Geoffroy, Véronique; El Chehadeh, Salima; Jung, Matthieu; Trojak, Benoit; Le Gras, Stéphanie; Lehalle, Daphné; Jost, Bernard; Maury, Stéphanie; Masurel, Alice; Edery, Patrick; Thauvin-Robinet, Christel; Gérard, Bénédicte; Mandel, Jean-Louis; Faivre, Laurence; Piton, Amélie

    2017-01-01

    Fragile-X syndrome (FXS) is a frequent genetic form of intellectual disability (ID). The main recurrent mutagenic mechanism causing FXS is the expansion of a CGG repeat sequence in the 5′-UTR of the FMR1 gene, therefore, routinely tested in ID patients. We report here three FMR1 intragenic pathogenic variants not affecting this sequence, identified using high-throughput sequencing (HTS): a previously reported hemizygous deletion encompassing the last exon of FMR1, too small to be detected by array-CGH and inducing decreased expression of a truncated form of FMRP protein, in three brothers with ID (family 1) and two splice variants in boys with sporadic ID: a de novo variant c.990+1G>A (family 2) and a maternally inherited c.420-8A>G variant (family 3). After clinical reevaluation, the five patients presented features consistent with FXS (mean Hagerman's scores=15). We conducted a systematic review of all rare non-synonymous variants previously reported in FMR1 in ID patients and showed that six of them are convincing pathogenic variants. This study suggests that intragenic FMR1 variants, although much less frequent than CGG expansions, are a significant mutational mechanism leading to FXS and demonstrates the interest of HTS approaches to detect them in ID patients with a negative standard work-up. PMID:28176767

  4. In Silico Analysis of FMR1 Gene Missense SNPs.

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    Tekcan, Akin

    2016-06-01

    The FMR1 gene, a member of the fragile X-related gene family, is responsible for fragile X syndrome (FXS). Missense single-nucleotide polymorphisms (SNPs) are responsible for many complex diseases. The effect of FMR1 gene missense SNPs is unknown. The aim of this study, using in silico techniques, was to analyze all known missense mutations that can affect the functionality of the FMR1 gene, leading to mental retardation (MR) and FXS. Data on the human FMR1 gene were collected from the Ensembl database (release 81), National Centre for Biological Information dbSNP Short Genetic Variations database, 1000 Genomes Browser, and NHLBI Exome Sequencing Project Exome Variant Server. In silico analysis was then performed. One hundred-twenty different missense SNPs of the FMR1 gene were determined. Of these, 11.66 % of the FMR1 gene missense SNPs were in highly conserved domains, and 83.33 % were in domains with high variety. The results of the in silico prediction analysis showed that 31.66 % of the FMR1 gene SNPs were disease related and that 50 % of SNPs had a pathogenic effect. The results of the structural and functional analysis revealed that although the R138Q mutation did not seem to have a damaging effect on the protein, the G266E and I304N SNPs appeared to disturb the interaction between the domains and affect the function of the protein. This is the first study to analyze all missense SNPs of the FMR1 gene. The results indicate the applicability of a bioinformatics approach to FXS and other FMR1-related diseases. I think that the analysis of FMR1 gene missense SNPs using bioinformatics methods would help diagnosis of FXS and other FMR1-related diseases.

  5. A nonsense mutation in FMR1 causing fragile X syndrome

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    Grønskov, Karen; Brøndum-Nielsen, Karen; Dedic, Alma

    2011-01-01

    Fragile X syndrome is a common cause of inherited intellectual disability. It is caused by lack of the FMR1 gene product FMRP. The most frequent cause is the expansion of a CGG repeat located in the 5'UTR of FMR1. Alleles with 200 or more repeats become hypermethylated and transcriptionally silent....... Only few patients with intragenic point mutations in FMR1 have been reported and, currently, routine analysis of patients referred for fragile X syndrome includes solely analysis for repeat expansion and methylation status. We identified a substitution in exon 2 of FMR1, c.80C>A, causing a nonsense...... mutation p.Ser27X, in a patient with classical clinical symptoms of fragile X syndrome. The mother who carried the mutation in heterozygous form presented with mild intellectual impairment. We conclude that further studies including western blot and DNA sequence analysis of the FMR1 gene should...

  6. Influence of the fragile X mental retardation (FMR1) gene on the brain and working memory in men with normal FMR1 alleles

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    Wang, Jun Yi; Hessl, David; Iwahashi, Christine; Cheung, Katherine; Schneider, Andrea; Hagerman, Randi J.; Hagerman, Paul J.; Rivera, Susan M.

    2012-01-01

    The fragile X mental retardation 1 (FMR1) gene plays an important role in the development and maintenance of neuronal circuits that are essential for cognitive functioning. We explored the functional linkage(s) among lymphocytic FMR1 gene expression, brain structure, and working memory in healthy adult males. We acquired T1-weighted and diffusion tensor imaging from 34 males (18–80 years, mean ± SD = 43.6 ± 18.4 years) with normal FMR1 alleles and performed genetic and working memory assessme...

  7. The mGluR5 antagonist AFQ056 does not affect methylation and transcription of the mutant FMR1 gene in vitro

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    Tabolacci Elisabetta

    2012-03-01

    Full Text Available Abstract Background Fragile X syndrome (FXS, the leading cause of inherited mental retardation, is due to expansion and methylation of a CGG sequence in the FMR1 gene, which result in its silencing and consequent absence of FMRP protein. This absence causes loss of repression of metabotropic glutamate receptor 5 (mGluR5-mediated pathways resulting in the behavioral and cognitive impairments associated with FXS. In a randomized, double-blind trial it was recently demonstrated a beneficial effect of AFQ056, a selective inhibitor of metabotrobic glutamate receptor type 5 (mGluR5, on fully methylated FXS patients respect to partially methylated FXS ones. Methods To determine whether AFQ056 may have secondary effects on the methylation and transcription of FMR1, here we treated three FXS lymphoblastoid cell lines and one normal control male line. A quantitative RT-PCR was performed to assess transcriptional reactivation of the FMR1 gene. To assess the methylation status of the FMR1 gene promoter it was carried out a bisulphite sequencing analysis. Results Both FMR1-mRNA levels and DNA methylation were unmodified with respect to untreated controls. Conclusions These results demonstrate that the AFQ056 effect on fully methylated FXS patients is not due to a secondary effect on DNA methylation and consequent transcriptional activation of FMR1.

  8. Deletion of Fmr1 results in sex-specific changes in behavior.

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    Nolan, Suzanne O; Reynolds, Conner D; Smith, Gregory D; Holley, Andrew J; Escobar, Brianna; Chandler, Matthew A; Volquardsen, Megan; Jefferson, Taylor; Pandian, Ashvini; Smith, Tileena; Huebschman, Jessica; Lugo, Joaquin N

    2017-10-01

    In this study, we used a systemic Fmr1 knockout in order to investigate both genotype- and sex-specific differences across multiple measures of sociability, repetitive behaviors, activity levels, anxiety, and fear-related learning and memory. Fragile X syndrome is the most common monogenic cause of intellectual disability and autism. Few studies to date have examined sex differences in a mouse model of Fragile X syndrome, though clinical data support the idea of differences in both overall prevalence and phenotype between the sexes. Using wild-type and systemic homozygous Fmr1 knockout mice, we assessed a variety of behavioral paradigms in adult animals, including the open field test, elevated plus maze, nose-poke assay, accelerating rotarod, social partition task, three-chambered social task, and two different fear conditioning paradigms. Tests were ordered such that the most invasive tests were performed last in the sequence, and testing paradigms for similar behaviors were performed in separate cohorts to minimize testing effects. Our results indicate several sex-specific changes in Fmr1 knockout mice, including male-specific increases in activity levels, and female-specific increases in repetitive behaviors on both the nose-poke assay and motor coordination on the accelerating rotarod task. The results also indicated that Fmr1 deletion results in deficits in fear learning and memory across both sexes, and no changes in social behavior across two tasks. These findings highlight the importance of including female subjects in preclinical studies, as simply studying the impact of genetic mutations in males does not yield a complete picture of the phenotype. Further research should explore these marked phenotypic differences among the sexes. Moreover, given that treatment strategies are typically equivalent between the sexes, the results highlight a potential need for sex-specific therapeutics.

  9. How the FMR1 gene became relevant to female fertility and reproductive medicine

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    Norbert eGleicher

    2014-08-01

    Full Text Available This manuscript describes the 6-year evolution of our center’s research into ovarian functions of the FMR1 gene, which led to the identification of a new normal CGGn range of 26-34. This new normal range, in turn, led to definitions of different alleles (haplotypes based on whether no, one or both alleles are within range. Specific alleles then were demonstrated to represent distinct ovarian aging patterns, suggesting an important FMR1 function in follicle recruitment and ovarian depletion of follicles. So called low alleles, characterized by CGGn34 alleles. Because low FMR1 alleles present in approximately 25% of all females, FMR1 testing at young ages may offer an opportunity for earlier diagnosis of OPOI than current practice allows. Earlier diagnosis of OPOI, in turn, would give young women the options of reassessing their reproductive schedules and/or pursue fertility preservation via oocyte cryopreservation when most effective.

  10. Correlation of normal-range FMR1 repeat length or genotypes and reproductive parameters.

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    Maslow, Bat-Sheva L; Davis, Stephanie; Engmann, Lawrence; Nulsen, John C; Benadiva, Claudio A

    2016-09-01

    This study aims to ascertain whether the length of normal-ranged CGG repeats on the FMR1 gene correlates with abnormal reproductive parameters. We performed a retrospective, cross-sectional study of all FMR1 carrier screening performed as part of routine care at a large university-based fertility center from January 2011 to March 2014. Correlations were performed between normal-range FMR1 length and baseline serum anti-Müllerian hormone (AMH), cycle day 3 follicle stimulating hormone (FSH), ovarian volumes (OV), antral follicle counts (AFC), and incidence of diminished ovarian reserve (DOR), while controlling for the effect of age. Six hundred three FMR1 screening results were collected. One subject was found to be a pre-mutation carrier and was excluded from the study. Baseline serum AMH, cycle day 3 FSH, OV, and AFC data were collected for the 602 subjects with normal-ranged CGG repeats. No significant difference in median age was noted amongst any of the FMR1 repeat genotypes. No significant correlation or association was found between any allele length or genotype, with any of the reproductive parameters or with incidence of DOR at any age (p > 0.05). However, subjects who were less than 35 years old with low/low genotype were significantly more likely to have below average AMH levels compared to those with normal/normal genotype (RR 3.82; 95 % CI 1.38-10.56). This large study did not demonstrate any substantial association between normal-range FMR1 repeat lengths and reproductive parameters.

  11. Brief Report: Altered Social Behavior in Isolation-Reared "Fmr1" Knockout Mice

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    Heitzer, Andrew M.; Roth, Alexandra K.; Nawrocki, Lauren; Wrenn, Craige C.; Valdovinos, Maria G.

    2013-01-01

    Social behavior abnormalities in Fragile X syndrome (FXS) are characterized by social withdrawal, anxiety, and deficits in social cognition. To assess these deficits, a model of FXS, the "Fmr1" knockout mouse ("Fmr1" KO), has been utilized. This mouse model has a null mutation in the fragile X mental retardation 1 gene ("Fmr1") and displays…

  12. Fragile X mental retardation 1 (FMR1) intron 1 methylation in blood predicts verbal cognitive impairment in female carriers of expanded FMR1 alleles: evidence from a pilot study.

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    Godler, David E; Slater, Howard R; Bui, Quang M; Storey, Elsdon; Ono, Michele Y; Gehling, Freya; Inaba, Yoshimi; Francis, David; Hopper, John L; Kinsella, Glynda; Amor, David J; Hagerman, Randi J; Loesch, Danuta Z

    2012-03-01

    Cognitive status in females with mutations in the FMR1 (fragile X mental retardation 1) gene is highly variable. A biomarker would be of value for predicting which individuals were liable to develop cognitive impairment and could benefit from early intervention. A detailed analysis of CpG sites bridging exon 1 and intron 1 of FMR1, known as fragile X-related epigenetic element 2 (FREE2), suggests that a simple blood test could identify these individuals. Study participants included 74 control females (Wechsler intelligence quotient (IQ) tests. We used MALDI-TOF mass spectrometry to determine the methylation status of FREE2 CpG sites that best identified low-functioning (IQ 200 CGG repeats), compared the results with those for Southern blot FMR1 activation ratios, and related these assessments to the level of production of the FMR1 protein product in blood. A methylation analysis of intron 1 CpG sites 10-12 showed the highest diagnostic sensitivity (100%) and specificity (98%) of all the molecular measures tested for detecting females with a standardized verbal IQ of <70 among the study participants. In the group consisting of only FM females, methylation of these sites was significantly correlated with full-scale IQ, verbal IQ, and performance IQ. Several verbal subtest scores showed strong correlation with the methylation of these sites (P = 1.2 × 10(-5)) after adjustment for multiple measures. The data suggest that hypermethylation of the FMR1 intron 1 sites in blood is predictive of cognitive impairment in FM females, with implications for improved fragile X syndrome diagnostics in young children and screening of the newborn population.

  13. 78 FR 36723 - Federal Management Regulation (FMR); Restrictions on International Transportation of Freight and...

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    2013-06-19

    ..., Sequence 1] RIN 3090-AJ34 Federal Management Regulation (FMR); Restrictions on International Transportation... Administration (GSA). ACTION: Proposed rule. SUMMARY: GSA is proposing to amend the Federal Management Regulation... Federal Management Regulation (FMR) to state clearly that this part applies to all agencies and wholly...

  14. Phenobarbital use and neurological problems in FMR1 premutation carriers.

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    Saldarriaga, Wilmar; Lein, Pamela; González Teshima, Laura Yuriko; Isaza, Carolina; Rosa, Lina; Polyak, Andrew; Hagerman, Randi; Girirajan, Santhosh; Silva, Marisol; Tassone, Flora

    2016-03-01

    Fragile X Syndrome (FXS) is a neurodevelopmental disorder caused by a CGG expansion in the FMR1 gene located at Xq27.3. Patients with the premutation in FMR1 present specific clinical problems associated with the number of CGG repeats (55-200 CGG repeats). Premutation carriers have elevated FMR1 mRNA expression levels, which have been associated with neurotoxicity potentially causing neurodevelopmental problems or neurological problems associated with aging. However, cognitive impairments or neurological problems may also be related to increased vulnerability of premutation carriers to neurotoxicants, including phenobarbital. Here we present a study of three sisters with the premutation who were exposed differentially to phenobarbital therapy throughout their lives, allowing us to compare the neurological effects of this drug in these patients. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. PSP-CBS with Dopamine Deficiency in a Female with a FMR1 Premutation.

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    Paucar, Martin; Beniaminov, Stanislav; Paslawski, Wojciech; Svenningsson, Per

    2016-10-01

    Premutations in the fragile X mental retardation 1 (FMR1) gene cause fragile X-associated tremor/ataxia syndrome (FXTAS) and FMR1-related primary ovarian insufficiency (POI). Female FMR1 premutation carriers rarely develop motor features. Dual pathology is an emerging phenomenon among FMR1 premutation carriers. Here, we describe a family affected by FMR1-related disorders in which the female index case has developed a rapidly progressive and disabling syndrome of atypical parkinsonism. This syndrome consists of early onset postural instability, echolalia, dystonia, and varying types of apraxia like early onset orobuccal apraxia and oculomotor apraxia. She has also developed supranuclear gaze palsy, increased latency of saccade initiation, and slow saccades. These features are compatible with progressive supranuclear palsy (PSP) of a corticobasal syndrome (CBS) variant. Imaging displays a marked reduction of presynaptic dopaminergic uptake and cerebrospinal fluid analysis showed reduced dopamine metabolism; however, the patient is unresponsive to levodopa. Midbrain atrophy ("hummingbird sign") and mild cerebellar atrophy were found on brain MRI. Her father was affected by a typical FXTAS presentation but also displayed dopamine deficiency along with the hummingbird sign. The mechanisms by which FMR1 premutations predispose to atypical parkinsonism and dopamine deficiency await further elucidation.

  16. Hyperactivity and lack of social discrimination in the adolescent Fmr1 knockout mouse.

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    Sørensen, Emilie M; Bertelsen, Freja; Weikop, Pia; Skovborg, Maria M; Banke, Tue; Drasbek, Kim R; Scheel-Krüger, Jørgen

    2015-12-01

    The aims of this study were to investigate behaviour relevant to human autism spectrum disorder (ASD) and the fragile X syndrome in adolescent Fmr1 knockout (KO) mice and to evaluate the tissue levels of striatal monoamines. Fmr1 KO mice were evaluated in the open field, marble burying and three-chamber test for the presence of hyperactivity, anxiety, repetitive behaviour, sociability and observation of social novelty compared with wild-type (WT) mice. The Fmr1 KO mice expressed anxiety and hyperactivity in the open field compared with WT mice. This increased level of hyperactivity was confirmed in the three-chamber test. Fmr1 KO mice spent more time with stranger mice compared with the WT. However, after a correction for hyperactivity, their apparent increase in sociability became identical to that of the WT. Furthermore, the Fmr1 KO mice could not differentiate between a familiar or a novel mouse. Monoamines were measured by HPLC: Fmr1 KO mice showed an increase in the striatal dopamine level. We conclude that the fragile X syndrome model seems to be useful for understanding certain aspects of ASD and may have translational interest for studies of social behaviour when hyperactivity coexists in ASD patients.

  17. FMR1 Knockout mice: A model to study fragile X mental retardation

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    Oostra, B.A.; Bakker, C.E.; Reyniers, E. [Erasmus Univ., Rotterdam (Netherlands)] [and others

    1994-09-01

    The fragile X syndrome is the most frequent form of inherited mental retardation in humans with an incidence of 1 in 1250 males and 1 in 2500 females. The clinical syndrome includes moderate to severe mental retardation, autistic behavior, macroorchidism, and facial features, such as long face with mandibular prognathism and large, everted ears. The molecular basis for this disease is a large expansion of a triplet repeat (CGG){sub n} in the 5{prime} untranslated region of the FMR1 gene. Due to this large expansion of the CGG repeat, the promoter region becomes methylated and the FMR1 gene is subsequently silenced. Hardly anything is known about the physiologic function of FMR1 and the pathologic mechanisms leading to these symptoms. Since the FMR1 gene is highly conserved in the mouse, we used the mouse to design a knockout model for the fragile X syndrome. These knockout mice lacking Fmrp have normal litter size suggesting that FMR1 is not essential in human gametogenesis and embryonic development. The knockout mice show the abnormalities also seen in the affected organs of human patients. Mutant mice show a gradual development through time of macroorchidism. In the knockout mice we observed cognitive defects in the form of deficits in learning (as shown by the hidden platform Morris water maze task) and behavioral abnormalities such as increased exploratory behavior and hyperactivity. Therefore this knockout mouse may serve as a valuable tool in studying the role of FMR1 in the fragile X syndrome and may serve as a model to elucidate the mechanisms involved in macroorchidism, abnormal behavior, and mental retardation.

  18. Low-Normal FMR1 CGG Repeat Length: Phenotypic Associations

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    Marsha eMailick

    2014-09-01

    Full Text Available This population-based study investigates genotype-phenotype correlations of low-normal CGG repeats in the fragile X mental retardation 1 (FMR1 gene. FMR1 plays an important role in brain development and function, and encodes FMRP (fragile X mental retardation protein, an RNA-binding protein that regulates protein synthesis impacting activity-dependent synaptic development and plasticity. Most past research has focused on CGG premutation expansions (41 to 200 CGG repeats and on fragile X syndrome (200+ CGG repeats, with considerably less attention on the other end of the spectrum of CGG repeats. Using existing data, older adults with 23 or fewer CGG repeats (2 SDs below the mean were compared with age-peers who have normal numbers of CGGs (24-40 with respect to cognition, mental health, cancer, and having children with disabilities. Men (n = 341 with an allele in the low-normal range and women (n = 46 with two low-normal alleles had significantly more difficulty with their memory and ability to solve day to day problems. Women with both FMR1 alleles in the low-normal category had significantly elevated odds of feeling that they need to drink more to get the same effect as in the past. These women also had two and one-half times the odds of having had breast cancer and four times the odds of uterine cancer. Men and women with low-normal CGGs had higher odds of having a child with a disability, either a developmental disability or a mental health condition. These findings are in line with the hypothesis that there is a need for tight neuronal homeostatic control mechanisms for optimal cognitive and behavioral functioning, and more generally that low numbers as well as high numbers of CGG repeats may be problematic for health.

  19. Resilience to audiogenic seizures is associated with p-ERK1/2 dephosphorylation in the subiculum of Fmr1 knockout mice

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    Giulia eCuria

    2013-04-01

    Full Text Available Young, but not adult, Fmr1 knockout (KO mice display audiogenic seizures (AGS that can be prevented by inhibiting extracellular signal-regulated kinases 1/2 (ERK1/2 phosphorylation. In order to identify the cerebral regions involved in these phenomena, we characterized the response to AGS in Fmr1 KO mice and wild type (WT controls at postnatal day (P 45 and P90. To characterize the diverse response to AGS in various cerebral regions, we evaluated the activity markers FosB/ΔFosB and phosphorylated ERK1/2 (p-ERK1/2. Wild running (100% of tested mice followed by clonic/tonic seizures (30% were observed in P45 Fmr1 KO mice, but not in WT mice. In P90 Fmr1 KO mice, wild running was only present in 25% of tested animals. Basal FosB/ΔFosB immunoreactivity was higher (P<0.01 vs WT in the CA1 and subiculum of P45 Fmr1 KO mice. Following the AGS test, FosB/ΔFosB expression consistently increased in most of the analyzed regions in both groups at P45, but not at P90. Interestingly, FosB/ΔFosB immunoreactivity was significantly higher in P45 Fmr1 KO mice in the medial geniculate body (P<0.05 vs WT and CA3 (P<0.01. Neurons presenting with immunopositivity to p-ERK1/2 were more abundant in the subiculum of Fmr1 KO mice in control condition (P<0.05 vs WT, in both age groups. In this region, p-ERK1/2-immunopositive cells significantly decreased (-75%, P<0.01 in P90 Fmr1 KO mice exposed to the AGS test, but no changes were found in P45 mice or in other brain regions. In both age groups of WT mice, p-ERK1/2-immunopositive cells increased in the subiculum after exposure to the acoustic test. Our findings illustrate that FosB/ΔFosB markers are overexpressed in the medial geniculate body and CA3 in Fmr1 KO mice experiencing AGS, and that p-ERK1/2 is markedly decreased in the subiculum of Fmr1 KO mice resistant to AGS induction. These findings suggest that resilience to AGS is associated with dephosphorylation of p-ERK1/2 in the subiculum of mature Fmr1 KO mice.

  20. Study of the Genetic Etiology of Primary Ovarian Insufficiency: FMR1 Gene

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    Maitane Barasoain

    2016-12-01

    Full Text Available Menopause is a period of women’s life characterized by the cessation of menses in a definitive way. The mean age for menopause is approximately 51 years. Primary ovarian insufficiency (POI refers to ovarian dysfunction defined as irregular menses and elevated gonadotrophin levels before or at the age of 40 years. The etiology of POI is unknown but several genes have been reported as being of significance. The fragile X mental retardation 1 gene (FMR1 is one of the most important genes associated with POI. The FMR1 gene contains a highly polymorphic CGG repeat in the 5′ untranslated region of exon 1. Four allelic forms have been defined with respect to CGG repeat length and instability during transmission. Normal (5–44 CGG alleles are usually transmitted from parent to offspring in a stable manner. The full mutation form consists of over 200 repeats, which induces hypermethylation of the FMR1 gene promoter and the subsequent silencing of the gene, associated with Fragile X Syndrome (FXS. Finally, FMR1 intermediate (45–54 CGG and premutation (55–200 CGG alleles have been principally associated with two phenotypes, fragile X tremor ataxia syndrome (FXTAS and fragile X primary ovarian insufficiency (FXPOI.

  1. Wild-type male offspring of fmr-1+/- mothers exhibit characteristics of the fragile X phenotype.

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    Zupan, Bojana; Toth, Miklos

    2008-10-01

    Fragile X syndrome is an X-linked disorder caused by the inactivation of the FMR-1 gene with symptoms ranging from impaired cognitive functions to seizures, anxiety, sensory abnormalities, and hyperactivity. Males are more severely affected than heterozygote (H) females, who, as carriers, have a 50% chance of transmitting the mutated allele in each pregnancy. fmr-1 knockout (KO) mice reproduce fragile X symptoms, including hyperactivity, seizures, and abnormal sensory processing. In contrast to the expectation that wild-type (WT) males born to H (fmr-1(+/-)) mothers (H>WT) are behaviorally normal and indistinguishable from WT males born to WT mothers (WT>WT); here, we show that H>WT offspring are more active than WT>WT offspring and that their hyperactivity is similar to male KO mice born to H or KO (fmr-1(-/-)) mothers (H>KO/KO>KO). H>WT mice, however, do not exhibit seizures or abnormal sensory processing. Consistent with their hyperactivity, the effect of the D2 agonist quinpirole is reduced in H>WT as well as in H>KO and KO>KO mice compared to WT>WT offspring, suggesting a diminished feedback inhibition of dopamine release. Our data indicate that some aspects of hyperactivity and associated dopaminergic changes in 'fragile X' mice are a maternal fmr-1 genotype rather than an offspring fmr-1 genotype effect.

  2. FMR1 epigenetic silencing commonly occurs in undifferentiated fragile X-affected embryonic stem cells.

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    Avitzour, Michal; Mor-Shaked, Hagar; Yanovsky-Dagan, Shira; Aharoni, Shira; Altarescu, Gheona; Renbaum, Paul; Eldar-Geva, Talia; Schonberger, Oshrat; Levy-Lahad, Ephrat; Epsztejn-Litman, Silvina; Eiges, Rachel

    2014-11-11

    Fragile X syndrome (FXS) is the most common heritable form of cognitive impairment. It results from epigenetic silencing of the X-linked FMR1 gene by a CGG expansion in its 5'-untranslated region. Taking advantage of a large set of FXS-affected human embryonic stem cell (HESC) lines and isogenic subclones derived from them, we show that FMR1 hypermethylation commonly occurs in the undifferentiated state (six of nine lines, ranging from 24% to 65%). In addition, we demonstrate that hypermethylation is tightly linked with FMR1 transcriptional inactivation in undifferentiated cells, coincides with loss of H3K4me2 and gain of H3K9me3, and is unrelated to CTCF binding. Taken together, these results demonstrate that FMR1 epigenetic gene silencing takes place in FXS HESCs and clearly highlights the importance of examining multiple cell lines when investigating FXS and most likely other epigenetically regulated diseases.

  3. FMR1 Epigenetic Silencing Commonly Occurs in Undifferentiated Fragile X-Affected Embryonic Stem Cells

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    Michal Avitzour

    2014-11-01

    Full Text Available Fragile X syndrome (FXS is the most common heritable form of cognitive impairment. It results from epigenetic silencing of the X-linked FMR1 gene by a CGG expansion in its 5′-untranslated region. Taking advantage of a large set of FXS-affected human embryonic stem cell (HESC lines and isogenic subclones derived from them, we show that FMR1 hypermethylation commonly occurs in the undifferentiated state (six of nine lines, ranging from 24% to 65%. In addition, we demonstrate that hypermethylation is tightly linked with FMR1 transcriptional inactivation in undifferentiated cells, coincides with loss of H3K4me2 and gain of H3K9me3, and is unrelated to CTCF binding. Taken together, these results demonstrate that FMR1 epigenetic gene silencing takes place in FXS HESCs and clearly highlights the importance of examining multiple cell lines when investigating FXS and most likely other epigenetically regulated diseases.

  4. Identifying intrinsic and extrinsic determinants that regulate internal initiation of translation mediated by the FMR1 5' leader

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    Timmerman Stephanie

    2008-10-01

    Full Text Available Abstract Background Regulating synthesis of the Fragile X gene (FMR1 product, FMRP alters neural plasticity potentially through its role in the microRNA pathway. Cap-dependent translation of the FMR1 mRNA, a process requiring ribosomal scanning through the 5' leader, is likely impeded by the extensive secondary structure generated by the high guanosine/cytosine nucleotide content including the CGG triplet nucleotide repeats in the 5' leader. An alternative mechanism to initiate translation – internal initiation often utilizes secondary structure to recruit the translational machinery. Consequently, studies were undertaken to confirm and extend a previous observation that the FMR1 5' leader contains an internal ribosomal entry site (IRES. Results Cellular transfection of a dicistronic DNA construct containing the FMR1 5' leader inserted into the intercistronic region yielded significant translation of the second cistron, but the FMR1 5' leader was also found to contain a cryptic promoter possibly confounding interpretation of these results. However, transfection of dicistronic and monocistronic RNA ex vivo or in vitro confirmed that the FMR1 5' leader contains an IRES. Moreover, inhibiting cap-dependent translation ex vivo did not affect the expression level of endogenous FMRP indicating a role for IRES-dependent translation of FMR1 mRNA. Analysis of the FMR1 5' leader revealed that the CGG repeats and the 5' end of the leader were vital for internal initiation. Functionally, exposure to potassium chloride or intracellular acidification and addition of polyinosinic:polycytidylic acid as mimics of neural activity and double stranded RNA, respectively, differentially affected FMR1 IRES activity. Conclusion Our results indicate that multiple stimuli influence IRES-dependent translation of the FMR1 mRNA and suggest a functional role for the CGG nucleotide repeats.

  5. FMR1 gene expansion and scans without evidence of dopaminergic deficits in parkinsonism patients.

    Science.gov (United States)

    Hall, D A; Jennings, D; Seibyl, J; Tassone, F; Marek, K

    2010-11-01

    To determine if patients with parkinsonism and fragile X mental retardation 1 (FMR1) gene expansions have a striatal dopamine deficit similar to Parkinson disease (PD) patients. The authors studied three patients with parkinsonism carrying small expansions in the FMR1 gene (41-60 CGG) with [(123)I]β-CIT SPECT imaging. The patients responded to dopaminergic medications, but had preserved dopamine transporter density. These results suggest that parkinsonism associated with smaller FMR1 expansions may be related to mechanisms other than pre-synaptic dopaminergic changes and may represent a potential explanation for at least some parkinsonian cases with scans without evidence of dopaminergic deficits (SWEDD). Copyright © 2010 Elsevier Ltd. All rights reserved.

  6. MicroRNA-130b targets Fmr1 and regulates embryonic neural progenitor cell proliferation and differentiation

    International Nuclear Information System (INIS)

    Gong, Xi; Zhang, Kunshan; Wang, Yanlu; Wang, Junbang; Cui, Yaru; Li, Siguang; Luo, Yuping

    2013-01-01

    Highlights: •We found that the 3′ UTR of the Fmr1 mRNA is a target of miR-130b. •MiR-130b suppresses the expression of Fmr1 in mouse embryonic stem cell. •MiR-130b alters the proliferation of mouse embryonic stem cell. •MiR-130b alters fate specification of mouse embryonic stem cell. -- Abstract: Fragile X syndrome, one of the most common forms of inherited mental retardation, is caused by expansion of the CGG repeat in the 5′-untranslated region of the X-linked Fmr1 gene, which results in transcriptional silencing and loss of expression of its encoded protein FMRP. The loss of FMRP increases proliferation and alters fate specification in adult neural progenitor cells (aNPCs). However, little is known about Fmr1 mRNA regulation at the transcriptional and post-transcriptional levels. In the present study, we report that miR-130b regulated Fmr1 expression by directly targeting its 3′-untranslated region (3′ UTR). Up-regulation of miR-130b in mouse embryonic neural progenitor cells (eNPCs) decreased Fmr1 expression, markedly increased eNPC proliferation and altered the differentiation tendency of eNPCs, suggesting that antagonizing miR-130b may be a new therapeutic entry point for treating Fragile X syndrome

  7. MicroRNA-130b targets Fmr1 and regulates embryonic neural progenitor cell proliferation and differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Xi [State Key Laboratory of Food Science and Technology, College of Life Sciences and Food Engineering, Nanchang University, Nanchang 330047 (China); Zhang, Kunshan [Department of Regenerative Medicine, Stem Cell Center, Tongji University School of Medicine, Shanghai 200092 (China); Wang, Yanlu; Wang, Junbang; Cui, Yaru [State Key Laboratory of Food Science and Technology, College of Life Sciences and Food Engineering, Nanchang University, Nanchang 330047 (China); Li, Siguang, E-mail: siguangli@163.com [Department of Regenerative Medicine, Stem Cell Center, Tongji University School of Medicine, Shanghai 200092 (China); Luo, Yuping, E-mail: luoyuping@163.com [State Key Laboratory of Food Science and Technology, College of Life Sciences and Food Engineering, Nanchang University, Nanchang 330047 (China)

    2013-10-04

    Highlights: •We found that the 3′ UTR of the Fmr1 mRNA is a target of miR-130b. •MiR-130b suppresses the expression of Fmr1 in mouse embryonic stem cell. •MiR-130b alters the proliferation of mouse embryonic stem cell. •MiR-130b alters fate specification of mouse embryonic stem cell. -- Abstract: Fragile X syndrome, one of the most common forms of inherited mental retardation, is caused by expansion of the CGG repeat in the 5′-untranslated region of the X-linked Fmr1 gene, which results in transcriptional silencing and loss of expression of its encoded protein FMRP. The loss of FMRP increases proliferation and alters fate specification in adult neural progenitor cells (aNPCs). However, little is known about Fmr1 mRNA regulation at the transcriptional and post-transcriptional levels. In the present study, we report that miR-130b regulated Fmr1 expression by directly targeting its 3′-untranslated region (3′ UTR). Up-regulation of miR-130b in mouse embryonic neural progenitor cells (eNPCs) decreased Fmr1 expression, markedly increased eNPC proliferation and altered the differentiation tendency of eNPCs, suggesting that antagonizing miR-130b may be a new therapeutic entry point for treating Fragile X syndrome.

  8. Activity Induces Fmr1-Sensitive Synaptic Capture of Anterograde Circulating Neuropeptide Vesicles.

    Science.gov (United States)

    Cavolo, Samantha L; Bulgari, Dinara; Deitcher, David L; Levitan, Edwin S

    2016-11-16

    Synaptic neuropeptide and neurotrophin stores are maintained by constitutive bidirectional capture of dense-core vesicles (DCVs) as they circulate in and out of the nerve terminal. Activity increases DCV capture to rapidly replenish synaptic neuropeptide stores following release. However, it is not known whether this is due to enhanced bidirectional capture. Here experiments at the Drosophila neuromuscular junction, where DCVs contain neuropeptides and a bone morphogenic protein, show that activity-dependent replenishment of synaptic neuropeptides following release is evident after inhibiting the retrograde transport with the dynactin disruptor mycalolide B or photobleaching DCVs entering a synaptic bouton by retrograde transport. In contrast, photobleaching anterograde transport vesicles entering a bouton inhibits neuropeptide replenishment after activity. Furthermore, tracking of individual DCVs moving through boutons shows that activity selectively increases capture of DCVs undergoing anterograde transport. Finally, upregulating fragile X mental retardation 1 protein (Fmr1, also called FMRP) acts independently of futsch/MAP-1B to abolish activity-dependent, but not constitutive, capture. Fmr1 also reduces presynaptic neuropeptide stores without affecting activity-independent delivery and evoked release. Therefore, presynaptic motoneuron neuropeptide storage is increased by a vesicle capture mechanism that is distinguished from constitutive bidirectional capture by activity dependence, anterograde selectivity, and Fmr1 sensitivity. These results show that activity recruits a separate mechanism than used at rest to stimulate additional synaptic capture of DCVs for future release of neuropeptides and neurotrophins. Synaptic release of neuropeptides and neurotrophins depends on presynaptic accumulation of dense-core vesicles (DCVs). At rest, DCVs are captured bidirectionally as they circulate through Drosophila motoneuron terminals by anterograde and retrograde

  9. Population-based estimates of the prevalence of FMR1 expansion mutations in women with early menopause and primary ovarian insufficiency.

    Science.gov (United States)

    Murray, Anna; Schoemaker, Minouk J; Bennett, Claire E; Ennis, Sarah; Macpherson, James N; Jones, Michael; Morris, Danielle H; Orr, Nick; Ashworth, Alan; Jacobs, Patricia A; Swerdlow, Anthony J

    2014-01-01

    Primary ovarian insufficiency before the age of 40 years affects 1% of the female population and is characterized by permanent cessation of menstruation. Genetic causes include FMR1 expansion mutations. Previous studies have estimated mutation prevalence in clinical referrals for primary ovarian insufficiency, but these are likely to be biased as compared with cases in the general population. The prevalence of FMR1 expansion mutations in early menopause (between the ages of 40 and 45 years) has not been published. We studied FMR1 CGG repeat number in more than 2,000 women from the Breakthrough Generations Study who underwent menopause before the age of 46 years. We determined the prevalence of premutation (55-200 CGG repeats) and intermediate (45-54 CGG repeats) alleles in women with primary ovarian insufficiency (n = 254) and early menopause (n = 1,881). The prevalence of the premutation was 2.0% in primary ovarian insufficiency, 0.7% in early menopause, and 0.4% in controls, corresponding to odds ratios of 5.4 (95% confidence interval = 1.7-17.4; P = 0.004) for primary ovarian insufficiency and 2.0 (95% confidence interval = 0.8-5.1; P = 0.12) for early menopause. Combining primary ovarian insufficiency and early menopause gave an odds ratio of 2.4 (95% confidence interval = 1.02-5.8; P = 0.04). Intermediate alleles were not significant risk factors for either early menopause or primary ovarian insufficiency. FMR1 premutations are not as prevalent in women with ovarian insufficiency as previous estimates have suggested, but they still represent a substantial cause of primary ovarian insufficiency and early menopause.

  10. Clinical, molecular, and pharmacological aspects of FMR1 related disorders.

    Science.gov (United States)

    Pugin, A; Faundes, V; Santa María, L; Curotto, B; Aliaga, S; Salas, I; Soto, P; Bravo, P; Peña, M I; Alliende, M A

    2017-05-01

    Fragile X syndrome, the most common inherited cause of intellectual disability, is associated with a broad spectrum of disorders across different generations of a single family. This study reviews the clinical manifestations of fragile X-associated disorders as well as the spectrum of mutations of the fragile X mental retardation 1 gene (FMR1) and the neurobiology of the fragile X mental retardation protein (FMRP), and also provides an overview of the potential therapeutic targets and genetic counselling. This disorder is caused by expansion of the CGG repeat (>200 repeats) in the 5 prime untranslated region of FMR1, resulting in a deficit or absence of FMRP. FMRP is an RNA-binding protein that regulates the translation of several genes that are important in synaptic plasticity and dendritic maturation. It is believed that CGG repeat expansions in the premutation range (55 to 200 repeats) elicit an increase in mRNA levels of FMR1, which may cause neuronal toxicity. These changes manifest clinically as developmental problems such as autism and learning disabilities as well as neurodegenerative diseases including fragile X-associated tremor/ataxia syndrome (FXTAS). Advances in identifying the molecular basis of fragile X syndrome may help us understand the causes of neuropsychiatric disorders, and they will probably contribute to development of new and specific treatments. Copyright © 2014 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

  11. Genetic-background modulation of core and variable autistic-like symptoms in Fmr1 knock-out mice.

    Directory of Open Access Journals (Sweden)

    Susanna Pietropaolo

    Full Text Available BACKGROUND: No animal models of autism spectrum disorders (ASD with good construct validity are currently available; using genetic models of pathologies characterized by ASD-like deficits, but with known causes, may be therefore a promising strategy. The Fmr1-KO mouse is an example of this approach, modeling Fragile X syndrome, a well-known genetic disorder presenting ASD symptoms. The Fmr1-KO is available on different genetic backgrounds (FVB versus C57BL/6, which may explain some of the conflicting results that have been obtained with these mutants up till now. METHODS: Fmr1 KO and their wild-type littermates on both the FVB and C57BL/6 genetic backgrounds were examined on a battery of tests modeling the clinical symptoms of ASD, including the triad of core symptoms (alterations in social interaction and communication, presence of repetitive behaviors, as well as the secondary symptoms (disturbances in sensori-motor reactivity and in circadian patterns of activity, epileptic events. RESULTS: Fmr1-KO mice displayed autistic-like core symptoms of altered social interaction and occurrence of repetitive behaviors with additional hyperactivity. The genetic background modulated the effects of the Fmr1 deletion and it appears that the C57BL/6 background may be more suitable for further research on core autistic-like symptoms. CONCLUSIONS: The Fmr1-mouse line does not recapitulate all of the main core and secondary ASD symptoms, but still can be useful to elucidate the neurobiological mechanisms underlying specific ASD-like endophenotypes.

  12. Length of FMR1 repeat alleles within the normal range does not substantially affect the risk of early menopause

    Science.gov (United States)

    Ruth, Katherine S.; Bennett, Claire E.; Schoemaker, Minouk J.; Weedon, Michael N.; Swerdlow, Anthony J.; Murray, Anna

    2016-01-01

    STUDY QUESTION Is the length of FMR1 repeat alleles within the normal range associated with the risk of early menopause? SUMMARY ANSWER The length of repeat alleles within the normal range does not substantially affect risk of early menopause. WHAT IS KNOWN ALREADY There is a strong, well-established relationship between length of premutation FMR1 alleles and age at menopause, suggesting that this relationship could continue into the normal range. Within the normal range, there is conflicting evidence; differences in ovarian reserve have been identified with FMR1 repeat allele length, but a recent population-based study did not find any association with age at menopause as a quantitative trait. STUDY DESIGN, SIZE, DURATION We analysed cross-sectional baseline survey data collected at recruitment from 2004 to 2010 from a population-based, prospective epidemiological cohort study of >110 000 women to investigate whether repeat allele length was associated with early menopause. PARTICIPANTS/MATERIALS, SETTING, METHOD We included 4333 women from the Breakthrough Generations Study (BGS), of whom 2118 were early menopause cases (menopause under 46 years) and 2215 were controls. We analysed the relationship between length of FMR1 alleles and early menopause using logistic regression with allele length as continuous and categorical variables. We also conducted analyses with the outcome age at menopause as a quantitative trait as well as appropriate sensitivity and exploratory analyses. MAIN RESULTS AND THE ROLE OF CHANCE There was no association of the shorter or longer FMR1 allele or their combined genotype with the clinically relevant end point of early menopause in our main analysis. Likewise, there were no associations with age at menopause as a quantitative trait in our secondary analysis. LIMITATIONS, REASONS FOR CAUTION Women with homozygous alleles in the normal range may have undetected FMR1 premutation alleles, although there was no evidence to suggest this. We

  13. FMR study of carbon nanotubes filled with Fe{sub 3}O{sub 4} nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Kopyl, S., E-mail: svitlanakopyl@ua.pt [NRD-TEMA, Department of Mechanical Engineering, Aveiro Institute of Nanotechnology (AIN), University of Aveiro, Aveiro 3810-193 (Portugal); Timopheev, A.A., E-mail: andreyt@ua.pt [Physics Department and I3N, University of Aveiro, Aveiro 3810-193 (Portugal); Bystrov, V.S. [Department of Materials and Ceramic Engineering and CICECO, University of Aveiro, Aveiro 3810-193 (Portugal); Institute of Mathematical Problems of Biology RAS, 142290 Pushchino (Russian Federation); Bdikin, I. [NRD-TEMA, Department of Mechanical Engineering, Aveiro Institute of Nanotechnology (AIN), University of Aveiro, Aveiro 3810-193 (Portugal); Teixeira, B.M.S. [Physics Department and I3N, University of Aveiro, Aveiro 3810-193 (Portugal); Maevskij, E. [Institute of Theoretical and Experimental Biophysics RAS, 142290 Puschino (Russian Federation); Sobolev, N.A. [Physics Department and I3N, University of Aveiro, Aveiro 3810-193 (Portugal); Sousa, A.C.M. [NRD-TEMA, Department of Mechanical Engineering, Aveiro Institute of Nanotechnology (AIN), University of Aveiro, Aveiro 3810-193 (Portugal)

    2014-05-01

    Ordered arrays of carbon nanotubes were produced using a non-catalytic chemical vapour deposition. The multiwall nanotubes with an inner diameter of 120 nm were grown inside porous alumina templates and then filled with a magnetic colloid of 7.5 nm Fe{sub 3}O{sub 4} particles. X-ray diffraction, electron microscopy and ferromagnetic resonance (FMR) were used to characterize structural and magnetic properties of the grown samples. To estimate the filling factor from the angular dependence of the FMR resonance field, we have derived an effective demagnetization factor for our system using the formalism proposed by Skomsky and Dubowik. Angular dependence of the FMR line width allows one to conclude about the non-uniform filling, while temperature dependent measurements reflect typical features of a superparamagnetic resonance. - Highlights: • Synthesis of CNTs inside of alumina membrane and filling it with Fe{sub 3}O{sub 4} particles. • X-ray diffraction and electron microscopy study of the samples. • Magnetic properties of the samples studied by FMR. • Filling factor has been determined from the angular dependences of FMR. • Resulted magnetic CNTs are attractive for production of magnetic nanofluids.

  14. Age-Dependent Long-Term Potentiation Deficits in the Prefrontal Cortex of the Fmr1 Knockout Mouse Model of Fragile X Syndrome.

    Science.gov (United States)

    Martin, Henry G S; Lassalle, Olivier; Brown, Jonathan T; Manzoni, Olivier J

    2016-05-01

    The most common inherited monogenetic cause of intellectual disability is Fragile X syndrome (FXS). The clinical symptoms of FXS evolve with age during adulthood; however, neurophysiological data exploring this phenomenon are limited. The Fmr1 knockout (Fmr1KO) mouse models FXS, but studies in these mice of prefrontal cortex (PFC) function are underrepresented, and aging linked data are absent. We studied synaptic physiology and activity-dependent synaptic plasticity in the medial PFC of Fmr1KO mice from 2 to 12 months. In young adult Fmr1KO mice, NMDA receptor (NMDAR)-mediated long-term potentiation (LTP) is intact; however, in 12-month-old mice this LTP is impaired. In parallel, there was an increase in the AMPAR/NMDAR ratio and a concomitant decrease of synaptic NMDAR currents in 12-month-old Fmr1KO mice. We found that acute pharmacological blockade of mGlu5 receptor in 12-month-old Fmr1KO mice restored a normal AMPAR/NMDAR ratio and LTP. Taken together, the data reveal an age-dependent deficit in LTP in Fmr1KO mice, which may correlate to some of the complex age-related deficits in FXS. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Chronic minocycline treatment improves social recognition memory in adult male Fmr1 knockout mice.

    Science.gov (United States)

    Yau, Suk Yu; Chiu, Christine; Vetrici, Mariana; Christie, Brian R

    2016-10-01

    Fragile X syndrome (FXS) is caused by a mutation in the Fmr1 gene that leads to silencing of the gene and a loss of its gene product, Fragile X mental retardation protein (FMRP). Some of the key behavioral phenotypes for FXS include abnormal social anxiety and sociability. Here we show that Fmr1 knock-out (KO) mice exhibit impaired social recognition when presented with a novel mouse, and they display normal social interactions in other sociability tests. Administering minocycline to Fmr1 KO mice throughout critical stages of neural development improved social recognition memory in the novel mouse recognition task. To determine if synaptic changes in the prefrontal cortex (PFC) could have played a role in this improvement, we examined PSD-95, a member of the membrane-associated guanylate kinase family, and signaling molecules (ERK1/2, and Akt) linked to synaptic plasticity in the PFC. Our analyses indicated that while minocycline treatment can enhance behavioral performance, it does not enhance expression of PSD-95, ERK1/2 or Akt in the PFC. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks

    Directory of Open Access Journals (Sweden)

    Zarnescu Daniela C

    2008-11-01

    Full Text Available Abstract Background In Drosophila, the genes sticky and dFmr1 have both been shown to regulate cytoskeletal dynamics and chromatin structure. These genes also genetically interact with Argonaute family microRNA regulators. Furthermore, in mammalian systems, both genes have been implicated in neuronal development. Given these genetic and functional similarities, we tested Drosophila sticky and dFmr1 for a genetic interaction and measured whole genome expression in both mutants to assess similarities in gene regulation. Results We found that sticky mutations can dominantly suppress a dFmr1 gain-of-function phenotype in the developing eye, while phenotypes produced by RNAi knock-down of sticky were enhanced by dFmr1 RNAi and a dFmr1 loss-of-function mutation. We also identified a large number of transcripts that were misexpressed in both mutants suggesting that sticky and dFmr1 gene products similarly regulate gene expression. By integrating gene expression data with a protein-protein interaction network, we found that mutations in sticky and dFmr1 resulted in misexpression of common gene networks, and consequently predicted additional specific phenotypes previously not known to be associated with either gene. Further phenotypic analyses validated these predictions. Conclusion These findings establish a functional link between two previously unrelated genes. Microarray analysis indicates that sticky and dFmr1 are both required for regulation of many developmental genes in a variety of cell types. The diversity of transcripts regulated by these two genes suggests a clear cause of the pleiotropy that sticky and dFmr1 mutants display and provides many novel, testable hypotheses about the functions of these genes. As both of these genes are implicated in the development and function of the mammalian brain, these results have relevance to human health as well as to understanding more general biological processes.

  17. Increased transient Na+ conductance and action potential output in layer 2/3 prefrontal cortex neurons of the fmr1-/y mouse.

    Science.gov (United States)

    Routh, Brandy N; Rathour, Rahul K; Baumgardner, Michael E; Kalmbach, Brian E; Johnston, Daniel; Brager, Darrin H

    2017-07-01

    Layer 2/3 neurons of the prefrontal cortex display higher gain of somatic excitability, responding with a higher number of action potentials for a given stimulus, in fmr1 -/y mice. In fmr1 -/y L2/3 neurons, action potentials are taller, faster and narrower. Outside-out patch clamp recordings revealed that the maximum Na + conductance density is higher in fmr1 -/y L2/3 neurons. Measurements of three biophysically distinct K + currents revealed a depolarizing shift in the activation of a rapidly inactivating (A-type) K + conductance. Realistic neuronal simulations of the biophysical observations recapitulated the elevated action potential and repetitive firing phenotype. Fragile X syndrome is the most common form of inherited mental impairment and autism. The prefrontal cortex is responsible for higher order cognitive processing, and prefrontal dysfunction is believed to underlie many of the cognitive and behavioural phenotypes associated with fragile X syndrome. We recently demonstrated that somatic and dendritic excitability of layer (L) 5 pyramidal neurons in the prefrontal cortex of the fmr1 -/y mouse is significantly altered due to changes in several voltage-gated ion channels. In addition to L5 pyramidal neurons, L2/3 pyramidal neurons play an important role in prefrontal circuitry, integrating inputs from both lower brain regions and the contralateral cortex. Using whole-cell current clamp recording, we found that L2/3 pyramidal neurons in prefrontal cortex of fmr1 -/y mouse fired more action potentials for a given stimulus compared with wild-type neurons. In addition, action potentials in fmr1 -/y neurons were significantly larger, faster and narrower. Voltage clamp of outside-out patches from L2/3 neurons revealed that the transient Na + current was significantly larger in fmr1 -/y neurons. Furthermore, the activation curve of somatic A-type K + current was depolarized. Realistic conductance-based simulations revealed that these biophysical changes in Na

  18. Object recognition impairment in Fmr1 knockout mice is reversed by amphetamine: involvement of dopamine in the medial prefrontal cortex.

    Science.gov (United States)

    Ventura, R; Pascucci, T; Catania, M V; Musumeci, S A; Puglisi-Allegra, S

    2004-09-01

    Fragile X syndrome is an X-linked form of mental retardation including, among others, symptoms such as stereotypic behaviour, hyperactivity, hyperarousal, and cognitive deficits. We hypothesized that hyperactivity and/or compromised attentional, cognitive functions may lead to impaired performance in cognitive tasks in Fmr1 knockout mice, the most widely used animal model of fragile X syndrome, and suggested that psychostimulant treatment may improve performance by acting on one or both components. Since hyperactivity and cognitive functions have been suggested to depend on striatal and prefrontal cortex dopaminergic dysfunction, we assessed whether amphetamine produced beneficial, positive effects by acting on dopaminergic corticostriatal systems. Our results show that Fmr1 knockout mice are not able to discriminate between a familiar object and a novel one in the object recognition test, thus showing a clear-cut cognitive impairment that, to date, has been difficult to demonstrate in other cognitive tasks. Amphetamine improved performance of Fmr1 knockout mice, leading to enhanced ability to discriminate novel versus familiar objects, without significantly affecting locomotor activity. In agreement with behavioural data, amphetamine produced a greater increase in dopamine release in the prefrontal cortex of Fmr1 knockout compared with the wild-type mice, while a weak striatal dopaminergic response was observed in Fmr1 knockout mice. Our data support the view that the psychostimulant ameliorates performance in Fmr1 knockout mice by improving merely cognitive functions through its action on prefrontal cortical dopamine, irrespective of its action on motor hyperactivity. These results indicate that prefrontal cortical dopamine plays a major role in cognitive impairments characterizing Fmr1 knockout mice, thus pointing to an important aetiological factor in the fragile X syndrome.

  19. Wild-Type Male Offspring of fmr-1+/− Mothers Exhibit Characteristics of the Fragile X Phenotype

    OpenAIRE

    Zupan, Bojana; Toth, Miklos

    2008-01-01

    Fragile X syndrome is an X-linked disorder caused by the inactivation of the FMR-1 gene with symptoms ranging from impaired cognitive functions to seizures, anxiety, sensory abnormalities, and hyperactivity. Males are more severely affected than heterozygote (H) females, who, as carriers, have a 50% chance of transmitting the mutated allele in each pregnancy. fmr-1 knockout (KO) mice reproduce fragile X symptoms, including hyperactivity, seizures, and abnormal sensory processing. In contrast ...

  20. β-glucuronidase use as a single internal control gene may confound analysis in FMR1 mRNA toxicity studies.

    Science.gov (United States)

    Kraan, Claudine M; Cornish, Kim M; Bui, Quang M; Li, Xin; Slater, Howard R; Godler, David E

    2018-01-01

    Relationships between Fragile X Mental Retardation 1 (FMR1) mRNA levels in blood and intragenic FMR1 CGG triplet expansions support the pathogenic role of RNA gain of function toxicity in premutation (PM: 55-199 CGGs) related disorders. Real-time PCR (RT-PCR) studies reporting these findings normalised FMR1 mRNA level to a single internal control gene called β-glucuronidase (GUS). This study evaluated FMR1 mRNA-CGG correlations in 33 PM and 33 age- and IQ-matched control females using three normalisation strategies in peripheral blood mononuclear cells (PBMCs): (i) GUS as a single internal control; (ii) the mean of GUS, Eukaryotic Translation Initiation Factor 4A2 (EIF4A2) and succinate dehydrogenase complex flavoprotein subunit A (SDHA); and (iii) the mean of EIF4A2 and SDHA (with no contribution from GUS). GUS mRNA levels normalised to the mean of EIF4A2 and SDHA mRNA levels and EIF4A2/SDHA ratio were also evaluated. FMR1mRNA level normalised to the mean of EIF4A2 and SDHA mRNA levels, with no contribution from GUS, showed the most significant correlation with CGG size and the greatest difference between PM and control groups (p = 10-11). Only 15% of FMR1 mRNA PM results exceeded the maximum control value when normalised to GUS, compared with over 42% when normalised to the mean of EIF4A2 and SDHA mRNA levels. Neither GUS mRNA level normalised to the mean RNA levels of EIF4A2 and SDHA, nor to the EIF4A2/SDHA ratio were correlated with CGG size. However, greater variability in GUS mRNA levels were observed for both PM and control females across the full range of CGG repeat as compared to the EIF4A2/SDHA ratio. In conclusion, normalisation with multiple control genes, excluding GUS, can improve assessment of the biological significance of FMR1 mRNA-CGG size relationships.

  1. Electric-field tunable spin diode FMR in patterned PMN-PT/NiFe structures

    Energy Technology Data Exchange (ETDEWEB)

    Ziętek, Slawomir, E-mail: zietek@agh.edu.pl; Skowroński, Witold; Stobiecki, Tomasz [AGH University of Science and Technology, Department of Electronics, Al. Mickiewicza 30, 30-059 Kraków (Poland); Ogrodnik, Piotr, E-mail: piotrogr@if.pw.edu.pl [AGH University of Science and Technology, Department of Electronics, Al. Mickiewicza 30, 30-059 Kraków (Poland); Faculty of Physics, Warsaw University of Technology, ul. Koszykowa 75, 00-662 Warszawa (Poland); Stobiecki, Feliks [Institute of Molecular Physics, Polish Academy of Sciences, ul. Smoluchowskiego 17, 60-179 Poznań (Poland); Dijken, Sebastiaan van [NanoSpin, Department of Applied Physics, Aalto University School of Science, P.O. Box 15100, FI-00076 Aalto (Finland); Barnaś, Józef [Faculty of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614 Poznań (Poland); Institute of Molecular Physics, Polish Academy of Sciences, ul. Smoluchowskiego 17, 60-179 Poznań (Poland)

    2016-08-15

    Dynamic properties of NiFe thin films on PMN-PT piezoelectric substrate are investigated using the spin-diode method. Ferromagnetic resonance (FMR) spectra of microstrips with varying width are measured as a function of magnetic field and frequency. The FMR frequency is shown to depend on the electric field applied across the substrate, which induces strain in the NiFe layer. Electric field tunability of up to 100 MHz per 1 kV/cm is achieved. An analytical model based on total energy minimization and the Landau-Lifshitz-Gilbert equation, taking into account the magnetostriction effect, is used to explain the measured dynamics. Based on this model, conditions for optimal electric-field tunable spin diode FMR in patterned NiFe/PMN-PT structures are derived.

  2. Microdeletions including FMR1 in three female patients with intellectual disability - further delineation of the phenotype and expression studies

    DEFF Research Database (Denmark)

    Zink, A M; Wohlleber, E; Engels, H

    2014-01-01

    Fragile X syndrome (FXS) is one of the most common causes of intellectual disability/developmental delay (ID/DD), especially in males. It is caused most often by CGG trinucleotide repeat expansions, and less frequently by point mutations and partial or full deletions of the FMR1 gene. The wide...... clinical spectrum of affected females partly depends on their X-inactivation status. Only few female ID/DD patients with microdeletions including FMR1 have been reported. We describe 3 female patients with 3.5-, 4.2- and 9.2-Mb de novo microdeletions in Xq27.3-q28 containing FMR1. X-inactivation was random...

  3. The effects of optimism, religion, and hope on mood and anxiety disorders in women with the FMR1 premutation.

    Science.gov (United States)

    Lowell, E P; Tonnsen, B L; Bailey, D B; Roberts, J E

    2017-10-01

    The FMR1 premutation, caused by a CGG trinucleotide repeat expansion on the FMR1 gene, has been identified as a genetic risk factor for mood and anxiety disorders. Building on recent studies identifying increased risk for mood and affective disorders in this population, we examined effects of potential protective factors (optimism, religion, hope) on depression and anxiety diagnoses in a prospective, longitudinal cohort. Eighty-three women with the FMR1 premutation participated in the Structured Clinical Interview for DSM-IV-TR Disorders at two-time points, 3 years apart. Participants also completed measures of optimism, religion, personal faith, hope, and child and family characteristics. We used logistic regression to examine correlates of major depressive disorder (MDD) and anxiety disorders at the initial assessment, as well as predictors of the diagnostic course over time. Lower optimism and higher religious participation relevant to fragile X syndrome at the initial assessment were associated with a lifetime history of MDD. Lower optimism also predicted the occurrence and reoccurrence of an anxiety disorder 3 years later. In women with the FMR1 premutation, elevated optimism may reduce the occurrence or severity of MDD and anxiety disorders. These findings underscore the importance of supporting mental health across the FMR1 spectrum of involvement. © 2017 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

  4. Repeat-mediated genetic and epigenetic changes at the FMR1 locus in the Fragile X-related disorders

    Science.gov (United States)

    Usdin, Karen; Hayward, Bruce E.; Kumari, Daman; Lokanga, Rachel A.; Sciascia, Nicholas; Zhao, Xiao-Nan

    2014-01-01

    The Fragile X-related disorders are a group of genetic conditions that include the neurodegenerative disorder, Fragile X-associated tremor/ataxia syndrome (FXTAS), the fertility disorder, Fragile X-associated primary ovarian insufficiency (FXPOI) and the intellectual disability, Fragile X syndrome (FXS). The pathology in all these diseases is related to the number of CGG/CCG-repeats in the 5′ UTR of the Fragile X mental retardation 1 (FMR1) gene. The repeats are prone to continuous expansion and the increase in repeat number has paradoxical effects on gene expression increasing transcription on mid-sized alleles and decreasing it on longer ones. In some cases the repeats can simultaneously both increase FMR1 mRNA production and decrease the levels of the FMR1 gene product, Fragile X mental retardation 1 protein (FMRP). Since FXTAS and FXPOI result from the deleterious consequences of the expression of elevated levels of FMR1 mRNA and FXS is caused by an FMRP deficiency, the clinical picture is turning out to be more complex than once appreciated. Added complications result from the fact that increasing repeat numbers make the alleles somatically unstable. Thus many individuals have a complex mixture of different sized alleles in different cells. Furthermore, it has become apparent that the eponymous fragile site, once thought to be no more than a useful diagnostic criterion, may have clinical consequences for females who inherit chromosomes that express this site. This review will cover what is currently known about the mechanisms responsible for repeat instability, for the repeat-mediated epigenetic changes that affect expression of the FMR1 gene, and for chromosome fragility. It will also touch on what current and future options are for ameliorating some of these effects. PMID:25101111

  5. ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing

    OpenAIRE

    Moncini, S.; Bedeschi, M.F.; Castronovo, P.; Crippa, M.; Calvello, M.; Garghentino, R.R.; Scuvera, G.; Finelli, P.; Venturin, M.

    2013-01-01

    In this report, we describe two adult brothers affected by moderate non-specific intellectual disability (ID). They showed minor facial anomalies, not clearly ascribable to any specific syndromic patterns, microcephaly, brachydactyly and broad toes. Both brothers presented seizures. Karyotype, subtelomeric and FMR1 analysis were normal in both cases. We performed array-CGH analysis that revealed no copy-number variations potentially associated with ID. Subsequent exome sequence analysis allow...

  6. Ferromagnetic resonance response of electron-beam patterned arrays of ferromagnetic nanoparticles

    Science.gov (United States)

    Jung, Sukkoo; Watkins, Byron; Feller, Jeffrey; Ketterson, John; Chandrasekhar, Venkat

    2001-03-01

    We report on the fabrication and the dynamic magnetic properties of periodic permalloy dot arrays. Electron-beam lithography and e-gun evaporation have been used to make the arrays with the aspect ratio of 2 (dot diameter : 40 nm, height : 80 nm) and periods of 100 - 200 nm. The magnetic properties of the arrays and their interactions have been investigated by ferromagnetic resonance (FMR), magnetic force microscopy (MFM), and SQUID magnetometry. The measured FMR data show that the position and magnitude of resonant absorption peaks strongly depend on the angle between magnetic field and the lattice structure. The results of dot arrays with various kinds of structural parameters will be presented. Supported by Army Research Office, DAAD19-99-1-0334/P001

  7. Inhibitors of Histone Deacetylases Are Weak Activators of the FMR1 Gene in Fragile X Syndrome Cell Lines

    Directory of Open Access Journals (Sweden)

    Alexander A. Dolskiy

    2017-01-01

    Full Text Available Fragile X syndrome is the most common cause of inherited intellectual disability in humans. It is a result of CGG repeat expansion in the 5′ untranslated region (5′ UTR of the FMR1 gene. This gene encodes the FMRP protein that is involved in neuronal development. Repeat expansion leads to heterochromatinization of the promoter, gene silencing, and the subsequent absence of FMRP. To date, there is no specific therapy for the syndrome. All treatments in clinic practice provide symptomatic therapy. The development of drug therapy for Fragile X syndrome treatment is connected with the search for inhibitors of enzymes that are responsible for heterochromatinization. Here, we report a weak transcriptional activity of the FMR1 gene and the absence of FMRP protein after Fragile X syndrome cell lines treatment with two FDA approved inhibitors of histone deacetylases, romidepsin and vorinostat. We demonstrate that romidepsin, an inhibitor of class I histone deacetylases, does not activate FMR1 expression in patient cell cultures, whereas vorinostat, an inhibitor of classes I and II histone deacetylases, activates a low level of FMR1 expression in some patient cell lines.

  8. Prenatal diagnosis of the fragile X syndrome : loss of mutation owing to a double recombinant or gene conversion event at the FMR1 locus

    NARCIS (Netherlands)

    Losekoot, M; Hoogendoorn, E; Olmer, R; Jansen, CCAM; Oosterwijk, JC; vandenOuweland, AMW; Halley, DJJ; Warren, ST; Willemsen, R; Oostra, BA; Bakker, E

    1997-01-01

    The fragile X syndrome, an X linked mental retardation syndrome, is caused by an expanded CGG repeat in the first exon of the FMR1 gene. In patients with an expanded repeat the FMR1 promoter is methylated and, consequently, the gene is silenced and no FMR1 protein (FMRP) is produced, thus leading to

  9. Social anxiety and autism spectrum traits among adult FMR1 premutation carriers.

    Science.gov (United States)

    López-Mourelo, O; Mur, E; Madrigal, I; Alvarez-Mora, M I; Gómez-Ansón, B; Pagonabarraga, J; Rodriguez-Revenga, L; Milà, M

    2017-01-01

    Behavioral symptoms and traits have been proposed as early markers in neurodegenerative diseases. The aim of this study was to evaluate social anxiety and autism in FMR1 premutation carriers using the Social Phobia Inventory (SPIN) and the Autism-Spectrum Quotient (AQ) questionnaires. Fifty-nine premutation carriers were compared with 50 controls. The SPIN test showed statistically significant differences between female but not male carriers. The AQ questionnaire found statistically significant differences between premutation carriers and controls in the total AQ as well as in the social skills and attention switching subdomains. A gender effect was only observed for the social skills subdomain. Spearman's correlation analysis revealed a moderately positive correlation with the total AQ scores as well as the social skills and communication subdomains. Our results show that fragile X-associated tremor/ataxia syndrome (FXTAS) patients have higher AQ scores. Moreover, this is the first study to find statistically significant differences between FXTAS and no-FXTAS premutation carriers in the communication and the imagination subdomains, suggesting that FXTAS patients present a broader autistic phenotype than premutation carriers without FXTAS. Based on our results, a wide range of behavioral/psychiatric traits should be included within the broader phenotypic presentation of individuals with the FMR1 premutation. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. The FMR1 gene and fragile X-associated tremor/ataxia syndrome

    NARCIS (Netherlands)

    J. Brouwer (Jaap); R.A. Willemsen (Ralph); B.A. Oostra (Ben)

    2009-01-01

    textabstractThe CGG-repeat present in the 5′UTR of the FMR1 gene is unstable upon transmission to the next generation. The repeat is up to 55 CGGs long in the normal population. In fragile X patients, a repeat length exceeding 200 CGGs (full mutation: FM) generally leads to methylation of the repeat

  11. Epigenetic characterization of the FMR1 gene and aberrant neurodevelopment in human induced pluripotent stem cell models of fragile X syndrome.

    Directory of Open Access Journals (Sweden)

    Steven D Sheridan

    Full Text Available Fragile X syndrome (FXS is the most common inherited cause of intellectual disability. In addition to cognitive deficits, FXS patients exhibit hyperactivity, attention deficits, social difficulties, anxiety, and other autistic-like behaviors. FXS is caused by an expanded CGG trinucleotide repeat in the 5' untranslated region of the Fragile X Mental Retardation (FMR1 gene leading to epigenetic silencing and loss of expression of the Fragile X Mental Retardation protein (FMRP. Despite the known relationship between FMR1 CGG repeat expansion and FMR1 silencing, the epigenetic modifications observed at the FMR1 locus, and the consequences of the loss of FMRP on human neurodevelopment and neuronal function remain poorly understood. To address these limitations, we report on the generation of induced pluripotent stem cell (iPSC lines from multiple patients with FXS and the characterization of their differentiation into post-mitotic neurons and glia. We show that clones from reprogrammed FXS patient fibroblast lines exhibit variation with respect to the predominant CGG-repeat length in the FMR1 gene. In two cases, iPSC clones contained predominant CGG-repeat lengths shorter than measured in corresponding input population of fibroblasts. In another instance, reprogramming a mosaic patient having both normal and pre-mutation length CGG repeats resulted in genetically matched iPSC clonal lines differing in FMR1 promoter CpG methylation and FMRP expression. Using this panel of patient-specific, FXS iPSC models, we demonstrate aberrant neuronal differentiation from FXS iPSCs that is directly correlated with epigenetic modification of the FMR1 gene and a loss of FMRP expression. Overall, these findings provide evidence for a key role for FMRP early in human neurodevelopment prior to synaptogenesis and have implications for modeling of FXS using iPSC technology. By revealing disease-associated cellular phenotypes in human neurons, these iPSC models will aid

  12. Depressed nNOS expression during spine transition in the developing hippocampus of FMR1 KO mice

    International Nuclear Information System (INIS)

    Xu, Qin; Zhu, Zhiwei; Xu, Jialu; Gu, Weizhong; Zhao, Zhengyan

    2012-01-01

    Nitric oxide (NO), synthesized as needed by NO synthase (NOS), is involved in spinogenesis and synaptogenesis. Immature spine morphology is characteristic of fragile X syndrome (FXS). The objective of this research was to investigate and compare changes of postnatal neuronal NOS (nNOS) expression in the hippocampus of male fragile X mental retardation 1 gene knockout mice (FMR1 KO mice, the animal model of FXS) and male wild-type mice (WT) at postnatal day 7 (P7), P14, P21, and P28. nNOS mRNA levels were analyzed by real-time quantitative PCR (N = 4-7) and nNOS protein was estimated by Western blot (N = 3) and immunohistochemistry (N = 1). In the PCR assessment, primers 5′-GTGGCCATCGTGTCCTACCATAC-3′ and 5′-GTTTCGAGGCAGGTGGAAGCTA-3′ were used for the detection of nNOS and primers 5′-CCGTTTCTCCTGGCTCAGTTTA-3′ and 5′-CCCCAATACCACATCATCCAT-3′ were used for the detection of β-actin. Compared to the WT group, nNOS mRNA expression was significantly decreased in FMR1 KO mice at P21 (KO: 0.2857 ± 0.0150, WT: 0.5646 ± 0.0657; P < 0.05). Consistently, nNOS immunoreactivity also revealed reduced staining intensity at P21 in the FMR1 KO group. Western blot analysis validated the immunostaining results by demonstrating a significant reduction in nNOS protein levels in the FMR1 KO group compared to the WT group at P21 (KO: 0.3015 ± 0.0897, WT: 1.7542 ± 0.5455; P < 0.05). These results suggest that nNOS was involved in the postnatal development of the hippocampus in FXS and impaired NO production may retard spine maturation in FXS

  13. Depressed nNOS expression during spine transition in the developing hippocampus of FMR1 KO mice

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Qin; Zhu, Zhiwei; Xu, Jialu [Department of Children' s Health Care, Children' s Hospital, Zhejiang University, Hangzhou Zhejiang (China); Gu, Weizhong [Department of Pathology, Children' s Hospital, Zhejiang University, Hangzhou Zhejiang (China); Zhao, Zhengyan [Department of Children' s Health Care, Children' s Hospital, Zhejiang University, Hangzhou Zhejiang (China)

    2012-10-05

    Nitric oxide (NO), synthesized as needed by NO synthase (NOS), is involved in spinogenesis and synaptogenesis. Immature spine morphology is characteristic of fragile X syndrome (FXS). The objective of this research was to investigate and compare changes of postnatal neuronal NOS (nNOS) expression in the hippocampus of male fragile X mental retardation 1 gene knockout mice (FMR1 KO mice, the animal model of FXS) and male wild-type mice (WT) at postnatal day 7 (P7), P14, P21, and P28. nNOS mRNA levels were analyzed by real-time quantitative PCR (N = 4-7) and nNOS protein was estimated by Western blot (N = 3) and immunohistochemistry (N = 1). In the PCR assessment, primers 5′-GTGGCCATCGTGTCCTACCATAC-3′ and 5′-GTTTCGAGGCAGGTGGAAGCTA-3′ were used for the detection of nNOS and primers 5′-CCGTTTCTCCTGGCTCAGTTTA-3′ and 5′-CCCCAATACCACATCATCCAT-3′ were used for the detection of β-actin. Compared to the WT group, nNOS mRNA expression was significantly decreased in FMR1 KO mice at P21 (KO: 0.2857 ± 0.0150, WT: 0.5646 ± 0.0657; P < 0.05). Consistently, nNOS immunoreactivity also revealed reduced staining intensity at P21 in the FMR1 KO group. Western blot analysis validated the immunostaining results by demonstrating a significant reduction in nNOS protein levels in the FMR1 KO group compared to the WT group at P21 (KO: 0.3015 ± 0.0897, WT: 1.7542 ± 0.5455; P < 0.05). These results suggest that nNOS was involved in the postnatal development of the hippocampus in FXS and impaired NO production may retard spine maturation in FXS.

  14. Depressed nNOS expression during spine transition in the developing hippocampus of FMR1 KO mice

    Directory of Open Access Journals (Sweden)

    Qin Xu

    2012-12-01

    Full Text Available Nitric oxide (NO, synthesized as needed by NO synthase (NOS, is involved in spinogenesis and synaptogenesis. Immature spine morphology is characteristic of fragile X syndrome (FXS. The objective of this research was to investigate and compare changes of postnatal neuronal NOS (nNOS expression in the hippocampus of male fragile X mental retardation 1 gene knockout mice (FMR1 KO mice, the animal model of FXS and male wild-type mice (WT at postnatal day 7 (P7, P14, P21, and P28. nNOS mRNA levels were analyzed by real-time quantitative PCR (N = 4-7 and nNOS protein was estimated by Western blot (N = 3 and immunohistochemistry (N = 1. In the PCR assessment, primers 5’-GTGGCCATCGTGTCCTACCATAC-3’ and 5’-GTTTCGAGGCAGGTGGAAGCTA-3’ were used for the detection of nNOS and primers 5’-CCGTTTCTCCTGGCTCAGTTTA-3’ and 5’-CCCCAATACCACATCATCCAT-3’ were used for the detection of β-actin. Compared to the WT group, nNOS mRNA expression was significantly decreased in FMR1 KO mice at P21 (KO: 0.2857 ± 0.0150, WT: 0.5646 ± 0.0657; P < 0.05. Consistently, nNOS immunoreactivity also revealed reduced staining intensity at P21 in the FMR1 KO group. Western blot analysis validated the immunostaining results by demonstrating a significant reduction in nNOS protein levels in the FMR1 KO group compared to the WT group at P21 (KO: 0.3015 ± 0.0897, WT: 1.7542 ± 0.5455; P < 0.05. These results suggest that nNOS was involved in the postnatal development of the hippocampus in FXS and impaired NO production may retard spine maturation in FXS.

  15. Repeat-mediated epigenetic dysregulation of the FMR1 gene in the fragile X-related disorders.

    Science.gov (United States)

    Usdin, Karen; Kumari, Daman

    2015-01-01

    The fragile X-related disorders are members of the Repeat Expansion Diseases, a group of genetic conditions resulting from an expansion in the size of a tandem repeat tract at a specific genetic locus. The repeat responsible for disease pathology in the fragile X-related disorders is CGG/CCG and the repeat tract is located in the 5' UTR of the FMR1 gene, whose protein product FMRP, is important for the proper translation of dendritic mRNAs in response to synaptic activation. There are two different pathological FMR1 allele classes that are distinguished only by the number of repeats. Premutation alleles have 55-200 repeats and confer risk of fragile X-associated tremor/ataxia syndrome and fragile X-associated primary ovarian insufficiency. Full mutation alleles on the other hand have >200 repeats and result in fragile X syndrome, a disorder that affects learning and behavior. Different symptoms are seen in carriers of premutation and full mutation alleles because the repeat number has paradoxical effects on gene expression: Epigenetic changes increase transcription from premutation alleles and decrease transcription from full mutation alleles. This review will cover what is currently known about the mechanisms responsible for these changes in FMR1 expression and how they may relate to other Repeat Expansion Diseases that also show repeat-mediated changes in gene expression.

  16. Fear-Specific Amygdala Function in Children and Adolescents on the Fragile X Spectrum: A Dosage Response of the FMR1 Gene

    Science.gov (United States)

    Kim, So-Yeon; Burris, Jessica; Bassal, Frederick; Koldewyn, Kami; Chattarji, Sumantra; Tassone, Flora; Hessl, David; Rivera, Susan M.

    2014-01-01

    Mutations of the fragile X mental retardation 1 (FMR1) gene are the genetic cause of fragile X syndrome (FXS). The presence of significant socioemotional problems has been well documented in FXS although the brain basis of those deficits remains unspecified. Here, we investigated amygdala dysfunction and its relation to socioemotional deficits and FMR1 gene expression in children and adolescents on the FX spectrum (i.e., individuals whose trinucleotide CGG repeat expansion from 55 to over 200 places them somewhere within the fragile X diagnostic range from premutation to full mutation). Participants performed an fMRI task in which they viewed fearful, happy, and scrambled faces. Neuroimaging results demonstrated that FX participants revealed significantly attenuated amygdala activation in Fearful > Scrambled and Fearful > Happy contrasts compared with their neurotypical counterparts, while showing no differences in amygdala volume. Furthermore, we found significant relationships between FMR1 gene expression, anxiety/social dysfunction scores, and reduced amygdala activation in the FX group. In conclusion, we report novel evidence regarding a dosage response of the FMR1 gene on fear-specific functions of the amygdala, which is associated with socioemotional deficits in FXS. PMID:23146966

  17. Hyperactivity and lack of social discrimination in the adolescent Fmr1 knockout mouse

    DEFF Research Database (Denmark)

    Sørensen, Emilie M; Bertelsen, Freja; Weikop, Pia

    2015-01-01

    . Monoamines were measured by HPLC: Fmr1 KO mice showed an increase in the striatal dopamine level. We conclude that the fragile X syndrome model seems to be useful for understanding certain aspects of ASD and may have translational interest for studies of social behaviour when hyperactivity coexists in ASD...

  18. The fragile x mental retardation syndrome 20 years after the FMR1 gene discovery: an expanding universe of knowledge.

    Science.gov (United States)

    Rousseau, François; Labelle, Yves; Bussières, Johanne; Lindsay, Carmen

    2011-08-01

    The fragile X mental retardation (FXMR) syndrome is one of the most frequent causes of mental retardation. Affected individuals display a wide range of additional characteristic features including behavioural and physical phenotypes, and the extent to which individuals are affected is highly variable. For these reasons, elucidation of the pathophysiology of this disease has been an important challenge to the scientific community. 1991 marks the year of the discovery of both the FMR1 gene mutations involved in this disease, and of their dynamic nature. Although a mouse model for the disease has been available for 16 years and extensive research has been performed on the FMR1 protein (FMRP), we still understand little about how the disease develops, and no treatment has yet been shown to be effective. In this review, we summarise current knowledge on FXMR with an emphasis on the technical challenges of molecular diagnostics, on its prevalence and dynamics among populations, and on the potential of screening for FMR1 mutations.

  19. The Fragile X Mental Retardation Syndrome 20 Years After the FMR1 Gene Discovery: an Expanding Universe of Knowledge

    Science.gov (United States)

    Rousseau, François; Labelle, Yves; Bussières, Johanne; Lindsay, Carmen

    2011-01-01

    The fragile X mental retardation (FXMR) syndrome is one of the most frequent causes of mental retardation. Affected individuals display a wide range of additional characteristic features including behavioural and physical phenotypes, and the extent to which individuals are affected is highly variable. For these reasons, elucidation of the pathophysiology of this disease has been an important challenge to the scientific community. 1991 marks the year of the discovery of both the FMR1 gene mutations involved in this disease, and of their dynamic nature. Although a mouse model for the disease has been available for 16 years and extensive research has been performed on the FMR1 protein (FMRP), we still understand little about how the disease develops, and no treatment has yet been shown to be effective. In this review, we summarise current knowledge on FXMR with an emphasis on the technical challenges of molecular diagnostics, on its prevalence and dynamics among populations, and on the potential of screening for FMR1 mutations. PMID:21912443

  20. Changes in expression of the long noncoding RNA FMR4 associate with altered gene expression during differentiation of human neural precursor cells

    Directory of Open Access Journals (Sweden)

    Veronica Julia Peschansky

    2015-08-01

    Full Text Available CGG repeat expansions in the Fragile X mental retardation 1 (FMR1 gene are responsible for a family of associated disorders characterized by either intellectual disability and autism (Fragile X Syndrome, FXS, or adult-onset neurodegeneration (Fragile X-associated Tremor/Ataxia Syndrome, FXTAS. However, the FMR1 locus is complex and encodes several long noncoding RNAs (lncRNAs, whose expression is altered by repeat expansion mutations.The role of these lncRNAs is thus far unknown; therefore we investigated the functionality of FMR4, which we previously identified. Full-length expansions of the FMR1 triplet repeat cause silencing of both FMR1 and FMR4, thus we are interested in potential loss-of-function that may add to phenotypic manifestation of FXS. Since the two transcripts do not exhibit cis-regulation of one another, we examined the potential for FMR4 to regulate target genes at distal genomic loci using gene expression microarrays. We identified FMR4-responsive genes, including the methyl-CpG-binding domain protein 4 (MBD4. Furthermore, we found that in differentiating human neural precursor cells (hNPCs, FMR4 expression is developmentally regulated in opposition to expression of both FMR1 (which is expected to share a bidirectional promoter with FMR4 and MBD4.We therefore propose that FMR4’s function is as a gene-regulatory lncRNA and that this transcript may function in normal development. Closer examination of FMR4 increases our understanding of the role of regulatory lncRNA and the consequences of FMR1 repeat expansions.

  1. Distribution of the FMR1 gene in females by race/ethnicity: women with diminished ovarian reserve versus women with normal fertility (SWAN study).

    Science.gov (United States)

    Pastore, Lisa M; Young, Steven L; Manichaikul, Ani; Baker, Valerie L; Wang, Xin Q; Finkelstein, Joel S

    2017-01-01

    To study whether reported, but inconsistent, associations between the FMR1 CGG repeat lengths in the intermediate, high normal, or low normal range differentiate women diagnosed with diminished ovarian reserve (DOR) from population controls and whether associations vary by race/ethnic group. Case-control study. Academic and private fertility clinics. DOR cases (n = 129; 95 Whites, 22 Asian, 12 other) from five U.S. fertility clinics were clinically diagnosed, with regular menses and no fragile X syndrome family history. Normal fertility controls (n = 803; 386 Whites, 219 African-Americans, 102 Japanese, 96 Chinese) from the United States-based SWAN Study had one or more menstrual period in the 3 months pre-enrollment, one or more pregnancy, no history of infertility or hormone therapy, and menopause ≥46 years. Previously, the SWAN Chinese and Japanese groups had similar FMR1 CGG repeat lengths, thus they were combined. None. FMR1 CGG repeat lengths. Median CGG repeats were nearly identical by case/control group. DOR cases had fewer CGG repeats in the shorter FMR1 allele than controls among Whites, but this was not significant among Asians. White cases had fewer CGG repeats in the shorter allele than Asian cases. No significant differences were found in the high normal/intermediate range between cases and controls or by race/ethnic group within cases in the longer allele. This study refutes prior reports of an association between DOR and high normal/intermediate repeats and confirms an association between DOR and low normal repeats in Whites. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  2. The RNA-binding proteins FMR1, rasputin and caprin act together with the UBA protein lingerer to restrict tissue growth in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Roland Baumgartner

    Full Text Available Appropriate expression of growth-regulatory genes is essential to ensure normal animal development and to prevent diseases like cancer. Gene regulation at the levels of transcription and translational initiation mediated by the Hippo and Insulin signaling pathways and by the TORC1 complex, respectively, has been well documented. Whether translational control mediated by RNA-binding proteins contributes to the regulation of cellular growth is less clear. Here, we identify Lingerer (Lig, an UBA domain-containing protein, as growth suppressor that associates with the RNA-binding proteins Fragile X mental retardation protein 1 (FMR1 and Caprin (Capr and directly interacts with and regulates the RNA-binding protein Rasputin (Rin in Drosophila melanogaster. lig mutant organs overgrow due to increased proliferation, and a reporter for the JAK/STAT signaling pathway is upregulated in a lig mutant situation. rin, Capr or FMR1 in combination as double mutants, but not the respective single mutants, display lig like phenotypes, implicating a redundant function of Rin, Capr and FMR1 in growth control in epithelial tissues. Thus, Lig regulates cell proliferation during development in concert with Rin, Capr and FMR1.

  3. The RNA-binding proteins FMR1, rasputin and caprin act together with the UBA protein lingerer to restrict tissue growth in Drosophila melanogaster.

    Science.gov (United States)

    Baumgartner, Roland; Stocker, Hugo; Hafen, Ernst

    2013-01-01

    Appropriate expression of growth-regulatory genes is essential to ensure normal animal development and to prevent diseases like cancer. Gene regulation at the levels of transcription and translational initiation mediated by the Hippo and Insulin signaling pathways and by the TORC1 complex, respectively, has been well documented. Whether translational control mediated by RNA-binding proteins contributes to the regulation of cellular growth is less clear. Here, we identify Lingerer (Lig), an UBA domain-containing protein, as growth suppressor that associates with the RNA-binding proteins Fragile X mental retardation protein 1 (FMR1) and Caprin (Capr) and directly interacts with and regulates the RNA-binding protein Rasputin (Rin) in Drosophila melanogaster. lig mutant organs overgrow due to increased proliferation, and a reporter for the JAK/STAT signaling pathway is upregulated in a lig mutant situation. rin, Capr or FMR1 in combination as double mutants, but not the respective single mutants, display lig like phenotypes, implicating a redundant function of Rin, Capr and FMR1 in growth control in epithelial tissues. Thus, Lig regulates cell proliferation during development in concert with Rin, Capr and FMR1.

  4. Delineation of the working memory profile in female FMR1 premutation carriers: the effect of cognitive load on ocular motor responses.

    Science.gov (United States)

    Shelton, Annie L; Cornish, Kim M; Godler, David E; Clough, Meaghan; Kraan, Claudine; Bui, Minh; Fielding, Joanne

    2015-04-01

    Fragile X mental retardation 1 (FMR1) premutation carriers (PM-carriers) are characterised as having mid-sized expansions of between 55 and 200 CGG repeats in the 5' untranslated region of the FMR1 gene. While there is evidence of executive dysfunction in PM-carriers, few studies have explicitly explored working memory capabilities in female PM-carriers. 14 female PM-carriers and 13 age- and IQ-matched healthy controls completed an ocular motor n-back working memory paradigm. This task examined working memory ability and the effect of measured increases in cognitive load. Female PM-carriers were found to have attenuated working memory capabilities. Increasing the cognitive load did not elicit the expected reciprocal increase in the task errors for female PM-carriers, as it did in controls. However female PM-carriers took longer to respond than controls, regardless of the cognitive load. Further, FMR1 mRNA levels were found to significantly predict PM-carrier response time. Although preliminary, these findings provide further evidence of executive dysfunction, specifically disruption to working memory processes, which were found to be associated with increases in FMR1 mRNA expression in female PM-carriers. With future validation, ocular motor paradigms such as the n-back paradigm will be critical to the development of behavioural biomarkers for identification of PM-carrier cognitive-affective phenotypes. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. FMR1 CGG repeat expansion mutation detection and linked haplotype analysis for reliable and accurate preimplantation genetic diagnosis of fragile X syndrome.

    Science.gov (United States)

    Rajan-Babu, Indhu-Shree; Lian, Mulias; Cheah, Felicia S H; Chen, Min; Tan, Arnold S C; Prasath, Ethiraj B; Loh, Seong Feei; Chong, Samuel S

    2017-07-19

    Fragile X mental retardation 1 (FMR1) full-mutation expansion causes fragile X syndrome. Trans-generational fragile X syndrome transmission can be avoided by preimplantation genetic diagnosis (PGD). We describe a robust PGD strategy that can be applied to virtually any couple at risk of transmitting fragile X syndrome. This novel strategy utilises whole-genome amplification, followed by triplet-primed polymerase chain reaction (TP-PCR) for robust detection of expanded FMR1 alleles, in parallel with linked multi-marker haplotype analysis of 13 highly polymorphic microsatellite markers located within 1 Mb of the FMR1 CGG repeat, and the AMELX/Y dimorphism for gender identification. The assay was optimised and validated on single lymphoblasts isolated from fragile X reference cell lines, and applied to a simulated PGD case and a clinical in vitro fertilisation (IVF)-PGD case. In the simulated PGD case, definitive diagnosis of the expected results was achieved for all 'embryos'. In the clinical IVF-PGD case, delivery of a healthy baby girl was achieved after transfer of an expansion-negative blastocyst. FMR1 TP-PCR reliably detects presence of expansion mutations and obviates reliance on informative normal alleles for determining expansion status in female embryos. Together with multi-marker haplotyping and gender determination, misdiagnosis and diagnostic ambiguity due to allele dropout is minimised, and couple-specific assay customisation can be avoided.

  6. Detecting bacterial magnetite in sediments: strengths and limitations of FMR spectroscopy

    Science.gov (United States)

    Winklhofer, M.

    2012-04-01

    Ferromagnetic resonance spectroscopy (FMR) is increasingly being used as a diagnostic tool for identifying bacterial magnetite in sediments [e.g., Kopp et al. 2007; Kind et al. 2011, Roberts et al. 2011 ], the reason being that magnetic bacteria have a characteristic FMR fingerprint which is not known from inorganic geological samples [Kopp & Kirschvink, 2008]. The diagnostic FMR features of single-stranded magnetite chains are a g-value 2, quite opposite to what we know from single-stranded chains. Therefore, in order to better understand possible biogenic FMR fingerprints and to refine the screen, there is a clear need to acquire FMR spectra of magnetic bacteria with different chain configurations and, in particular, of greigite producing bacteria.

  7. Pragmatic Language Features of Mothers with the "FMR1" Premutation Are Associated with the Language Outcomes of Adolescents and Young Adults with Fragile X Syndrome

    Science.gov (United States)

    Klusek, Jessica; McGrath, Sara E.; Abbeduto, Leonard; Roberts, Jane E.

    2016-01-01

    Purpose: Pragmatic language difficulties have been documented as part of the FMR1 premutation phenotype, yet the interplay between these features in mothers and the language outcomes of their children with fragile X syndrome is unknown. This study aimed to determine whether pragmatic language difficulties in mothers with the "FMR1"…

  8. Impacts of yttrium substitution on FMR line-width and magnetic properties of nickel spinel ferrites

    Energy Technology Data Exchange (ETDEWEB)

    Ishaque, M., E-mail: ishaqdgk1@gmail.com [Department of Physics, Bahauddin Zakariya University, Multan 60800 (Pakistan); Khan, Muhammad Azhar, E-mail: azhar.khan@iub.edu.pk [Department of Physics, The Islamia University of Bahawalpur, Bahawalpur 63100 (Pakistan); Ali, Irshad; Khan, Hasan M. [Department of Physics, Bahauddin Zakariya University, Multan 60800 (Pakistan); Iqbal, M. Asif [Department of Physics, Bahauddin Zakariya University, Multan 60800 (Pakistan); College of E & ME, National University of Science and Technology, Islamabad (Pakistan); Islam, M.U. [Department of Physics, Bahauddin Zakariya University, Multan 60800 (Pakistan); Warsi, Muhammad Farooq [Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur 63100 (Pakistan)

    2015-05-15

    The influence of yttrium (Y) substitution on ferromagnetic resonance (FMR), initial permeability, and magnetic properties of NiFe{sub 2}O{sub 4} ferrites were investigated. It was observed that the FMR line-width decreases with yttrium contents for the substitution level 0≤×≤0.06. Beyond this, the FMR line-width increases with yttrium contents. The nominal composition NiY{sub 0.12}Fe{sub 1.88}O{sub 4} exhibited the smallest FMR line-width ~282 Oe. A significant change in FMR position of nickel–yttrium (Ni–Y) ferrites was observed and it found to exist between 4150 and 4600 Oe. The saturation magnetization was observed to decrease with the increase of yttrium contents and this was referred to the redistribution of cations on octahedral. The coercivity increased from 15 Oe to 59 Oe by increasing the yttrium concentration. The initial permeability decreased from 110 to 35 at 1 MHz by the incorporation of yttrium and this was attributed to the smaller grains which may obstruct the domain wall movement and impede the domain wall motion. The magnetic loss factors of substituted samples exhibit decreasing behavior in the frequency range 1 kHz to 10 MHz. The smaller FMR line-width and reduced magnetic loss factor of the investigated samples suggest the possible use of these materials in high frequency applications. - Highlights: • Influence of Y{sup 3+} substitution on the properties of nickel ferrites is investigated. • Very small FMR line-width (282 Oe) is exhibited by these substituted ferrites. • Fourfold increase in coercivity was observed for NiY{sub 0.24}Fe{sub 1.76}O{sub 4} ferrites.

  9. 76 FR 6792 - Federal Management Regulation; FMR Bulletin PBS-2011-B1; Redesignations of Federal Buildings

    Science.gov (United States)

    2011-02-08

    ... Management Regulation; FMR Bulletin PBS-2011-B1; Redesignations of Federal Buildings AGENCY: Public Buildings... announces the redesignations of three Federal buildings. DATES: Expiration Date: This bulletin announcement expires June 30, 2011. The building redesignations remain in effect until canceled or superseded by...

  10. Reversal of fragile X phenotypes by manipulation of AβPP/Aβ levels in Fmr1KO mice.

    Directory of Open Access Journals (Sweden)

    Cara J Westmark

    Full Text Available Fragile X syndrome (FXS is the most common form of inherited intellectual disability and the leading known genetic cause of autism. Fragile X mental retardation protein (FMRP, which is absent or expressed at substantially reduced levels in FXS, binds to and controls the postsynaptic translation of amyloid β-protein precursor (AβPP mRNA. Cleavage of AβPP can produce β-amyloid (Aβ, a 39-43 amino acid peptide mis-expressed in Alzheimer's disease (AD and Down syndrome (DS. Aβ is over-expressed in the brain of Fmr1(KO mice, suggesting a pathogenic role in FXS. To determine if genetic reduction of AβPP/Aβ rescues characteristic FXS phenotypes, we assessed audiogenic seizures (AGS, anxiety, the ratio of mature versus immature dendritic spines and metabotropic glutamate receptor (mGluR-mediated long-term depression (LTD in Fmr1(KO mice after removal of one App allele. All of these phenotypes were partially or completely reverted to normal. Plasma Aβ(1-42 was significantly reduced in full-mutation FXS males compared to age-matched controls while cortical and hippocampal levels were somewhat increased, suggesting that Aβ is sequestered in the brain. Evolving therapies directed at reducing Aβ in AD may be applicable to FXS and Aβ may serve as a plasma-based biomarker to facilitate disease diagnosis or assess therapeutic efficacy.

  11. Development of Genetic Testing for Fragile X Syndrome and Associated Disorders, and Estimates of the Prevalence of FMR1 Expansion Mutations

    Directory of Open Access Journals (Sweden)

    James N. Macpherson

    2016-11-01

    Full Text Available The identification of a trinucleotide (CGG expansion as the chief mechanism of mutation in Fragile X syndrome in 1991 heralded a new chapter in molecular diagnostic genetics and generated a new perspective on mutational mechanisms in human genetic disease, which rapidly became a central paradigm (“dynamic mutation” as more and more of the common hereditary neurodevelopmental disorders were ascribed to this novel class of mutation. The progressive expansion of a CGG repeat in the FMR1 gene from “premutation” to “full mutation” provided an explanation for the “Sherman paradox,” just as similar expansion mechanisms in other genes explained the phenomenon of “anticipation” in their pathogenesis. Later, FMR1 premutations were unexpectedly found associated with two other distinct phenotypes: primary ovarian insufficiency and tremor-ataxia syndrome. This review will provide a historical perspective on procedures for testing and reporting of Fragile X syndrome and associated disorders, and the population genetics of FMR1 expansions, including estimates of prevalence and the influence of AGG interspersions on the rate and probability of expansion.

  12. An integrated multiple capillary array electrophoresis system for high-throughput DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Lu, X.

    1998-03-27

    A capillary array electrophoresis system was chosen to perform DNA sequencing because of several advantages such as rapid heat dissipation, multiplexing capabilities, gel matrix filling simplicity, and the mature nature of the associated manufacturing technologies. There are two major concerns for the multiple capillary systems. One concern is inter-capillary cross-talk, and the other concern is excitation and detection efficiency. Cross-talk is eliminated through proper optical coupling, good focusing and immersing capillary array into index matching fluid. A side-entry excitation scheme with orthogonal detection was established for large capillary array. Two 100 capillary array formats were used for DNA sequencing. One format is cylindrical capillary with 150 {micro}m o.d., 75 {micro}m i.d and the other format is square capillary with 300 {micro}m out edge and 75 {micro}m inner edge. This project is focused on the development of excitation and detection of DNA as well as performing DNA sequencing. The DNA injection schemes are discussed for the cases of single and bundled capillaries. An individual sampling device was designed. The base-calling was performed for a capillary from the capillary array with the accuracy of 98%.

  13. Magnetic characterization by SQUID and FMR of a biocompatible ferrofluid based on Fe3O4

    International Nuclear Information System (INIS)

    Gamarra, L F; Amaro Jr, E; Pontuschka, W M; Mamani, J B; Cornejo, D R; Oliveira, T R; Vieira, E D; Costa-Filho, A J

    2009-01-01

    Biocompatible superparamagnetic iron oxide nanoparticles of magnetite coated with dextran were magnetically characterized using the techniques of SQUID (superconducting quantum interference device) magnetometry and ferromagnetic resonance (FMR). The SQUID magnetometry characterization was performed by isothermal measurements under applied magnetic field using the methods of zero-field-cooling (ZFC) and field-cooling (FC). The magnetic behavior of the nanoparticles indicated their superparamagnetic nature and it was assumed that they consisted exclusively of monodomains. The transition to a blocked state was observed at the temperature T B = (43 ± 1) K for frozen ferrofluid and at (52 ± 1) K for the lyophilized ferrofluid samples. The FMR analysis showed that the derivative peak-to-peak linewidth (ΔH PP ), gyromagnetic factor (g), number of spins (N S ), and spin-spin relaxation time (T 2 ) were strongly dependent on both temperature and super-exchange interaction. This information is important for possible nanotechnological applications, mainly those which are strongly dependent on the magnetic parameters.

  14. A Special Extract of Bacopa monnieri (CDRI-08-Restored Memory in CoCl2-Hypoxia Mimetic Mice Is Associated with Upregulation of Fmr-1 Gene Expression in Hippocampus

    Directory of Open Access Journals (Sweden)

    Anupama Rani

    2015-01-01

    Full Text Available Fragile X mental retardation protein (FMRP is a neuronal translational repressor and has been implicated in learning, memory, and cognition. However, the role of Bacopa monnieri extract (CDRI-08 in enhancing cognitive abilities in hypoxia-induced memory impairment via Fmr-1 gene expression is not known. Here, we have studied effects of CDRI-08 on the expression of Fmr-1 gene in the hippocampus of well validated cobalt chloride (CoCl2-induced hypoxia mimetic mice and analyzed the data with alterations in spatial memory. Results obtained from Morris water maze test suggest that CoCl2 treatment causes severe loss of spatial memory and CDRI-08 is capable of reversing it towards that in the normal control mice. Our semiquantitative RT-PCR, Western blot, and immunofluorescence microscopic data reveal that CoCl2-induced hypoxia significantly upregulates the expression of Hif-1α and downregulates the Fmr-1 expression in the hippocampus, respectively. Further, CDRI-08 administration reverses the memory loss and this is correlated with significant downregulation of Hif-1α and upregulation of Fmr-1 expression. Our data are novel and may provide mechanisms of hypoxia-induced impairments in the spatial memory and action of CDRI-08 in the recovery of hypoxia led memory impairment involving Fmr-1 gene encoded protein called FMRP.

  15. The fragile X syndrome: Isolation of the FMR-1 gene and characterization of the fragile X mutation

    NARCIS (Netherlands)

    B.A. Oostra (Ben); A. Verkerk

    1992-01-01

    markdownabstractConclusion Rapid progress has been made in the analysis of the fragile X syndrome during 1991. Different groups have discovered that fragile X chromosomes are preferentially methylated. In these X chromosomes an insertion has been found in the methylated region. The FMR-1 gene,

  16. High Throughput Sample Preparation and Analysis for DNA Sequencing, PCR and Combinatorial Screening of Catalysis Based on Capillary Array Technique

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yonghua [Iowa State Univ., Ames, IA (United States)

    2000-01-01

    Sample preparation has been one of the major bottlenecks for many high throughput analyses. The purpose of this research was to develop new sample preparation and integration approach for DNA sequencing, PCR based DNA analysis and combinatorial screening of homogeneous catalysis based on multiplexed capillary electrophoresis with laser induced fluorescence or imaging UV absorption detection. The author first introduced a method to integrate the front-end tasks to DNA capillary-array sequencers. protocols for directly sequencing the plasmids from a single bacterial colony in fused-silica capillaries were developed. After the colony was picked, lysis was accomplished in situ in the plastic sample tube using either a thermocycler or heating block. Upon heating, the plasmids were released while chromsomal DNA and membrane proteins were denatured and precipitated to the bottom of the tube. After adding enzyme and Sanger reagents, the resulting solution was aspirated into the reaction capillaries by a syringe pump, and cycle sequencing was initiated. No deleterious effect upon the reaction efficiency, the on-line purification system, or the capillary electrophoresis separation was observed, even though the crude lysate was used as the template. Multiplexed on-line DNA sequencing data from 8 parallel channels allowed base calling up to 620 bp with an accuracy of 98%. The entire system can be automatically regenerated for repeated operation. For PCR based DNA analysis, they demonstrated that capillary electrophoresis with UV detection can be used for DNA analysis starting from clinical sample without purification. After PCR reaction using cheek cell, blood or HIV-1 gag DNA, the reaction mixtures was injected into the capillary either on-line or off-line by base stacking. The protocol was also applied to capillary array electrophoresis. The use of cheaper detection, and the elimination of purification of DNA sample before or after PCR reaction, will make this approach an

  17. Nonlinear FMR spectra in yttrium iron garnet

    Directory of Open Access Journals (Sweden)

    Yu.M. Bunkov, P.M. Vetoshko, I.G. Motygullin, T.R. Safin, M.S. Tagirov, N.A. Tukmakova

    2015-12-01

    Full Text Available Results of demagnetizing effect studies in yttrium iron garnet Y3Fe5O12 thin films are reported. Experiments were performed on X-Band of electron paramagnetic resonance spectrometer at room temperature. The ferromagnetic resonance (FMR spectra were obtained for one-layer single crystal YIG films for different values of the applied microwave power. Nonlinear FMR spectra transformation by the microwave power increasing in various directions of magnetic field sweep was observed. It is explained by the influence of the demagnetization action of nonequilibrium magnons.

  18. Array-based techniques for fingerprinting medicinal herbs

    Directory of Open Access Journals (Sweden)

    Xue Charlie

    2011-05-01

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

  19. The history of magnetization process influence on FMR response of particle systems

    International Nuclear Information System (INIS)

    Dumitru, Ioan; Stancu, Alexandru

    2007-01-01

    In order to express the history of magnetization process dependence on ferromagnetic resonance (FMR) for a particle system we use a statistical model based on the Preisach model. The precedent magnetization processes define in Preisach plane a configuration of particle magnetization orientations. The particles are considered single domain and saturated and are modeled as Stoner-Wohlfarth particles. The FMR response of the system is computed by summarizing the individual dynamic susceptibility of the particles, keeping account of the initial directions of the particle magnetizations. The FMR spectra of the particle system is determined considering three initial magnetization states: the demagnetized state, the positive saturated state in which all the particles have the magnetization in the static field direction and the negative saturated state when all the particles have the magnetization in the opposite field direction. The static field dependence of the resonance frequency and linewidth are determined as functions of the initial magnetization states

  20. Compact field programmable gate array-based pulse-sequencer and radio-frequency generator for experiments with trapped atoms

    Energy Technology Data Exchange (ETDEWEB)

    Pruttivarasin, Thaned, E-mail: thaned.pruttivarasin@riken.jp [Quantum Metrology Laboratory, RIKEN, Wako-shi, Saitama 351-0198 (Japan); Katori, Hidetoshi [Quantum Metrology Laboratory, RIKEN, Wako-shi, Saitama 351-0198 (Japan); Innovative Space-Time Project, ERATO, JST, Bunkyo-ku, Tokyo 113-8656 (Japan); Department of Applied Physics, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656 (Japan)

    2015-11-15

    We present a compact field-programmable gate array (FPGA) based pulse sequencer and radio-frequency (RF) generator suitable for experiments with cold trapped ions and atoms. The unit is capable of outputting a pulse sequence with at least 32 transistor-transistor logic (TTL) channels with a timing resolution of 40 ns and contains a built-in 100 MHz frequency counter for counting electrical pulses from a photo-multiplier tube. There are 16 independent direct-digital-synthesizers RF sources with fast (rise-time of ∼60 ns) amplitude switching and sub-mHz frequency tuning from 0 to 800 MHz.

  1. A fully automated 384 capillary array for DNA sequencer. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Li, Qingbo; Kane, T

    2003-03-20

    Phase I SpectruMedix has successfully developed an automatic 96-capillary array DNA prototype based on the multiplexed capillary electrophoresis system originated from Ames Laboratory-USDOE, Iowa State University. With computer control of all steps involved in a 96-capillary array running cycle, the prototype instrument (the SCE9600) is now capable of sequencing 450 base pairs (bp) per capillary, or 48,000 bp per instrument run within 2 hrs. Phase II of this grant involved the advancement of the core 96 capillary technologies, as well as designing a high density 384 capillary prototype. True commercialization of the 96 capillary instrument involved finalization of the gel matrix, streamlining the instrument hardware, creating a more reliable capillary cartridge, and further advancement of the data processing software. Together these silos of technology create a truly commercializable product (the SCE9610) capable of meeting the operation needs of the sequencing centers.

  2. 41 CFR 102-2.30 - Where and in what formats is the FMR published?

    Science.gov (United States)

    2010-07-01

    ... formats is the FMR published? 102-2.30 Section 102-2.30 Public Contracts and Property Management Federal... published? Proposed rules are published in the Federal Register. FMR bulletins are published in looseleaf format. FMR interim and final rules are published in the following formats— (a) Federal Register under...

  3. Validation of a screening tool for the rapid and reliable detection of CGG trinucleotide repeat expansions in FMR1.

    Science.gov (United States)

    Basehore, Monica J; Marlowe, Natalia M; Jones, Julie R; Behlendorf, Deborah E; Laver, Thomas A; Friez, Michael J

    2012-06-01

    Most individuals with intellectual disability and/or autism are tested for Fragile X syndrome at some point in their lifetime. Greater than 99% of individuals with Fragile X have an expanded CGG trinucleotide repeat motif in the promoter region of the FMR1 gene, and diagnostic testing involves determining the size of the CGG repeat as well as methylation status when an expansion is present. Using a previously described triplet repeat-primed polymerase chain reaction, we have performed additional validation studies using two cohorts with previous diagnostic testing results available for comparison purposes. The first cohort (n=88) consisted of both males and females and had a high percentage of abnormal samples, while the second cohort (n=624) consisted of only females and was not enriched for expansion mutations. Data from each cohort were completely concordant with the results previously obtained during the course of diagnostic testing. This study further demonstrates the utility of using laboratory-developed triplet repeat-primed FMR1 testing in a clinical setting.

  4. 78 FR 49994 - Federal Management Regulation (FMR); Obligating Authority

    Science.gov (United States)

    2013-08-16

    ... Party Logistics (3PL) is an entity that provides multiple logistics services for use by customers. Among... Logistics (3PL) or Transportation Service Provider (TSP), issue bills of lading, and otherwise perform the... GENERAL SERVICES ADMINISTRATION 41 CFR Part 102-117 [FMR Case 2013-102-1; Docket 2013-0009...

  5. Modelamiento de Fluidos Magnetoreológicos (FMR Producidos con Magnetita Mineral

    Directory of Open Access Journals (Sweden)

    Claudia Molina

    2015-07-01

    Full Text Available Esta investigación establece la correlación entre los resultados del cambio de densidad de un FMR, expuesto a un campo magnético de intensidad variable, con los resultados de la simulación del sistema por elementos finitos, en ANSYS. A nivel de laboratorio se prepararon doce muestras de FMR, con: magnetita mineral como material magnético molida a 325, 400 y 500 mallas; aceites 20W30 y 20W50 como fluidos de transporte y, aditivos antigravitacionales y antiaglomerantes. Con el FMR de mayor estabilidad fisicoquímica (baja reactividad y sedimentación, se realizaron pruebas de variación de la densidad, en función de la intensidad de un campo magnético. La correlación de los resultados de las pruebas de laboratorio con los resultados de la simulación, fue de 0.92, lo cual indica que la predicción del comportamiento de la densidad del FMR, en presencia de un campo magnético de intensidad variable, es un procedimiento confiable.

  6. Early Retinal Defects in Fmr1-/y Mice: Toward a Critical Role of Visual Dys-Sensitivity in the Fragile X Syndrome Phenotype?

    Science.gov (United States)

    Perche, Olivier; Felgerolle, Chloé; Ardourel, Maryvonne; Bazinet, Audrey; Pâris, Arnaud; Rossignol, Rafaëlle; Meyer-Dilhet, Géraldine; Mausset-Bonnefont, Anne-Laure; Hébert, Betty; Laurenceau, David; Montécot-Dubourg, Céline; Menuet, Arnaud; Bizot, Jean-Charles; Pichon, Jacques; Ranchon-Cole, Isabelle; Briault, Sylvain

    2018-01-01

    Fragile X Syndrome (FXS) is caused by a deficiency in Fragile X Mental Retardation Protein (FMRP) leading to global sensorial abnormalities, among which visual defects represent a critical part. These visual defects are associated with cerebral neuron immaturity especially in the primary visual cortex. However, we recently demonstrated that retinas of adult Fmr1 -/y mice, the FXS murine model, present molecular, cellular and functional alterations. However, no data are currently available on the evolution pattern of such defects. As retinal stimulation through Eye Opening (EO) is a crucial signal for the cerebral visual system maturation, we questioned the precocity of molecular and functional retinal phenotype. To answer this question, we studied the retinal molecular phenotype of Fmr1 -/y mice before EO until adult age and the consequences of the retinal loss of Fmrp on retinal function in young and adult mice. We showed that retinal molecular defects are present before EO and remain stable at adult age, leading to electrophysiological impairments without any underlying structural changes. We underlined that loss of Fmrp leads to a wide range of defects in the retina, settled even before EO. Our work demonstrates a critical role of the sensorial dysfunction in the Fmr1 -/y mice overall phenotype, and provides evidence that altered peripheral perception is a component of the sensory processing defect in FXS conditions.

  7. Age- and region-specific imbalances of basal amino acids and monoamine metabolism in limbic regions of female Fmr1 knock-out mice.

    Science.gov (United States)

    Gruss, Michael; Braun, Katharina

    2004-07-01

    The Fragile X syndrome, a common form of mental retardation in humans, originates from the loss of expression of the Fragile X mental retardation gene leading to the absence of the encoded Fragile X mental retardation protein 1 (FMRP). A broad pattern of morphological and behavioral abnormalities is well described for affected humans as well as Fmr1 knock-out mice, a transgenic animal model for the human Fragile X syndrome. In the present study, we examined neurochemical differences between female Fmr1 knock-out and wildtype mice with particular focus on neurotransmission. Significant age- and region-specific differences of basal tissue neurotransmitter and metabolite levels measured by high performance liquid chromatography were found. Those differences were more numerous in juvenile animals (postnatal day (PND) 28-31) compared to adults (postnatal day 209-221). In juvenile female knock-out mice, especially aspartate and taurine were increased in cortical regions, striatum, cerebellum, and brainstem. Furthermore, compared to the wildtype animals, the juvenile knock-out mice displayed an increased level of neuronal inhibition in the hippocampus and brainstem reflected by decreased ratios of (aspartate + glutamate)/(taurine + GABA), as well as an increased dopamine (DA) turnover in cortical regions, striatum, and hippocampus. These results provide the first evidence that the lack of FMRP expression in female Fmr1 knock-out mice is accompanied by age-dependent, region-specific alterations in brain amino acids, and monoamine turnover, which might be related to the reported synaptical and behavioural alterations in these animals.

  8. Health Profiles of Mosaic Versus Non-mosaic FMR1 Premutation Carrier Mothers of Children With Fragile X Syndrome

    Directory of Open Access Journals (Sweden)

    Marsha R. Mailick

    2018-05-01

    Full Text Available The FMR1 premutation is of increasing interest to the FXS community, as questions about a primary premutation phenotype warrant research attention. 100 FMR1 premutation carrier mothers (mean age = 58; 67–138 CGG repeats of adults with fragile X syndrome were studied with respect to their physical and mental health, motor, and neurocognitive characteristics. We explored the correlates of CGG repeat mosaicism in women with expanded alleles. Mothers provided buccal swabs from which DNA was extracted and the FMR1 CGG genotyping was performed (Amplidex Kit, Asuragen. Mothers were categorized into three groups: Group 1: premutation non-mosaic (n = 45; Group 2: premutation mosaic (n = 41, and Group 3: premutation/full mutation mosaic (n = 14. Group 2 mothers had at least two populations of cells with different allele sizes in the premutation range besides their major expanded allele. Group 3 mothers had a very small population of cells in the full mutation range (>200 CGGs in addition to one or multiple populations of cells with different allele sizes in the premutation range. Machine learning (random forest was used to identify symptoms and conditions that correctly classified mothers with respect to mosaicism; follow-up comparisons were made to characterize the three groups. In categorizing mosaicism, the random forest yielded significantly better classification than random classification, with overall area under the receiver operating characteristic curve (AUROC of 0.737. Among the most important symptoms and conditions that contributed to the classification were anxiety, menopause symptoms, executive functioning limitations, and difficulty walking several blocks, with the women who had full mutation mosaicism (Group 3 unexpectedly having better health. Although only 14 premutation carrier mothers in the present sample also had a small population of full mutation cells, their profile of comparatively better health, mental health, and executive

  9. CoCr/NiFe double layers studied by FMR and VSM

    NARCIS (Netherlands)

    Stam, M.T.H.C.W.; Gerritsma, G.J.; Lodder, J.C.; Popma, T.J.A.

    1987-01-01

    CoCr/NiFe double layers were investigated by FMR and VSM. The FMR linewidth of NiFe of the double layer is about twice that of a single NiFe layer. The resonance field is the same in both cases. Using the VSM the coercive field of the CoCr layer of the double layer was obtained. It is approximately

  10. Male carriers of the FMR1 premutation show altered hippocampal-prefrontal function during memory encoding

    Directory of Open Access Journals (Sweden)

    John M Wang

    2012-10-01

    Full Text Available Previous functional MRI (fMRI studies have shown that fragile X mental retardation 1 (FMR1 premutation allele carriers (FXPCs exhibit decreased hippocampal activation during a recall task and lower inferior frontal activation during a working memory task compared to matched controls. The molecular characteristics of FXPCs includes 55 to 200 CGG trinucleoutide expansions, increased FMR1 mRNA levels, and decreased FMRP levels especially at higher repeat sizes. In the current study, we utilized MRI to examine differences in hippocampal volume and function during an encoding task in young male FXPCs. While no decreases in either hippocampal volume or hippocampal activity were observed during the encoding task in FXPCs, FMRP level (measured in blood correlated with decreases in parahippocampal activation. In addition, activity in the right dorsolateral prefrontal cortex during correctly encoded trials correlated negatively with mRNA levels. These results, as well as the established biological effects associated with elevated mRNA levels and decreased FMRP levels on dendritic maturation and axonal growth, prompted us to explore functional connectivity between the hippocampus, prefrontal cortex, and parahippocampal gyrus using a psychophysiological interaction analysis. In FXPCs, the right hippocampus evinced significantly lower connectivity with right ventrolateral prefrontal cortex (VLPFC and right parahippocampal gyrus. Furthermore, the weaker connectivity between the right hippocampus and VLPFC was associated with reduced FMRP in the FXPC group. These results suggest that while FXPCs show relatively typical brain response during encoding, faulty connectivity between frontal and hippocampal regions may have subsequent effects on recall and working memory.

  11. Ferromagnetic resonance investigation in permalloy magnetic antidot arrays on alumina nanoporous membranes

    Energy Technology Data Exchange (ETDEWEB)

    Rodríguez-Suárez, R.L., E-mail: rrodriguez@fis.puc.cl [Facultad de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860 Casilla 306, Santiago (Chile); Palma, J.L.; Burgos, E.O. [Departamento de Física, Universidad de Santiago de Chile (USACH), Avda. Ecuador 3493, 917-0124 Santiago (Chile); Michea, S. [Facultad de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860 Casilla 306, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile (USACH), Avda. Ecuador 3493, 917-0124 Santiago (Chile); Escrig, J.; Denardin, J.C. [Departamento de Física, Universidad de Santiago de Chile (USACH), Avda. Ecuador 3493, 917-0124 Santiago (Chile); Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Avda. Ecuador 3493, 917-0124 Santiago (Chile); Aliaga, C. [Center for the Development of Nanoscience and Nanotechnology (CEDENNA), Avda. Ecuador 3493, 917-0124 Santiago (Chile); Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40, Correo 33, Santiago (Chile)

    2014-01-15

    The magnetic properties of Ni{sub 80}Fe{sub 20} antidot arrays with hole diameters of 18 and 70 nm fabricated by a template-assisted method were investigated using the ferromagnetic resonance technique. Tuning the antidot arrays by changing the hole diameter enables control on the angular dependence of the ferromagnetic resonance field. The scanning electron microscope images reveal a quite regular hexagonal arrangement of the pores, however the angular dependence of the resonance field do not exhibit the six-fold symmetry expected for this symmetry. Micromagnetic simulations performed on a perfect hexagonal lattice, when compared with those made on our real system taken from the scanning microscope images, reveal that the presence of defects in the antidot lattice affects the ferromagnetic resonance field symmetry. - Highlights: • We use the FMR technique to investigate the magnetic properties of Py antidots. • We studied the effect of pore diameter on FMR angular measurement. • FMR field does not exhibit the six-fold symmetry. • For all angular positions there are two resonance modes always present. • Micromagnetic simulations agree with the experimental results with defects.

  12. Molecular analysis and test of linkage between the FMR-I gene and infantile autism in multiplex families

    Energy Technology Data Exchange (ETDEWEB)

    Hallmayer, J.; Pintado, E.; Lotspeich, L.; Spiker, D.; Kraemer, H.C.; Lee Wong, D.; Lin, A.; Herbert, J.; Cavalli-Sforza, L.L.; Ciaranello, R.D. [Stanford Univ., CA (United States)] [and others

    1994-11-01

    Approximately 2%-5% of autistic children show cytogenetic evidence of the fragile X syndrome. This report tests whether infantile autism in multiplex autism families arises from an unusual manifestion of the fragile X syndrome. This could arise either by expansion of the (CGG)n trinucleotide repeat in FMR-1 or from a mutation elsewhere in the gene. We studied 35 families that met stringent criteria for multiplex autism. Amplification of the trinucleotide repeat and analysis of methylation status were performed in 79 autistic children and in 31 of their unaffected siblings by Southern blot analysis. No examples of amplified repeats were seen in the autistic or control children or in their parents or grandparents. We next examined the hypothesis that there was a mutation elsewhere in the FMR-1 gene, by linkage analysis in 32 of these families. We tested four different dominant models and a recessive model. Linkage to FMR-1 could be excluded (lod score between -24 and -62) in all models by using probes DXS548, FRAXAC1, and FRAXAC2 and the CGG repeat itself. Tests for heterogeneity in this sample were negative, and the occurrence of positive lod scores in this data set could be attributed to chance. Analysis of the data by the affected-sib method also did not show evidence for linkage of any marker to autism. These results enable us to reject the hypothesis that multiplex autism arises from expansion of the (CGG)n trinucleotide repeat in FMR-1. Further, because the overall lod scores for all probes in all models tested were highly negative, linkage to FMR-1 can also be ruled out in multiplex autistic families. 35 refs., 2 figs., 5 tabs.

  13. Early Retinal Defects in Fmr1−/y Mice: Toward a Critical Role of Visual Dys-Sensitivity in the Fragile X Syndrome Phenotype?

    Science.gov (United States)

    Perche, Olivier; Felgerolle, Chloé; Ardourel, Maryvonne; Bazinet, Audrey; Pâris, Arnaud; Rossignol, Rafaëlle; Meyer-Dilhet, Géraldine; Mausset-Bonnefont, Anne-Laure; Hébert, Betty; Laurenceau, David; Montécot-Dubourg, Céline; Menuet, Arnaud; Bizot, Jean-Charles; Pichon, Jacques; Ranchon-Cole, Isabelle; Briault, Sylvain

    2018-01-01

    Fragile X Syndrome (FXS) is caused by a deficiency in Fragile X Mental Retardation Protein (FMRP) leading to global sensorial abnormalities, among which visual defects represent a critical part. These visual defects are associated with cerebral neuron immaturity especially in the primary visual cortex. However, we recently demonstrated that retinas of adult Fmr1−/y mice, the FXS murine model, present molecular, cellular and functional alterations. However, no data are currently available on the evolution pattern of such defects. As retinal stimulation through Eye Opening (EO) is a crucial signal for the cerebral visual system maturation, we questioned the precocity of molecular and functional retinal phenotype. To answer this question, we studied the retinal molecular phenotype of Fmr1−/y mice before EO until adult age and the consequences of the retinal loss of Fmrp on retinal function in young and adult mice. We showed that retinal molecular defects are present before EO and remain stable at adult age, leading to electrophysiological impairments without any underlying structural changes. We underlined that loss of Fmrp leads to a wide range of defects in the retina, settled even before EO. Our work demonstrates a critical role of the sensorial dysfunction in the Fmr1−/y mice overall phenotype, and provides evidence that altered peripheral perception is a component of the sensory processing defect in FXS conditions. PMID:29681800

  14. Early Retinal Defects in Fmr1−/y Mice: Toward a Critical Role of Visual Dys-Sensitivity in the Fragile X Syndrome Phenotype?

    Directory of Open Access Journals (Sweden)

    Olivier Perche

    2018-04-01

    Full Text Available Fragile X Syndrome (FXS is caused by a deficiency in Fragile X Mental Retardation Protein (FMRP leading to global sensorial abnormalities, among which visual defects represent a critical part. These visual defects are associated with cerebral neuron immaturity especially in the primary visual cortex. However, we recently demonstrated that retinas of adult Fmr1−/y mice, the FXS murine model, present molecular, cellular and functional alterations. However, no data are currently available on the evolution pattern of such defects. As retinal stimulation through Eye Opening (EO is a crucial signal for the cerebral visual system maturation, we questioned the precocity of molecular and functional retinal phenotype. To answer this question, we studied the retinal molecular phenotype of Fmr1−/y mice before EO until adult age and the consequences of the retinal loss of Fmrp on retinal function in young and adult mice. We showed that retinal molecular defects are present before EO and remain stable at adult age, leading to electrophysiological impairments without any underlying structural changes. We underlined that loss of Fmrp leads to a wide range of defects in the retina, settled even before EO. Our work demonstrates a critical role of the sensorial dysfunction in the Fmr1−/y mice overall phenotype, and provides evidence that altered peripheral perception is a component of the sensory processing defect in FXS conditions.

  15. A Female Patient with FMR1 Premutation and Mosaic X Chromosome Aneuploidy and Two Sons with Intellectual Disability.

    Science.gov (United States)

    Galanina, Ekaterina M; Tulupov, Andrey A; Lemskaya, Natalya A; Korostyshevskaya, Aleksandra M; Maksimova, Yuliya V; Shorina, Asia R; Savelov, Andrey A; Sergeeva, Irina G; Isanova, Evgeniya R; Grishchenko, Irina V; Yudkin, Dmitry V

    2017-03-01

    In this report, we describe a molecular cytogenetic study of a family burdened with intellectual disability (ID) and suicide. Our study revealed that the mother has a heterozygous premutation in the FMR1 gene and supernumerary X chromosomes as well as X-derived marker chromosomes. Both of her sons have ID and a normal chromosome number. One of the sons has fragile X syndrome, and the other has ID of an unclear nature.

  16. 2-Methyl-6-(phenylethynyl pyridine (MPEP reverses maze learning and PSD-95 deficits in Fmr1 knock-out mice.

    Directory of Open Access Journals (Sweden)

    Réno Michelle Gandhi

    2014-03-01

    Full Text Available Fragile X syndrome (FXS is caused by the lack of expression of the fragile X mental retardation protein (FMRP, which results in intellectual disability and other debilitating symptoms including impairment of visual-spatial functioning. FXS is the only single-gene disorder that is highly co-morbid with autism spectrum disorder and can therefore provide insight into its pathophysiology. Lack of FMRP results in altered group I metabotropic glutamate receptor (mGluR signalling, which is a target for putative treatments. The Hebb-Williams (H-W mazes are a set of increasingly complex spatial navigation problems that depend on intact hippocampal and thus mGluR-5 functioning. In the present investigation, we examined whether an antagonist of mGluR-5 would reverse previously described behavioural deficits in Fmr1 KO mice. Mice were trained on a subset of the H-W mazes and then treated with either 20 mg/kg of an mGluR-5 antagonist, 2-Methyl-6-(phenylethynyl pyridine (MPEP; n = 11 or an equivalent dose of saline (n = 11 prior to running test mazes. Latency and errors were dependent variables recorded during the test phase. Immediately after completing each test, marble-burying behavior was assessed which confirmed that the drug treatment was pharmacologically active during maze learning. Although latency was not statistically different between the groups, MPEP treated Fmr1 KO mice made significantly fewer errors on mazes deemed more difficult suggesting a reversal of the behavioural deficit. MPEP treated mice were also less perseverative and impulsive when navigating mazes. Furthermore, MPEP treatment reversed PSD-95 protein deficits in Fmr1 KO treated mice, whereas levels of a control protein (β-tubulin remained unchanged. These data further validate MPEP as a potentially beneficial treatment for FXS. Our findings also suggest that adapted H-W mazes may be a useful tool to document alterations in behavioural functioning following pharmacological

  17. Permanent magnetic ferrite based power-tunable metamaterials

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guanqiao; Lan, Chuwen [State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China); Gao, Rui [High Temperature Thermochemistry Laboratory, Department of Mining and Materials Engineering, McGill University, Montreal, Quebec H3A 0C5 (Canada); Zhou, Ji, E-mail: zhouji@tsinghua.edu.cn [State Key Laboratory of New Ceramics and Fine Processing, School of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China)

    2017-08-15

    Highlights: • Power-tunable metamaterials based on barium permanent magnetic ferrite have been proposed and fabricated. • It is observed that resonant frequency of the array shifts upon altering the output power. • This kind of power-tunable behavior is due to the temperature rise as a result of FMR-induced heat buildup. • This work offers a practical idea to tune ferrite metamaterials besides magneto-tunability and thermal-tunability. - Abstract: Power-tunable metamaterials based on barium permanent magnetic ferrite have been proposed and fabricated in this research. Scattering parameter measurements confirm a shift in resonant frequency in correlation to changes in incident electromagnetic power within microwave frequency band. The tunable phenomenon represented by a blue-shift in transmission spectra in the metamaterials array can be attributed to a decrease in saturation magnetization resulting from FMR-induced temperature elevation upon resonant conditions. This power-dependent behavior offers a simple and practical route towards dynamically fine-tunable ferrite metamaterials.

  18. SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences.

    Science.gov (United States)

    Pickett, B D; Karlinsey, S M; Penrod, C E; Cormier, M J; Ebbert, M T W; Shiozawa, D K; Whipple, C J; Ridge, P G

    2016-09-01

    Simple Sequence Repeats (SSRs) are used to address a variety of research questions in a variety of fields (e.g. population genetics, phylogenetics, forensics, etc.), due to their high mutability within and between species. Here, we present an innovative algorithm, SA-SSR, based on suffix and longest common prefix arrays for efficiently detecting SSRs in large sets of sequences. Existing SSR detection applications are hampered by one or more limitations (i.e. speed, accuracy, ease-of-use, etc.). Our algorithm addresses these challenges while being the most comprehensive and correct SSR detection software available. SA-SSR is 100% accurate and detected >1000 more SSRs than the second best algorithm, while offering greater control to the user than any existing software. SA-SSR is freely available at http://github.com/ridgelab/SA-SSR CONTACT: perry.ridge@byu.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  19. Analysis of unstable DNA sequence in FRM1 gene in Polish families with fragile X syndrome

    International Nuclear Information System (INIS)

    Milewski, Michal; Bal, Jerzy; Obersztyn, Ewa; Bocian, Ewa; Mazurczak, Tadeusz; Zygulska, Marta; Horst, Juergen; Deelen, Wout H.; Halley, Dicky J.J.

    1996-01-01

    The unstable DNA sequence in the FMR1 gene was analyzed in 85 individuals from Polish families with fragile X syndrome in order to characterize mutations responsible for the disease in Poland. In all affected individuals classified on the basis of clinical features and expression of the fragile site at X(q27.3) a large expansion of the unstable sequence (full mutation) was detected. About 5% (2 of 43) of individuals with full mutation did not express the fragile site. Among normal alleles, ranging in size from 20 to 41 CGC repeats, allele with 29 repeats was the most frequent (37%). Transmission of premutated and fully mutated alleles to the offspring was always associated with size increase. No change in repeat number was found when normal alleles were transmitted. (author). 19 refs., 4 figs, 1 tab

  20. Concurrent array-based queue

    Science.gov (United States)

    Heidelberger, Philip; Steinmacher-Burow, Burkhard

    2015-01-06

    According to one embodiment, a method for implementing an array-based queue in memory of a memory system that includes a controller includes configuring, in the memory, metadata of the array-based queue. The configuring comprises defining, in metadata, an array start location in the memory for the array-based queue, defining, in the metadata, an array size for the array-based queue, defining, in the metadata, a queue top for the array-based queue and defining, in the metadata, a queue bottom for the array-based queue. The method also includes the controller serving a request for an operation on the queue, the request providing the location in the memory of the metadata of the queue.

  1. Characterization and validation of noninvasive oxygen tension measurements in human glioma xenografts by 19F-MR relaxometry

    International Nuclear Information System (INIS)

    Sanden, Boudewijn P.J. van der; Heerschap, Arend; Simonetti, Arjan W.; Rijken, Paul F.J.W.; Peters, Hans P.W.; Stbeen, Georg; Kogel, Albert J. van der

    1999-01-01

    Purpose: The aim of this study was to characterize and to validate noninvasive 19 F-magnetic resonance relaxometry for the measurement of oxygen tensions in human glioma xenografts in nude mice. The following three questions were addressed: 1. When perfluorocarbon compounds (PFCs) are administrated intravenously, which tumor regions are assessed by 19 F-MR relaxometry? 2. Are oxygen tension as detected by 19 F-MR relaxometry (pO 2/relaxo ) comparable to Eppendorf O 2 -electrode measurements (pO 2/electrode )? 3. Can 19 F-MR relaxometry be used to detect oxygen tension changes in tumor tissue during carbogen breathing? Methods and Materials: Slice-selective 19 F-MR relaxometry was carried out with perfluoro-15-crown-5-ether as oxygen sensor. The PFC was injected i.v. 3 days before the 19 F-MR experiments. Two datasets were acquired before and two after the start of carbogen breathing. The distribution of PFCs and necrotic areas were analyzed in 19 F-Spin Echo (SE) density MR images and T 2 -weighted 1 H-SE MR images, respectively. One day after the MR investigations, oxygen tensions were measured by oxygen electrodes in the same slice along two perpendicular tracks. These measurements were followed by (immuno)histochemical analysis of the 2D distribution of perfused microvessels, hypoxic cells, necrotic areas, and macrophages. Results: The PFCs mainly became sequestered in perfused regions at the tumor periphery; thus, 19 F-MR relaxometry probed mean oxygen tensions in these regions throughout the selected MR slice. In perfused regions of the tumor, mean pO 2/relaxo values were comparable to mean pO 2/electrode values, and varied from 0.03 to 9 mmHg. Median pO 2/electrode values of both tracks were lower than mean pO 2/relaxo values, because low pO 2/electrode values that originate from hypoxic and necrotic areas were also included in calculations of median pO 2/electrode values. After 8-min carbogen breathing, the average pO 2/relaxo increase was 3.3 ± 0.8 (SEM

  2. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.

    Science.gov (United States)

    Chen, Wen; Djama, Zeinab Robleh; Coffey, Michael D; Martin, Frank N; Bilodeau, Guillaume J; Radmer, Lorien; Denton, Geoff; Lévesque, C André

    2013-01-01

    Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

  3. High Performance Systolic Array Core Architecture Design for DNA Sequencer

    Directory of Open Access Journals (Sweden)

    Saiful Nurdin Dayana

    2018-01-01

    Full Text Available This paper presents a high performance systolic array (SA core architecture design for Deoxyribonucleic Acid (DNA sequencer. The core implements the affine gap penalty score Smith-Waterman (SW algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA and improved in the core area by 90% reduction.

  4. Expanded clinical phenotype of women with the FMR1 premutation.

    Science.gov (United States)

    Coffey, Sarah M; Cook, Kylee; Tartaglia, Nicole; Tassone, Flora; Nguyen, Danh V; Pan, Ruiqin; Bronsky, Hannah E; Yuhas, Jennifer; Borodyanskaya, Mariya; Grigsby, Jim; Doerflinger, Melanie; Hagerman, Paul J; Hagerman, Randi J

    2008-04-15

    Fragile X-associated tremor/ataxia syndrome (FXTAS) is generally considered to be uncommon in older female carriers of premutation alleles (55-200 CGG repeats) of the fragile X mental retardation 1 (FMR1) gene; however, neither prevalence, nor the nature of the clinical phenotype, has been well characterized in female carriers. In this study, we evaluated 146 female carriers (mean, 42.3 years; range, 20-75 years) with and without core features of FXTAS (tremor; gait ataxia), and 69 age-matched controls (mean, 45.8 years; range, 21-78 years). Compared with controls, carriers with definite or probable FXTAS had greater medical co-morbidity, with increased prevalence of thyroid disease (P = 0.0096), hypertension (P = 0.0020), seizures (P = 0.0077), peripheral neuropathy (P = 0.0040), and fibromyalgia (P = 0.0097), in addition to the typical symptoms of FXTAS-tremor (P < 0.0001) and ataxia (P < 0.0001). The non-FXTAS premutation group had more complaints of chronic muscle pain (P = 0.0097), persistent paraesthesias in extremities (P < 0.0001), and history of tremor (P < 0.0123) than controls. The spectrum of clinical involvement in female carriers with FXTAS is quite broad, encompassing a number of medical co-morbidities as well as the core movement disorder. The remarkable degree of thyroid dysfunction (17% in the non-FXTAS group and 50% in the FXTAS group) warrants consideration of thyroid function studies in all female premutation carriers, particularly those with core features of FXTAS. Copyright 2008 Wiley-Liss, Inc.

  5. Study of spin dynamics and damping on the magnetic nanowire arrays with various nanowire widths

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Jaehun [Department of Physics, Inha University, Incheon, 402-751 (Korea, Republic of); Fujii, Yuya; Konioshi, Katsunori [Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531 (Japan); Yoon, Jungbum [Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117576 (Singapore); Kim, Nam-Hui; Jung, Jinyong [Department of Physics, Inha University, Incheon, 402-751 (Korea, Republic of); Miwa, Shinji [Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531 (Japan); Jung, Myung-Hwa [Department of Physics, Sogang University, Seoul, 121-742 (Korea, Republic of); Suzuki, Yoshishige [Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531 (Japan); You, Chun-Yeol, E-mail: cyyou@inha.ac.kr [Department of Physics, Inha University, Incheon, 402-751 (Korea, Republic of)

    2016-07-01

    We investigate the spin dynamics including Gilbert damping in the ferromagnetic nanowire arrays. We have measured the ferromagnetic resonance of ferromagnetic nanowire arrays using vector-network analyzer ferromagnetic resonance (VNA-FMR) and analyzed the results with the micromagnetic simulations. We find excellent agreement between the experimental VNA-FMR spectra and micromagnetic simulations result for various applied magnetic fields. We find that the same tendency of the demagnetization factor for longitudinal and transverse conditions, N{sub z} (N{sub y}) increases (decreases) as increasing the nanowire width in the micromagnetic simulations while N{sub x} is almost zero value in transverse case. We also find that the Gilbert damping constant increases from 0.018 to 0.051 as the increasing nanowire width for the transverse case, while it is almost constant as 0.021 for the longitudinal case. - Highlights: • We investigate the spin dynamic properties in the ferromagnetic nanowire arrays. • The demagnetization factors have similar tendency with the prism geometry results. • The Gilbert damping constant is increased from 0.018 to 0.051 as the increasing nanowire width for the transverse. • The Gilbert damping constant is almost constant as 0.021 for the longitudinal case.

  6. High-Throughput Analysis With 96-Capillary Array Electrophoresis and Integrated Sample Preparation for DNA Sequencing Based on Laser Induced Fluorescence Detection

    Energy Technology Data Exchange (ETDEWEB)

    Xue, Gang [Iowa State Univ., Ames, IA (United States)

    2001-01-01

    The purpose of this research was to improve the fluorescence detection for the multiplexed capillary array electrophoresis, extend its use beyond the genomic analysis, and to develop an integrated micro-sample preparation system for high-throughput DNA sequencing. The authors first demonstrated multiplexed capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) separations in a 96-capillary array system with laser-induced fluorescence detection. Migration times of four kinds of fluoresceins and six polyaromatic hydrocarbons (PAHs) are normalized to one of the capillaries using two internal standards. The relative standard deviations (RSD) after normalization are 0.6-1.4% for the fluoresceins and 0.1-1.5% for the PAHs. Quantitative calibration of the separations based on peak areas is also performed, again with substantial improvement over the raw data. This opens up the possibility of performing massively parallel separations for high-throughput chemical analysis for process monitoring, combinatorial synthesis, and clinical diagnosis. The authors further improved the fluorescence detection by step laser scanning. A computer-controlled galvanometer scanner is adapted for scanning a focused laser beam across a 96-capillary array for laser-induced fluorescence detection. The signal at a single photomultiplier tube is temporally sorted to distinguish among the capillaries. The limit of detection for fluorescein is 3 x 10-11 M (S/N = 3) for 5-mW of total laser power scanned at 4 Hz. The observed cross-talk among capillaries is 0.2%. Advantages include the efficient utilization of light due to the high duty-cycle of step scan, good detection performance due to the reduction of stray light, ruggedness due to the small mass of the galvanometer mirror, low cost due to the simplicity of components, and flexibility due to the independent paths for excitation and emission.

  7. Prevalence of carriers of premutation-size alleles of the FMR1 gene-and implications for the population genetics of the fragile X syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Rousseau, F.; Rouillard, P.; Morel, M.L. [Universite Laval, Quebec City (Canada)] [and others

    1995-11-01

    The fragile X syndrome is the second leading cause of mental retardation after Down syndrome. Fragile X premutations are not associated with any clinical phenotype but are at high risk of expanding to full mutations causing the disease when they are transmitted by a carrier woman. There is no reliable estimate of the prevalence of women who are carriers of fragile X premutations. We have screened 10,624 unselected women by Southern blot for the presence of FMR1 premutation alleles and have confirmed their size by PCR analysis. We found 41 carriers of alleles with 55-101 CGG repeats, a prevalence of 1/259 women (95% confidence interval 1/373-1/198). Thirty percent of these alleles carry an inferred haplotype that corresponds to the most frequent haplotype found in fragile X males and may indeed constitute premutations associated with a significant risk of expansion on transmission by carrier women. We identified another inferred haplotype that is rare in both normal and fragile X chromosomes but that is present on 13 (57%) of 23 chromosomes carrying FMR1 alleles with 53-64 CGG repeats. This suggests either (1) that this haplotype may be stable or (2) that the associated premutation-size alleles have not yet reached equilibrium in this population and that the incidence of fragile X syndrome may increase in the future. 42 refs., 3 figs., 4 tabs.

  8. Interaction between scene-based and array-based contextual cueing.

    Science.gov (United States)

    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.

  9. DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR-cas Array and Capsular Profiling

    Directory of Open Access Journals (Sweden)

    Pauline Ogrodzki

    2017-09-01

    Full Text Available The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping. This article updates the application of three genotyping methods across the Cronobacter genus. The three genotyping methods were multilocus sequence typing (MLST, capsular profiling of the K-antigen and colanic acid (CA biosynthesis regions, and CRISPR-cas array profiling. A total of 1654 MLST profiled and 286 whole genome sequenced strains, available by open access at the PubMLST Cronobacter database, were used this analysis. The predominance of C. sakazakii and C. malonaticus in clinical infections was confirmed. The majority of clinical strains being in the C. sakazakii clonal complexes (CC 1 and 4, sequence types (ST 8 and 12 and C. malonaticus ST7. The capsular profile K2:CA2, previously proposed as being strongly associated with C. sakazakii and C. malonaticus isolates from severe neonatal infections, was also found in C. turicensis, C. dublinensis and C. universalis. The majority of CRISPR-cas types across the genus was the I-E (Ecoli type. Some strains of C. dublinensis and C. muytjensii encoded the I-F (Ypseudo type, and others lacked the cas gene loci. The significance of the expanding profiling will be of benefit to researchers as well as governmental and industrial risk assessors.

  10. DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR-cas Array and Capsular Profiling.

    Science.gov (United States)

    Ogrodzki, Pauline; Forsythe, Stephen J

    2017-01-01

    The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping. This article updates the application of three genotyping methods across the Cronobacter genus. The three genotyping methods were multilocus sequence typing (MLST), capsular profiling of the K -antigen and colanic acid (CA) biosynthesis regions, and CRISPR- cas array profiling. A total of 1654 MLST profiled and 286 whole genome sequenced strains, available by open access at the PubMLST Cronobacter database, were used this analysis. The predominance of C. sakazakii and C. malonaticus in clinical infections was confirmed. The majority of clinical strains being in the C. sakazakii clonal complexes (CC) 1 and 4, sequence types (ST) 8 and 12 and C. malonaticus ST7. The capsular profile K2:CA2, previously proposed as being strongly associated with C. sakazakii and C. malonaticus isolates from severe neonatal infections, was also found in C. turicensis , C. dublinensis and C. universalis . The majority of CRISPR- cas types across the genus was the I-E (Ecoli) type. Some strains of C. dublinensis and C. muytjensii encoded the I-F (Ypseudo) type, and others lacked the cas gene loci. The significance of the expanding profiling will be of benefit to researchers as well as governmental and industrial risk assessors.

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

    Science.gov (United States)

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

    2018-05-01

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

  12. Ultrasensitive DNA sequence detection using nanoscale ZnO sensor arrays

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Nitin; Dorfman, Adam; Hahm, Jong-in [Department of Chemical Engineering, Pennsylvania State University, 160 Fenske Laboratory, University Park, PA 16802 (United States)

    2006-06-28

    We report that engineered nanoscale zinc oxide structures can be effectively used for the identification of the biothreat agent, Bacillus anthracis by successfully discriminating its DNA sequence from other genetically related species. We explore both covalent and non-covalent linking schemes in order to couple probe DNA strands to the zinc oxide nanostructures. Hybridization reactions are performed with various concentrations of target DNA strands whose sequence is unique to Bacillus anthracis. The use of zinc oxide nanomaterials greatly enhances the fluorescence signal collected after carrying out duplex formation reaction. Specifically, the covalent strategy allows detection of the target species at sample concentrations at a level as low as a few femtomolar as compared to the detection sensitivity in the tens of nanomolar range when using the non-covalent scheme. The presence of the underlying zinc oxide nanomaterials is critical in achieving increased fluorescence detection of hybridized DNA and, therefore, accomplishing rapid and extremely sensitive identification of the biothreat agent. We also demonstrate the easy integration potential of nanoscale zinc oxide into high density arrays by using various types of zinc oxide sensor prototypes in the DNA sequence detection. When combined with conventional automatic sample handling apparatus and computerized fluorescence detection equipment, our approach can greatly promote the use of zinc oxide nanomaterials as signal enhancing platforms for rapid, multiplexed, high-throughput, highly sensitive, DNA sensor arrays.

  13. Ultrasensitive DNA sequence detection using nanoscale ZnO sensor arrays

    International Nuclear Information System (INIS)

    Kumar, Nitin; Dorfman, Adam; Hahm, Jong-in

    2006-01-01

    We report that engineered nanoscale zinc oxide structures can be effectively used for the identification of the biothreat agent, Bacillus anthracis by successfully discriminating its DNA sequence from other genetically related species. We explore both covalent and non-covalent linking schemes in order to couple probe DNA strands to the zinc oxide nanostructures. Hybridization reactions are performed with various concentrations of target DNA strands whose sequence is unique to Bacillus anthracis. The use of zinc oxide nanomaterials greatly enhances the fluorescence signal collected after carrying out duplex formation reaction. Specifically, the covalent strategy allows detection of the target species at sample concentrations at a level as low as a few femtomolar as compared to the detection sensitivity in the tens of nanomolar range when using the non-covalent scheme. The presence of the underlying zinc oxide nanomaterials is critical in achieving increased fluorescence detection of hybridized DNA and, therefore, accomplishing rapid and extremely sensitive identification of the biothreat agent. We also demonstrate the easy integration potential of nanoscale zinc oxide into high density arrays by using various types of zinc oxide sensor prototypes in the DNA sequence detection. When combined with conventional automatic sample handling apparatus and computerized fluorescence detection equipment, our approach can greatly promote the use of zinc oxide nanomaterials as signal enhancing platforms for rapid, multiplexed, high-throughput, highly sensitive, DNA sensor arrays

  14. Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences

    Directory of Open Access Journals (Sweden)

    Alessandra Traini

    2013-01-01

    Full Text Available Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

  15. Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences.

    Science.gov (United States)

    Traini, Alessandra; Iorizzo, Massimo; Mann, Harpartap; Bradeen, James M; Carputo, Domenico; Frusciante, Luigi; Chiusano, Maria Luisa

    2013-01-01

    Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

  16. Microcomputer based system to control the load of a capacitor array in the TJ-1 Tokamak

    International Nuclear Information System (INIS)

    Alberdi Primicia, J.; Asenjo, L.; Sanz, J.A.

    1990-01-01

    The power to create the magnetic field in the TJ-1 TOKAMAK is provide by an array of 16 capacitor sets. The total capacity of this array is 8.1F. This work describes a computer system based on the Motorola M-6800 microprocessor which controls the load of the capacitor set-and establishes the conditions for the reactor trigger. (author)

  17. Microcomputer Based System to control the Load of a Capacitor Array in the TJ-1 Tokamak

    International Nuclear Information System (INIS)

    Alberdi, J.; Asenso, L.; Sanz, J. A.

    1990-01-01

    The power to create the magnetic fields in the TJ-1 Tokamak is provides by an array of 16 capacitor sets. The total capacity of this array is 8. 1F. This work describes a computer system based on the Motorola M-6800 micro- processor which controls the load of the capacitor set and stablished the conditions for the reactor trigger. (Author)

  18. The magnetic-resonance properties study of nanostructures for spintronics by FMR

    International Nuclear Information System (INIS)

    Kupriyanova, G; Zyubin, A; Astashonok, A; Orlova, A; Prokhorenko, E

    2011-01-01

    In this work we report the study of the magnetic-resonance properties such as magnetic anisotropy, magnetic damping, and interlayer exchange coupling between ferromagnetic layers separated by a nonmagnetic spacer by FMR to assess their applicability in a functional magnetic tunnel junction.

  19. HIV-1 envelope sequence-based diversity measures for identifying recent infections.

    Directory of Open Access Journals (Sweden)

    Alexis Kafando

    Full Text Available Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC of the receiver operating characteristic (ROC. Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001. Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806, gp120 C2_3 (AUC = 0.805 and gp120 V3 (AUC = 0.812. Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency.

  20. Protocols for 16S rDNA Array Analyses of Microbial Communities by Sequence-Specific Labeling of DNA Probes

    Directory of Open Access Journals (Sweden)

    Knut Rudi

    2003-01-01

    Full Text Available Analyses of complex microbial communities are becoming increasingly important. Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity. Novel protocols for DNA array-based analyses of microbial communities are presented. In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization. The gene encoding 16S ribosomal RNA was chosen as the target in these analyses. This gene contains both universally conserved regions and regions with relatively high variability. The universally conserved regions are used for PCR amplification primers, while the variable regions are used for the specific probes. Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations.

  1. Quantitation of heteroplasmy of mtDNA sequence variants identified in a population of AD patients and controls by array-based resequencing.

    Science.gov (United States)

    Coon, Keith D; Valla, Jon; Szelinger, Szabolics; Schneider, Lonnie E; Niedzielko, Tracy L; Brown, Kevin M; Pearson, John V; Halperin, Rebecca; Dunckley, Travis; Papassotiropoulos, Andreas; Caselli, Richard J; Reiman, Eric M; Stephan, Dietrich A

    2006-08-01

    The role of mitochondrial dysfunction in the pathogenesis of Alzheimer's disease (AD) has been well documented. Though evidence for the role of mitochondria in AD seems incontrovertible, the impact of mitochondrial DNA (mtDNA) mutations in AD etiology remains controversial. Though mutations in mitochondrially encoded genes have repeatedly been implicated in the pathogenesis of AD, many of these studies have been plagued by lack of replication as well as potential contamination of nuclear-encoded mitochondrial pseudogenes. To assess the role of mtDNA mutations in the pathogenesis of AD, while avoiding the pitfalls of nuclear-encoded mitochondrial pseudogenes encountered in previous investigations and showcasing the benefits of a novel resequencing technology, we sequenced the entire coding region (15,452 bp) of mtDNA from 19 extremely well-characterized AD patients and 18 age-matched, unaffected controls utilizing a new, reliable, high-throughput array-based resequencing technique, the Human MitoChip. High-throughput, array-based DNA resequencing of the entire mtDNA coding region from platelets of 37 subjects revealed the presence of 208 loci displaying a total of 917 sequence variants. There were no statistically significant differences in overall mutational burden between cases and controls, however, 265 independent sites of statistically significant change between cases and controls were identified. Changed sites were found in genes associated with complexes I (30.2%), III (3.0%), IV (33.2%), and V (9.1%) as well as tRNA (10.6%) and rRNA (14.0%). Despite their statistical significance, the subtle nature of the observed changes makes it difficult to determine whether they represent true functional variants involved in AD etiology or merely naturally occurring dissimilarity. Regardless, this study demonstrates the tremendous value of this novel mtDNA resequencing platform, which avoids the pitfalls of erroneously amplifying nuclear-encoded mtDNA pseudogenes, and

  2. ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing.

    Science.gov (United States)

    Moncini, S; Bedeschi, M F; Castronovo, P; Crippa, M; Calvello, M; Garghentino, R R; Scuvera, G; Finelli, P; Venturin, M

    2013-12-01

    In this report, we describe two adult brothers affected by moderate non-specific intellectual disability (ID). They showed minor facial anomalies, not clearly ascribable to any specific syndromic patterns, microcephaly, brachydactyly and broad toes. Both brothers presented seizures. Karyotype, subtelomeric and FMR1 analysis were normal in both cases. We performed array-CGH analysis that revealed no copy-number variations potentially associated with ID. Subsequent exome sequence analysis allowed the identification of the ATRX c.109C>T (p.R37X) mutation in both the affected brothers. Sanger sequencing confirmed the presence of the mutation in the brothers and showed that the mother is a healthy carrier. Mutations in the ATRX gene cause the X-linked alpha thalassemia/mental retardation (ATR-X) syndrome (MIM #301040), a severe clinical condition usually associated with profound ID, facial dysmorphism and alpha thalassemia. However, the syndrome is clinically heterogeneous and some mutations, including the c.109C>T, are associated with a broad phenotypic spectrum, with patients displaying a less severe phenotype with only mild-moderate ID. In the case presented here, exome sequencing provided an effective strategy to achieve the molecular diagnosis of ATR-X syndrome, which otherwise would have been difficult to consider due to the mild non-specific phenotype and the absence of a family history with typical severe cases.

  3. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration

    Directory of Open Access Journals (Sweden)

    Fasold Mario

    2010-04-01

    Full Text Available Abstract Background The brightness of the probe spots on expression microarrays intends to measure the abundance of specific mRNA targets. Probes with runs of at least three guanines (G in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis. Results Longer runs of three or more consecutive G along the probe sequence and in particular triple degenerated G at its solution end ((GGG1-effect are associated with exceptionally large probe intensities on GeneChip expression arrays. This intensity bias is related to non-specific hybridization and affects both perfect match and mismatch probes. The (GGG1-effect tends to increase gradually for microarrays of later GeneChip generations. It was found for DNA/RNA as well as for DNA/DNA probe/target-hybridization chemistries. Amplification of sample RNA using T7-primers is associated with strong positive amplitudes of the G-bias whereas alternative amplification protocols using random primers give rise to much smaller and partly even negative amplitudes. We applied positional dependent sensitivity models to analyze the specifics of probe intensities in the context of all possible short sequence motifs of one to four adjacent nucleotides along the 25meric probe sequence. Most of the longer motifs are adequately described using a nearest-neighbor (NN model. In contrast, runs of degenerated guanines require explicit consideration of next nearest neighbors (GGG terms. Preprocessing methods such as vsn, RMA, dChip, MAS5 and gcRMA only insufficiently remove the G-bias from data. Conclusions Positional and motif dependent sensitivity models accounts for sequence effects of oligonucleotide probe intensities. We propose a positional dependent NN+GGG hybrid model to correct the intensity bias associated with probes containing poly-G motifs. It is implemented as a single-chip based calibration

  4. Structural protein descriptors in 1-dimension and their sequence-based predictions.

    Science.gov (United States)

    Kurgan, Lukasz; Disfani, Fatemeh Miri

    2011-09-01

    The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods.

  5. A 5 tesla superconducting magnet and cryostats for an EPR/FMR spectrometer

    NARCIS (Netherlands)

    Reuvekamp, E.M.C.M.; Gerritsma, G.J.; ten Kate, Herman H.J.; van de Klundert, L.J.M.

    1988-01-01

    A description is given of the cryogenic part of an electron paramagnetic resonance (EPR)/ferromagnetic resonance (FMR) spectrometer using Ka-band (26.5-40 GHz) and U-band (40-60 GHz) frequencies for resonance measurements on large magnetic thin-films. The unit has two cryostats; the first has a

  6. 41 CFR 102-2.5 - What is the Federal Management Regulation (FMR)?

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What is the Federal Management Regulation (FMR)? 102-2.5 Section 102-2.5 Public Contracts and Property Management Federal... MANAGEMENT REGULATION SYSTEM Regulation System General § 102-2.5 What is the Federal Management Regulation...

  7. NSAMD: A new approach to discover structured contiguous substrings in sequence datasets using Next-Symbol-Array.

    Science.gov (United States)

    Pari, Abdolvahed; Baraani, Ahmad; Parseh, Saeed

    2016-10-01

    In many sequence data mining applications, the goal is to find frequent substrings. Some of these applications like extracting motifs in protein and DNA sequences are looking for frequently occurring approximate contiguous substrings called simple motifs. By approximate we mean that some mismatches are allowed during similarity test between substrings, and it helps to discover unknown patterns. Structured motifs in DNA sequences are frequent structured contiguous substrings which contains two or more simple motifs. There are some works that have been done to find simple motifs but these works have problems such as low scalability, high execution time, no guarantee to find all patterns, and low flexibility in adaptation to other application. The Flame is the only algorithm that can find all unknown structured patterns in a dataset and has solved most of these problems but its scalability for very large sequences is still weak. In this research a new approach named Next-Symbol-Array based Motif Discovery (NSAMD) is represented to improve scalability in extracting all unknown simple and structured patterns. To reach this goal a new data structure has been presented called Next-Symbol-Array. This data structure makes change in how to find patterns by NSAMD in comparison with Flame and helps to find structured motif faster. Proposed algorithm is as accurate as Flame and extracts all existing patterns in dataset. Performance comparisons show that NSAMD outperforms Flame in extracting structured motifs in both execution time (51% faster) and memory usage (more than 99%). Proposed algorithm is slower in extracting simple motifs but considerable improvement in memory usage (more than 99%) makes NSAMD more scalable than Flame. This advantage of NSAMD is very important in biological applications in which very large sequences are applied. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Investigating the relationship between FMR1 allele length and cognitive ability in children: a subtle effect of the normal allele range on the normal ability range?

    Science.gov (United States)

    Loat, C S; Craig, G; Plomin, R; Craig, I W

    2006-09-01

    The FMR1 gene contains a trinucleotide repeat tract which can expand from a normal size of around 30 repeats to over 200 repeats, causing mental retardation (Fragile X Syndrome). Evidence suggests that premutation males (55-200 repeats) are susceptible to a late-onset tremor/ataxia syndrome and females to premature ovarian failure, and that intermediate alleles ( approximately 41-55 repeats) and premutations may be in excess in samples with special educational needs. We explored the relationship between FMR1 allele length and cognitive ability in 621 low ability and control children assessed at 4 and 7 years, as well as 122 students with high IQ. The low and high ability and control samples showed no between-group differences in incidence of longer alleles. In males there was a significant negative correlation between allele length and non-verbal ability at 4 years (p = 0.048), academic achievement in maths (p = 0.003) and English (p = 0.011) at 7 years, and IQ in the high ability group (p = 0.018). There was a significant negative correlation between allele length and a standardised score for IQ and general cognitive ability at age 7 in the entire male sample (p = 0.002). This suggests that, within the normal spectrum of allele length, increased repeat numbers may have a limiting influence on cognitive performance.

  9. Avanços tecnológicos e variabilidade genética da expansão CGG da região promotora do gene FMR1

    OpenAIRE

    Gigonzac, Marc Alexandre Duarte

    2016-01-01

    A Síndrome do X-Frágil (SXF) é a principal causa de deficiência intelectual herdável no mundo e a segunda de etiologia genética, com uma prevalência estimada de 1/4000 homens e 1/8000 mulheres. O mecanismo molecular mais comum na SXF é decorrente de alterações na expressão do gene FMR1, localizado em Xq27.3, devido a expansões trinucleotídicas CGG na região promotora e subsequente metilação do gene. Apesar de apresentar achados clínicos consistentes, os mesmos não são exclusivos, e a existênc...

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

    DEFF Research Database (Denmark)

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

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

  11. Pseudo-reorganization of language cortical function at fMR imaging: a consequence of tumor-induced neurovascular uncoupling.

    Science.gov (United States)

    Ulmer, John L; Krouwer, Hendrikus G; Mueller, Wade M; Ugurel, M Sahin; Kocak, Mehmet; Mark, Leighton P

    2003-02-01

    A left-handed patient with a grade II left frontal lobe astrocytoma had spontaneous seizures causing speech arrest and uncontrolled right upper extremity movements. Word-generation functional MR (fMR) imaging showed activity nearly exclusively in the right inferior frontal gyrus. The clinical history of the speech arrest and the intraoperative mapping proved left-hemisphere language dominance. Tumor involvement of the left inferior frontal gyrus caused uncoupling of the blood oxygenation level-dependent (BOLD) and neuronal response, leading to the erroneous fMR imaging appearance of right-hemisphere language dominance. Discrepancies between BOLD and intraoperative mapping in areas near lesions illustrate the complementary nature of these techniques.

  12. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.

    Science.gov (United States)

    Antanaviciute, Laima; Fernández-Fernández, Felicidad; Jansen, Johannes; Banchi, Elisa; Evans, Katherine M; Viola, Roberto; Velasco, Riccardo; Dunwell, Jim M; Troggio, Michela; Sargent, Daniel J

    2012-05-25

    A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny. Of the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the 'Golden Delicious' genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the 'Golden Delicious' pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence. We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been

  13. Permanent magnetic ferrite based power-tunable metamaterials

    Science.gov (United States)

    Zhang, Guanqiao; Lan, Chuwen; Gao, Rui; Zhou, Ji

    2017-08-01

    Power-tunable metamaterials based on barium permanent magnetic ferrite have been proposed and fabricated in this research. Scattering parameter measurements confirm a shift in resonant frequency in correlation to changes in incident electromagnetic power within microwave frequency band. The tunable phenomenon represented by a blue-shift in transmission spectra in the metamaterials array can be attributed to a decrease in saturation magnetization resulting from FMR-induced temperature elevation upon resonant conditions. This power-dependent behavior offers a simple and practical route towards dynamically fine-tunable ferrite metamaterials.

  14. Spatially Defined Oligonucleotide Arrays. Technical Report for Phase II; FINAL

    International Nuclear Information System (INIS)

    None

    2000-01-01

    The goal of the Human Genome Project is to sequence all 3 billion base pairs of the human genome. Progress in this has been rapid; GenBank(reg s ign) finished 1994 with 286 million bases of sequence and grew by 2470 in the first quarter of 1995. The challenge to the scientific community is to understand the biological relevance of this genetic information. In most cases the sequence being generated for any single region of the genome represents the genotype of a single individual. A complete understanding of the function of specific genes and other regions of the genome and their role in human disease and development will only become apparent when the sequence of many more individuals is known. Access to genetic information is ultimately limited by the ability to screen DNA sequence. Although the pioneering sequencing methods of Sanger et al. (15) and Maxam and Gilbert (11) have become standard in virtually all molecular biology laboratories, the basic protocols remain largely unchanged. The throughput of this sequencing technology is now becoming the rate-limiting step in both large-scale sequencing projects such as the Human Genome Project and the subsequent efforts to understand genetic diversity. This has inspired the development of advanced DNA sequencing technologies (9), Incremental improvements to Sanger sequencing have been made in DNA labeling and detection. High-speed electrophoresis methods using ultrathin gels or capillary arrays are now being more widely employed. However, these methods are throughput-limited by their sequential nature and the speed and resolution of separations. This limitation will become more pronounced as the need to rapidly screen newly discovered genes for biologically relevant polymorphisms increases. An alternative to gel-based sequencing is to use high-density oligonucleotide probe arrays. Oligonucleotide probe arrays display specific oligonucleotide probes at precise locations in a high density, information-rich format (5,4,1

  15. Impaired cognitive discrimination and discoordination of coupled theta-gamma oscillations in Fmr1 knockout mice

    Science.gov (United States)

    Radwan, Basma; Dvorak, Dino; Fenton, André

    2016-01-01

    Fragile X syndrome (FXS) patients do not make the fragile X mental retardation protein (FMRP). Absence of FMRP causes dysregulated translation, abnormal synaptic plasticity and the most common form of inherited intellectual disability. But FMRP loss has minimal effects on memory itself, making it difficult to understand why absence of FMRP impairs memory discrimination and increases risk of autistic symptoms in patients, such as exaggerated responses to environmental changes. While Fmr1 knockout (KO) and wild-type (WT) mice perform cognitive discrimination tasks, we find abnormal patterns of coupling between theta and gamma oscillations in perisomatic and dendritic hippocampal CA1 local field potentials of the KO. Perisomatic CA1 theta-gamma phase-amplitude coupling (PAC) decreases with familiarity in both the WT and KO, but activating an invisible shock zone, subsequently changing its location, or turning it off, changes the pattern of oscillatory events in the LFPs recorded along the somato-dendritic axis of CA1. The cognition-dependent changes of this pattern of neural activity are relatively constrained in WT mice compared to KO mice, which exhibit abnormally weak changes during the cognitive challenge caused by changing the location of the shock zone and exaggerated patterns of change when the shock zone is turned off. Such pathophysiology might explain how dysregulated translation leads to intellectual disability in FXS. These findings demonstrate major functional abnormalities after the loss of FMRP in the dynamics of neural oscillations and that these impairments would be difficult to detect by steady-state measurements with the subject at rest or in steady conditions. PMID:26792400

  16. Smart-phone based computational microscopy using multi-frame contact imaging on a fiber-optic array.

    Science.gov (United States)

    Navruz, Isa; Coskun, Ahmet F; Wong, Justin; Mohammad, Saqib; Tseng, Derek; Nagi, Richie; Phillips, Stephen; Ozcan, Aydogan

    2013-10-21

    We demonstrate a cellphone based contact microscopy platform, termed Contact Scope, which can image highly dense or connected samples in transmission mode. Weighing approximately 76 grams, this portable and compact microscope is installed on the existing camera unit of a cellphone using an opto-mechanical add-on, where planar samples of interest are placed in contact with the top facet of a tapered fiber-optic array. This glass-based tapered fiber array has ~9 fold higher density of fiber optic cables on its top facet compared to the bottom one and is illuminated by an incoherent light source, e.g., a simple light-emitting-diode (LED). The transmitted light pattern through the object is then sampled by this array of fiber optic cables, delivering a transmission image of the sample onto the other side of the taper, with ~3× magnification in each direction. This magnified image of the object, located at the bottom facet of the fiber array, is then projected onto the CMOS image sensor of the cellphone using two lenses. While keeping the sample and the cellphone camera at a fixed position, the fiber-optic array is then manually rotated with discrete angular increments of e.g., 1-2 degrees. At each angular position of the fiber-optic array, contact images are captured using the cellphone camera, creating a sequence of transmission images for the same sample. These multi-frame images are digitally fused together based on a shift-and-add algorithm through a custom-developed Android application running on the smart-phone, providing the final microscopic image of the sample, visualized through the screen of the phone. This final computation step improves the resolution and also removes spatial artefacts that arise due to non-uniform sampling of the transmission intensity at the fiber optic array surface. We validated the performance of this cellphone based Contact Scope by imaging resolution test charts and blood smears.

  17. Genetic mapping using the Diversity Arrays Technology (DArT) : application and validation using the whole-genome sequences of Arabidopsis thaliana and the fungal wheat pathogen Mycosphaerella graminicola

    NARCIS (Netherlands)

    Wittenberg, A.H.J.

    2007-01-01

    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- to thousands of restriction site based polymorphisms between genotypes and does not require DNA sequence

  18. 77 FR 40358 - Federal Management Regulation; FMR Bulletin PBS-2012-03; Redesignations of Federal Buildings...

    Science.gov (United States)

    2012-07-09

    ... Management Regulation; FMR Bulletin PBS-2012-03; Redesignations of Federal Buildings: Correction AGENCY: Public Buildings Service (PBS), General Services Administration (GSA). ACTION: Notice of a bulletin..., 2012, a bulletin announcing the designation and redesignation of three Federal buildings. Inadvertently...

  19. Tomographical properties of uniformly redundant arrays

    International Nuclear Information System (INIS)

    Cannon, T.M.; Fenimore, E.E.

    1978-01-01

    Recent work in coded aperture imaging has shown that the uniformly redundant array (URA) can image distant planar radioactive sources with no artifacts. The performance of two URA apertures when used in a close-up tomographic imaging system is investigated. It is shown that a URA based on m sequences is superior to one based on quadratic residues. The m sequence array not only produces less obnoxious artifacts in tomographic imaging, but is also more resilient to some described detrimental effects of close-up imaging. It is shown that in spite of these close-up effects, tomographic depth resolution increases as the source is moved closer to the detector

  20. 77 FR 35393 - Federal Management Regulation; FMR Bulletin PBS-2012-03; Redesignations of Federal Buildings

    Science.gov (United States)

    2012-06-13

    ... Management Regulation; FMR Bulletin PBS-2012-03; Redesignations of Federal Buildings AGENCY: Public Buildings... bulletin announces the designation and redesignation of three Federal buildings. Expiration Date: This bulletin announcement expires October 31, 2012. The building designation and redesignations remains in...

  1. A sequence in subdomain 2 of DBL1α of Plasmodium falciparum erythrocyte membrane protein 1 induces strain transcending antibodies.

    Directory of Open Access Journals (Sweden)

    Karin Blomqvist

    Full Text Available Immunity to severe malaria is the first level of immunity acquired to Plasmodium falciparum. Antibodies to the variant antigen PfEMP1 (P. falciparum erythrocyte membrane protein 1 present at the surface of the parasitized red blood cell (pRBC confer protection by blocking microvascular sequestration. Here we have generated antibodies to peptide sequences of subdomain 2 of PfEMP1-DBL1α previously identified to be associated with severe or mild malaria. A set of sera generated to the amino acid sequence KLQTLTLHQVREYWWALNRKEVWKA, containing the motif ALNRKE, stained the live pRBC. 50% of parasites tested (7/14 were positive both in flow cytometry and immunofluorescence assays with live pRBCs including both laboratory strains and in vitro adapted clinical isolates. Antibodies that reacted selectively with the sequence REYWWALNRKEVWKA in a 15-mer peptide array of DBL1α-domains were also found to react with the pRBC surface. By utilizing a peptide array to map the binding properties of the elicited anti-DBL1α antibodies, the amino acids WxxNRx were found essential for antibody binding. Complementary experiments using 135 degenerate RDSM peptide sequences obtained from 93 Ugandan patient-isolates showed that antibody binding occurred when the amino acids WxLNRKE/D were present in the peptide. The data suggests that the ALNRKE sequence motif, associated with severe malaria, induces strain-transcending antibodies that react with the pRBC surface.

  2. A 7T spine array based on electric dipole transmitters.

    Science.gov (United States)

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

    2015-10-01

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

  3. Microcomputer based system to control the load of a capacitor array in the TJ-1 Tokamak; Sistema de control de carga de condensadores del TJ-1

    Energy Technology Data Exchange (ETDEWEB)

    Alberdi, J.; Asenjo, L.; Sanz, J.A.

    1990-12-31

    The power to create the magnetic field in the TJ-1 TOKAMAK is provide by an array of 16 capacitor sets. The total capacity of this array is 8.1F. This work describes a computer system based on the Motorola M-6800 microprocessor which controls the load of the capacitor set-and stablishes the conditions for the reactor trigger. (author)

  4. Microcomputer based system to control the load of a capacitor array in the TJ-1 Tokamak. Sistema de control de carga de condensadores del TJ-1

    Energy Technology Data Exchange (ETDEWEB)

    Alberdi, J.; Asenjo, L.; Sanz, J.A.

    1990-01-01

    The power to create the magnetic field in the TJ-1 TOKAMAK is provide by an array of 16 capacitor sets. The total capacity of this array is 8.1F. This work describes a computer system based on the Motorola M-6800 microprocessor which controls the load of the capacitor set-and stablishes the conditions for the reactor trigger. (author)

  5. Microcomputer Based System to control the Load of a Capacitor Array in the TJ-1 Tokamak; Sistema de Control de Carga de Condensadores del TJ-1

    Energy Technology Data Exchange (ETDEWEB)

    Alberdi, J; Asenso, L; Sanz, J A

    1990-07-01

    The power to create the magnetic fields in the TJ-1 Tokamak is provides by an array of 16 capacitor sets. The total capacity of this array is 8. 1F. This work describes a computer system based on the Motorola M-6800 micro- processor which controls the load of the capacitor set and stablished the conditions for the reactor trigger. (Author)

  6. Nine-channel mid-power bipolar pulse generator based on a field programmable gate array

    Energy Technology Data Exchange (ETDEWEB)

    Haylock, Ben, E-mail: benjamin.haylock2@griffithuni.edu.au; Lenzini, Francesco; Kasture, Sachin; Fisher, Paul; Lobino, Mirko [Centre for Quantum Dynamics, Griffith University, Brisbane (Australia); Queensland Micro and Nanotechnology Centre, Griffith University, Brisbane (Australia); Streed, Erik W. [Centre for Quantum Dynamics, Griffith University, Brisbane (Australia); Institute for Glycomics, Griffith University, Gold Coast (Australia)

    2016-05-15

    Many channel arbitrary pulse sequence generation is required for the electro-optic reconfiguration of optical waveguide networks in Lithium Niobate. Here we describe a scalable solution to the requirement for mid-power bipolar parallel outputs, based on pulse patterns generated by an externally clocked field programmable gate array. Positive and negative pulses can be generated at repetition rates up to 80 MHz with pulse width adjustable in increments of 1.6 ns across nine independent outputs. Each channel can provide 1.5 W of RF power and can be synchronised with the operation of other components in an optical network such as light sources and detectors through an external clock with adjustable delay.

  7. Report for Development of a Census Array and Evaluation of the Array to Detect Biothreat Agents and Environmental Samples for DHS

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C; Jackson, P

    2011-04-14

    The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. This report focuses on the design, testing and results of samples on the Census Array. We designed a Census/Detection Array to detect all sequenced viruses (including phage), bacteria (eubacteria), and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms, and to be unique relative to the human genome. A combination of 'detection' probes with high levels of conservation within a family plus 'census' probes targeting strain/isolate specific regions enabled detection and taxonomic classification from the level of family down to the strain. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. We tested the array with purified bacterial and viral DNA/RNA samples, artificial mixes of known bacterial/viral samples, spiked DNA against complex background including BW aerosol samples and soil samples, and environmental samples to evaluate the array's sensitivity and forensic capability. The data were analyzed using our novel maximum likelihood software. For most of the organisms tested, we have achieved at least species level discrimination.

  8. 41 CFR 102-2.140 - What elements of plain language appear in the FMR?

    Science.gov (United States)

    2010-07-01

    ... MANAGEMENT REGULATION SYSTEM Plain Language Regulatory Style § 102-2.140 What elements of plain language... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false What elements of plain language appear in the FMR? 102-2.140 Section 102-2.140 Public Contracts and Property Management Federal...

  9. Digital chaotic sequence generator based on coupled chaotic systems

    International Nuclear Information System (INIS)

    Shu-Bo, Liu; Jing, Sun; Jin-Shuo, Liu; Zheng-Quan, Xu

    2009-01-01

    Chaotic systems perform well as a new rich source of cryptography and pseudo-random coding. Unfortunately their digital dynamical properties would degrade due to the finite computing precision. Proposed in this paper is a modified digital chaotic sequence generator based on chaotic logistic systems with a coupling structure where one chaotic subsystem generates perturbation signals to disturb the control parameter of the other one. The numerical simulations show that the length of chaotic orbits, the output distribution of chaotic system, and the security of chaotic sequences have been greatly improved. Moreover the chaotic sequence period can be extended at least by one order of magnitude longer than that of the uncoupled logistic system and the difficulty in decrypting increases 2 128 *2 128 times indicating that the dynamical degradation of digital chaos is effectively improved. A field programmable gate array (FPGA) implementation of an algorithm is given and the corresponding experiment shows that the output speed of the generated chaotic sequences can reach 571.4 Mbps indicating that the designed generator can be applied to the real-time video image encryption. (general)

  10. Modeling Fragile X Syndrome in Drosophila

    Science.gov (United States)

    Drozd, Małgorzata; Bardoni, Barbara; Capovilla, Maria

    2018-01-01

    Intellectual disability (ID) and autism are hallmarks of Fragile X Syndrome (FXS), a hereditary neurodevelopmental disorder. The gene responsible for FXS is Fragile X Mental Retardation gene 1 (FMR1) encoding the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein involved in RNA metabolism and modulating the expression level of many targets. Most cases of FXS are caused by silencing of FMR1 due to CGG expansions in the 5′-UTR of the gene. Humans also carry the FXR1 and FXR2 paralogs of FMR1 while flies have only one FMR1 gene, here called dFMR1, sharing the same level of sequence homology with all three human genes, but functionally most similar to FMR1. This enables a much easier approach for FMR1 genetic studies. Drosophila has been widely used to investigate FMR1 functions at genetic, cellular, and molecular levels since dFMR1 mutants have many phenotypes in common with the wide spectrum of FMR1 functions that underlay the disease. In this review, we present very recent Drosophila studies investigating FMRP functions at genetic, cellular, molecular, and electrophysiological levels in addition to research on pharmacological treatments in the fly model. These studies have the potential to aid the discovery of pharmacological therapies for FXS. PMID:29713264

  11. Efficient decoupling schemes with bounded controls based on Eulerian orthogonal arrays

    International Nuclear Information System (INIS)

    Wocjan, Pawel

    2006-01-01

    The task of decoupling, i.e., removing unwanted internal couplings of a quantum system and its couplings to an environment, plays an important role in quantum control theory. There are many efficient decoupling schemes based on combinatorial concepts such as orthogonal arrays, difference schemes, and Hadamard matrices. So far these combinatorial decoupling schemes have relied on the ability to effect sequences of instantaneous, arbitrarily strong control Hamiltonians (bang-bang controls). To overcome the shortcomings of bang-bang control, Viola and Knill proposed a method called 'Eulerian decoupling' that allows the use of bounded-strength controls for decoupling. However, their method was not directly designed to take advantage of the local structure of internal couplings and couplings to an environment that typically occur in multipartite quantum systems. In this paper we define a combinatorial structure called Eulerian orthogonal array. It merges the desirable properties of orthogonal arrays and Eulerian cycles in Cayley graphs (that are the basis of Eulerian decoupling). We show that this structure gives rise to decoupling schemes with bounded-strength control Hamiltonians that can be used to remove both internal couplings and couplings to an environment of a multipartite quantum system. Furthermore, we show how to construct Eulerian orthogonal arrays having good parameters in order to obtain efficient decoupling schemes

  12. 76 FR 54772 - Federal Management Regulation; FMR Bulletin PBS-2011-B2; Redesignations of Federal Buildings

    Science.gov (United States)

    2011-09-02

    ... Management Regulation; FMR Bulletin PBS-2011-B2; Redesignations of Federal Buildings AGENCY: Public Buildings... announces the designation and redesignation of two Federal buildings. Expiration Date: This bulletin announcement expires January 31, 2012. The building designation and redesignation remains in effect until...

  13. 75 FR 69080 - Federal Management Regulation; FMR Bulletin PBS-2010-B5; Redesignations of Federal Buildings

    Science.gov (United States)

    2010-11-10

    ... Management Regulation; FMR Bulletin PBS-2010-B5; Redesignations of Federal Buildings AGENCY: Public Buildings... announces the designation and redesignation of two Federal buildings. DATES: Expiration Date: This bulletin announcement expires April 30, 2011. The building designation and redesignation remains in effect until...

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

    Directory of Open Access Journals (Sweden)

    Aihua Liu

    2017-01-01

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

  15. Extracting flat-field images from scene-based image sequences using phase correlation

    Energy Technology Data Exchange (ETDEWEB)

    Caron, James N., E-mail: Caron@RSImd.com [Research Support Instruments, 4325-B Forbes Boulevard, Lanham, Maryland 20706 (United States); Montes, Marcos J. [Naval Research Laboratory, Code 7231, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States); Obermark, Jerome L. [Naval Research Laboratory, Code 8231, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States)

    2016-06-15

    Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method uses sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.

  16. Post-processing Free Quantum Random Number Generator Based on Avalanche Photodiode Array

    International Nuclear Information System (INIS)

    Li Yang; Liao Sheng-Kai; Liang Fu-Tian; Shen Qi; Liang Hao; Peng Cheng-Zhi

    2016-01-01

    Quantum random number generators adopting single photon detection have been restricted due to the non-negligible dead time of avalanche photodiodes (APDs). We propose a new approach based on an APD array to improve the generation rate of random numbers significantly. This method compares the detectors' responses to consecutive optical pulses and generates the random sequence. We implement a demonstration experiment to show its simplicity, compactness and scalability. The generated numbers are proved to be unbiased, post-processing free, ready to use, and their randomness is verified by using the national institute of standard technology statistical test suite. The random bit generation efficiency is as high as 32.8% and the potential generation rate adopting the 32 × 32 APD array is up to tens of Gbits/s. (paper)

  17. A novel fragile X syndrome mutation reveals a conserved role for the carboxy-terminus in FMRP localization and function.

    Science.gov (United States)

    Okray, Zeynep; de Esch, Celine E F; Van Esch, Hilde; Devriendt, Koen; Claeys, Annelies; Yan, Jiekun; Verbeeck, Jelle; Froyen, Guy; Willemsen, Rob; de Vrij, Femke M S; Hassan, Bassem A

    2015-04-01

    Loss of function of the FMR1 gene leads to fragile X syndrome (FXS), the most common form of intellectual disability. The loss of FMR1 function is usually caused by epigenetic silencing of the FMR1 promoter leading to expansion and subsequent methylation of a CGG repeat in the 5' untranslated region. Very few coding sequence variations have been experimentally characterized and shown to be causal to the disease. Here, we describe a novel FMR1 mutation and reveal an unexpected nuclear export function for the C-terminus of FMRP. We screened a cohort of patients with typical FXS symptoms who tested negative for CGG repeat expansion in the FMR1 locus. In one patient, we identified a guanine insertion in FMR1 exon 15. This mutation alters the open reading frame creating a short novel C-terminal sequence, followed by a stop codon. We find that this novel peptide encodes a functional nuclear localization signal (NLS) targeting the patient FMRP to the nucleolus in human cells. We also reveal an evolutionarily conserved nuclear export function associated with the endogenous C-terminus of FMRP. In vivo analyses in Drosophila demonstrate that a patient-mimetic mutation alters the localization and function of Dfmrp in neurons, leading to neomorphic neuronal phenotypes. © 2015 The Authors. Published under the terms of the CC BY 4.0 license.

  18. 75 FR 44264 - Federal Management Regulation; FMR Bulletin PBS-2010-B4; Redesignation of Federal Building

    Science.gov (United States)

    2010-07-28

    ... Management Regulation; FMR Bulletin PBS-2010-B4; Redesignation of Federal Building AGENCY: Public Buildings... announces the redesignation of a Federal building. DATES: Expiration Date: This bulletin expires December 31, 2010. However, the building redesignation announced by this bulletin will remain in effect until...

  19. ArrayExpress update--trends in database growth and links to data analysis tools.

    Science.gov (United States)

    Rustici, Gabriella; Kolesnikov, Nikolay; Brandizi, Marco; Burdett, Tony; Dylag, Miroslaw; Emam, Ibrahim; Farne, Anna; Hastings, Emma; Ison, Jon; Keays, Maria; Kurbatova, Natalja; Malone, James; Mani, Roby; Mupo, Annalisa; Pedro Pereira, Rui; Pilicheva, Ekaterina; Rung, Johan; Sharma, Anjan; Tang, Y Amy; Ternent, Tobias; Tikhonov, Andrew; Welter, Danielle; Williams, Eleanor; Brazma, Alvis; Parkinson, Helen; Sarkans, Ugis

    2013-01-01

    The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

  20. Flexible eddy current coil arrays

    International Nuclear Information System (INIS)

    Krampfner, Y.; Johnson, D.P.

    1987-01-01

    A novel approach was devised to overcome certain limitations of conventional eddy current testing. The typical single-element hand-wound probe was replaced with a two dimensional array of spirally wound probe elements deposited on a thin, flexible polyimide substrate. This provides full and reliable coverage of the test area and eliminates the need for scanning. The flexible substrate construction of the array allows the probes to conform to irregular part geometries, such as turbine blades and tubing, thereby eliminating the need for specialized probes for each geometry. Additionally, the batch manufacturing process of the array can yield highly uniform and reproducible coil geometries. The array is driven by a portable computer-based eddy current instrument, smartEDDY/sup TM/, capable of two-frequency operation, and offers a great deal of versatility and flexibility due to its software-based architecture. The array is coupled to the instrument via an 80-switch multiplexer that can be configured to address up to 1600 probes. The individual array elements may be addressed in any desired sequence, as defined by the software

  1. Paper-based immune-affinity arrays for detection of multiple mycotoxins in cereals.

    Science.gov (United States)

    Li, Li; Chen, Hongpu; Lv, Xiaolan; Wang, Min; Jiang, Xizhi; Jiang, Yifei; Wang, Heye; Zhao, Yongfu; Xia, Liru

    2018-03-01

    Mycotoxins produced by different species of fungi may coexist in cereals and feedstuffs, and could be highly toxic for humans and animals. For quantification of multiple mycotoxins in cereals, we developed a paper-based mycotoxin immune-affinity array. First, paper-based microzone arrays were fabricated by photolithography. Then, monoclonal mycotoxin antibodies were added in a copolymerization reaction with a cross-linker to form an immune-affinity monolith on the paper-based microzone array. With use of a competitive immune-response format, paper-based mycotoxin immune-affinity arrays were successfully applied to detect mycotoxins in samples. The detection limits for deoxynivalenol, zearalenone, T-2 toxin, and HT-2 toxin were 62.7, 10.8, 0.36, and 0.23 μg·kg -1 , respectively, which meet relevant requirements for these compounds in food. The recovery rates were 81-86% for deoxynivalenol, 89-117% for zearalenone, 79-86% for T-2 toxin, and 78-83% for HT-2 toxin, and showed the paper-based immune-affinity arrays had good reproducibility. In summary, the paper-based mycotoxin immune-affinity array provides a sensitive, rapid, accurate, stable, and convenient platform for detection of multiple mycotoxins in agro-foods. Graphical abstract Paper-based immune-affinity monolithic array. DON deoxynivalenol, HT-2 HT-2 toxin, T-2 T-2 toxin, PEGDA polyethylene glycol diacrylate, ZEN zearalenone.

  2. Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

    International Nuclear Information System (INIS)

    Oudes, Asa J; Roach, Jared C; Walashek, Laura S; Eichner, Lillian J; True, Lawrence D; Vessella, Robert L; Liu, Alvin Y

    2005-01-01

    Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis. Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases

  3. Ferrite LTCC based phased array antennas

    KAUST Repository

    Ghaffar, Farhan A.

    2016-11-02

    Two phased array antennas realized in multilayer ferrite LTCC technology are presented in this paper. The use of embedded bias windings in these designs allows the negation of external magnets which are conventionally employed with bulk ferrite medium. This reduces the required magnetostatic field strength by 90% as compared to the traditional designs. The phase shifters are implemented using the SIW technology. One of the designs is operated in the half mode waveguide topology while the other design is based on standard full mode waveguide operation. The two phase shifter designs are integrated with two element patch antenna array and slotted SIW array respectively. The array designs demonstrate a beam steering of 30° and ±19° respectively for a current excitation of 200 mA. The designs, due to their small factor can be easily integrated in modern communication systems which is not possible in the case of bulk ferrite based designs.

  4. Computationally assisted screening and design of cell-interactive peptides by a cell-based assay using peptide arrays and a fuzzy neural network algorithm.

    Science.gov (United States)

    Kaga, Chiaki; Okochi, Mina; Tomita, Yasuyuki; Kato, Ryuji; Honda, Hiroyuki

    2008-03-01

    We developed a method of effective peptide screening that combines experiments and computational analysis. The method is based on the concept that screening efficiency can be enhanced from even limited data by use of a model derived from computational analysis that serves as a guide to screening and combining the model with subsequent repeated experiments. Here we focus on cell-adhesion peptides as a model application of this peptide-screening strategy. Cell-adhesion peptides were screened by use of a cell-based assay of a peptide array. Starting with the screening data obtained from a limited, random 5-mer library (643 sequences), a rule regarding structural characteristics of cell-adhesion peptides was extracted by fuzzy neural network (FNN) analysis. According to this rule, peptides with unfavored residues in certain positions that led to inefficient binding were eliminated from the random sequences. In the restricted, second random library (273 sequences), the yield of cell-adhesion peptides having an adhesion rate more than 1.5-fold to that of the basal array support was significantly high (31%) compared with the unrestricted random library (20%). In the restricted third library (50 sequences), the yield of cell-adhesion peptides increased to 84%. We conclude that a repeated cycle of experiments screening limited numbers of peptides can be assisted by the rule-extracting feature of FNN.

  5. DNA Array-Based Gene Profiling

    Science.gov (United States)

    Mocellin, Simone; Provenzano, Maurizio; Rossi, Carlo Riccardo; Pilati, Pierluigi; Nitti, Donato; Lise, Mario

    2005-01-01

    Cancer is a heterogeneous disease in most respects, including its cellularity, different genetic alterations, and diverse clinical behaviors. Traditional molecular analyses are reductionist, assessing only 1 or a few genes at a time, thus working with a biologic model too specific and limited to confront a process whose clinical outcome is likely to be governed by the combined influence of many genes. The potential of functional genomics is enormous, because for each experiment, thousands of relevant observations can be made simultaneously. Accordingly, DNA array, like other high-throughput technologies, might catalyze and ultimately accelerate the development of knowledge in tumor cell biology. Although in its infancy, the implementation of DNA array technology in cancer research has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to carcinogenesis, tumor aggressiveness, and sensitivity to antiblastic agents. Given the revolutionary implications that the use of this technology might have in the clinical management of patients with cancer, principles of DNA array-based tumor gene profiling need to be clearly understood for the data to be correctly interpreted and appreciated. In the present work, we discuss the technical features characterizing this powerful laboratory tool and review the applications so far described in the field of oncology. PMID:15621987

  6. 41 CFR 102-2.145 - To what do pronouns refer when used in the FMR?

    Science.gov (United States)

    2010-07-01

    ... MANAGEMENT REGULATION SYSTEM Plain Language Regulatory Style § 102-2.145 To what do pronouns refer when used... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false To what do pronouns refer when used in the FMR? 102-2.145 Section 102-2.145 Public Contracts and Property Management Federal...

  7. Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array.

    Science.gov (United States)

    van Geest, Geert; Voorrips, Roeland E; Esselink, Danny; Post, Aike; Visser, Richard Gf; Arens, Paul

    2017-08-07

    Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Further, we present a method for dosage scoring in hexaploids from signal intensities of the array based on mixture models (2) and validation of selection steps in the SNP selection pipeline (3). The resulting genotypic data is used to draw conclusions on the mode of inheritance in chrysanthemum (4), and to make an inference on allelic expression bias (5). With use of the mixture model approach, we successfully called the dosage of 73,936 out of 183,130 SNPs (40.4%) that segregated in any of the bi-parental populations. To investigate the mode of inheritance, we analysed markers that segregated in the large bi-parental population (n = 405). Analysis of segregation of duplex x nulliplex SNPs resulted in evidence for genome-wide hexasomic inheritance. This evidence was substantiated by the absence of strong linkage between markers in repulsion, which indicated absence of full disomic inheritance. We present the success rate of SNP discovery out of RNA sequencing data as affected by different selection steps, among which SNP coverage over genotypes and use of different types of sequence read mapping software. Genomic dosage highly correlated with relative allele coverage from the RNA sequencing data, indicating that most alleles are expressed according to their genomic dosage. The large population, genotyped with a very large number of markers, is a unique framework for extensive genetic analyses in hexaploid chrysanthemum. As starting point, we show conclusive evidence for genome-wide hexasomic inheritance.

  8. Study of LCP based flexible patch antenna array

    KAUST Repository

    Ghaffar, Farhan A.

    2012-07-01

    Wrapping of a two element LCP based patch antenna array is studied in this work. For the first time, the designed array is bent in both E and H planes to observe the effect on the radiation and impedance performance of the antenna. The 38 GHz simulation results reveal better performance for H plane bending as compared to E plane bending. A 100 um thick substrate is used for the design which is best suited for flexible antenna applications. Gain variations of 1.1 dB and 1.4 dB are observed for the two orientations while a significantly increased impedance bandwidth of 3 % is obtained with H plane wrapping. The design is highly suitable for broadband micro-cellular backhaul applications. © 2012 IEEE.

  9. Exome sequencing of a multigenerational human pedigree.

    Directory of Open Access Journals (Sweden)

    Dale J Hedges

    2009-12-01

    Full Text Available Over the next few years, the efficient use of next-generation sequencing (NGS in human genetics research will depend heavily upon the effective mechanisms for the selective enrichment of genomic regions of interest. Recently, comprehensive exome capture arrays have become available for targeting approximately 33 Mb or approximately 180,000 coding exons across the human genome. Selective genomic enrichment of the human exome offers an attractive option for new experimental designs aiming to quickly identify potential disease-associated genetic variants, especially in family-based studies. We have evaluated a 2.1 M feature human exome capture array on eight individuals from a three-generation family pedigree. We were able to cover up to 98% of the targeted bases at a long-read sequence read depth of > or = 3, 86% at a read depth of > or = 10, and over 50% of all targets were covered with > or = 20 reads. We identified up to 14,284 SNPs and small indels per individual exome, with up to 1,679 of these representing putative novel polymorphisms. Applying the conservative genotype calling approach HCDiff, the average rate of detection of a variant allele based on Illumina 1 M BeadChips genotypes was 95.2% at > or = 10x sequence. Further, we propose an advantageous genotype calling strategy for low covered targets that empirically determines cut-off thresholds at a given coverage depth based on existing genotype data. Application of this method was able to detect >99% of SNPs covered > or = 8x. Our results offer guidance for "real-world" applications in human genetics and provide further evidence that microarray-based exome capture is an efficient and reliable method to enrich for chromosomal regions of interest in next-generation sequencing experiments.

  10. Internal Transcribed Spacer 1 (ITS1 based sequence typing reveals phylogenetically distinct Ascaris population

    Directory of Open Access Journals (Sweden)

    Koushik Das

    2015-01-01

    Full Text Available Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout the world is certainly crucial. Ascaris population from human has been genetically characterized based on the widely used genetic marker, internal transcribed spacer1 (ITS1. Along with previously reported and prevalent genotype G1, 8 new sequence variants of ITS1 have been identified. Genotype G1 was significantly present among female patients aged between 10 to 15 years. Intragenic linkage disequilibrium (LD analysis at target locus within our study population has identified an incomplete LD value with potential recombination events. A separate cluster of Indian isolates with high bootstrap value indicate their distinct phylogenetic position in comparison to the global Ascaris population. Genetic shuffling through recombination could be a possible reason for high population diversity and frequent emergence of new sequence variants, identified in present and other previous studies. This study explores the genetic organization of Indian Ascaris population for the first time which certainly includes some fundamental information on the molecular epidemiology of Ascariasis.

  11. The use of a phased-array surface coil and breath-holding in MRI of the liver. Comparison of conventional SE, fat-suppressed GRE, and TSE sequences

    International Nuclear Information System (INIS)

    Helmberger, T.; Holzknecht, N.; Lackerbauer, C.A.; Mueller-Lisse, U.; Schnarkowski, P.; Gauger, J.; Reiser, M.

    1995-01-01

    To determine the efficacy of fast MRI techniques using a taylored imaging design (breathhold and array-surface coil), conventional T1-, T2-weighted spin-echo (SE) sequences and breathhold gradient-echo (GRE) T1- and breathhold fast SE T2-weighted images were compared. 20 patients with proven focal liver lesions were studied on a 1.5 Tesla system. Conventional SE T1- und T2-weighted imaging, as well as GRE T1- and fast SE T2-weighted imaging was performed. Fast imaging was done during breathhold using an array-surface coil. For all sequences signal-to-noise ratios (S/N) and liver-to-lesion-contrast ratios (L/L) were measured and statistically compared. Regarding image quality parameters, S/N and L/L, there was no significant difference between the conventional and fast imaging techniques. However, GRE imaging was superior (84.8%) to conventional imaging for breathing and pulsation artifacts, while fast SE T2 imaging was equal regarding breathing artifacts, but superior (51.5%) regarding pulsation artifacts. The number of detected hepatic lesions was identical in all sequences. The fast MRI techniques demonstrated a superiority to conventional imaging regarding image quality and presence of artifacts. (orig.) [de

  12. PDMS-based triboelectric and transparent nanogenerators with ZnO nanorod arrays.

    Science.gov (United States)

    Ko, Yeong Hwan; Nagaraju, Goli; Lee, Soo Hyun; Yu, Jae Su

    2014-05-14

    Vertically-grown ZnO nanorod arrays (NRAs) on indium tin oxide (ITO)-coated polyethylene terephthalate (PET), as a top electrode of nanogenerators, were investigated for the antireflective property as well as an efficient contact surface in bare polydimethysiloxane (PDMS)-based triboelectric nanogenerators. Compared to conventional ITO-coated PET (i.e., ITO/PET), the ZnO NRAs considerably suppressed the reflectance from 20 to 9.7% at wavelengths of 300-1100 nm, creating a highly transparent top electrode, as demonstrated by theoretical analysis. Also, the interval time between the peaks of generated output voltage under external pushing forces was significantly decreased from 1.84 to 0.19 s because the reduced contact area of the PDMS by discrete surfaces of the ZnO NRAs on ITO/PET causes a rapid sequence for triboelectric charge generation process including rubbing and separating. Therefore, the use of this top electrode enabled to operate the transparent PDMS-based triboelectric nanogenerator at high frequency of external pushing force. Under different external forces of 0.3-10 kgf, the output voltage and current were also characterized.

  13. Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Knudsen, Steen

    2002-01-01

    PROBEWIZ designs PCR primers for amplifying probes for cDNA arrays. The probes are designed to have minimal homology to other expressed sequences from a given organism. The primer selection is based on user-defined penalties for homology, primer quality, and proximity to the 3' end.......PROBEWIZ designs PCR primers for amplifying probes for cDNA arrays. The probes are designed to have minimal homology to other expressed sequences from a given organism. The primer selection is based on user-defined penalties for homology, primer quality, and proximity to the 3' end....

  14. Two sequence motifs from HIF-1α bind to the DNA-binding site of p53

    OpenAIRE

    Hansson, Lars O.; Friedler, Assaf; Freund, Stefan; Rüdiger, Stefan; Fersht, Alan R.

    2002-01-01

    There is evidence that hypoxia-inducible factor-1α (HIF-1α) interacts with the tumor suppressor p53. To characterize the putative interaction, we mapped the binding of the core domain of p53 (p53c) to an array of immobilized HIF-1α-derived peptides and found two peptide-sequence motifs that bound to p53c with micromolar affinity in solution. One sequence was adjacent to and the other coincided with the two proline residues of the oxygen-dependent degradation domain (P402 and P564) that act as...

  15. Generalized min-max bound-based MRI pulse sequence design framework for wide-range T1 relaxometry: A case study on the tissue specific imaging sequence.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    Full Text Available This paper proposes a new design strategy for optimizing MRI pulse sequences for T1 relaxometry. The design strategy optimizes the pulse sequence parameters to minimize the maximum variance of unbiased T1 estimates over a range of T1 values using the Cramér-Rao bound. In contrast to prior sequences optimized for a single nominal T1 value, the optimized sequence using our bound-based strategy achieves improved precision and accuracy for a broad range of T1 estimates within a clinically feasible scan time. The optimization combines the downhill simplex method with a simulated annealing process. To show the effectiveness of the proposed strategy, we optimize the tissue specific imaging (TSI sequence. Preliminary Monte Carlo simulations demonstrate that the optimized TSI sequence yields improved precision and accuracy over the popular driven-equilibrium single-pulse observation of T1 (DESPOT1 approach for normal brain tissues (estimated T1 700-2000 ms at 3.0T. The relative mean estimation error (MSE for T1 estimation is less than 1.7% using the optimized TSI sequence, as opposed to less than 7.0% using DESPOT1 for normal brain tissues. The optimized TSI sequence achieves good stability by keeping the MSE under 7.0% over larger T1 values corresponding to different lesion tissues and the cerebrospinal fluid (up to 5000 ms. The T1 estimation accuracy using the new pulse sequence also shows improvement, which is more pronounced in low SNR scenarios.

  16. Paper-Based Active Tactile Sensor Array.

    Science.gov (United States)

    Zhong, Qize; Zhong, Junwen; Cheng, Xiaofeng; Yao, Xu; Wang, Bo; Li, Wenbo; Wu, Nan; Liu, Kang; Hu, Bin; Zhou, Jun

    2015-11-25

    A paper-based active tactile sensor -array (PATSA) with a dynamic sensitivity of 0.35 V N(-1) is demonstrated. The pixel position of the PATSA can be routed by analyzing the real-time recording voltages in the pressing process. The PATSA performance, which remains functional when removing partial areas, reveals that the device has a potential application to customized electronic skins. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. 16.1% Efficient Hysteresis-Free Mesostructured Perovskite Solar Cells Based on Synergistically Improved ZnO Nanorod Arrays

    KAUST Repository

    Mahmood, Khalid

    2015-06-01

    Significant efficiency improvements are reported in mesoscopic perovskite solar cells based on the development of a low-temperature solution-processed ZnO nanorod (NR) array exhibiting higher NR aspect ratio, enhanced electron density, and substantially reduced work function than conventional ZnO NRs. These features synergistically result in hysteresis-free, scan-independent, and stabilized devices with an efficiency of 16.1%. Electron-rich, nitrogen-doped ZnO (N:ZnO) NR-based electron transporting materials (ETMs) with enhanced electron mobility produced using ammonium acetate show consistently higher efficiencies by one to three power points than undoped ZnO NRs. Additionally, the preferential electrostatic interaction between the -nonpolar facets of N:ZnO and the conjugated polyelectrolyte polyethylenimine (PEI) has been relied on to promote the hydrothermal growth of high aspect ratio NR arrays and substantially improve the infiltration of the perovskite light absorber into the ETM. Using the same interactions, a conformal PEI coating on the electron-rich high aspect ratio N:ZnO NR arrays is -successfully applied, resulting in a favorable work function shift and altogether leading to the significant boost in efficiency from <10% up to >16%. These results largely surpass the state-of-the-art PCE of ZnO-based perovskite solar cells and highlight the benefits of synergistically combining mesoscale control with doping and surface modification. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Array processors based on Gaussian fraction-free method

    Energy Technology Data Exchange (ETDEWEB)

    Peng, S; Sedukhin, S [Aizu Univ., Aizuwakamatsu, Fukushima (Japan); Sedukhin, I

    1998-03-01

    The design of algorithmic array processors for solving linear systems of equations using fraction-free Gaussian elimination method is presented. The design is based on a formal approach which constructs a family of planar array processors systematically. These array processors are synthesized and analyzed. It is shown that some array processors are optimal in the framework of linear allocation of computations and in terms of number of processing elements and computing time. (author)

  19. Capillarity-based preparation system for optical colorimetric sensor arrays.

    Science.gov (United States)

    Luo, Xiao-Gang; Yi, Xin; Bu, Xiang-Nan; Hou, Chang-Jun; Huo, Dan-Qun; Yang, Mei; Fa, Huan-Bao; Lei, Jin-Can

    2017-03-01

    In recent years, optical colorimetric sensor arrays have demonstrated beneficial features, including rapid response, high selectivity, and high specificity; as a result, it has been extensively applied in food inspection and chemical studies, among other fields. There are instruments in the current market available for the preparation of an optical colorimetric sensor array, but it lacks the corresponding research of the preparation mechanism. Therefore, in connection with the main features of this kind of sensor array such as consistency, based on the preparation method of contact spotting, combined with a capillary fluid model, Washburn equation, Laplace equation, etc., this paper develops a diffusion model of an optical colorimetric sensor array during its preparation and sets up an optical colorimetric sensor array preparation system based on this diffusion model. Finally, this paper compares and evaluates the sensor arrays prepared by the system and prepared manually in three aspects such as the quality of array point, response of array, and response result, and the results show that the performance index of the sensor array prepared by a system under this diffusion model is better than that of the sensor array of manual spotting, which meets the needs of the experiment.

  20. Analyzing Plasmodium falciparum erythrocyte membrane protein 1 gene expression by a next generation sequencing based method

    DEFF Research Database (Denmark)

    Jespersen, Jakob S.; Petersen, Bent; Seguin-Orlando, Andaine

    2013-01-01

    at identifying PfEMP1 features associated with high virulence. Here we present the first effective method for sequence analysis of var genes expressed in field samples: a sequential PCR and next generation sequencing based technique applied on expressed var sequence tags and subsequently on long range PCR......, encoded by ~60 highly variable 'var' genes per haploid genome. PfEMP1 is exported to the surface of infected erythrocytes and is thought to be fundamental to immune evasion by adhesion to host and parasite factors. The highly variable nature has constituted a roadblock in var expression studies aimed...

  1. Complete genome sequence of Klebsiella pneumoniae J1, a protein-based microbial flocculant-producing bacterium.

    Science.gov (United States)

    Pang, Changlong; Li, Ang; Cui, Di; Yang, Jixian; Ma, Fang; Guo, Haijuan

    2016-02-20

    Klebsiella pneumoniae J1 is a Gram-negative strain, which belongs to a protein-based microbial flocculant-producing bacterium. However, little genetic information is known about this species. Here we carried out a whole-genome sequence analysis of this strain and report the complete genome sequence of this organism and its genetic basis for carbohydrate metabolism, capsule biosynthesis and transport system. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Hybridization and sequencing of nucleic acids using base pair mismatches

    Science.gov (United States)

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  3. Negative Effects of Chronic Rapamycin Treatment on Behavior in a Mouse Model of Fragile X Syndrome

    Directory of Open Access Journals (Sweden)

    Rachel M. Saré

    2018-01-01

    Full Text Available Fragile X syndrome (FXS, the most common form of inherited intellectual disability, is also highly associated with autism spectrum disorders (ASD. It is caused by expansion of a CGG repeat sequence on the X chromosome resulting in silencing of the FMR1 gene. This is modeled in the mouse by deletion of Fmr1 (Fmr1 KO. Fmr1 KO mice recapitulate many of the behavioral features of the disorder including seizure susceptibility, hyperactivity, impaired social behavior, sleep problems, and learning and memory deficits. The mammalian target of rapamycin pathway (mTORC1 is upregulated in Fmr1 KO mice and is thought to be important for the pathogenesis of this disorder. We treated Fmr1 KO mice chronically with an mTORC1 inhibitor, rapamycin, to determine if rapamycin treatment could reverse behavioral phenotypes. We performed open field, zero maze, social behavior, sleep, passive avoidance, and audiogenic seizure testing. We found that pS6 was upregulated in Fmr1 KO mice and normalized by rapamycin treatment, but, except for an anxiogenic effect, it did not reverse any of the behavioral phenotypes examined. In fact, rapamycin treatment had an adverse effect on sleep and social behavior in both control and Fmr1 KO mice. These results suggest that targeting the mTOR pathway in FXS is not a good treatment strategy and that other pathways should be considered.

  4. An Effective Amperometric Biosensor Based on Gold Nanoelectrode Arrays

    Directory of Open Access Journals (Sweden)

    Zhu Yingchun

    2008-01-01

    Full Text Available Abstract A sensitive amperometric biosensor based on gold nanoelectrode array (NEA was investigated. The gold nanoelectrode array was fabricated by template-assisted electrodeposition on general electrodes, which shows an ordered well-defined 3D structure of nanowires. The sensitivity of the gold NEA to hydrogen peroxide is 37 times higher than that of the conventional electrode. The linear range of the platinum NEA toward H2O2is from 1 × 10−6to 1 × 10−2 M, covering four orders of magnitudes with detection limit of 1 × 10−7 M and a single noise ratio (S/N of four. The enzyme electrode exhibits an excellent response performance to glucose with linear range from 1 × 10−5to 1 × 10−2 M and a fast response time within 8 s. The Michaelis–Menten constantkm and the maximum current densityi maxof the enzyme electrode were 4.97 mM and 84.60 μA cm−2, respectively. This special nanoelectrode may find potential application in other biosensors based on amperometric signals.

  5. 75 FR 32484 - Array-Based Cytogenetic Tests: Questions on Performance Evaluation, Result Reporting and...

    Science.gov (United States)

    2010-06-08

    ...] Array-Based Cytogenetic Tests: Questions on Performance Evaluation, Result Reporting and Interpretation... public meeting: Array-Based Cytogenetic Tests: Questions on Performance Evaluation, Result Reporting and... cytogenetic tests. Date and Time: The meeting will be held on June 30, 2010, from 1:30 p.m. to 5 p.m. Location...

  6. Polymerase-free measurement of microRNA-122 with single base specificity using single molecule arrays: Detection of drug-induced liver injury.

    Directory of Open Access Journals (Sweden)

    David M Rissin

    Full Text Available We have developed a single probe method for detecting microRNA from human serum using single molecule arrays, with sequence specificity down to a single base, and without the use of amplification by polymerases. An abasic peptide nucleic acid (PNA probe-containing a reactive amine instead of a nucleotide at a specific position in the sequence-for detecting a microRNA was conjugated to superparamagnetic beads. These beads were incubated with a sample containing microRNA, a biotinylated reactive nucleobase-containing an aldehyde group-that was complementary to the missing base in the probe sequence, and a reducing agent. When a target molecule with an exact match in sequence hybridized to the capture probe, the reactive nucleobase was covalently attached to the backbone of the probe by a dynamic covalent chemical reaction. Single molecules of the biotin-labeled probe were then labeled with streptavidin-β-galactosidase (SβG, the beads were resuspended in a fluorogenic enzyme substrate, loaded into an array of femtoliter wells, and sealed with oil. The array was imaged fluorescently to determine which beads were associated with single enzymes, and the average number of enzymes per bead was determined. The assay had a limit of detection of 500 fM, approximately 500 times more sensitive than a corresponding analog bead-based assay, with target specificity down to a single base mis-match. This assay was used to measure microRNA-122 (miR-122-an established biomarker of liver toxicity-extracted from the serum of patients who had acute liver injury due to acetaminophen, and control healthy patients. All patients with liver injury had higher levels of miR-122 in their serum compared to controls, and the concentrations measured correlated well with those determined using RT-qPCR. This approach allows rapid quantification of circulating microRNA with single-based specificity and a limit of quantification suitable for clinical use.

  7. Design of area array CCD image acquisition and display system based on FPGA

    Science.gov (United States)

    Li, Lei; Zhang, Ning; Li, Tianting; Pan, Yue; Dai, Yuming

    2014-09-01

    With the development of science and technology, CCD(Charge-coupled Device) has been widely applied in various fields and plays an important role in the modern sensing system, therefore researching a real-time image acquisition and display plan based on CCD device has great significance. This paper introduces an image data acquisition and display system of area array CCD based on FPGA. Several key technical challenges and problems of the system have also been analyzed and followed solutions put forward .The FPGA works as the core processing unit in the system that controls the integral time sequence .The ICX285AL area array CCD image sensor produced by SONY Corporation has been used in the system. The FPGA works to complete the driver of the area array CCD, then analog front end (AFE) processes the signal of the CCD image, including amplification, filtering, noise elimination, CDS correlation double sampling, etc. AD9945 produced by ADI Corporation to convert analog signal to digital signal. Developed Camera Link high-speed data transmission circuit, and completed the PC-end software design of the image acquisition, and realized the real-time display of images. The result through practical testing indicates that the system in the image acquisition and control is stable and reliable, and the indicators meet the actual project requirements.

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

    Directory of Open Access Journals (Sweden)

    Chang-Hyun Lee

    2016-10-01

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

  9. Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.

    Science.gov (United States)

    Gowrisankar, Sivakumar; Lerner-Ellis, Jordan P; Cox, Stephanie; White, Emily T; Manion, Megan; LeVan, Kevin; Liu, Jonathan; Farwell, Lisa M; Iartchouk, Oleg; Rehm, Heidi L; Funke, Birgit H

    2010-11-01

    Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.

  10. Black GE based on crystalline/amorphous core/shell nanoneedle arrays

    Science.gov (United States)

    Javey, Ali; Chueh, Yu-Lun; Fan, Zhiyong

    2014-03-04

    Direct growth of black Ge on low-temperature substrates, including plastics and rubber is reported. The material is based on highly dense, crystalline/amorphous core/shell Ge nanoneedle arrays with ultrasharp tips (.about.4 nm) enabled by the Ni catalyzed vapor-solid-solid growth process. Ge nanoneedle arrays exhibit remarkable optical properties. Specifically, minimal optical reflectance (<1%) is observed, even for high angles of incidence (.about.75.degree.) and for relatively short nanoneedle lengths (.about.1 .mu.m). Furthermore, the material exhibits high optical absorption efficiency with an effective band gap of .about.1 eV. The reported black Ge can have important practical implications for efficient photovoltaic and photodetector applications on nonconventional substrates.

  11. DNA detection on ultrahigh-density optical fiber-based nanoarrays.

    Science.gov (United States)

    Tam, Jenny M; Song, Linan; Walt, David R

    2009-04-15

    Nanoarrays for DNA detection were fabricated on etched nanofiber bundles based on recently developed techniques for microscale arrays. Two different-sized nanoarrays were created: one with 700 nm feature sizes and a 1 microm center-to-center pitch (approximately 1x10(6) array elements/mm(2)) and one with 300 nm feature sizes and a 500 nm center-to-center pitch (4.6x10(6) array elements/mm(2)). A random, multiplexed array composed of oligonucleotide-functionalized nanospheres was constructed and used for parallel detection and analysis of fluorescently labeled DNA targets. We have used these arrays to detect a variety of target sequences including Bacillus thuringiensis kurstaki and vaccina virus sequences, two potential biowarfare agents, as well as interleukin-2 sequences, an immune system modulator that has been used for the diagnosis of HIV.

  12. Efficient oligonucleotide probe selection for pan-genomic tiling arrays

    Directory of Open Access Journals (Sweden)

    Zhang Wei

    2009-09-01

    Full Text Available Abstract Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray applications, requires adequate coverage of probes targeting the regions of interest. An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. However, such a whole-genome tiling requires that the genome sequence is known in advance. For the accurate analysis of uncharacterized bacteria, an array must query a fully representative set of sequences from the species' pan-genome. Prior microarrays have included only a single strain per array or the conserved sequences of gene families. These arrays omit potentially important genes and sequence variants from the pan-genome. Results This paper presents a new probe selection algorithm (PanArray that can tile multiple whole genomes using a minimal number of probes. Unlike arrays built on clustered gene families, PanArray uses an unbiased, probe-centric approach that does not rely on annotations, gene clustering, or multi-alignments. Instead, probes are evenly tiled across all sequences of the pan-genome at a consistent level of coverage. To minimize the required number of probes, probes conserved across multiple strains in the pan-genome are selected first, and additional probes are used only where necessary to span polymorphic regions of the genome. The viability of the algorithm is demonstrated by array designs for seven different bacterial pan-genomes and, in particular, the design of a 385,000 probe array that fully tiles the genomes of 20 different Listeria monocytogenes strains with overlapping probes at greater than twofold coverage. Conclusion PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on

  13. Expected Science Performance of the Square Kilometre Array Phase 1 (SKA1)

    Science.gov (United States)

    Bourke, Tyler; Braun, Robert; Bonaldi, Anna; Garcia-Miro, Cristina; Keane, Evan; Wagg, Jeff; SKAO Science Team

    2018-01-01

    The Square Kilometre Array (SKA) will be the world’s largest radio telescope when Phase 1 (SKA1) is completed in the next decade. The past few years have seen great progress toward this goal, through extensive design activities, with construction to start before the end of this decade, and early operations anticipated to begin around 2026. This poster describes the SKA and presents the expected performance and capabilities of SKA1 based on the modelling and proto-typing to date.

  14. Sequence- vs. chip-assisted genomic selection: accurate biological information is advised.

    Science.gov (United States)

    Pérez-Enciso, Miguel; Rincón, Juan C; Legarra, Andrés

    2015-05-09

    The development of next-generation sequencing technologies (NGS) has made the use of whole-genome sequence data for routine genetic evaluations possible, which has triggered a considerable interest in animal and plant breeding fields. Here, we investigated whether complete or partial sequence data can improve upon existing SNP (single nucleotide polymorphism) array-based selection strategies by simulation using a mixed coalescence - gene-dropping approach. We simulated 20 or 100 causal mutations (quantitative trait nucleotides, QTN) within 65 predefined 'gene' regions, each 10 kb long, within a genome composed of ten 3-Mb chromosomes. We compared prediction accuracy by cross-validation using a medium-density chip (7.5 k SNPs), a high-density (HD, 17 k) and sequence data (335 k). Genetic evaluation was based on a GBLUP method. The simulations showed: (1) a law of diminishing returns with increasing number of SNPs; (2) a modest effect of SNP ascertainment bias in arrays; (3) a small advantage of using whole-genome sequence data vs. HD arrays i.e. ~4%; (4) a minor effect of NGS errors except when imputation error rates are high (≥20%); and (5) if QTN were known, prediction accuracy approached 1. Since this is obviously unrealistic, we explored milder assumptions. We showed that, if all SNPs within causal genes were included in the prediction model, accuracy could also dramatically increase by ~40%. However, this criterion was highly sensitive to either misspecification (including wrong genes) or to the use of an incomplete gene list; in these cases, accuracy fell rapidly towards that reached when all SNPs from sequence data were blindly included in the model. Our study shows that, unless an accurate prior estimate on the functionality of SNPs can be included in the predictor, there is a law of diminishing returns with increasing SNP density. As a result, use of whole-genome sequence data may not result in a highly increased selection response over high

  15. Cloth-based hybridization array system for expanded identification of the animal species origin of derived materials in feeds.

    Science.gov (United States)

    Murphy, Johanna; Armour, Jennifer; Blais, Burton W

    2007-12-01

    A cloth-based hybridization array system (CHAS) previously developed for the detection of animal species for which prohibited materials have been specified (cattle, sheep, goat, elk, and deer) has been expanded to include the detection of animal species for which there are no prohibitions (pig and horse) in Canadian and American animal feeds. Animal species were identified by amplification of mitochondrial DNA sequences by PCR and subsequent hybridization of the amplicons with an array of species-specific oligonucleotide capture probes immobilized on a polyester cloth support, followed by an immunoenzymatic assay of the bound PCR products. The CHAS permitted sensitive and specific detection of meat meals from different animal species blended in a grain-based feed and should provide a useful adjunct to microscopic examination for the identification of prohibited materials in animal feeds.

  16. Method and apparatus for synthesis of arrays of DNA probes

    Science.gov (United States)

    Cerrina, Francesco; Sussman, Michael R.; Blattner, Frederick R.; Singh-Gasson, Sangeet; Green, Roland

    2002-04-23

    The synthesis of arrays of DNA probes sequences, polypeptides, and the like is carried out using a patterning process on an active surface of a substrate. An image is projected onto the active surface of the substrate utilizing an image former that includes a light source that provides light to a micromirror device comprising an array of electronically addressable micromirrors, each of which can be selectively tilted between one of at least two positions. Projection optics receives the light reflected from the micromirrors along an optical axis and precisely images the micromirrors onto the active surface of the substrate, which may be used to activate the surface of the substrate. The first level of bases may then be applied to the substrate, followed by development steps, and subsequent exposure of the substrate utilizing a different pattern of micromirrors, with further repeats until the elements of a two dimensional array on the substrate surface have an appropriate base bound thereto. The micromirror array can be controlled in conjunction with a DNA synthesizer supplying appropriate reagents to a flow cell containing the active substrate to control the sequencing of images presented by the micromirror array in coordination of the reagents provided to the substrate.

  17. Spaced training rescues memory and ERK1/2 signaling in fragile X syndrome model mice.

    Science.gov (United States)

    Seese, Ronald R; Wang, Kathleen; Yao, Yue Qin; Lynch, Gary; Gall, Christine M

    2014-11-25

    Recent studies have shown that short, spaced trains of afferent stimulation produce much greater long-term potentiation (LTP) than that obtained with a single, prolonged stimulation episode. The present studies demonstrate that spaced training regimens, based on these LTP timing rules, facilitate learning in wild-type (WT) mice and can offset learning and synaptic signaling impairments in the fragile X mental retardation 1 (Fmr1) knockout (KO) model of fragile X syndrome. We determined that 5 min of continuous training supports object location memory (OLM) in WT but not Fmr1 KO mice. However, the same amount of training distributed across three short trials, spaced by one hour, produced robust long-term memory in the KOs. At least three training trials were needed to realize the benefit of spacing, and intertrial intervals shorter or longer than 60 min were ineffective. Multiple short training trials also rescued novel object recognition in Fmr1 KOs. The spacing effect was surprisingly potent: just 1 min of OLM training, distributed across three trials, supported robust memory in both genotypes. Spacing also rescued training-induced activation of synaptic ERK1/2 in dorsal hippocampus of Fmr1 KO mice. These results show that a spaced training regimen designed to maximize synaptic potentiation facilitates recognition memory in WT mice and can offset synaptic signaling and memory impairments in a model of congenital intellectual disability.

  18. Model-based processing for underwater acoustic arrays

    CERN Document Server

    Sullivan, Edmund J

    2015-01-01

    This monograph presents a unified approach to model-based processing for underwater acoustic arrays. The use of physical models in passive array processing is not a new idea, but it has been used on a case-by-case basis, and as such, lacks any unifying structure. This work views all such processing methods as estimation procedures, which then can be unified by treating them all as a form of joint estimation based on a Kalman-type recursive processor, which can be recursive either in space or time, depending on the application. This is done for three reasons. First, the Kalman filter provides a natural framework for the inclusion of physical models in a processing scheme. Second, it allows poorly known model parameters to be jointly estimated along with the quantities of interest. This is important, since in certain areas of array processing already in use, such as those based on matched-field processing, the so-called mismatch problem either degrades performance or, indeed, prevents any solution at all. Third...

  19. Characterization of Kerfless Linear Arrays Based on PZT Thick Film.

    Science.gov (United States)

    Zawada, Tomasz; Bierregaard, Louise Moller; Ringgaard, Erling; Xu, Ruichao; Guizzetti, Michele; Levassort, Franck; Certon, Dominique

    2017-09-01

    Multielement transducers enabling novel cost-effective fabrication of imaging arrays for medical applications have been presented earlier. Due to the favorable low lateral coupling of the screen-printed PZT, the elements can be defined by the top electrode pattern only, leading to a kerfless design with low crosstalk between the elements. The thick-film-based linear arrays have proved to be compatible with a commercial ultrasonic scanner and to support linear array beamforming as well as phased array beamforming. The main objective of the presented work is to investigate the performance of the devices at the transducer level by extensive measurements of the test structures. The arrays have been characterized by several different measurement techniques. First, electrical impedance measurements on several elements in air and liquid have been conducted in order to support material parameter identification using the Krimholtz-Leedom-Matthaei model. It has been found that electromechanical coupling is at the level of 35%. The arrays have also been characterized by a pulse-echo system. The measured sensitivity is around -60 dB, and the fractional bandwidth is close to 60%, while the center frequency is about 12 MHz over the whole array. Finally, laser interferometry measurements have been conducted indicating very good displacement level as well as pressure. The in-depth characterization of the array structure has given insight into the performance parameters for the array based on PZT thick film, and the obtained information will be used to optimize the key parameters for the next generation of cost-effective arrays based on piezoelectric thick film.

  20. Multispot array combined with S1 nuclease-mediated elimination of unpaired nucleotides

    DEFF Research Database (Denmark)

    Yoo, Seung Min; Kim, Dong Min; Lee, Sang Yup

    2015-01-01

    The accurate detection of mismatched base pairs is critical to many DNA hybridization-based applications in basic research and diagnostics. We herein demonstrate that mismatched DNAs on a multispot array can be accurately detected in a multiplexed way by employing the S1 nuclease-based mismatched...... base pair-specific cleavage system. After the optimization of the reaction condition, mismatched DNAs present in various pathogenic bacteria and genetic disorders could be successfully detected with stable hybridization signals regardless of the position of the fluorescent label relative to the probe......-target duplex. This technique of performing S1 nuclease-mediated cleavage on a multispot array offers high specificity and high-throughput detection of mismatched DNAs. It is expected that this assay system will prove useful for single-assay genotyping and/or the diagnosis of various diseases and pathogens....

  1. Study of LCP based flexible patch antenna array

    KAUST Repository

    Ghaffar, Farhan A.; Shamim, Atif; Roy, Langis

    2012-01-01

    Wrapping of a two element LCP based patch antenna array is studied in this work. For the first time, the designed array is bent in both E and H planes to observe the effect on the radiation and impedance performance of the antenna. The 38 GHz

  2. Accurate Local-Ancestry Inference in Exome-Sequenced Admixed Individuals via Off-Target Sequence Reads

    Science.gov (United States)

    Hu, Youna; Willer, Cristen; Zhan, Xiaowei; Kang, Hyun Min; Abecasis, Gonçalo R.

    2013-01-01

    Estimates of the ancestry of specific chromosomal regions in admixed individuals are useful for studies of human evolutionary history and for genetic association studies. Previously, this ancestry inference relied on high-quality genotypes from genome-wide association study (GWAS) arrays. These high-quality genotypes are not always available when samples are exome sequenced, and exome sequencing is the strategy of choice for many ongoing genetic studies. Here we show that off-target reads generated during exome-sequencing experiments can be combined with on-target reads to accurately estimate the ancestry of each chromosomal segment in an admixed individual. To reconstruct local ancestry, our method SEQMIX models aligned bases directly instead of relying on hard genotype calls. We evaluate the accuracy of our method through simulations and analysis of samples sequenced by the 1000 Genomes Project and the NHLBI Grand Opportunity Exome Sequencing Project. In African Americans, we show that local-ancestry estimates derived by our method are very similar to those derived with Illumina’s Omni 2.5M genotyping array and much improved in relation to estimates that use only exome genotypes and ignore off-target sequencing reads. Software implementing this method, SEQMIX, can be applied to analysis of human population history or used for genetic association studies in admixed individuals. PMID:24210252

  3. Ultrasound beam characteristics of a symmetric nodal origami based array

    Science.gov (United States)

    Bilgunde, Prathamesh N.; Bond, Leonard J.

    2018-04-01

    Origami-the ancient art of paper folding-is being explored in acoustics for effective focusing of sound. In this short communication, we present a numerical investigation of beam characteristics for an origami based ultrasound array. A spatial re-configuration of array elements is performed based upon the symmetric nodal origami. The effect of fold angle on the ultrasound beam is evaluated using frequency domain and transient finite element analysis. It was found that increase in the fold angle reduces near field length by 58% and also doubles the beam intensity as compared to the linear array. Transient analysis also indicated 80% reduction in the -6dB beam width, which can improve the lateral resolution of phased array. Such a spatially re-configurable array could potentially be used in the future to reduce the cost of electronics in the phased array instrumentation.

  4. Tin Oxide Nanorod Array-Based Electrochemical Hydrogen Peroxide Biosensor

    Directory of Open Access Journals (Sweden)

    Liu Jinping

    2010-01-01

    Full Text Available Abstract SnO2 nanorod array grown directly on alloy substrate has been employed as the working electrode of H2O2 biosensor. Single-crystalline SnO2 nanorods provide not only low isoelectric point and enough void spaces for facile horseradish peroxidase (HRP immobilization but also numerous conductive channels for electron transport to and from current collector; thus, leading to direct electrochemistry of HRP. The nanorod array-based biosensor demonstrates high H2O2 sensing performance in terms of excellent sensitivity (379 μA mM−1 cm−2, low detection limit (0.2 μM and high selectivity with the apparent Michaelis–Menten constant estimated to be as small as 33.9 μM. Our work further demonstrates the advantages of ordered array architecture in electrochemical device application and sheds light on the construction of other high-performance enzymatic biosensors.

  5. Fiber-optic microsphere-based antibody array for the analysis of inflammatory cytokines in saliva.

    Science.gov (United States)

    Blicharz, Timothy M; Siqueira, Walter L; Helmerhorst, Eva J; Oppenheim, Frank G; Wexler, Philip J; Little, Frédéric F; Walt, David R

    2009-03-15

    Antibody microarrays have emerged as useful tools for high-throughput protein analysis and candidate biomarker screening. We describe here the development of a multiplexed microsphere-based antibody array capable of simultaneously measuring 10 inflammatory protein mediators. Cytokine-capture microspheres were fabricated by covalently coupling monoclonal antibodies specific for cytokines of interest to fluorescently encoded 3.1 microm polymer microspheres. An optical fiber bundle containing approximately 50,000 individual 3.1 microm diameter fibers was chemically etched to create microwells in which cytokine-capture microspheres could be deposited. Microspheres were randomly distributed in the wells to produce an antibody array for performing a multiplexed sandwich immunoassay. The array responded specifically to recombinant cytokine solutions in a concentration-dependent fashion. The array was also used to examine endogenous mediator patterns in saliva supernatants from patients with pulmonary inflammatory diseases such as asthma and chronic obstructive pulmonary disease (COPD). This array technology may prove useful as a laboratory-based platform for inflammatory disease research and diagnostics, and its small footprint could also enable integration into a microfluidic cassette for use in point-of-care testing.

  6. A Ferrite LTCC-Based Monolithic SIW Phased Antenna Array

    KAUST Repository

    Nafe, Ahmed A.; Ghaffar, Farhan A.; Farooqui, Muhammad Fahad; Shamim, Atif

    2016-01-01

    In this work, we present a novel configuration for realizing monolithic SIW-based phased antenna arrays using Ferrite LTCC technology. Unlike the current common schemes for realizing SIW phased arrays that rely on surface-mount component (p-i-n diodes, etc) for controlling the phase of the individual antenna elements, here the phase is tuned by biasing of the ferrite filling of the SIW. This approach eliminates the need for mounting of any additional RF components and enables seamless monolithic integration of phase shifters and antennas in SIW technology. As a proof of concept, a two-element slotted SIW-based phased array is designed, fabricated and measured. The prototype exhibits a gain of 4.9 dBi at 13.2 GHz and a maximum E-plane beam-scanning of 28 degrees using external windings for biasing the phase shifters. Moreover, the array can achieve a maximum beam-scanning of 19 degrees when biased with small windings that are embedded in the package. This demonstration marks the first time a fully monolithic SIW-based phased array is realized in Ferrite LTCC technology and paves the way for future larger-size implementations.

  7. A Ferrite LTCC-Based Monolithic SIW Phased Antenna Array

    KAUST Repository

    Nafe, Ahmed

    2016-11-17

    In this work, we present a novel configuration for realizing monolithic SIW-based phased antenna arrays using Ferrite LTCC technology. Unlike the current common schemes for realizing SIW phased arrays that rely on surface-mount component (p-i-n diodes, etc) for controlling the phase of the individual antenna elements, here the phase is tuned by biasing of the ferrite filling of the SIW. This approach eliminates the need for mounting of any additional RF components and enables seamless monolithic integration of phase shifters and antennas in SIW technology. As a proof of concept, a two-element slotted SIW-based phased array is designed, fabricated and measured. The prototype exhibits a gain of 4.9 dBi at 13.2 GHz and a maximum E-plane beam-scanning of 28 degrees using external windings for biasing the phase shifters. Moreover, the array can achieve a maximum beam-scanning of 19 degrees when biased with small windings that are embedded in the package. This demonstration marks the first time a fully monolithic SIW-based phased array is realized in Ferrite LTCC technology and paves the way for future larger-size implementations.

  8. Thermal crosstalk in arrays of III-N-based Lasers

    International Nuclear Information System (INIS)

    Kuc, Maciej; Sarzała, Robert P.; Nakwaski, Włodzimierz

    2013-01-01

    This paper presents a 3D comprehensive thermal-electrical self-consistent model of the continuous-wave (CW) operation of one-dimensional arrays of III-N-based laser diodes at room-temperature (RT). Their performance is mostly limited by thermal processes, in particular by thermal crosstalk between array emitters. Based on data collected from a range of secondary sources, the temperature dependence of the thermal and electrical conductivities of III-N materials used to manufacture nitride-based devices is shown to be a function of the thickness, aluminum mole fractions and Si- and Mg-doping levels of the nitride layers. The impact of substrate width and thickness on increasing the efficiency of heat-flux transport and reducing thermal crosstalk is investigated. As expected, the application of a top-mounted diamond heat spreader was found to have considerable influence on the thermal crosstalk between array emitters, enabling the RT CW operation of laser diode arrays with additional emitters

  9. From MAD to SAD: The Italian experience for the low-frequency aperture array of SKA1-LOW

    Science.gov (United States)

    Bolli, P.; Pupillo, G.; Virone, G.; Farooqui, M. Z.; Lingua, A.; Mattana, A.; Monari, J.; Murgia, M.; Naldi, G.; Paonessa, F.; Perini, F.; Pluchino, S.; Rusticelli, S.; Schiaffino, M.; Schillirò, F.; Tartarini, G.; Tibaldi, A.

    2016-03-01

    This paper describes two small aperture array demonstrators called Medicina and Sardinia Array Demonstrators (MAD and SAD, respectively). The objectives of these instruments are to acquire experience and test new technologies for a possible application to the low-frequency aperture array of the low-frequency telescope of the Square Kilometer Array phase 1 (SKA1-LOW). The MAD experience was concluded in 2014, and it turned out to be an important test bench for implementing calibration techniques based on an artificial source mounted in an aerial vehicle. SAD is based on 128 dual-polarized Vivaldi antennas and is 1 order of magnitude larger than MAD. The architecture and the station size of SAD, which is along the construction phase, are more similar to those under evaluation for SKA1-LOW, and therefore, SAD is expected to provide useful hints for SKA1-LOW.

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

    Science.gov (United States)

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

    2016-10-13

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

  11. EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

    Directory of Open Access Journals (Sweden)

    Zhu Yuelin

    2008-01-01

    Full Text Available Abstract Background Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. With accumulating microarray data deposited in public databases, easy-to-use programs to re-analyze previously published microarray data are in high demand. Results EzArray is a web-based Affymetrix expression array data management and analysis system for researchers who need to organize microarray data efficiently and get data analyzed instantly. EzArray organizes microarray data into projects that can be analyzed online with predefined or custom procedures. EzArray performs data preprocessing and detection of differentially expressed genes with statistical methods. All analysis procedures are optimized and highly automated so that even novice users with limited pre-knowledge of microarray data analysis can complete initial analysis quickly. Since all input files, analysis parameters, and executed scripts can be downloaded, EzArray provides maximum reproducibility for each analysis. In addition, EzArray integrates with Gene Expression Omnibus (GEO and allows instantaneous re-analysis of published array data. Conclusion EzArray is a novel Affymetrix expression array data analysis and sharing system. EzArray provides easy-to-use tools for re-analyzing published microarray data and will help both novice and experienced users perform initial analysis of their microarray data from the location of data storage. We believe EzArray will be a useful system for facilities with microarray services and laboratories with multiple members involved in microarray data analysis. EzArray is freely available from http://www.ezarray.com/.

  12. Design for an IO block array in a tile-based FPGA

    International Nuclear Information System (INIS)

    Ding Guangxin; Chen Lingdou; Liu Zhongli

    2009-01-01

    A design for an IO block array in a tile-based FPGA is presented. Corresponding with the characteristics of the FPGA, each IO cell is composed of a signal path, local routing pool and configurable input/output buffers. Shared programmable registers in the signal path can be configured for the function of JTAG, without specific boundary scan registers/latches, saving layout area. The local routing pool increases the flexibility of routing and the routability of the whole FPGA. An auxiliary power supply is adopted to increase the performance of the IO buffers at different configured IO standards. The organization of the IO block array is described in an architecture description file, from which the array layout can be accomplished through use of an automated layout assembly tool. This design strategy facilitates the design of FPGAs with different capacities or architectures in an FPGA family series. The bond-out schemes of the same FPGA chip in different packages are also considered. The layout is based on SMIC 0.13 μm logic 1P8M salicide 1.2/2.5 V CMOS technology. Our performance is comparable with commercial SRAM-based FPGAs which use a similar process. (semiconductor integrated circuits)

  13. Three-dimensional digital imaging based on shifted point-array encoding.

    Science.gov (United States)

    Tian, Jindong; Peng, Xiang

    2005-09-10

    An approach to three-dimensional (3D) imaging based on shifted point-array encoding is presented. A kind of point-array structure light is projected sequentially onto the reference plane and onto the object surface to be tested and thus forms a pair of point-array images. A mathematical model is established to formulize the imaging process with the pair of point arrays. This formulation allows for a description of the relationship between the range image of the object surface and the lateral displacement of each point in the point-array image. Based on this model, one can reconstruct each 3D range image point by computing the lateral displacement of the corresponding point on the two point-array images. The encoded point array can be shifted digitally along both the lateral and the longitudinal directions step by step to achieve high spatial resolution. Experimental results show good agreement with the theoretical predictions. This method is applicable for implementing 3D imaging of object surfaces with complex topology or large height discontinuities.

  14. Control of recollection by slow gamma dominating mid-frequency gamma in hippocampus CA1

    Science.gov (United States)

    Dvorak, Dino; Radwan, Basma; Sparks, Fraser T.; Talbot, Zoe Nicole

    2018-01-01

    Behavior is used to assess memory and cognitive deficits in animals like Fmr1-null mice that model Fragile X Syndrome, but behavior is a proxy for unknown neural events that define cognitive variables like recollection. We identified an electrophysiological signature of recollection in mouse dorsal Cornu Ammonis 1 (CA1) hippocampus. During a shocked-place avoidance task, slow gamma (SG) (30–50 Hz) dominates mid-frequency gamma (MG) (70–90 Hz) oscillations 2–3 s before successful avoidance, but not failures. Wild-type (WT) but not Fmr1-null mice rapidly adapt to relocating the shock; concurrently, SG/MG maxima (SGdom) decrease in WT but not in cognitively inflexible Fmr1-null mice. During SGdom, putative pyramidal cell ensembles represent distant locations; during place avoidance, these are avoided places. During shock relocation, WT ensembles represent distant locations near the currently correct shock zone, but Fmr1-null ensembles represent the formerly correct zone. These findings indicate that recollection occurs when CA1 SG dominates MG and that accurate recollection of inappropriate memories explains Fmr1-null cognitive inflexibility. PMID:29346381

  15. A new sieving matrix for DNA sequencing, genotyping and mutation detection and high-throughput genotyping with a 96-capillary array system

    Energy Technology Data Exchange (ETDEWEB)

    Gao, David [Iowa State Univ., Ames, IA (United States)

    1999-11-08

    Capillary electrophoresis has been widely accepted as a fast separation technique in DNA analysis. In this dissertation, a new sieving matrix is described for DNA analysis, especially DNA sequencing, genetic typing and mutation detection. A high-throughput 96 capillary array electrophoresis system was also demonstrated for simultaneous multiple genotyping. The authors first evaluated the influence of different capillary coatings on the performance of DNA sequencing. A bare capillary was compared with a DB-wax, an FC-coated and a polyvinylpyrrolidone dynamically coated capillary with PEO as sieving matrix. It was found that covalently-coated capillaries had no better performance than bare capillaries while PVP coating provided excellent and reproducible results. The authors also developed a new sieving Matrix for DNA separation based on commercially available poly(vinylpyrrolidone) (PVP). This sieving matrix has a very low viscosity and an excellent self-coating effect. Successful separations were achieved in uncoated capillaries. Sequencing of M13mp18 showed good resolution up to 500 bases in treated PVP solution. Temperature gradient capillary electrophoresis and PVP solution was applied to mutation detection. A heteroduplex sample and a homoduplex reference were injected during a pair of continuous runs. A temperature gradient of 10 C with a ramp of 0.7 C/min was swept throughout the capillary. Detection was accomplished by laser induced fluorescence detection. Mutation detection was performed by comparing the pattern changes between the homoduplex and the heteroduplex samples. High throughput, high detection rate and easy operation were achieved in this system. They further demonstrated fast and reliable genotyping based on CTTv STR system by multiple-capillary array electrophoresis. The PCR products from individuals were mixed with pooled allelic ladder as an absolute standard and coinjected with a 96-vial tray. Simultaneous one-color laser-induced fluorescence

  16. Measurement of magnetization of Ga1−xMnxAs by ferromagnetic resonance

    International Nuclear Information System (INIS)

    Hagmann, J.A.; Traudt, K.; Zhou, Y.Y.; Liu, X.; Dobrowolska, M.; Furdyna, J.K.

    2014-01-01

    In this paper, we extend ferromagnetic resonance (FMR) studies of thin layers of the ferromagnetic semiconductor Ga 1−x Mn x As to the analysis of the integrated intensity of the resonance in order to obtain information on the total spin in the sample directly involved in ferromagnetically-ordered magnetization. A theoretical model is proposed for the dependences of the FMR integrated intensity and linewidth on the orientation of the applied magnetic field as the field direction is varied from in-plane to normal-to-the-plane of the Ga 1−x Mn x As layer. The strain-induced magnetic anisotropy of Ga 1−x Mn x As presents a significant challenge to conventional FMR linewidth and integrated intensity models. The new model predicts that the integrated FMR intensity is proportional to the saturation magnetization M S of the sample, with the constant of proportionality varying as a function of the polar and azimuthal angles of the applied magnetic field. The angular and temperature behaviors of the integrated intensity and linewidth of the FMR predicted by the proposed model are in good qualitative agreement with measurements. - Highlights: • We extend ferromagnetic resonance to the analysis of total magnetization of thin film Ga 1−x Mn x As. • We formulate a theoretical model for FMR integrated intensity and linewidth. • The model predicts that integrated FMR intensity is proportional to magnetization. • Predictions made by the model are in good qualitative agreement with measurements

  17. Irregular Polyomino-Shaped Subarrays for Space-Based Active Arrays

    Directory of Open Access Journals (Sweden)

    R. J. Mailloux

    2009-01-01

    Full Text Available This paper presents new results showing the application of polyomino-based subarrays to limited field of view and wideband, wide-angle scanning. This technology can reduce the number of phase controls in arrays used for limited sector coverage or the number of time delay devices for wideband radar or communications, and so can reduce the cost of space-based active arrays. We concentrate on the wideband application. Results are presented by comparing the gain and peak sidelobe results of irregular polyomino subarray-based arrays with those of rectangular subarrays. It is shown that using irregular polyomino subarrays can result in a major decrease in sidelobes while presenting, in most cases, only a few tenths of a dB gain reduction compared to rectangular subarrays.

  18. Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population

    Directory of Open Access Journals (Sweden)

    Tae-Joon Park

    2015-01-01

    Full Text Available Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip.

  19. Imaging 2015 Mw 7.8 Gorkha Earthquake and Its Aftershock Sequence Combining Multiple Calibrated Global Seismic Arrays

    Science.gov (United States)

    LI, B.; Ghosh, A.

    2016-12-01

    The 2015 Mw 7.8 Gorkha earthquake provides a good opportunity to study the tectonics and earthquake hazards in the Himalayas, one of the most seismically active plate boundaries. Details of the seismicity patterns and associated structures in the Himalayas are poorly understood mainly due to limited instrumentation. Here, we apply a back-projection method to study the mainshock rupture and the following aftershock sequence using four large aperture global seismic arrays. All the arrays show eastward rupture propagation of about 130 km and reveal similar evolution of seismic energy radiation, with strong high-frequency energy burst about 50 km north of Kathmandu. Each single array, however, is typically limited by large azimuthal gap, low resolution, and artifacts due to unmodeled velocity structures. Therefore, we use a self-consistent empirical calibration method to combine four different arrays to image the Gorkha event. It greatly improves the resolution, can better track rupture and reveal details that cannot be resolved by any individual array. In addition, we also use the same arrays at teleseismic distances and apply a back-projection technique to detect and locate the aftershocks immediately following the Gorkha earthquake. We detect about 2.5 times the aftershocks recorded by the Advance National Seismic System comprehensive earthquake catalog during the 19 days following the mainshock. The aftershocks detected by the arrays show an east-west trend in general, with majority of the aftershocks located at the eastern part of the rupture patch and surrounding the rupture zone of the largest Mw 7.3 aftershock. Overall spatiotemporal aftershock pattern agrees well with global catalog, with our catalog showing more details relative to the standard global catalog. The improved aftershock catalog enables us to better study the aftershock dynamics, stress evolution in this region. Moreover, rapid and better imaging of aftershock distribution may aid rapid response

  20. DNA suspension arrays: silencing discrete artifacts for high-sensitivity applications.

    Directory of Open Access Journals (Sweden)

    Matthew S Lalonde

    2010-11-01

    Full Text Available Detection of low frequency single nucleotide polymorphisms (SNPs has important implications in early screening for tumorgenesis, genetic disorders and pathogen drug resistance. Nucleic acid arrays are a powerful tool for genome-scale SNP analysis, but detection of low-frequency SNPs in a mixed population on an array is problematic. We demonstrate a model assay for HIV-1 drug resistance mutations, wherein ligase discrimination products are collected on a suspension array. In developing this system, we discovered that signal from multiple polymorphisms was obscured by two discrete hybridization artifacts. Specifically: 1 tethering of unligated probes on the template DNA elicited false signal and 2 unpredictable probe secondary structures impaired probe capture and suppressed legitimate signal from the array. Two sets of oligonucleotides were used to disrupt these structures; one to displace unligated reporter labels from the bead-bound species and another to occupy sequences which interfered with array hybridization. This artifact silencing system resulted in a mean 21-fold increased sensitivity for 29 minority variants of 17 codons in our model assay for mutations most commonly associated with HIV-1 drug resistance. Furthermore, since the artifacts we characterized are not unique to our system, their specific inhibition might improve the quality of data from solid-state microarrays as well as from the growing number of multiple analyte suspension arrays relying on sequence-specific nucleic acid target capture.

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

    Science.gov (United States)

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

    2010-01-01

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

  2. Characterizing leader sequences of CRISPR loci

    DEFF Research Database (Denmark)

    Alkhnbashi, Omer; Shah, Shiraz Ali; Garrett, Roger Antony

    2016-01-01

    The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR...... array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs...... sequences by focusing on the consensus repeat of the adjacent CRISPR array and weak upstream conservation signals. We applied our tool to the analysis of a comprehensive genomic database and identified several characteristic properties of leader sequences specific to archaea and bacteria, ranging from...

  3. A Broadband Metasurface-Based Terahertz Flat-Lens Array

    KAUST Repository

    Wang, Qiu; Zhang, Xueqian; Xu, Yuehong; Tian, Zhen; Gu, Jianqiang; Yue, Weisheng; Zhang, Shuang; Han, Jiaguang; Zhang, Weili; Zhang, Weili

    2015-01-01

    A metasurface-based terahertz flat-lens array is proposed, comprising C-shaped split-ring resonators exhibiting locally engineerable phase discontinuities. Possessing a high numerical aperture, the planar lens array is flexible, robust, and shows excellent focusing characteristics in a broadband terahertz frequency. It could be an important step towards the development of planar terahertz focusing devices for practical applications.

  4. A Broadband Metasurface-Based Terahertz Flat-Lens Array

    KAUST Repository

    Wang, Qiu

    2015-02-12

    A metasurface-based terahertz flat-lens array is proposed, comprising C-shaped split-ring resonators exhibiting locally engineerable phase discontinuities. Possessing a high numerical aperture, the planar lens array is flexible, robust, and shows excellent focusing characteristics in a broadband terahertz frequency. It could be an important step towards the development of planar terahertz focusing devices for practical applications.

  5. Evaluating imputation algorithms for low-depth genotyping-by-sequencing (GBS) data

    Science.gov (United States)

    Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordabl...

  6. RESEARCH NOTE Genome-based exome-sequencing analysis ...

    Indian Academy of Sciences (India)

    Navya

    2017-02-22

    Feb 22, 2017 ... Genome-based exome-sequencing analysis identifies GYG1, DIS3L, DDRGK1 genes ... Cardiology Division, Department of Internal Medicine, Severance .... with p values of <0.05 byanalyzing differences in allele distribution.

  7. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  8. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  9. A functional gene array for detection of bacterial virulence elements

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  10. Performance Evaluation of a Biometric System Based on Acoustic Images

    Science.gov (United States)

    Izquierdo-Fuente, Alberto; del Val, Lara; Jiménez, María I.; Villacorta, Juan J.

    2011-01-01

    An acoustic electronic scanning array for acquiring images from a person using a biometric application is developed. Based on pulse-echo techniques, multifrequency acoustic images are obtained for a set of positions of a person (front, front with arms outstretched, back and side). Two Uniform Linear Arrays (ULA) with 15 λ/2-equispaced sensors have been employed, using different spatial apertures in order to reduce sidelobe levels. Working frequencies have been designed on the basis of the main lobe width, the grating lobe levels and the frequency responses of people and sensors. For a case-study with 10 people, the acoustic profiles, formed by all images acquired, are evaluated and compared in a mean square error sense. Finally, system performance, using False Match Rate (FMR)/False Non-Match Rate (FNMR) parameters and the Receiver Operating Characteristic (ROC) curve, is evaluated. On the basis of the obtained results, this system could be used for biometric applications. PMID:22163708

  11. Performance Evaluation of a Biometric System Based on Acoustic Images

    Directory of Open Access Journals (Sweden)

    Juan J. Villacorta

    2011-10-01

    Full Text Available An acoustic electronic scanning array for acquiring images from a person using a biometric application is developed. Based on pulse-echo techniques, multifrequency acoustic images are obtained for a set of positions of a person (front, front with arms outstretched, back and side. Two Uniform Linear Arrays (ULA with 15 l/2-equispaced sensors have been employed, using different spatial apertures in order to reduce sidelobe levels. Working frequencies have been designed on the basis of the main lobe width, the grating lobe levels and the frequency responses of people and sensors. For a case-study with 10 people, the acoustic profiles, formed by all images acquired, are evaluated and compared in a mean square error sense. Finally, system performance, using False Match Rate (FMR/False Non-Match Rate (FNMR parameters and the Receiver Operating Characteristic (ROC curve, is evaluated. On the basis of the obtained results, this system could be used for biometric applications.

  12. An optomechatronic curvature measurement array based on fiber Bragg gratings

    International Nuclear Information System (INIS)

    Chang, Hsing-Cheng; Lin, Shyan-Lung; Hung, San-Shan; Chang, I-Nan; Chen, Ya-Hui; Lin, Jung-Chih; Liu, Wen-Fung

    2014-01-01

    This study investigated an optomechatronic array-integrated signal processing module and a human–machine interface based on fiber Bragg grating sensing elements embedded in an elastic support matrix that involves using a self-located electromagnetic mechanism for curvature sensing and solid contour reconstruction. Using bilinear interpolation and average calculation methods, the smooth and accurate surface contours of convex and concave lenses are reconstructed in real-time. The elastic supporting optical sensing array is self-balanced to reduce operational errors. Compared with our previous single-head sensor, the sensitivity of the proposed array is improved by more than 15%. In the curvature range from −20.15 to +27.09 m −1 , the sensitivities are 3.53 pm m for the convex measurement and 2.15 pm m for the concave measurement with an error rate below 8.89%. The curvature resolutions are 0.283 and 0.465 m −1 for convex and concave lenses, respectively. This array could be applied in the curvature measurement of solar collectors to monitor energy conversion efficiency or could be used to monitor the wafer-level thin-film fabrication process. (paper)

  13. Estrategia de genotipado del gen FMR1: Método de diagnóstico alternativo para el Síndrome X Frágil y otras enfermedades por expansión de trinucleotidos

    Directory of Open Access Journals (Sweden)

    Saúl Lindo-Samanamud

    2013-10-01

    Full Text Available Objetivos: Diseñar una estrategia alternativa por PCR para el genotipado de secuencias ricas en citosinas, basada en modificación nucleotídica. Material y métodos: Se modificó el gen FMR1 nativo de ocho individuos clínicamente no afectados por el Síndrome X frágil, cambiando las citosinas por uracilos, empleando bisulfito de sodio. El ADN modificado fue purificado y cuantificado por espectrofotometría. Las estructuras alternativas y potenciales islas CpG que adopta el microsatélite inestable fueron simuladas con los programas MFOLD y CpGplot. Se generaron cebadores específicos que hibriden tanto con el microsatélite modificado (Primer T y con una secuencia modificada de las islas CpG (Primer M, utilizando el programa MethPrimer. Finalmente, ambas secuencias fueron amplificadas por PCR y los amplicones fueron separados por electroforesis en gel de poliacrilamida (PAGE por sus siglas en inglés al 6% y visualizados con tinción de nitrato de plata. Resultados: La modificación del ADN fue evidenciada por espectrofotometría al uracilo. Las estructuras observadas en la simulación fueron las horquillas encontrándose dos potenciales islas CpG. La amplificación con los cebadores T, confirmó el diseño in silico desarrollado para abordar la estructura en horquillas. La amplificación con los cebadores M permitió detectar metilación de la primera isla CpG del gen FMR1.Conclusión: Se propone un diseño alternativo para amplificación de secuencias de microsatélite que contengan citosinas metiladas y no metiladas. Se requieren estudios posteriores con muestras de ADN que contengan microsatélites muy expandidos para validar su aplicación para diagnóstico molecular.

  14. Investigating Microbial Habitats in Hydrothermal Chimneys using Ti-Thermocouple Arrays: Microbial Diversity

    Science.gov (United States)

    Pagé, A.; Tivey, M. K.; Stakes, D. S.; Bradley, A. M.; Seewald, J. S.; Wheat, C. G.; Reysenbach, A.

    2004-12-01

    In order to examine the changes that occur in the microbial community composition as a deep-sea hydrothermal vent chimney develops, we deployed Ti-thermocouple arrays over high temperature vents at two active sites of the Guaymas Basin Southern Trough. Chimney material that precipitated around the arrays was recovered after 4 and 72 days. Chimney material that precipitated prior to deployment of the arrays was also recovered at one of the sites (Busted Shroom). Culture-independent analysis based on the small subunit rRNA sequence (cloning and DGGE) was used to determine the microbial diversity associated with subsamples of each chimney. The original Busted Shroom chimney (BSO) was dominated by members of the Crenarchaeota Marine Group I, a group of cosmopolitan marine Archaea, ɛ -Proteobacteria, and γ -Proteobacteria, two divisions of Bacteria that are common to deep-sea vents. The 4 days old Busted Shroom chimney (BSD1) was dominated by members of the Methanocaldococcaceae, hyperthermophilic methanogens, and the 72 days old chimney (BSD2) by members of the Methanosarcinaceae, mesophilic and thermophilic methanogens. At the second site, Toadstool, the 72 days old chimney material that had precipitated around the array (TS) revealed the dominance of sequences from uncultured marine Archaea, the DHVE group I and II, and from the ɛ -Proteobacteria. Additionally, sequences belonging to the Methanocaldococcaceae and Desulfurococcaceae were recovered next to thermocouples that were at temperatures of 109° C (at Busted Shroom) and 116° C (at Toadstool), respectively. These temperatures are higher than the upper limit for growth of cultured representatives from each family.

  15. Combining gene expression data from different generations of oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Kong Sek

    2004-10-01

    Full Text Available Abstract Background One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism or structure can be obtained. However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform. Results We first describe the extent of discordance between the results derived from two generations of Affymetrix oligonucleotide arrays, as revealed in cluster analysis and in identification of differentially expressed genes. We then propose a method for increasing comparability. The dataset we use consists of a set of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays. We find that the use of the probe set matching table for comparative analysis provided by Affymetrix produces better results than matching by UniGene or LocusLink identifiers but still remains inadequate. Rescaling of expression values for each gene across samples and data filtering by expression values enhance comparability but only for few specific analyses. As a generic method for improving comparability, we select a subset of probes with overlapping sequence segments in the two array types and recalculate expression values based only on the selected probes. We show that this filtering of probes significantly improves the comparability while retaining a sufficient number of probe sets for further analysis. Conclusions Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different

  16. Flexible Supercapacitors Based on Polyaniline Arrays Coated Graphene Aerogel Electrodes.

    Science.gov (United States)

    Yang, Yu; Xi, Yunlong; Li, Junzhi; Wei, Guodong; Klyui, N I; Han, Wei

    2017-12-01

    Flexible supercapacitors(SCs) made by reduced graphene oxide (rGO)-based aerogel usually suffer from the low energy density, short cycle life and bad flexibility. In this study, a new, synthetic strategy was developed for enhancing the electrochemical performances of rGO aerogel-based supercapacitor via electrodeposition polyaniline arrays on the prepared ultralight rGO aerogel. The novel hybrid composites with coated polyaniline (PANI) arrays growing on the rGO surface can take full advantage of the rich open-pore and excellent conductivity of the crosslinking framework structure of 3D rGO aerogel and high capacitance contribution from the PANI. The obtained hybrid composites exhibit excellent electrochemical performance with a specific capacitance of 432 F g -1 at the current density of 1 A g -1 , robust cycling stability to maintain 85% after 10,000 charge/discharge cycles and high energy density of 25 W h kg -1 . Furthermore, the flexible all-solid-state supercapacitor have superior flexibility and outstanding stability under different bending states from the straight state to the 90° status. The high-performance flexible all-solid-state SCs together with the lighting tests demonstrate it possible for applications in portable electronics.

  17. Peptide array-based interaction assay of solid-bound peptides and anchorage-dependant cells and its effectiveness in cell-adhesive peptide design.

    Science.gov (United States)

    Kato, Ryuji; Kaga, Chiaki; Kunimatsu, Mitoshi; Kobayashi, Takeshi; Honda, Hiroyuki

    2006-06-01

    Peptide array, the designable peptide library covalently synthesized on cellulose support, was applied to assay peptide-cell interaction, between solid-bound peptides and anchorage-dependant cells, to study objective peptide design. As a model case, cell-adhesive peptides that could enhance cell growth as tissue engineering scaffold material, was studied. On the peptide array, the relative cell-adhesion ratio of NIH/3T3 cells was 2.5-fold higher on the RGDS (Arg-Gly-Asp-Ser) peptide spot as compared to the spot with no peptide, thus indicating integrin-mediated peptide-cell interaction. Such strong cell adhesion mediated by the RGDS peptide was easily disrupted by single residue substitution on the peptide array, thus indicating that the sequence recognition accuracy of cells was strictly conserved in our optimized scheme. The observed cellular morphological extension with active actin stress-fiber on the RGD motif-containing peptide supported our strategy that peptide array-based interaction assay of solid-bound peptide and anchorage-dependant cells (PIASPAC) could provide quantitative data on biological peptide-cell interaction. The analysis of 180 peptides obtained from fibronectin type III domain (no. 1447-1629) yielded 18 novel cell-adhesive peptides without the RGD motif. Taken together with the novel candidates, representative rules of ineffective amino acid usage were obtained from non-effective candidate sequences for the effective designing of cell-adhesive peptides. On comparing the amino acid usage of the top 20 and last 20 peptides from the 180 peptides, the following four brief design rules were indicated: (i) Arg or Lys of positively charged amino acids (except His) could enhance cell adhesion, (ii) small hydrophilic amino acids are favored in cell-adhesion peptides, (iii) negatively charged amino acids and small amino acids (except Gly) could reduce cell adhesion, and (iv) Cys and Met could be excluded from the sequence combination since they have

  18. Vision communications based on LED array and imaging sensor

    Science.gov (United States)

    Yoo, Jong-Ho; Jung, Sung-Yoon

    2012-11-01

    In this paper, we propose a brand new communication concept, called as "vision communication" based on LED array and image sensor. This system consists of LED array as a transmitter and digital device which include image sensor such as CCD and CMOS as receiver. In order to transmit data, the proposed communication scheme simultaneously uses the digital image processing and optical wireless communication scheme. Therefore, the cognitive communication scheme is possible with the help of recognition techniques used in vision system. By increasing data rate, our scheme can use LED array consisting of several multi-spectral LEDs. Because arranged each LED can emit multi-spectral optical signal such as visible, infrared and ultraviolet light, the increase of data rate is possible similar to WDM and MIMO skills used in traditional optical and wireless communications. In addition, this multi-spectral capability also makes it possible to avoid the optical noises in communication environment. In our vision communication scheme, the data packet is composed of Sync. data and information data. Sync. data is used to detect the transmitter area and calibrate the distorted image snapshots obtained by image sensor. By making the optical rate of LED array be same with the frame rate (frames per second) of image sensor, we can decode the information data included in each image snapshot based on image processing and optical wireless communication techniques. Through experiment based on practical test bed system, we confirm the feasibility of the proposed vision communications based on LED array and image sensor.

  19. Development and validation of an Haemophilus influenzae supragenome hybridization (SGH array for transcriptomic analyses.

    Directory of Open Access Journals (Sweden)

    Benjamin A Janto

    Full Text Available We previously carried out the design and testing of a custom-built Haemophilus influenzae supragenome hybridization (SGH array that contains probe sequences to 2,890 gene clusters identified by whole genome sequencing of 24 strains of H. influenzae. The array was originally designed as a tool to interrogate the gene content of large numbers of clinical isolates without the need for sequencing, however, the data obtained is quantitative and is thus suitable for transcriptomic analyses. In the current study RNA was extracted from H. influenzae strain CZ4126/02 (which was not included in the design of the array converted to cDNA, and labelled and hybridized to the SGH arrays to assess the quality and reproducibility of data obtained from these custom-designed chips to serve as a tool for transcriptomics. Three types of experimental replicates were analyzed with all showing very high degrees of correlation, thus validating both the array and the methods used for RNA profiling. A custom filtering pipeline for two-condition unpaired data using five metrics was developed to minimize variability within replicates and to maximize the identification of the most significant true transcriptional differences between two samples. These methods can be extended to transcriptional analysis of other bacterial species utilizing supragenome-based arrays.

  20. Automation and integration of multiplexed on-line sample preparation with capillary electrophoresis for DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Tan, H.

    1999-03-31

    The purpose of this research is to develop a multiplexed sample processing system in conjunction with multiplexed capillary electrophoresis for high-throughput DNA sequencing. The concept from DNA template to called bases was first demonstrated with a manually operated single capillary system. Later, an automated microfluidic system with 8 channels based on the same principle was successfully constructed. The instrument automatically processes 8 templates through reaction, purification, denaturation, pre-concentration, injection, separation and detection in a parallel fashion. A multiplexed freeze/thaw switching principle and a distribution network were implemented to manage flow direction and sample transportation. Dye-labeled terminator cycle-sequencing reactions are performed in an 8-capillary array in a hot air thermal cycler. Subsequently, the sequencing ladders are directly loaded into a corresponding size-exclusion chromatographic column operated at {approximately} 60 C for purification. On-line denaturation and stacking injection for capillary electrophoresis is simultaneously accomplished at a cross assembly set at {approximately} 70 C. Not only the separation capillary array but also the reaction capillary array and purification columns can be regenerated after every run. DNA sequencing data from this system allow base calling up to 460 bases with accuracy of 98%.

  1. Developing barbed microtip-based electrode arrays for biopotential measurement.

    Science.gov (United States)

    Hsu, Li-Sheng; Tung, Shu-Wei; Kuo, Che-Hsi; Yang, Yao-Joe

    2014-07-10

    This study involved fabricating barbed microtip-based electrode arrays by using silicon wet etching. KOH anisotropic wet etching was employed to form a standard pyramidal microtip array and HF/HNO3 isotropic etching was used to fabricate barbs on these microtips. To improve the electrical conductance between the tip array on the front side of the wafer and the electrical contact on the back side, a through-silicon via was created during the wet etching process. The experimental results show that the forces required to detach the barbed microtip arrays from human skin, a polydimethylsiloxane (PDMS) polymer, and a polyvinylchloride (PVC) film were larger compared with those required to detach microtip arrays that lacked barbs. The impedances of the skin-electrode interface were measured and the performance levels of the proposed dry electrode were characterized. Electrode prototypes that employed the proposed tip arrays were implemented. Electroencephalogram (EEG) and electrocardiography (ECG) recordings using these electrode prototypes were also demonstrated.

  2. Developing Barbed Microtip-Based Electrode Arrays for Biopotential Measurement

    Directory of Open Access Journals (Sweden)

    Li-Sheng Hsu

    2014-07-01

    Full Text Available This study involved fabricating barbed microtip-based electrode arrays by using silicon wet etching. KOH anisotropic wet etching was employed to form a standard pyramidal microtip array and HF/HNO3 isotropic etching was used to fabricate barbs on these microtips. To improve the electrical conductance between the tip array on the front side of the wafer and the electrical contact on the back side, a through-silicon via was created during the wet etching process. The experimental results show that the forces required to detach the barbed microtip arrays from human skin, a polydimethylsiloxane (PDMS polymer, and a polyvinylchloride (PVC film were larger compared with those required to detach microtip arrays that lacked barbs. The impedances of the skin-electrode interface were measured and the performance levels of the proposed dry electrode were characterized. Electrode prototypes that employed the proposed tip arrays were implemented. Electroencephalogram (EEG and electrocardiography (ECG recordings using these electrode prototypes were also demonstrated.

  3. Waveguide-Based Antenna Arrays for 5G Networks

    Directory of Open Access Journals (Sweden)

    Arismar Cerqueira Sodré

    2018-01-01

    Full Text Available This work reports the development of two high-performance waveguide-based antenna arrays for 5G cellular networks, operating in the underutilized millimetre wave (mm-wave frequency spectrum. Two different scenarios of mm-wave communications are proposed for illustrating the applicability of the proposed arrays, which provide specific radiation patterns, namely, 12 dBi gain omnidirectional coverage in the 28 GHz band and dual-band sectorial coverage using the 28 and 38 GHz bands with gain up to 15.6 dBi. Numerical and experimental results of the array reflection coefficient, radiation pattern, and gain have been shown in an excellent agreement.

  4. Fiber-array based optogenetic prosthetic system for stimulation therapy

    Science.gov (United States)

    Gu, Ling; Cote, Chris; Tejeda, Hector; Mohanty, Samarendra

    2012-02-01

    Recent advent of optogenetics has enabled activation of genetically-targeted neuronal cells using low intensity blue light with high temporal precision. Since blue light is attenuated rapidly due to scattering and absorption in neural tissue, optogenetic treatment of neurological disorders may require stimulation of specific cell types in multiple regions of the brain. Further, restoration of certain neural functions (vision, and auditory etc) requires accurate spatio-temporal stimulation patterns rather than just precise temporal stimulation. In order to activate multiple regions of the central nervous system in 3D, here, we report development of an optogenetic prosthetic comprising of array of fibers coupled to independently-controllable LEDs. This design avoids direct contact of LEDs with the brain tissue and thus does not require electrical and heat isolation, which can non-specifically stimulate and damage the local brain regions. The intensity, frequency, and duty cycle of light pulses from each fiber in the array was controlled independently using an inhouse developed LabView based program interfaced with a microcontroller driving the individual LEDs. While the temporal profile of the light pulses was controlled by varying the current driving the LED, the beam profile emanating from each fiber tip could be sculpted by microfabrication of the fiber tip. The fiber array was used to stimulate neurons, expressing channelrhodopsin-2, in different locations within the brain or retina. Control of neural activity in the mice cortex, using the fiber-array based prosthetic, is evaluated from recordings made with multi-electrode array (MEA). We also report construction of a μLED array based prosthetic for spatio-temporal stimulation of cortex.

  5. Sequence-Based Identification of Aspergillus, Fusarium, and Mucorales in the Clinical Laboratory: Where Are We and Where Should We Go From Here?

    Science.gov (United States)

    Accurate identification of fungal species helps establish or exclude a fungal cause of disease. In the past, clinical microbiology labs were restricted to a limited array of phenotypic criteria for categorizing isolates to the species level. This scenario is shifting in favour of DNA sequence-base...

  6. Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications

    Energy Technology Data Exchange (ETDEWEB)

    Hashimoto, Hideharu; Zhang, Xing; Zheng, Yu; Wilson, Geoffrey G.; Cheng, Xiaodong

    2016-09-04

    Mutations in human zinc-finger transcription factor WT1 result in abnormal development of the kidneys and genitalia and an array of pediatric problems including nephropathy, blastoma, gonadal dysgenesis and genital discordance. Several overlapping phenotypes are associated with WT1 mutations, including Wilms tumors, Denys-Drash syndrome (DDS), Frasier syndrome (FS) and WAGR syndrome (Wilms tumor, aniridia, genitourinary malformations, and mental retardation). These conditions vary in severity from individual to individual; they can be fatal in early childhood, or relatively benign into adulthood. DDS mutations cluster predominantly in zinc fingers (ZF) 2 and 3 at the C-terminus of WT1, which together with ZF4 determine the sequence-specificity of DNA binding. We examined three DDS associated mutations in ZF2 of human WT1 where the normal glutamine at position 369 is replaced by arginine (Q369R), lysine (Q369K) or histidine (Q369H). These mutations alter the sequence-specificity of ZF2, we find, changing its affinity for certain bases and certain epigenetic forms of cytosine. X-ray crystallography of the DNA binding domains of normal WT1, Q369R and Q369H in complex with preferred sequences revealed the molecular interactions responsible for these affinity changes. DDS is inherited in an autosomal dominant fashion, implying a gain of function by mutant WT1 proteins. This gain, we speculate, might derive from the ability of the mutant proteins to sequester WT1 into unproductive oligomers, or to erroneously bind to variant target sequences.

  7. 16.1% Efficient Hysteresis-Free Mesostructured Perovskite Solar Cells Based on Synergistically Improved ZnO Nanorod Arrays

    KAUST Repository

    Mahmood, Khalid; Swain, Bhabani Sankar; Amassian, Aram

    2015-01-01

    Significant efficiency improvements are reported in mesoscopic perovskite solar cells based on the development of a low-temperature solution-processed ZnO nanorod (NR) array exhibiting higher NR aspect ratio, enhanced electron density

  8. Multicoil resonance-based parallel array for smart wireless power delivery.

    Science.gov (United States)

    Mirbozorgi, S A; Sawan, M; Gosselin, B

    2013-01-01

    This paper presents a novel resonance-based multicoil structure as a smart power surface to wirelessly power up apparatus like mobile, animal headstage, implanted devices, etc. The proposed powering system is based on a 4-coil resonance-based inductive link, the resonance coil of which is formed by an array of several paralleled coils as a smart power transmitter. The power transmitter employs simple circuit connections and includes only one power driver circuit per multicoil resonance-based array, which enables higher power transfer efficiency and power delivery to the load. The power transmitted by the driver circuit is proportional to the load seen by the individual coil in the array. Thus, the transmitted power scales with respect to the load of the electric/electronic system to power up, and does not divide equally over every parallel coils that form the array. Instead, only the loaded coils of the parallel array transmit significant part of total transmitted power to the receiver. Such adaptive behavior enables superior power, size and cost efficiency then other solutions since it does not need to use complex detection circuitry to find the location of the load. The performance of the proposed structure is verified by measurement results. Natural load detection and covering 4 times bigger area than conventional topologies with a power transfer efficiency of 55% are the novelties of presented paper.

  9. Array-based sensing using nanoparticles: an alternative approach for cancer diagnostics.

    Science.gov (United States)

    Le, Ngoc D B; Yazdani, Mahdieh; Rotello, Vincent M

    2014-07-01

    Array-based sensing using nanoparticles (NPs) provides an attractive alternative to specific biomarker-focused strategies for cancer diagnosis. The physical and chemical properties of NPs provide both the recognition and transduction capabilities required for biosensing. Array-based sensors utilize a combined response from the interactions between sensors and analytes to generate a distinct pattern (fingerprint) for each analyte. These interactions can be the result of either the combination of multiple specific biomarker recognition (specific binding) or multiple selective binding responses, known as chemical nose sensing. The versatility of the latter array-based sensing using NPs can facilitate the development of new personalized diagnostic methodologies in cancer diagnostics, a necessary evolution in the current healthcare system to better provide personalized treatments. This review will describe the basic principle of array-based sensors, along with providing examples of both invasive and noninvasive samples used in cancer diagnosis.

  10. CRISPRDetect: A flexible algorithm to define CRISPR arrays.

    Science.gov (United States)

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

    2016-05-17

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

  11. Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA

    Directory of Open Access Journals (Sweden)

    Chan Alan

    2006-06-01

    Full Text Available Abstract Background Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length. Results In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A. Conclusion Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.

  12. Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA.

    Science.gov (United States)

    Gibbons, Brian; Datta, Parikkhit; Wu, Ying; Chan, Alan; Al Armour, John

    2006-06-30

    Current methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH) we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene International. In this new method, electrophoretic analysis of amplified products is replaced with photometric analysis of a probed oligonucleotide array. Copy number analysis of hybridised probes is based on a dual-label approach by comparing the intensity of Cy3-labelled MAPH probes amplified from test samples co-hybridised with similarly amplified Cy5-labelled reference MAPH probes. The key feature of using a hybridisation-based end point with MAPH is that discrimination of amplified probes is based on sequence and not fragment length. In this study we showed that microarray MAPH measurement of PMP22 gene dosage correlates well with PMP22 gene dosage determined by capillary MAPH and that copy number was accurately reported in analyses of DNA from 38 individuals, 12 of which were known to have Charcot-Marie-Tooth disease type 1A (CMT1A). Measurement of microarray-based endpoints for MAPH appears to be of comparable accuracy to electrophoretic methods, and holds the prospect of fully exploiting the potential multiplicity of MAPH. The technology has the potential to simplify copy number assays for genes with a large number of exons, or of expanded sets of probes from dispersed genomic locations.

  13. Large-scale Identification of Expressed Sequence Tags (ESTs from Nicotianatabacum by Normalized cDNA Library Sequencing

    Directory of Open Access Journals (Sweden)

    Alvarez S Perez

    2014-12-01

    Full Text Available An expressed sequence tags (EST resource for tobacco plants (Nicotianatabacum was established using high-throughput sequencing of randomly selected clones from one cDNA library representing a range of plant organs (leaf, stem, root and root base. Over 5000 ESTs were generated from the 3’ ends of 8000 clones, analyzed by BLAST searches and categorized functionally. All annotated ESTs were classified into 18 functional categories, unique transcripts involved in energy were the largest group accounting for 831 (32.32% of the annotated ESTs. After excluding 2450 non-significant tentative unique transcripts (TUTs, 100 unique sequences (1.67% of total TUTs were identified from the N. tabacum database. In the array result two genes strongly related to the tobacco mosaic virus (TMV were obtained, one basic form of pathogenesis-related protein 1 precursor (TBT012G08 and ubiquitin (TBT087G01. Both of them were found in the variety Hongda, some other important genes were classified into two groups, one of these implicated in plant development like those genes related to a photosynthetic process (chlorophyll a-b binding protein, photosystem I, ferredoxin I and III, ATP synthase and a further group including genes related to plant stress response (ubiquitin, ubiquitin-like protein SMT3, glycine-rich RNA binding protein, histones and methallothionein. The interesting finding in this study is that two of these genes have never been reported before in N. tabacum (ubiquitin-like protein SMT3 and methallothionein. The array results were confirmed using quantitative PCR.

  14. Successive Standardization of Rectangular Arrays

    Directory of Open Access Journals (Sweden)

    Richard A. Olshen

    2012-02-01

    Full Text Available In this note we illustrate and develop further with mathematics and examples, the work on successive standardization (or normalization that is studied earlier by the same authors in [1] and [2]. Thus, we deal with successive iterations applied to rectangular arrays of numbers, where to avoid technical difficulties an array has at least three rows and at least three columns. Without loss, an iteration begins with operations on columns: first subtract the mean of each column; then divide by its standard deviation. The iteration continues with the same two operations done successively for rows. These four operations applied in sequence completes one iteration. One then iterates again, and again, and again, ... In [1] it was argued that if arrays are made up of real numbers, then the set for which convergence of these successive iterations fails has Lebesgue measure 0. The limiting array has row and column means 0, row and column standard deviations 1. A basic result on convergence given in [1] is true, though the argument in [1] is faulty. The result is stated in the form of a theorem here, and the argument for the theorem is correct. Moreover, many graphics given in [1] suggest that except for a set of entries of any array with Lebesgue measure 0, convergence is very rapid, eventually exponentially fast in the number of iterations. Because we learned this set of rules from Bradley Efron, we call it “Efron’s algorithm”. More importantly, the rapidity of convergence is illustrated by numerical examples.

  15. Swarm-based Sequencing Recommendations in E-learning

    NARCIS (Netherlands)

    Van den Berg, Bert; Tattersall, Colin; Janssen, José; Brouns, Francis; Kurvers, Hub; Koper, Rob

    2005-01-01

    Van den Berg, B., Tattersall, C., Janssen, J., Brouns, F., Kurvers, H., & Koper, R. (2006). Swarm-based Sequencing Recommendations in E-learning. International Journal of Computer Science & Applications, III(III), 1-11.

  16. Preliminary Investigation of an SOI-based Arrayed Waveguide Grating Demodulation Integration Microsystem

    Science.gov (United States)

    Li, Hongqiang; Zhou, Wenqian; Liu, Yu; Dong, Xiaye; Zhang, Cheng; Miao, Changyun; Zhang, Meiling; Li, Enbang; Tang, Chunxiao

    2014-05-01

    An arrayed waveguide grating (AWG) demodulation integration microsystem is investigated in this study. The system consists of a C-band on-chip LED, a 2 × 2 silicon nanowire-based coupler, a fiber Bragg grating (FBG) array, a 1 × 8 AWG, and a photoelectric detector array. The coupler and AWG are made from silicon-on-insulator wafers using electron beam exposure and response-coupled plasma technology. Experimental results show that the excess loss in the MMI coupler with a footprint of 6 × 100 μm2 is 0.5423 dB. The 1 × 8 AWG with a footprint of 267 × 381 μm2 and a waveguide width of 0.4 μm exhibits a central channel loss of -3.18 dB, insertion loss non-uniformity of -1.34 dB, and crosstalk level of -23.1 dB. The entire system is preliminarily tested. Wavelength measurement precision is observed to reach 0.001 nm. The wavelength sensitivity of each FBG is between 0.04 and 0.06 nm/dB.

  17. SMITH: a LIMS for handling next-generation sequencing workflows

    OpenAIRE

    Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

    2014-01-01

    Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to ...

  18. A 15-year-long Southern blotting analysis of FMR1 to detect female carriers and for prenatal diagnosis of fragile X syndrome in Taiwan.

    Science.gov (United States)

    Tzeng, C-C; Tsai, L-P; Chang, Y-K; Hung, Y-J; Chang, Y-Y; Su, Y-P; Jiang, J-J; Liang, H-M

    2017-08-01

    Here, we review the results of Southern blotting analyses of the FMR1 gene performed in our reference laboratory in Taiwan over a 15-year period. In total, 725 high-risk women with a family history of fragile X syndrome (FXS) or idiopathic intellectual disability, 3911 low-risk pregnant women without such family history, and prenatal diagnosis data for 32 foetuses from 24 carrier mothers were included. Only 2 carriers were in the low-risk group, which indicated a prevalence of 1 of 1955 women (95% confidence interval: 1/7156-1/539). A total of 100 carriers were found to be in the high-risk group, thus revealing a significantly higher frequency than the low-risk group (100/725 vs 2/3911, P<0.0001). Eight of the 14 foetuses that inherited the maternal mutant allele were verified to have a full mutation, with the smallest maternal pre-mutation allele carrying 56 CGG repeats. The overall findings confirmed that the carrier prevalence among low-risk women in Taiwan is significantly lower than that reported in western countries. Therefore, the most important step for preventing FXS in Taiwan would be to focus on high-risk women by promoting general awareness of this disease and spreading knowledge regarding the benefits of carrier screening and prenatal testing. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  19. High specific radioactivity (1R,2S)-4-[18F]fluorometaraminol: a PET radiotracer for mapping sympathetic nerves of the heart

    International Nuclear Information System (INIS)

    Langer, Oliver; Valette, Heric; Dolle, Frederic; Halldin, Christer; Loc'h, Christian; Fuseau, Chantal; Coulon, Christine; Ottaviani, Michele; Bottlaender, Michel; Maziere, Bernard; Crouzel, Christian

    2000-01-01

    The radiolabeled catecholamine analogue (1R,2S)-6-[ 18 F]fluorometaraminol (6-[ 18 F]FMR) is a substrate for the neuronal norepinephrine transporter. It has been used as a positron emission tomography (PET) ligand to map sympathetic nerves in dog heart. 6-[ 18 F]FMR could be only synthesized with low specific radioactivity, which precluded its use in human subjects. We have recently prepared (1R,2S)-4-[ 18 F]fluorometaraminol (4-[ 18 F]FMR), a new fluoro-analogue of metaraminol, with high specific radioactivity (56-106 GBq/μmol). In the present study, we demonstrate in rats that 4-[ 18 F]FMR possesses similar affinity toward myocardial norepinephrine transport mechanisms as 6-[ 18 F]FMR. When compared with control animals, an 80% and 76% reduction in myocardial uptake was observed in animals pretreated with desipramine (an inhibitor of the neuronal norepinephrine transporter) and with reserpine (a blocker of the vesicular storage of monoamines), respectively. The entire radioactivity in rat myocardium represented unmetabolized parent tracer as determined by high performance liquid chromatography analysis of tissue extracts. In dogs, myocardial kinetics of 4-[ 18 F]FMR were assessed using PET. A rapid and high uptake was observed, followed by prolonged cardiac retention. A heart-to-lung ratio of 15 was reached 10 min after injection of the radiotracer. Pretreatment with desipramine reduced the heart half-life of 4-[ 18 F]FMR by 90% compared with control. Moreover, an infusion of tyramine caused a rapid decline of radioactivity in the heart. This demonstrates that 4-[ 18 F]FMR specifically visualizes sympathetic neurons in dog heart. High specific radioactivity 4-[ 18 F]FMR is a promising alternative to 6-[ 18 F]FMR for myocardial neuronal mapping with PET in humans

  20. Microneedle-based drug and vaccine delivery via nanoporous microneedle arrays

    OpenAIRE

    Maaden, van der, Koen; Lüttge, R Regina; Vos, PJW; Bouwstra, Joke A; Kersten, Gideon FA; Ploemen, IHJ Ingmar

    2015-01-01

    In the literature, several types of microneedles have been extensively described. However, porous microneedle arrays only received minimal attention. Hence, only little is known about drug delivery via these microneedles. However, porous microneedle arrays may have potential for future microneedle-based drug and vaccine delivery and could be a valuable addition to the other microneedle-based drug delivery approaches. To gain more insight into porous microneedle technologies, the scientific an...

  1. Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

    Science.gov (United States)

    Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

    2012-01-01

    The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

  2. Passive high-frequency devices based on superlattice ferromagnetic nanowires

    International Nuclear Information System (INIS)

    Ye, B.; Li, F.; Cimpoesu, D.; Wiley, J.B.; Jung, J.-S.; Stancu, A.; Spinu, L.

    2007-01-01

    In this paper we propose to tailor the bandwidth of a microwave filter by exploitation of shape anisotropy of nanowires. In order to achieve this control of shape anisotropy, we considered superlattice wires containing varying-sized ferromagnetic regions separated by nonferromagnetic regions. Superlattice wires of Ni and Au with a nominal diameter of 200 nm were grown using standard electrodeposition techniques. The microwave properties were probed using X-band (9.8 GHz) ferromagnetic resonance (FMR) experiments performed at room temperature. In order to investigate the effectiveness of the shape anisotropy on the superlattice nanowire based filter the FMR spectrum of superlattice structure is compared to the FMR spectra of nanowires samples with constant length

  3. Quantitative kinetics of proteolytic enzymes determined by a surface concentration-based assay using peptide arrays.

    Science.gov (United States)

    Jung, Se-Hui; Kong, Deok-Hoon; Park, Seoung-Woo; Kim, Young-Myeong; Ha, Kwon-Soo

    2012-08-21

    Peptide arrays have emerged as a key technology for drug discovery, diagnosis, and cell biology. Despite the promise of these arrays, applications of peptide arrays to quantitative analysis of enzyme kinetics have been limited due to the difficulty in obtaining quantitative information of enzymatic reaction products. In this study, we developed a new approach for the quantitative kinetics analysis of proteases using fluorescence-conjugated peptide arrays, a surface concentration-based assay with solid-phase peptide standards using dry-off measurements, and compared it with an applied concentration-based assay. For fabrication of the peptide arrays, substrate peptides of cMMP-3, caspase-3, caspase-9, and calpain-1 were functionalized with TAMRA and cysteine, and were immobilized onto amine-functionalized arrays using a heterobifunctional linker, N-[γ-maleimidobutyloxy]succinimide ester. The proteolytic activities of the four enzymes were quantitatively analyzed by calculating changes induced by enzymatic reactions in the concentrations of peptides bound to array surfaces. In addition, this assay was successfully applied for calculating the Michaelis constant (K(m,surf)) for the four enzymes. Thus, this new assay has a strong potential for use in the quantitative evaluation of proteases, and for drug discovery through kinetics studies including the determination of K(m) and V(max).

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  5. LLNL Genomic Assessment: Viral and Bacterial Sequencing Needs for TMTI, Task 1.4.2 Report

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T; Borucki, M; Lam, M; Lenhoff, R; Vitalis, E

    2010-01-26

    Good progress has been made on both bacterial and viral sequencing by the TMTI centers. While access to appropriate samples is a limiting factor to throughput, excellent progress has been made with respect to getting agreements in place with key sources of relevant materials. Sharing of sequenced genomes funded by TMTI has been extremely limited to date. The April 2010 exercise should force a resolution to this, but additional managerial pressures may be needed to ensure that rapid sharing of TMTI-funded sequencing occurs, regardless of collaborator constraints concerning ultimate publication(s). Policies to permit TMTI-internal rapid sharing of sequenced genomes should be written into all TMTI agreements with collaborators now being negotiated. TMTI needs to establish a Web-based system for tracking samples destined for sequencing. This includes metadata on sample origins and contributor, information on sample shipment/receipt, prioritization by TMTI, assignment to one or more sequencing centers (including possible TMTI-sponsored sequencing at a contributor site), and status history of the sample sequencing effort. While this system could be a component of the AFRL system, it is not part of any current development effort. Policy and standardized procedures are needed to ensure appropriate verification of all TMTI samples prior to the investment in sequencing. PCR, arrays, and classical biochemical tests are examples of potential verification methods. Verification is needed to detect miss-labeled, degraded, mixed or contaminated samples. Regular QC exercises are needed to ensure that the TMTI-funded centers are meeting all standards for producing quality genomic sequence data.

  6. Highly accurate fluorogenic DNA sequencing with information theory-based error correction.

    Science.gov (United States)

    Chen, Zitian; Zhou, Wenxiong; Qiao, Shuo; Kang, Li; Duan, Haifeng; Xie, X Sunney; Huang, Yanyi

    2017-12-01

    Eliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory-based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.

  7. Miniaturized optical sensors based on lens arrays

    DEFF Research Database (Denmark)

    Hanson, Steen Grüner; Jakobsen, M.L.; Larsen, H.E.

    2005-01-01

    A suite of optical sensors based on the use of lenticular arrays for probing mechanical deflections will be displayed. The optical systems are well suited for miniaturization, and utilize speckles as the information-carriers. This implementation allows for acquiring directional information...

  8. High specific radioactivity (1R,2S)-4-[{sup 18}F]fluorometaraminol: a PET radiotracer for mapping sympathetic nerves of the heart

    Energy Technology Data Exchange (ETDEWEB)

    Langer, Oliver; Valette, Heric; Dolle, Frederic E-mail: dolle@dsvidf.cea.fr; Halldin, Christer; Loc' h, Christian; Fuseau, Chantal; Coulon, Christine; Ottaviani, Michele; Bottlaender, Michel; Maziere, Bernard; Crouzel, Christian

    2000-04-01

    The radiolabeled catecholamine analogue (1R,2S)-6-[{sup 18}F]fluorometaraminol (6-[{sup 18}F]FMR) is a substrate for the neuronal norepinephrine transporter. It has been used as a positron emission tomography (PET) ligand to map sympathetic nerves in dog heart. 6-[{sup 18}F]FMR could be only synthesized with low specific radioactivity, which precluded its use in human subjects. We have recently prepared (1R,2S)-4-[{sup 18}F]fluorometaraminol (4-[{sup 18}F]FMR), a new fluoro-analogue of metaraminol, with high specific radioactivity (56-106 GBq/{mu}mol). In the present study, we demonstrate in rats that 4-[{sup 18}F]FMR possesses similar affinity toward myocardial norepinephrine transport mechanisms as 6-[{sup 18}F]FMR. When compared with control animals, an 80% and 76% reduction in myocardial uptake was observed in animals pretreated with desipramine (an inhibitor of the neuronal norepinephrine transporter) and with reserpine (a blocker of the vesicular storage of monoamines), respectively. The entire radioactivity in rat myocardium represented unmetabolized parent tracer as determined by high performance liquid chromatography analysis of tissue extracts. In dogs, myocardial kinetics of 4-[{sup 18}F]FMR were assessed using PET. A rapid and high uptake was observed, followed by prolonged cardiac retention. A heart-to-lung ratio of 15 was reached 10 min after injection of the radiotracer. Pretreatment with desipramine reduced the heart half-life of 4-[{sup 18}F]FMR by 90% compared with control. Moreover, an infusion of tyramine caused a rapid decline of radioactivity in the heart. This demonstrates that 4-[{sup 18}F]FMR specifically visualizes sympathetic neurons in dog heart. High specific radioactivity 4-[{sup 18}F]FMR is a promising alternative to 6-[{sup 18}F]FMR for myocardial neuronal mapping with PET in humans.

  9. Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences

    KAUST Repository

    Shibl, Ahmed A.; Haroon, Mohamed; Ngugi, David; Thompson, Luke R.; Stingl, Ulrich

    2016-01-01

    The marine picocyanobacteria Prochlorococcus represent a significant fraction of the global pelagic bacterioplankton community. Specifically, in the surface waters of the Red Sea, they account for around 91% of the phylum Cyanobacteria. Previous work suggested a widespread presence of high-light (HL)-adapted ecotypes in the Red Sea with the occurrence of low-light (LL)-adapted ecotypes at intermediate depths in the water column. To obtain a more comprehensive dataset over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze the diversity of the Prochlorococcus rpoC1 gene from a total of 113 samples at various depths (up to 500 m) from 45 stations spanning the Red Sea basin from north to south. In addition, we analyzed 45 metagenomes from eight stations using hidden Markov models based on a set of reference Prochlorococcus genomes to (1) estimate the relative abundance of Prochlorococcus based on 16S rRNA gene sequences, and (2) identify and classify rpoC1 sequences as an assessment of the community structure of Prochlorococcus in the northern, central and southern regions of the basin without amplification bias. Analyses of metagenomic data indicated that Prochlorococcus occurs at a relative abundance of around 9% in samples from surface waters (25, 50, 75 m), 3% in intermediate waters (100 m) and around 0.5% in deep-water samples (200–500 m). Results based on rpoC1 sequences using both methods showed that HL II cells dominate surface waters and were also present in deep-water samples. Prochlorococcus communities in intermediate waters (100 m) showed a higher diversity and co-occurrence of low-light and high-light ecotypes. Prochlorococcus communities at each depth range (surface, intermediate, deep sea) did not change significantly over the sampled transects spanning most of the Saudi waters in the Red Sea. Statistical analyses of rpoC1 sequences from metagenomes indicated that the vertical distribution of Prochlorococcus in the water

  10. Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences

    KAUST Repository

    Shibl, Ahmed A.

    2016-06-25

    The marine picocyanobacteria Prochlorococcus represent a significant fraction of the global pelagic bacterioplankton community. Specifically, in the surface waters of the Red Sea, they account for around 91% of the phylum Cyanobacteria. Previous work suggested a widespread presence of high-light (HL)-adapted ecotypes in the Red Sea with the occurrence of low-light (LL)-adapted ecotypes at intermediate depths in the water column. To obtain a more comprehensive dataset over a wider biogeographical scope, we used a 454-pyrosequencing approach to analyze the diversity of the Prochlorococcus rpoC1 gene from a total of 113 samples at various depths (up to 500 m) from 45 stations spanning the Red Sea basin from north to south. In addition, we analyzed 45 metagenomes from eight stations using hidden Markov models based on a set of reference Prochlorococcus genomes to (1) estimate the relative abundance of Prochlorococcus based on 16S rRNA gene sequences, and (2) identify and classify rpoC1 sequences as an assessment of the community structure of Prochlorococcus in the northern, central and southern regions of the basin without amplification bias. Analyses of metagenomic data indicated that Prochlorococcus occurs at a relative abundance of around 9% in samples from surface waters (25, 50, 75 m), 3% in intermediate waters (100 m) and around 0.5% in deep-water samples (200–500 m). Results based on rpoC1 sequences using both methods showed that HL II cells dominate surface waters and were also present in deep-water samples. Prochlorococcus communities in intermediate waters (100 m) showed a higher diversity and co-occurrence of low-light and high-light ecotypes. Prochlorococcus communities at each depth range (surface, intermediate, deep sea) did not change significantly over the sampled transects spanning most of the Saudi waters in the Red Sea. Statistical analyses of rpoC1 sequences from metagenomes indicated that the vertical distribution of Prochlorococcus in the water

  11. Vector network analyzer ferromagnetic resonance spectrometer with field differential detection

    Science.gov (United States)

    Tamaru, S.; Tsunegi, S.; Kubota, H.; Yuasa, S.

    2018-05-01

    This work presents a vector network analyzer ferromagnetic resonance (VNA-FMR) spectrometer with field differential detection. This technique differentiates the S-parameter by applying a small binary modulation field in addition to the DC bias field to the sample. By setting the modulation frequency sufficiently high, slow sensitivity fluctuations of the VNA, i.e., low-frequency components of the trace noise, which limit the signal-to-noise ratio of the conventional VNA-FMR spectrometer, can be effectively removed, resulting in a very clean FMR signal. This paper presents the details of the hardware implementation and measurement sequence as well as the data processing and analysis algorithms tailored for the FMR spectrum obtained with this technique. Because the VNA measures a complex S-parameter, it is possible to estimate the Gilbert damping parameter from the slope of the phase variation of the S-parameter with respect to the bias field. We show that this algorithm is more robust against noise than the conventional algorithm based on the linewidth.

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

    Science.gov (United States)

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

    2017-10-01

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

  13. A Compute Environment of ABC95 Array Computer Based on Multi-FPGA Chip

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    ABC95 array computer is a multi-function network's computer based on FPGA technology, The multi-function network supports processors conflict-free access data from memory and supports processors access data from processors based on enhanced MESH network.ABC95 instruction's system includes control instructions, scalar instructions, vectors instructions.Mostly net-work instructions are introduced.A programming environment of ABC95 array computer assemble language is designed.A programming environment of ABC95 array computer for VC++ is advanced.It includes load function of ABC95 array computer program and data, store function, run function and so on.Specially, The data type of ABC95 array computer conflict-free access is defined.The results show that these technologies can develop programmer of ABC95 array computer effectively.

  14. Sequencing-based breast cancer diagnostics as an alternative to routine biomarkers.

    Science.gov (United States)

    Rantalainen, Mattias; Klevebring, Daniel; Lindberg, Johan; Ivansson, Emma; Rosin, Gustaf; Kis, Lorand; Celebioglu, Fuat; Fredriksson, Irma; Czene, Kamila; Frisell, Jan; Hartman, Johan; Bergh, Jonas; Grönberg, Henrik

    2016-11-30

    Sequencing-based breast cancer diagnostics have the potential to replace routine biomarkers and provide molecular characterization that enable personalized precision medicine. Here we investigate the concordance between sequencing-based and routine diagnostic biomarkers and to what extent tumor sequencing contributes clinically actionable information. We applied DNA- and RNA-sequencing to characterize tumors from 307 breast cancer patients with replication in up to 739 patients. We developed models to predict status of routine biomarkers (ER, HER2,Ki-67, histological grade) from sequencing data. Non-routine biomarkers, including mutations in BRCA1, BRCA2 and ERBB2(HER2), and additional clinically actionable somatic alterations were also investigated. Concordance with routine diagnostic biomarkers was high for ER status (AUC = 0.95;AUC(replication) = 0.97) and HER2 status (AUC = 0.97;AUC(replication) = 0.92). The transcriptomic grade model enabled classification of histological grade 1 and histological grade 3 tumors with high accuracy (AUC = 0.98;AUC(replication) = 0.94). Clinically actionable mutations in BRCA1, BRCA2 and ERBB2(HER2) were detected in 5.5% of patients, while 53% had genomic alterations matching ongoing or concluded breast cancer studies. Sequencing-based molecular profiling can be applied as an alternative to histopathology to determine ER and HER2 status, in addition to providing improved tumor grading and clinically actionable mutations and molecular subtypes. Our results suggest that sequencing-based breast cancer diagnostics in a near future can replace routine biomarkers.

  15. Improved Focusing Method for 3-D Imaging using Row–Column-Addressed 2-D Arrays

    DEFF Research Database (Denmark)

    Bouzari, Hamed; Engholm, Mathias; Stuart, Matthias Bo

    2017-01-01

    A row–column-addressed (RCA) 2-D array can be interpreted as two orthogonal 1-D arrays. By transmitting with row elements and receiving the echoes through column elements or vice versa, a rectilinear volume in front of the array can be beamformed. Since the transmit and receive 1-D arrays are ort...... measurements with a PZT λ/2-pitch 3 MHz 62+62 RCA 2-D transducer probe. A synthetic aperture imaging sequence with single element transmissions at a time, is designed for imaging down to 14 cm at a volume rate of 44 Hz....

  16. Carcinogen-DNA interaction study by base sequence footprinting. Progress report, July 1, 1985-January 21, 1986

    International Nuclear Information System (INIS)

    Bases, R.

    1986-01-01

    Acetyl-aminofluorene (AAF) modified plasmid pSV 2 CAT is being studied to learn how the adducts influence expression of chloramphenicol acetyltransferase (CAT) genes. phi X-174 RF DNA exhibits specific base sequence abnormalities induced by the formation of AAF adducts. The DNAase I sensitive state of AAF modified DNA sequences could presumably lead to enhanced expression of genes since it is a well-known characteristic of active or potentially active derepressed genes. DNAase I hypersensitive sites are necessary but not sufficient for transcription. We observed enhanced expression of CAT genes in CV-1 cells after transfection with modified plasmids, using electroporation to introduce the plasmids into the cells. 34 refs., 2 figs

  17. The research on multi-projection correction based on color coding grid array

    Science.gov (United States)

    Yang, Fan; Han, Cheng; Bai, Baoxing; Zhang, Chao; Zhao, Yunxiu

    2017-10-01

    There are many disadvantages such as lower timeliness, greater manual intervention in multi-channel projection system, in order to solve the above problems, this paper proposes a multi-projector correction technology based on color coding grid array. Firstly, a color structured light stripe is generated by using the De Bruijn sequences, then meshing the feature information of the color structured light stripe image. We put the meshing colored grid intersection as the center of the circle, and build a white solid circle as the feature sample set of projected images. It makes the constructed feature sample set not only has the perceptual localization, but also has good noise immunity. Secondly, we establish the subpixel geometric mapping relationship between the projection screen and the individual projectors by using the structure of light encoding and decoding based on the color array, and the geometrical mapping relation is used to solve the homography matrix of each projector. Lastly the brightness inconsistency of the multi-channel projection overlap area is seriously interfered, it leads to the corrected image doesn't fit well with the observer's visual needs, and we obtain the projection display image of visual consistency by using the luminance fusion correction algorithm. The experimental results show that this method not only effectively solved the problem of distortion of multi-projection screen and the issue of luminance interference in overlapping region, but also improved the calibration efficient of multi-channel projective system and reduced the maintenance cost of intelligent multi-projection system.

  18. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1.

    Directory of Open Access Journals (Sweden)

    Binhua Liang

    Full Text Available BACKGROUND: Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. METHODOLOGY/PRINCIPAL FINDINGS: HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. CONCLUSIONS/SIGNIFICANCE: Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies.

  19. The ITS1-5.8S-ITS2 sequence region in the Musaceae: structure, diversity and use in molecular phylogeny.

    Directory of Open Access Journals (Sweden)

    Eva Hřibová

    2011-03-01

    Full Text Available Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades--Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes.

  20. Molecular Profiling of Microbial Communities from Contaminated Sources: Use of Subtractive Cloning Methods and rDNA Spacer Sequences; FINAL

    International Nuclear Information System (INIS)

    Robb, Frank T.

    2001-01-01

    The major objective of this research was to provide appropriate sequences and assemble a DNA array of oligonucleotides to be used for rapid profiling of microbial populations from polluted areas and other areas of interest. The sequences to be assigned to the DNA array were chosen from cloned genomic DNA taken from groundwater sites having well characterized pollutant histories at Hanford Nuclear Plant and Lawrence Livermore Site 300. Glass-slide arrays were made and tested; and a new multiplexed, bead-based method was developed that uses nucleic acid hybridization on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences. The test data revealed considerable strain variation between sample sites showing a striking distribution of sequences. It also suggests that diversity varies greatly with bioremediation, and that there are many bacterial intergenic spacer region sequences that can indicate its effects. The bead method exhibited superior sequence discrimination and has features for easier and more accurate measurement

  1. High-efficiency perovskite solar cells based on anatase TiO{sub 2} nanotube arrays

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yan, E-mail: huangyan@ecust.edu.cn [School of Chemistry and Molecular Engineering, East China University of Science & Technology, Shanghai 200237 (China); Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA 15261 (United States); Wu, Jiamin; Gao, Di [Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA 15261 (United States)

    2016-01-01

    Perovskite solar cells (PSCs) based on one-dimensional anatase TiO{sub 2} nanotube arrays were prepared by using a two-step deposition method to fill the arrays of TiO{sub 2} nanotubes in different lengths with perovskite. The photovoltaic performance of PSCs was found to be significantly dependent on the length of the TiO{sub 2} nanotubes, and the power conversion efficiency decreased as the length of the TiO{sub 2} nanotubes increased from ~ 0.40 μm to ~ 0.65 and then to ~ 0.93 μm. The PSC fabricated with ~ 0.40 μm-long anatase TiO{sub 2} nanotube arrays yielded a power conversion efficiency of 11.3% and a fill factor of 0.68 under illumination of 100 mW/cm{sup 2} AM 1.5G simulated sunlight, which is significantly higher than previously reported solar cells based on 1-D TiO{sub 2} nanostructures. Incident photon-to-current efficiency and electrochemical impedance spectroscopy measurements indicated that longer TiO{sub 2} nanotubes led to higher recombination losses of charge carriers, possibly due to poor filling of the nanotube arrays with perovskite. - Highlights: • 1D anatase TiO{sub 2} nanotubes were used to fabricate perovskite solar cells. • The best efficiency of 11.3% was achieved with ~ 0.40 μm-long TiO{sub 2} nanotubes. • The efficiency of the devices decreased with increasing TiO{sub 2} nanotube lengths.

  2. Selecting Sums in Arrays

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Jørgensen, Allan Grønlund

    2008-01-01

    In an array of n numbers each of the \\binomn2+nUnknown control sequence '\\binom' contiguous subarrays define a sum. In this paper we focus on algorithms for selecting and reporting maximal sums from an array of numbers. First, we consider the problem of reporting k subarrays inducing the k largest...... sums among all subarrays of length at least l and at most u. For this problem we design an optimal O(n + k) time algorithm. Secondly, we consider the problem of selecting a subarray storing the k’th largest sum. For this problem we prove a time bound of Θ(n · max {1,log(k/n)}) by describing...... an algorithm with this running time and by proving a matching lower bound. Finally, we combine the ideas and obtain an O(n· max {1,log(k/n)}) time algorithm that selects a subarray storing the k’th largest sum among all subarrays of length at least l and at most u....

  3. Genetic analysis of presbycusis by arrayed primer extension.

    Science.gov (United States)

    Rodriguez-Paris, Juan; Ballay, Charles; Inserra, Michelle; Stidham, Katrina; Colen, Tahl; Roberson, Joseph; Gardner, Phyllis; Schrijver, Iris

    2008-01-01

    Using the Hereditary Hearing Loss arrayed primer extension (APEX) array, which contains 198 mutations across 8 hearing loss-associated genes (GJB2, GJB6, GJB3, GJA1, SLC26A4, SLC26A5, 12S-rRNA, and tRNA Ser), we compared the frequency of sequence variants in 94 individuals with early presbycusis to 50 unaffected controls and aimed to identify possible genetic contributors. This cross-sectional study was performed at Stanford University with presbycusis samples from the California Ear Institute. The patients were between ages 20 and 65 yr, with adult-onset sensorineural hearing loss of unknown etiology, and carried a clinical diagnosis of early presbycusis. Exclusion criteria comprised known causes of hearing loss such as significant noise exposure, trauma, ototoxic medication, neoplasm, and congenital infection or syndrome, as well as congenital or pediatric onset. Sequence changes were identified in 11.7% and 10% of presbycusis and control alleles, respectively. Among the presbycusis group, these solely occurred within the GJB2 and SLC26A4 genes. Homozygous and compound heterozygous pathogenic mutations were exclusively seen in affected individuals. We were unable to detect a statistically significant difference between our control and affected populations regarding the frequency of sequence variants detected with the APEX array. Individuals who carry two mild mutations in the GJB2 gene possibly have an increased risk of developing early presbycusis.

  4. A method of incident angle estimation for high resolution spectral recovery in filter-array-based spectrometers

    Science.gov (United States)

    Kim, Cheolsun; Lee, Woong-Bi; Ju, Gun Wu; Cho, Jeonghoon; Kim, Seongmin; Oh, Jinkyung; Lim, Dongsung; Lee, Yong Tak; Lee, Heung-No

    2017-02-01

    In recent years, there has been an increasing interest in miniature spectrometers for research and development. Especially, filter-array-based spectrometers have advantages of low cost and portability, and can be applied in various fields such as biology, chemistry and food industry. Miniaturization in optical filters causes degradation of spectral resolution due to limitations on spectral responses and the number of filters. Nowadays, many studies have been reported that the filter-array-based spectrometers have achieved resolution improvements by using digital signal processing (DSP) techniques. The performance of the DSP-based spectral recovery highly depends on the prior information of transmission functions (TFs) of the filters. The TFs vary with respect to an incident angle of light onto the filter-array. Conventionally, it is assumed that the incident angle of light on the filters is fixed and the TFs are known to the DSP. However, the incident angle is inconstant according to various environments and applications, and thus TFs also vary, which leads to performance degradation of spectral recovery. In this paper, we propose a method of incident angle estimation (IAE) for high resolution spectral recovery in the filter-array-based spectrometers. By exploiting sparse signal reconstruction of the L1- norm minimization, IAE estimates an incident angle among all possible incident angles which minimizes the error of the reconstructed signal. Based on IAE, DSP effectively provides a high resolution spectral recovery in the filter-array-based spectrometers.

  5. Detection of M-Sequences from Spike Sequence in Neuronal Networks

    Directory of Open Access Journals (Sweden)

    Yoshi Nishitani

    2012-01-01

    Full Text Available In circuit theory, it is well known that a linear feedback shift register (LFSR circuit generates pseudorandom bit sequences (PRBS, including an M-sequence with the maximum period of length. In this study, we tried to detect M-sequences known as a pseudorandom sequence generated by the LFSR circuit from time series patterns of stimulated action potentials. Stimulated action potentials were recorded from dissociated cultures of hippocampal neurons grown on a multielectrode array. We could find several M-sequences from a 3-stage LFSR circuit (M3. These results show the possibility of assembling LFSR circuits or its equivalent ones in a neuronal network. However, since the M3 pattern was composed of only four spike intervals, the possibility of an accidental detection was not zero. Then, we detected M-sequences from random spike sequences which were not generated from an LFSR circuit and compare the result with the number of M-sequences from the originally observed raster data. As a result, a significant difference was confirmed: a greater number of “0–1” reversed the 3-stage M-sequences occurred than would have accidentally be detected. This result suggests that some LFSR equivalent circuits are assembled in neuronal networks.

  6. Acoustic Source Localization via Subspace Based Method Using Small Aperture MEMS Arrays

    Directory of Open Access Journals (Sweden)

    Xin Zhang

    2014-01-01

    Full Text Available Small aperture microphone arrays provide many advantages for portable devices and hearing aid equipment. In this paper, a subspace based localization method is proposed for acoustic source using small aperture arrays. The effects of array aperture on localization are analyzed by using array response (array manifold. Besides array aperture, the frequency of acoustic source and the variance of signal power are simulated to demonstrate how to optimize localization performance, which is carried out by introducing frequency error with the proposed method. The proposed method for 5 mm array aperture is validated by simulations and experiments with MEMS microphone arrays. Different types of acoustic sources can be localized with the highest precision of 6 degrees even in the presence of wind noise and other noises. Furthermore, the proposed method reduces the computational complexity compared with other methods.

  7. SEQUENCING OF FLAX LIS-1 INSERTION SITE IN THE ALBIDUM GENOTYPE

    Directory of Open Access Journals (Sweden)

    Jana Žiarovská

    2012-12-01

    Full Text Available The paper presents a methodology of identifying the insertion site of LIS-1-1 (Linum Insertion Sequence 1 element in flax Albidum variety when growing under the in vitro combined with environmental stress conditions. Abiotic stress was induced by a reduced nutrient content in a growth medium. The LIS-1 insertion site amplification was reaLIS-1ed using the forward LIS-L: 5'-GGG CAG TTT AAC TGT AAC GAA - 3 'and revers LIS-R: 5'-GCT TGG ATT TAG ACT TGG CAA C - 3' primers by PCR. PCR product was sequenced by direct sequencing method to proove the nucleotide sequence for matching with database LIS-1 sequence. A comparison has been matched with the sequence of the amplified segment in the database for all nucleotides except the 11-position in the 5'-3 ' direction, where instead of the three adenine pair is a couple in the Albidum variety. Changes caused by mobile elements or insertion sequences result in common flax in variability that can be used for the purposes of development of effective marker identification or environment based markers development.

  8. Generation of miniaturized planar ecombinant antibody arrays using a microcantilever-based printer

    Science.gov (United States)

    Petersson, Linn; Berthet Duroure, Nathalie; Auger, Angèle; Dexlin-Mellby, Linda; Borrebaeck, Carl AK; Ait Ikhlef, Ali; Wingren, Christer

    2014-07-01

    Miniaturized (Ø 10 μm), multiplexed (>5-plex), and high-density (>100 000 spots cm-2) antibody arrays will play a key role in generating protein expression profiles in health and disease. However, producing such antibody arrays is challenging, and it is the type and range of available spotters which set the stage. This pilot study explored the use of a novel microspotting tool, BioplumeTM—consisting of an array of micromachined silicon cantilevers with integrated microfluidic channels—to produce miniaturized, multiplexed, and high-density planar recombinant antibody arrays for protein expression profiling which targets crude, directly labelled serum. The results demonstrated that 16-plex recombinant antibody arrays could be produced—based on miniaturized spot features (78.5 um2, Ø 10 μm) at a 7-125-times increased spot density (250 000 spots cm-2), interfaced with a fluorescent-based read-out. This prototype platform was found to display adequate reproducibility (spot-to-spot) and an assay sensitivity in the pM range. The feasibility of the array platform for serum protein profiling was outlined.

  9. Generation of miniaturized planar ecombinant antibody arrays using a microcantilever-based printer

    International Nuclear Information System (INIS)

    Petersson, Linn; Dexlin-Mellby, Linda; Borrebaeck, Carl AK; Wingren, Christer; Berthet Duroure, Nathalie; Auger, Angèle; Ait Ikhlef, Ali

    2014-01-01

    Miniaturized (Ø 10 μm), multiplexed (>5-plex), and high-density (>100 000 spots cm −2 ) antibody arrays will play a key role in generating protein expression profiles in health and disease. However, producing such antibody arrays is challenging, and it is the type and range of available spotters which set the stage. This pilot study explored the use of a novel microspotting tool, Bioplume TM —consisting of an array of micromachined silicon cantilevers with integrated microfluidic channels—to produce miniaturized, multiplexed, and high-density planar recombinant antibody arrays for protein expression profiling which targets crude, directly labelled serum. The results demonstrated that 16-plex recombinant antibody arrays could be produced—based on miniaturized spot features (78.5 um 2 , Ø 10 μm) at a 7–125-times increased spot density (250 000 spots cm −2 ), interfaced with a fluorescent-based read-out. This prototype platform was found to display adequate reproducibility (spot-to-spot) and an assay sensitivity in the pM range. The feasibility of the array platform for serum protein profiling was outlined. (paper)

  10. On-line monitoring system of PV array based on internet of things technology

    Science.gov (United States)

    Li, Y. F.; Lin, P. J.; Zhou, H. F.; Chen, Z. C.; Wu, L. J.; Cheng, S. Y.; Su, F. P.

    2017-11-01

    The Internet of Things (IoT) Technology is used to inspect photovoltaic (PV) array which can greatly improve the monitoring, performance and maintenance of the PV array. In order to efficiently realize the remote monitoring of PV operating environment, an on-line monitoring system of PV array based on IoT is designed in this paper. The system includes data acquisition, data gateway and PV monitoring centre (PVMC) website. Firstly, the DSP-TMS320F28335 is applied to collect indicators of PV array using sensors, then the data are transmitted to data gateway through ZigBee network. Secondly, the data gateway receives the data from data acquisition part, obtains geographic information via GPS module, and captures the scenes around PV array via USB camera, then uploads them to PVMC website. Finally, the PVMC website based on Laravel framework receives all data from data gateway and displays them with abundant charts. Moreover, a fault diagnosis approach for PV array based on Extreme Learning Machine (ELM) is applied in PVMC. Once fault occurs, a user alert can be sent via E-mail. The designed system enables users to browse the operating conditions of PV array on PVMC website, including electrical, environmental parameters and video. Experimental results show that the presented monitoring system can efficiently real-time monitor the PV array, and the fault diagnosis approach reaches a high accuracy of 97.5%.

  11. Coupled-oscillator based active-array antennas

    CERN Document Server

    Pogorzelski, Ronald J

    2012-01-01

    Describing an innovative approach to phased-array control in antenna design This book explores in detail phased-array antennas that use coupled-oscillator arrays, an arrangement featuring a remarkably simple beam steering control system and a major reduction in complexity compared with traditional methods of phased-array control. It brings together in one convenient, self-contained volume the many salient research results obtained over the past ten to fifteen years in laboratories around the world, including the California Institute of Technology's Jet Propulsion Laboratory.

  12. Piezo-Phototronic Enhanced UV Sensing Based on a Nanowire Photodetector Array.

    Science.gov (United States)

    Han, Xun; Du, Weiming; Yu, Ruomeng; Pan, Caofeng; Wang, Zhong Lin

    2015-12-22

    A large array of Schottky UV photodetectors (PDs) based on vertical aligned ZnO nanowires is achieved. By introducing the piezo-phototronic effect, the performance of the PD array is enhanced up to seven times in photoreponsivity, six times in sensitivity, and 2.8 times in detection limit. The UV PD array may have applications in optoelectronic systems, adaptive optical computing, and communication. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Establishment of a Molecular Serotyping Scheme and a Multiplexed Luminex-Based Array for Enterobacter aerogenes.

    Science.gov (United States)

    Guo, Xi; Wang, Min; Wang, Lu; Wang, Yao; Chen, Tingting; Wu, Pan; Chen, Min; Liu, Bin; Feng, Lu

    2018-01-01

    Serotyping based on surface polysaccharide antigens is important for the clinical detection and epidemiological surveillance of pathogens. Polysaccharide gene clusters (PSgcs) are typically responsible for the diversity of bacterial surface polysaccharides. Through whole-genome sequencing and analysis, eight putative PSgc types were identified in 23 Enterobacter aerogenes strains from several geographic areas, allowing us to present the first molecular serotyping system for E. aerogenes . A conventional antigenic scheme was also established and correlated well with the molecular serotyping system that was based on PSgc genetic variation, indicating that PSgc-based molecular typing and immunological serology provide equally valid results. Further, a multiplex Luminex-based array was developed, and a double-blind test was conducted with 97 clinical specimens from Shanghai, China, to validate our array. The results of these analyses indicated that strains containing PSgc4 and PSgc7 comprised the predominant groups. We then examined 86 publicly available E. aerogenes strain genomes and identified an additional seven novel PSgc types, with PSgc10 being the most abundant type. In total, our study identified 15 PSgc types in E. aerogenes , providing the basis for a molecular serotyping scheme. From these results, differing epidemic patterns were identified between strains that were predominant in different regions. Our study highlights the feasibility and reliability of a serotyping system based on PSgc diversity, and for the first time, presents a molecular serotyping system, as well as an antigenic scheme for E. aerogenes , providing the basis for molecular diagnostics and epidemiological surveillance of this important emerging pathogen.

  14. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  15. Detection of viral sequence fragments of HIV-1 subfamilies yet unknown

    Directory of Open Access Journals (Sweden)

    Stanke Mario

    2011-04-01

    Full Text Available Abstract Background Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI, has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments. Results We have developed Unknown Subtype Finder (USF, an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM for each known subtype and an additional pHMM for an unknown subtype. The emission probabilities of the latter are estimated using the emission frequencies of the known subtypes by means of a (position-wise probabilistic model for the emergence of new subtypes. We have applied USF to SIV and HIV-1 sequences formerly classified as having emerged from an unknown subtype. Moreover, we have evaluated its performance on artificial HIV-1 recombinants and non-recombinant HIV-1 sequences. The results have been compared with the corresponding results of the BI. Conclusions Our results demonstrate that USF is suitable for detecting segments in HIV-1 sequences stemming from yet unknown subtypes. Comparing USF with the BI shows that our algorithm performs as good as the BI or better.

  16. Genome and Transcriptome Sequencing of the Ostreid herpesvirus 1 From Tomales Bay, California

    Science.gov (United States)

    Burge, C. A.; Langevin, S.; Closek, C. J.; Roberts, S. B.; Friedman, C. S.

    2016-02-01

    Mass mortalities of larval and seed bivalve molluscs attributed to the Ostreid herpesvirus 1 (OsHV-1) occur globally. OsHV-1 was fully sequenced and characterized as a member of the Family Malacoherpesviridae. Multiple strains of OsHV-1 exist and may vary in virulence, i.e. OsHV-1 µvar. For most global variants of OsHV-1, sequence data is limited to PCR-based sequencing of segments, including two recent genomes. In the United States, OsHV-1 is limited to detection in adjacent embayments in California, Tomales and Drakes bays. Limited DNA sequence data of OsHV-1 infecting oysters in Tomales Bay indicates the virus detected in Tomales Bay is similar but not identical to any one global variant of OsHV-1. In order to better understand both strain variation and virulence of OsHV-1 infecting oysters in Tomales Bay, we used genomic and transcriptomic sequencing. Meta-genomic sequencing (Illumina MiSeq) was conducted from infected oysters (n=4 per year) collected in 2003, 2007, and 2014, where full OsHV-1 genome sequences and low overall microbial diversity were achieved from highly infected oysters. Increased microbial diversity was detected in three of four samples sequenced from 2003, where qPCR based genome copy numbers of OsHV-1 were lower. Expression analysis (SOLiD RNA sequencing) of OsHV-1 genes expressed in oyster larvae at 24 hours post exposure revealed a nearly complete transcriptome, with several highly expressed genes, which are similar to recent transcriptomic analyses of other OsHV-1 variants. Taken together, our results indicate that genome and transcriptome sequencing may be powerful tools in understanding both strain variation and virulence of non-culturable marine viruses.

  17. A new ion detector array and digital-signal-processor-based interface

    International Nuclear Information System (INIS)

    Langstaff, D.P.; McGinnity, T.M.; Forbes, D.M.; Birkinshaw, K.; Lawton, M.W.

    1994-01-01

    A new one-dimensional ion detector array on a silicon chip has been developed for use in mass spectrometry. It is much smaller and simpler than electro-optical arrays currently in use and in addition has a higher resolution and a zero noise level. The array consists of a one-dimensional array of metal strips (electrodes) with a pitch of 25 μm on the top surface of a silicon chip, each electrode having its own charge pulse sensor, 8-bit counter and control/interface circuitry. The chip is mounted on a ceramic substrate and is preceded by a micro-channel plate electron multiplier. Chips are butted to give a longer array. Test results show a stable operating region. A digital-signal-processor-based interface is described, which controls the mode of operation and reads the accumulated array data at the maximum rate to avoid counter overflow. (author)

  18. A new ion detector array and digital-signal-processor-based interface

    Energy Technology Data Exchange (ETDEWEB)

    Langstaff, D.P.; McGinnity, T.M.; Forbes, D.M.; Birkinshaw, K. (University Coll. of Wales, Aberystwyth (United Kingdom). Dept. of Physics); Lawton, M.W. (University of Wales Aberystwyth (United Kingdom). Dept. of Computer Science)

    1994-04-01

    A new one-dimensional ion detector array on a silicon chip has been developed for use in mass spectrometry. It is much smaller and simpler than electro-optical arrays currently in use and in addition has a higher resolution and a zero noise level. The array consists of a one-dimensional array of metal strips (electrodes) with a pitch of 25 [mu]m on the top surface of a silicon chip, each electrode having its own charge pulse sensor, 8-bit counter and control/interface circuitry. The chip is mounted on a ceramic substrate and is preceded by a micro-channel plate electron multiplier. Chips are butted to give a longer array. Test results show a stable operating region. A digital-signal-processor-based interface is described, which controls the mode of operation and reads the accumulated array data at the maximum rate to avoid counter overflow. (author).

  19. A FPGA-based signal processing unit for a GEM array detector

    International Nuclear Information System (INIS)

    Yen, W.W.; Chou, H.P.

    2013-06-01

    in the present study, a signal processing unit for a GEM one-dimensional array detector is presented to measure the trajectory of photoelectrons produced by cosmic X-rays. The present GEM array detector system has 16 signal channels. The front-end unit provides timing signals from trigger units and energy signals from charge sensitive amplifies. The prototype of the processing unit is implemented using commercial field programmable gate array circuit boards. The FPGA based system is linked to a personal computer for testing and data analysis. Tests using simulated signals indicated that the FPGA-based signal processing unit has a good linearity and is flexible for parameter adjustment for various experimental conditions (authors)

  20. Micro-array versus nano-array platforms: a comparative study for ODN detection based on SPR enhanced ellipsometry

    International Nuclear Information System (INIS)

    Celen, Burcu; Piskin, Erhan; Demirel, Goekhan

    2011-01-01

    The rapid and sensitive detection of DNA has recently attracted worldwide attention for a variety of disease diagnoses and detection of harmful bacteria in food and drink. In this paper, we carried out a comparative study based on surface plasmon resonance enhanced ellipsometry (SPREE) for the detection of oligodeoxynucleotides (ODNs) using micro- and nano-array platforms. The micro-arrayed surfaces were fabricated by a photolithography approach using different types of mask having varying size and shape. Well-ordered arrays of high aspect ratio polymeric nanotubes were also obtained using high molecular weight polystyrene (PS) and anodic aluminum oxide (AAO) membranes having 200 nm pore diameters. The SPREE sensors were then prepared by direct coupling of thiolated probe-ODNs, which contain suitable spacer arms, on gold-coated micro- and nano-arrayed surfaces. We experimentally demonstrated that, for the first time, gold-coated free standing polymeric nano-arrayed platforms can easily be produced and lead to a significant sensor sensitivity gain compared to that of the conventional SPREE surfaces of about four times. We believe that such an enhancement in sensor response could be useful for next generation sensor systems.

  1. Micro-array versus nano-array platforms: a comparative study for ODN detection based on SPR enhanced ellipsometry

    Science.gov (United States)

    Celen, Burcu; Demirel, Gökhan; Piskin, Erhan

    2011-04-01

    The rapid and sensitive detection of DNA has recently attracted worldwide attention for a variety of disease diagnoses and detection of harmful bacteria in food and drink. In this paper, we carried out a comparative study based on surface plasmon resonance enhanced ellipsometry (SPREE) for the detection of oligodeoxynucleotides (ODNs) using micro- and nano-array platforms. The micro-arrayed surfaces were fabricated by a photolithography approach using different types of mask having varying size and shape. Well-ordered arrays of high aspect ratio polymeric nanotubes were also obtained using high molecular weight polystyrene (PS) and anodic aluminum oxide (AAO) membranes having 200 nm pore diameters. The SPREE sensors were then prepared by direct coupling of thiolated probe-ODNs, which contain suitable spacer arms, on gold-coated micro- and nano-arrayed surfaces. We experimentally demonstrated that, for the first time, gold-coated free standing polymeric nano-arrayed platforms can easily be produced and lead to a significant sensor sensitivity gain compared to that of the conventional SPREE surfaces of about four times. We believe that such an enhancement in sensor response could be useful for next generation sensor systems.

  2. Propagation of rotational Risley-prism-array-based Gaussian beams in turbulent atmosphere

    Science.gov (United States)

    Chen, Feng; Ma, Haotong; Dong, Li; Ren, Ge; Qi, Bo; Tan, Yufeng

    2018-03-01

    Limited by the size and weight of prism and optical assembling, Rotational Risley-prism-array system is a simple but effective way to realize high power and superior beam quality of deflecting laser output. In this paper, the propagation of the rotational Risley-prism-array-based Gaussian beam array in atmospheric turbulence is studied in detail. An analytical expression for the average intensity distribution at the receiving plane is derived based on nonparaxial ray tracing method and extended Huygens-Fresnel principle. Power in the diffraction-limited bucket is chosen to evaluate beam quality. The effect of deviation angle, propagation distance and intensity of turbulence on beam quality is studied in detail by quantitative simulation. It reveals that with the propagation distance increasing, the intensity distribution gradually evolves from multiple-petal-like shape into the pattern that contains one main-lobe in the center with multiple side-lobes in weak turbulence. The beam quality of rotational Risley-prism-array-based Gaussian beam array with lower deviation angle is better than its counterpart with higher deviation angle when propagating in weak and medium turbulent (i.e. Cn2 beam quality of higher deviation angle arrays degrades faster as the intensity of turbulence gets stronger. In the case of propagating in strong turbulence, the long propagation distance (i.e. z > 10km ) and deviation angle have no influence on beam quality.

  3. Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle.

    Science.gov (United States)

    Sahana, G; Guldbrandtsen, B; Thomsen, B; Holm, L-E; Panitz, F; Brøndum, R F; Bendixen, C; Lund, M S

    2014-11-01

    Mastitis is a mammary disease that frequently affects dairy cattle. Despite considerable research on the development of effective prevention and treatment strategies, mastitis continues to be a significant issue in bovine veterinary medicine. To identify major genes that affect mastitis in dairy cattle, 6 chromosomal regions on Bos taurus autosome (BTA) 6, 13, 16, 19, and 20 were selected from a genome scan for 9 mastitis phenotypes using imputed high-density single nucleotide polymorphism arrays. Association analyses using sequence-level variants for the 6 targeted regions were carried out to map causal variants using whole-genome sequence data from 3 breeds. The quantitative trait loci (QTL) discovery population comprised 4,992 progeny-tested Holstein bulls, and QTL were confirmed in 4,442 Nordic Red and 1,126 Jersey cattle. The targeted regions were imputed to the sequence level. The highest association signal for clinical mastitis was observed on BTA 6 at 88.97 Mb in Holstein cattle and was confirmed in Nordic Red cattle. The peak association region on BTA 6 contained 2 genes: vitamin D-binding protein precursor (GC) and neuropeptide FF receptor 2 (NPFFR2), which, based on known biological functions, are good candidates for affecting mastitis. However, strong linkage disequilibrium in this region prevented conclusive determination of the causal gene. A different QTL on BTA 6 located at 88.32 Mb in Holstein cattle affected mastitis. In addition, QTL on BTA 13 and 19 were confirmed to segregate in Nordic Red cattle and QTL on BTA 16 and 20 were confirmed in Jersey cattle. Although several candidate genes were identified in these targeted regions, it was not possible to identify a gene or polymorphism as the causal factor for any of these regions. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  4. An integrated semiconductor device enabling non-optical genome sequencing.

    Science.gov (United States)

    Rothberg, Jonathan M; Hinz, Wolfgang; Rearick, Todd M; Schultz, Jonathan; Mileski, William; Davey, Mel; Leamon, John H; Johnson, Kim; Milgrew, Mark J; Edwards, Matthew; Hoon, Jeremy; Simons, Jan F; Marran, David; Myers, Jason W; Davidson, John F; Branting, Annika; Nobile, John R; Puc, Bernard P; Light, David; Clark, Travis A; Huber, Martin; Branciforte, Jeffrey T; Stoner, Isaac B; Cawley, Simon E; Lyons, Michael; Fu, Yutao; Homer, Nils; Sedova, Marina; Miao, Xin; Reed, Brian; Sabina, Jeffrey; Feierstein, Erika; Schorn, Michelle; Alanjary, Mohammad; Dimalanta, Eileen; Dressman, Devin; Kasinskas, Rachel; Sokolsky, Tanya; Fidanza, Jacqueline A; Namsaraev, Eugeni; McKernan, Kevin J; Williams, Alan; Roth, G Thomas; Bustillo, James

    2011-07-20

    The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.

  5. Detection and Quantification of the Fragile X Mental Retardation Protein 1 (FMRP).

    Science.gov (United States)

    LaFauci, Giuseppe; Adayev, Tatyana; Kascsak, Richard; Brown, W Ted

    2016-12-09

    The final product of FMR1 gene transcription, Fragile X Mental Retardation Protein 1 (FMRP), is an RNA binding protein that acts as a repressor of translation. FMRP is expressed in several tissues and plays important roles in neurogenesis, synaptic plasticity, and ovarian functions and has been implicated in a number of neuropsychological disorders. The loss of FMRP causes Fragile X Syndrome (FXS). In most cases, FXS is due to large expansions of a CGG repeat in FMR1 -normally containing 6-54 repeats-to over 200 CGGs and identified as full mutation (FM). Hypermethylation of the repeat induces FMR1 silencing and lack of FMRP expression in FM male. Mosaic FM males express low levels of FMRP and present a less severe phenotype that inversely correlates with FMRP levels. Carriers of pre-mutations (55-200 CGG) show increased mRNA, and normal to reduced FMRP levels. Alternative splicing of FMR1 mRNA results in 24 FMRP predicted isoforms whose expression are tissues and developmentally regulated. Here, we summarize the approaches used by several laboratories including our own to (a) detect and estimate the amount of FMRP in different tissues, developmental stages and various pathologies; and (b) to accurately quantifying FMRP for a direct diagnosis of FXS in adults and newborns.

  6. Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

    Science.gov (United States)

    Morse, Alison M; Calabro, Kaitlyn R; Fear, Justin M; Bloom, David C; McIntyre, Lauren M

    2017-08-16

    High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines. Here, we evaluate two approaches for the identification of genetic variants in HSV1 strains using Illumina short read sequencing data. The first, a reference-based approach, identifies variants from reads aligned to a reference sequence and the second, a de novo assembly approach, identifies variants from reads aligned to de novo assembled consensus sequences. Of critical importance for both approaches is the reduction in the number of low complexity regions through the construction of a non-redundant reference genome. We compared variants identified in the two methods. Our results indicate that approximately 85% of variants are identified regardless of the approach. The reference-based approach to variant discovery captures an additional 15% representing variants divergent from the HSV1 reference possibly due to viral passage. Reference-based approaches are significantly less labor-intensive and identify variants across the genome where de novo assembly-based approaches are limited to regions where contigs have been successfully assembled. In addition, regions of poor quality assembly can lead to false variant identification in de novo consensus sequences. For viruses with a well-assembled reference genome, a reference-based approach is recommended.

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

    Science.gov (United States)

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

    2016-04-01

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

  8. MEMS-Based Solid Propellant Rocket Array Thruster

    Science.gov (United States)

    Tanaka, Shuji; Hosokawa, Ryuichiro; Tokudome, Shin-Ichiro; Hori, Keiichi; Saito, Hirobumi; Watanabe, Masashi; Esashi, Masayoshi

    The prototype of a solid propellant rocket array thruster for simple attitude control of a 10 kg class micro-spacecraft was completed and tested. The prototype has 10×10 φ0.8 mm solid propellant micro-rockets arrayed at a pitch of 1.2 mm on a 20×22 mm substrate. To realize such a dense array of micro-rockets, each ignition heater is powered from the backside of the thruster through an electrical feedthrough which passes along a propellant cylinder wall. Boron/potassium nitrate propellant (NAB) is used with/without lead rhodanide/potassium chlorate/nitrocellulose ignition aid (RK). Impulse thrust was measured by a pendulum method in air. Ignition required electric power of at least 3 4 W with RK and 4 6 W without RK. Measured impulse thrusts were from 2×10-5 Ns to 3×10-4 Ns after the calculation of compensation for air dumping.

  9. Fragile X syndrome and fragile X-associated tremor ataxia syndrome.

    Science.gov (United States)

    Hall, Deborah A; Berry-Kravis, Elizabeth

    2018-01-01

    Fragile X-associated disorders encompass several conditions, which are caused by expansion mutations in the fragile X mental retardation 1 (FMR1) gene. Fragile X syndrome is the most common inherited etiology of intellectual disability and results from a full mutation or >200 CGG repeats in FMR1. It is associated with developmental delay, autism spectrum disorder, and seizures. Fragile X-associated tremor/ataxia syndrome is a progressive neurodegenerative disease that occurs in premutation carriers of 55-200 CGG repeats in FMR1 and is characterized by kinetic tremor, gait ataxia, parkinsonism, executive dysfunction, and neuropathy. Fragile X-associated primary ovarian insufficiency also occurs in premutation carrier women and manifests with infertility and early menopause. The diseases constituting fragile X-associated disorders differ mechanistically, due to the distinct molecular properties of premutation versus full mutations. Fragile X syndrome occurs when there is a lack of fragile X mental retardation protein (FMRP) due to FMR1 methylation and silencing. In fragile X-associated tremor ataxia syndrome, a toxic gain of function is postulated with the production of excess CGG repeat-containing FMR1 mRNA, abnormal translation of the repeat sequence leading to production of polyglycine, polyalanine, and other polypeptides and to outright deficits in translation leading to reduced FMRP at larger premutation sizes. The changes in underlying brain chemistry due to FMR1 mutations have led to therapeutic studies in these disorders, with some progress being made in fragile X syndrome. This paper also summarizes indications for testing, genetic counseling issues, and what the future holds for these disorders. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping.

    Science.gov (United States)

    Milius, Robert P; Heuer, Michael; Valiga, Daniel; Doroschak, Kathryn J; Kennedy, Caleb J; Bolon, Yung-Tsi; Schneider, Joel; Pollack, Jane; Kim, Hwa Ran; Cereb, Nezih; Hollenbach, Jill A; Mack, Steven J; Maiers, Martin

    2015-12-01

    We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and Sequence Based Typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  11. Highly selective gas sensor arrays based on thermally reduced graphene oxide.

    Science.gov (United States)

    Lipatov, Alexey; Varezhnikov, Alexey; Wilson, Peter; Sysoev, Victor; Kolmakov, Andrei; Sinitskii, Alexander

    2013-06-21

    The electrical properties of reduced graphene oxide (rGO) have been previously shown to be very sensitive to surface adsorbates, thus making rGO a very promising platform for highly sensitive gas sensors. However, poor selectivity of rGO-based gas sensors remains a major problem for their practical use. In this paper, we address the selectivity problem by employing an array of rGO-based integrated sensors instead of focusing on the performance of a single sensing element. Each rGO-based device in such an array has a unique sensor response due to the irregular structure of rGO films at different levels of organization, ranging from nanoscale to macroscale. The resulting rGO-based gas sensing system could reliably recognize analytes of nearly the same chemical nature. In our experiments rGO-based sensor arrays demonstrated a high selectivity that was sufficient to discriminate between different alcohols, such as methanol, ethanol and isopropanol, at a 100% success rate. We also discuss a possible sensing mechanism that provides the basis for analyte differentiation.

  12. Performance study of solar cell arrays based on a Trough Concentrating Photovoltaic/Thermal system

    International Nuclear Information System (INIS)

    Li, Ming; Ji, Xu; Li, Guoliang; Wei, Shengxian; Li, YingFeng; Shi, Feng

    2011-01-01

    Highlights: → The performances of solar cell arrays based on a Trough Concentrating Photovoltaic/Thermal (TCPV/T) system have been studied. → The optimum concentration ratios for the single crystalline silicon cell, the Super cells and the GaAs cells were studied by experiments. → The influences between the solar cell's performance and the series resistances, the working temperature, solar irradiation intensity were explored. - Abstract: The performances of solar cell arrays based on a Trough Concentrating Photovoltaic/Thermal (TCPV/T) system have been studied via both experiment and theoretical calculation. The I-V characteristics of the solar cell arrays and the output performances of the TCPV/T system demonstrated that among the investigated four types of solar cell arrays, the triple junction GaAs cells possessed good performance characteristics and the polysilicon cells exhibited poor performance characteristics under concentrating conditions. The optimum concentration ratios for the single crystalline silicon cell, the Super cells and the GaAs cells were also studied by experiments. The optimum concentration ratios for the single crystalline silicon cells and Super cells were 4.23 and 8.46 respectively, and the triple junction GaAs cells could work well at higher concentration ratio. Besides, some theoretical calculations and experiments were performed to explore the influences of the series resistances and the working temperature. When the series resistances R s changed from 0 Ω to 1 Ω, the maximum power P m of the single crystalline silicon, the polycrystalline silicon, the Super cell and the GaAs cell arrays decreased by 67.78%, 74.93%, 77.30% and 58.07% respectively. When the cell temperature increased by 1 K, the short circuit current of the four types of solar cell arrays decreased by 0.11818 A, 0.05364 A, 0.01387 A and 0.00215 A respectively. The research results demonstrated that the output performance of the solar cell arrays with lower

  13. Group I mGluR antagonist rescues the deficit of D1-induced LTP in a mouse model of fragile X syndrome

    Directory of Open Access Journals (Sweden)

    Xu Zhao-Hui

    2012-05-01

    Full Text Available Abstract Background Fragile X syndrome (FXS is caused by the absence of the mRNA-binding protein Fragile X mental retardation protein (FMRP, encoded by the Fmr1 gene. Overactive signaling by group 1 metabotropic glutamate receptor (Grp1 mGluR could contribute to slowed synaptic development and other symptoms of FXS. Our previous study has identified that facilitation of synaptic long-term potentiation (LTP by D1 receptor is impaired in Fmr1 knockout (KO mice. However, the contribution of Grp1 mGluR to the facilitation of synaptic plasticity by D1 receptor stimulation in the prefrontal cortex has been less extensively studied. Results Here we demonstrated that DL-AP3, a Grp1 mGluR antagonist, rescued LTP facilitation by D1 receptor agonist SKF81297 in Fmr1KO mice. Grp1 mGluR inhibition restored the GluR1-subtype AMPA receptors surface insertion by D1 activation in the cultured Fmr1KO neurons. Simultaneous treatment of Grp1 mGluR antagonist with D1 agonist recovered the D1 receptor signaling by reversing the subcellular redistribution of G protein-coupled receptor kinase 2 (GRK2 in the Fmr1KO neurons. Treatment of SKF81297 alone failed to increase the phosphorylation of NR2B-containing N-methyl D-aspartate receptors (NMDARs at Tyr-1472 (p-NR2B-Tyr1472 in the cultures from KO mice. However, simultaneous treatment of DL-AP3 could rescue the level of p-NR2B-Tyr1472 by SKF81297 in the cultures from KO mice. Furthermore, behavioral tests indicated that simultaneous treatment of Grp1 mGluR antagonist with D1 agonist inhibited hyperactivity and improved the learning ability in the Fmr1KO mice. Conclusion The findings demonstrate that mGluR1 inhibition is a useful strategy to recover D1 receptor signaling in the Fmr1KO mice, and combination of Grp1 mGluR antagonist and D1 agonist is a potential drug therapy for the FXS.

  14. Two novel deletions (array CGH findings) in pigment dispersion syndrome.

    Science.gov (United States)

    Mikelsaar, Ruth; Molder, Harras; Bartsch, Oliver; Punab, Margus

    2007-12-01

    We report the first male with pigment dispersion syndrome and a balanced translocation t(10;15)(p11.1;q11.1). Cytogenetic analyses using Giemsa banding and FISH methods, and array CGH were performed. Array CGH analyses did not show altered DNA sequences in the breakpoints of the translocation, but revealed two novel deletions in 2q22.1 and 18q22.1. We suppose that the coexistence of t(10;15) and pigment dispersion syndrome in our patient is a coincidence. The deletion in 2q22.1, where the gene LRP1B has been located, may play a major role in the dysembryogenesis of the eye and cause the disorder.

  15. Pulse Splitting for Harmonic Beamforming in Time-Modulated Linear Arrays

    Directory of Open Access Journals (Sweden)

    Lorenzo Poli

    2014-01-01

    Full Text Available A novel strategy for harmonic beamforming in time-modulated linear arrays is proposed. The pulse splitting technique is exploited to simultaneously generate two harmonic patterns, one at the central frequency and another at a preselected harmonic of arbitrary order, while controlling the maximum level of the remaining sideband radiations. An optimization strategy based on the particle swarm optimizer is developed in order to determine the optimal parameters describing the pulse sequence used to modulate the excitation weights of the array elements. Representative numerical results are reported and discussed to point out potentialities and limitations of the proposed approach.

  16. Bicolor Light-Emitting Diode Based on Zinc Oxide Nanorod Arrays and Poly(2-methoxy,5-octoxy)-1,4-phenylenevinylene

    Science.gov (United States)

    Song, Jizhong; He, Ying; Chen, Jie; Zhu, Di; Pan, Zhaodong; Zhang, Yaofei; Wang, Jun-An

    2012-03-01

    The current study reports a novel inorganic/organic light-emitting diode (LED), consisting of zinc oxide (ZnO) nanorod arrays and poly(2-methoxy, 5-octoxy)-1,4-phenylenevinylene (MOPPV). ZnO nanorod arrays passivated using polyacrylamide (PAM) with 70 nm diameter were successfully prepared by a simple polymer-assisted chemical method. Enhancement of the ZnO defect emission is caused by PAM passivation, as observed in photoluminescence spectra. Infrared absorption spectra reveal that PAM is chemically or physically adsorbed on the surfaces of ZnO nanorod arrays. The electroluminescence (EL) spectrum shows bluish light at 406 nm from ZnO transition emission, and light emission with center at 600 nm from exciton emission in MOPPV. The potential EL mechanism is electron transition to zinc vacancy in PAM/ZnO nanorod arrays, and exciton radiation luminescence in MOPPV film. This novel PAM/ZnO-MOPPV device may be helpful to promote development of multicolor LEDs.

  17. Peptide array-based screening of human mesenchymal stem cell-adhesive peptides derived from fibronectin type III domain

    International Nuclear Information System (INIS)

    Okochi, Mina; Nomura, Shigeyuki; Kaga, Chiaki; Honda, Hiroyuki

    2008-01-01

    Human mesenchymal stem cell-adhesive peptides were screened based on the amino acid sequence of fibronectin type III domain 8-11 (FN-III 8-11 ) using a peptide array synthesized by the Fmoc-chemistry. Using hexameric peptide library of FN-III 8-11 scan, we identified the ALNGR (Ala-Leu-Asn-Gly-Arg) peptide that induced cell adhesion as well as RGDS (Arg-Gly-Asp-Ser) peptide. After incubation for 2 h, approximately 68% of inoculated cells adhere to the ALNGR peptide disk. Adhesion inhibition assay with integrin antibodies showed that the ALNGR peptide interacts with integrin β1 but not with αvβ3, indicating that the receptors for ALNGR are different from RGDS. Additionally, the ALNGR peptide expressed cell specificities for adhesion: cell adhesion was promoted for fibroblasts but not for keratinocytes or endotherial cells. The ALNGR peptide induced cell adhesion and promoted cell proliferation without changing its property. It is therefore useful for the construction of functional biomaterials

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

    Science.gov (United States)

    Zhang, Yun; Baheti, Saurabh; Sun, Zhifu

    2018-05-01

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

  19. GaN-based micro-LED arrays on flexible substrates for optical cochlear implants

    International Nuclear Information System (INIS)

    Goßler, Christian; Bierbrauer, Colin; Moser, Rüdiger; Kunzer, Michael; Holc, Katarzyna; Pletschen, Wilfried; Köhler, Klaus; Wagner, Joachim; Schwarz, Ulrich T; Schwaerzle, Michael; Ruther, Patrick; Paul, Oliver; Neef, Jakob; Keppeler, Daniel; Hoch, Gerhard; Moser, Tobias

    2014-01-01

    Currently available cochlear implants are based on electrical stimulation of the spiral ganglion neurons. Optical stimulation with arrays of micro-sized light-emitting diodes (µLEDs) promises to increase the number of distinguishable frequencies. Here, the development of a flexible GaN-based micro-LED array as an optical cochlear implant is reported for application in a mouse model. The fabrication of 15 µm thin and highly flexible devices is enabled by a laser-based layer transfer process of the GaN-LEDs from sapphire to a polyimide-on-silicon carrier wafer. The fabricated 50 × 50 µm 2 LEDs are contacted via conducting paths on both p- and n-sides of the LEDs. Up to three separate channels could be addressed. The probes, composed of a linear array of the said µLEDs bonded to the flexible polyimide substrate, are peeled off the carrier wafer and attached to flexible printed circuit boards. Probes with four µLEDs and a width of 230 µm are successfully implanted in the mouse cochlea both in vitro and in vivo. The LEDs emit 60 µW at 1 mA after peel-off, corresponding to a radiant emittance of 6 mW mm −2 . (paper)

  20. Toward Wearable Energy Storage Devices: Paper-Based Biofuel Cells based on a Screen-Printing Array Structure.

    Science.gov (United States)

    Shitanda, Isao; Momiyama, Misaki; Watanabe, Naoto; Tanaka, Tomohiro; Tsujimura, Seiya; Hoshi, Yoshinao; Itagaki, Masayuki

    2017-10-01

    A novel paper-based biofuel cell with a series/parallel array structure has been fabricated, in which the cell voltage and output power can easily be adjusted as required by printing. The output of the fabricated 4-series/4-parallel biofuel cell reached 0.97±0.02 mW at 1.4 V, which is the highest output power reported to date for a paper-based biofuel cell. This work contributes to the development of flexible, wearable energy storage device.

  1. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

    Directory of Open Access Journals (Sweden)

    Moreau Yves

    2005-05-01

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

  2. Enhanced immunization via dissolving microneedle array-based delivery system incorporating subunit vaccine and saponin adjuvant

    Directory of Open Access Journals (Sweden)

    Zhao JH

    2017-07-01

    Full Text Available Ji-Hui Zhao,1,* Qi-Bo Zhang,1,* Bao Liu,2 Xiang-Hua Piao,1 Yu-Lu Yan,1 Xiao-Ge Hu,1 Kuan Zhou,1 Yong-Tai Zhang,1 Nian-Ping Feng1 1School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China; 2Anethesiology Department, Augusta University, Augusta, GA, USA *These authors contributed equally to this work Purpose: To enhance the immunogenicity of the model subunit vaccine, ovalbumin (OVA was combined with platycodin (PD, a saponin adjuvant. To reduce the toxicity of PD, OVA, and adjuvant were loaded together into liposomes before being incorporated into a dissolving microneedle array.Methods: OVA- and PD-loaded liposomes (OVA-PD-Lipos were prepared using the film dispersion method. Their uptake behavior, toxicity to mouse bone marrow dendritic cells (BMDCs, and hemolytic activity to rabbit red blood cells (RBCs were evaluated. The OVA-PD-Lipos were incorporated into a dissolving microneedle array. The chemical stability of OVA and the physical stability of OVA-PD-Lipos in microneedle arrays were investigated. The immune response of Institute of Cancer Research mice and potential skin irritation reaction of rabbits to OVA-PD-Lipos-MNs were evaluated.Results: The uptake of OVA by mouse BMDCs was greatly enhanced when OVA was prepared as OVA-PD-Lipos, and in this form, the toxicity of PD was dramatically reduced. OVA was chemically stable as OVA-PD-Lipos, when OVA-PD-Lipos was incorporated into a dissolving microneedle array. Institute of Cancer Research mice treated with OVA-PD-Lipos-MNs showed a significantly enhanced immune response. PD combined with OVA elicited a balanced Th1 and Th2 humoral immune response in mice, with minimal irritation in rabbit skin.Conclusion: The dissolving microneedle array-based system is a promising delivery vehicle for subunit vaccine and its adjuvant. Keywords: subunit vaccine, saponin adjuvant, liposomes, dissolving microneedle array, intradermal vaccination

  3. High-performance flexible supercapacitor based on porous array electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Shieh, Jen-Yu; Tsai, Sung-Ying; Li, Bo-Yan [Institute of Electro-Optical and Materials Science, National Formosa University, 64 Wenhua Road, Huwei, Yunlin 63208, Taiwan (China); Yu, Hsin Her, E-mail: hhyu@nfu.edu.tw [Department of Biotechnology, National Formosa University, 64 Wenhua Road, Huwei, Yunlin 63208, Taiwan (China)

    2017-07-01

    In this study, an array of polystyrene (PS) spheres was synthesized by a dispersion-polymerization technique as a template onto which a porous polydimethylsiloxane (PDMS) microarray structure was fabricated by soft lithography. A conducting layer was coated on the surface of the microarray after a suspension of multi-walled carbon nanotubes (MWCNTs) mixed with graphene (G) had been poured into the porous array. A PDMS-based porous supercapacitor was assembled by sandwiching a separator between two porous electrodes filled with a H{sub 3}PO{sub 4}/polyvinyl alcohol (PVA) gel electrolyte. The specific capacitance, electrochemical properties, and cycle stability of the porous electrode supercapacitors were explored. The porous PDMS-electrode-based supercapacitor exhibited high specific capacitance and good cycle stability, indicating its enormous potential for future applications in wearable and portable electronic products. - Highlights: • Porous electrode was prepared using an array of polystyrene spheres as template. • The porous electrodes provided increased contact area with the electrolyte. • A gel electrolyte averted problems with leakage and poor interfacial contact. • A larger separator pore size effectively reduced the internal resistance, iR{sub drop}. • Porous PDMS supercapacitor showed superior flexibility and cycling stability.

  4. Comparison of Nasal Epithelial Smoking-Induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays

    Directory of Open Access Journals (Sweden)

    Xiaoling Zhang

    2013-01-01

    Full Text Available We have previously defined the impact of tobacco smoking on nasal epithelium gene expression using Affymetrix Exon 1.0 ST arrays. In this paper, we compared the performance of the Affymetrix GeneChip Human Gene 1.0 ST array with the Human Exon 1.0 ST array for detecting nasal smoking-related gene expression changes. RNA collected from the nasal epithelium of five current smokers and five never smokers was hybridized to both arrays. While the intersample correlation within each array platform was relatively higher in the Gene array than that in the Exon array, the majority of the genes most changed by smoking were tightly correlated between platforms. Although neither array dataset was powered to detect differentially expressed genes (DEGs at a false discovery rate (FDR <0.05, we identified more DEGs than expected by chance using the Gene ST array. These findings suggest that while both platforms show a high degree of correlation for detecting smoking-induced differential gene expression changes, the Gene ST array may be a more cost-effective platform in a clinical setting for gene-level genomewide expression profiling and an effective tool for exploring the host response to cigarette smoking and other inhaled toxins.

  5. Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.

    Science.gov (United States)

    Delong, Allison K; Wu, Mingham; Bennett, Diane; Parkin, Neil; Wu, Zhijin; Hogan, Joseph W; Kantor, Rami

    2012-08-01

    Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802 PR and 44,432 RT sequences) from the published literature ( http://hivdb.Stanford.edu ). Nucleic acid sequences are read into SQUAT, identified, aligned, and translated. Nucleic acid sequences are flagged if with >five 1-2-base insertions; >one 3-base insertion; >one deletion; >six PR or >18 RT ambiguous bases; >three consecutive PR or >four RT nucleic acid mutations; >zero stop codons; >three PR or >six RT ambiguous amino acids; >three consecutive PR or >four RT amino acid mutations; >zero unique amino acids; or 15% genetic distance from another submitted sequence. Thresholds are user modifiable. SQUAT output includes a summary report with detailed comments for troubleshooting of flagged sequences, histograms of pairwise genetic distances, neighbor joining phylogenetic trees, and aligned nucleic and amino acid sequences. SQUAT is a stand-alone, free, web-independent tool to ensure use of high-quality HIV PR/RT sequences in interpretation and reporting of drug resistance, while increasing awareness and expertise and facilitating troubleshooting of potentially problematic sequences.

  6. Flow-through nanohole array based sensor implemented on analogue smartphone components

    Science.gov (United States)

    Gomez-Cruz, Juan; Nair, Srijit; Ascanio, Gabriel; Escobedo, Carlos

    2017-08-01

    Mobile communications have massively populated the consumer electronics market over the past few years and it is now ubiquitous, providing a timeless opportunity for the development of smartphone-based technologies as point-of-care (POC) diagnosis tools1 . The expectation for a fully integrated smartphone-based sensor that enables applications such as environmental monitoring, explosive detection and biomedical analysis has increased among the scientific community in the past few years2,3. The commercialization forecast for smartphone-based sensing technologies is very promising, but reliable, miniature and cost-effective sensing platforms that can adapt to portable electronics in still under development. In this work, we present an integrated sensing platform based on flow-through metallic nanohole arrays. The nanohole arrays are 260 nm in diameter and 520 nm in pitch, fabricated using Focused Ion Beam (FIB) lithography. A white LED resembling a smartphone flash LED serves as light source to excite surface plasmons and the signal is recorded via a Complementary Metal-Oxide-Semiconductor (CMOS) module. The sensing abilities of the integrated sensing platform is demonstrated for the detection of (i) changes in bulk refractive index (RI), (ii) real-time monitoring of surface modification by receptor-analyte system of streptavidin-biotin.

  7. Adaptive Basis Selection for Exponential Family Smoothing Splines with Application in Joint Modeling of Multiple Sequencing Samples

    OpenAIRE

    Ma, Ping; Zhang, Nan; Huang, Jianhua Z.; Zhong, Wenxuan

    2017-01-01

    Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments in parallel. After the resulting sequences (short reads) are mapped to the genome, one gets a sequence of short read counts along the genome. Effective extraction of signals in these short read counts is the key to the success of sequencing technologies. No...

  8. A backing device based on an embedded stiffener and retractable insertion tool for thin-film cochlear arrays

    Science.gov (United States)

    Tewari, Radheshyam

    Intracochlear trauma from surgical insertion of bulky electrode arrays and inadequate pitch perception are areas of concern with current hand-assembled commercial cochlear implants. Parylene thin-film arrays with higher electrode densities and lower profiles are a potential solution, but lack rigidity and hence depend on manually fabricated permanently attached polyethylene terephthalate (PET) tubing based bulky backing devices. As a solution, we investigated a new backing device with two sub-systems. The first sub-system is a thin poly(lactic acid) (PLA) stiffener that will be embedded in the parylene array. The second sub-system is an attaching and detaching mechanism, utilizing a poly(N-vinylpyrrolidone)-block-poly(d,l-lactide) (PVP-b-PDLLA) copolymer-based biodegradable and water soluble adhesive, that will help to retract the PET insertion tool after implantation. As a proof-of-concept of sub-system one, a microfabrication process for patterning PLA stiffeners embedded in parylene has been developed. Conventional hot-embossing, mechanical micromachining, and standard cleanroom processes were integrated for patterning fully released and discrete stiffeners coated with parylene. The released embedded stiffeners were thermoformed to demonstrate that imparting perimodiolar shapes to stiffener-embedded arrays will be possible. The developed process when integrated with the array fabrication process will allow fabrication of stiffener-embedded arrays in a single process. As a proof-of-concept of sub-system two, the feasibility of the attaching and detaching mechanism was demonstrated by adhering 1x and 1.5x scale PET tube-based insertion tools and PLA stiffeners embedded in parylene using the copolymer adhesive. The attached devices survived qualitative adhesion tests, thermoforming, and flexing. The viability of the detaching mechanism was tested by aging the assemblies in-vitro in phosphate buffer solution. The average detachment times, 2.6 minutes and 10 minutes

  9. Low Power Systolic Array Based Digital Filter for DSP Applications

    Directory of Open Access Journals (Sweden)

    S. Karthick

    2015-01-01

    Full Text Available Main concepts in DSP include filtering, averaging, modulating, and correlating the signals in digital form to estimate characteristic parameter of a signal into a desirable form. This paper presents a brief concept of low power datapath impact for Digital Signal Processing (DSP based biomedical application. Systolic array based digital filter used in signal processing of electrocardiogram analysis is presented with datapath architectural innovations in low power consumption perspective. Implementation was done with ASIC design methodology using TSMC 65 nm technological library node. The proposed systolic array filter has reduced leakage power up to 8.5% than the existing filter architectures.

  10. Microneedle-based drug and vaccine delivery via nanoporous microneedle arrays.

    Science.gov (United States)

    van der Maaden, Koen; Luttge, Regina; Vos, Pieter Jan; Bouwstra, Joke; Kersten, Gideon; Ploemen, Ivo

    2015-08-01

    In the literature, several types of microneedles have been extensively described. However, porous microneedle arrays only received minimal attention. Hence, only little is known about drug delivery via these microneedles. However, porous microneedle arrays may have potential for future microneedle-based drug and vaccine delivery and could be a valuable addition to the other microneedle-based drug delivery approaches. To gain more insight into porous microneedle technologies, the scientific and patent literature is reviewed, and we focus on the possibilities and constraints of porous microneedle technologies for dermal drug delivery. Furthermore, we show preliminary data with commercially available porous microneedles and describe future directions in this field of research.

  11. Molecular identification of common Salmonella serovars using multiplex DNA sensor-based suspension array.

    Science.gov (United States)

    Aydin, Muhsin; Carter-Conger, Jacqueline; Gao, Ning; Gilmore, David F; Ricke, Steven C; Ahn, Soohyoun

    2018-04-01

    Salmonella is one of major foodborne pathogens and the leading cause of foodborne illness-related hospitalizations and deaths. It is critical to develop a sensitive and rapid detection assay that can identify Salmonella to ensure food safety. In this study, a DNA sensor-based suspension array system of high multiplexing ability was developed to identify eight Salmonella serovars commonly associated with foodborne outbreaks to the serotype level. Each DNA sensor was prepared by activating pre-encoded microspheres with oligonucleotide probes that are targeting virulence genes and serovar-specific regions. The mixture of 12 different types of DNA sensors were loaded into a 96-well microplate and used as a 12-plex DNA sensor array platform. DNA isolated from Salmonella was amplified by multiplex polymerase chain reaction (mPCR), and the presence of Salmonella was determined by reading fluorescent signals from hybridization between probes on DNA sensors and fluorescently labeled target DNA using the Bio-Plex® system. The developed multiplex array was able to detect synthetic DNA at the concentration as low as 100 fM and various Salmonella serovars as low as 100 CFU/mL within 1 h post-PCR. Sensitivity of this assay was further improved to 1 CFU/mL with 6-h enrichment. The array system also correctly and specifically identified serotype of tested Salmonella strains without any cross-reactivity with other common foodborne pathogens. Our results indicate the developed DNA sensor suspension array can be a rapid and reliable high-throughput method for simultaneous detection and molecular identification of common Salmonella serotypes.

  12. Detection and Quantification of the Fragile X Mental Retardation Protein 1 (FMRP

    Directory of Open Access Journals (Sweden)

    Giuseppe LaFauci

    2016-12-01

    Full Text Available The final product of FMR1 gene transcription, Fragile X Mental Retardation Protein 1 (FMRP, is an RNA binding protein that acts as a repressor of translation. FMRP is expressed in several tissues and plays important roles in neurogenesis, synaptic plasticity, and ovarian functions and has been implicated in a number of neuropsychological disorders. The loss of FMRP causes Fragile X Syndrome (FXS. In most cases, FXS is due to large expansions of a CGG repeat in FMR1—normally containing 6–54 repeats—to over 200 CGGs and identified as full mutation (FM. Hypermethylation of the repeat induces FMR1 silencing and lack of FMRP expression in FM male. Mosaic FM males express low levels of FMRP and present a less severe phenotype that inversely correlates with FMRP levels. Carriers of pre-mutations (55–200 CGG show increased mRNA, and normal to reduced FMRP levels. Alternative splicing of FMR1 mRNA results in 24 FMRP predicted isoforms whose expression are tissues and developmentally regulated. Here, we summarize the approaches used by several laboratories including our own to (a detect and estimate the amount of FMRP in different tissues, developmental stages and various pathologies; and (b to accurately quantifying FMRP for a direct diagnosis of FXS in adults and newborns.

  13. Probing Contaminant-Induced Alterations in Chlorophyll Fluorescence by AC-Dielectrophoresis-Based 2D-Algal Array

    Directory of Open Access Journals (Sweden)

    Coralie Siebman

    2018-02-01

    Full Text Available The investigation of contaminant impact on algae requires rapid and reliable cell collection and optical detection. The capability of alternative current (AC dielectrophoresis (DEP collection of whole cell arrays with combined fluorescence microscopy detection to follow the alterations of chlorophyll fluorescence during environmental contaminant exposure was explored. The application of an AC-field of 100 V cm−1, 100 Hz for 30 min to capture and immobilize the cells of green alga Chlamydomonas reinhardtii in two-dimensional (2D arrays does not induce changes in chlorophyll fluorescence. The results demonstrate that DEP-based 2D-arrays allow non-invasive detection of chlorophyll fluorescence change upon exposure to high concentrations of copper oxide nanoparticles and ionic copper. These results were in agreement with data obtained by flow cytometry used as a comparative method. The tool was also applied to follow the effect of a number of ubiquitous contaminants such as inorganic mercury, methylmercury, and diuron. However, a statistically significant short-term effect was observed only for mercury. Overall, DEP-based 2D-arrays of algal cells with fluorescence detection appear to be suitable for stain-free probing the effects on the photosynthetic microorganisms in highly polluted environment.

  14. An approach to fabricating chemical sensors based on ZnO nanorod arrays

    International Nuclear Information System (INIS)

    Park, Jae Young; Song, Dong Eon; Kim, Sang Sub

    2008-01-01

    Vertically and laterally aligned ZnO nanorod arrays were synthesized on Pt-coated Si substrates by catalyst-free metal organic chemical vapor deposition. An approach to fabricating chemical sensors based on the nanorod arrays using a coating-and-etching process with a photo-resist is reported. Tests of the devices as oxygen gas sensors have been performed. Our results demonstrate that the approach holds promise for the realization of sensitive and reliable nanorod array chemical sensors

  15. Noninvasive prenatal paternity testing (NIPAT) through maternal plasma DNA sequencing

    DEFF Research Database (Denmark)

    Jiang, Haojun; Xie, Yifan; Li, Xuchao

    2016-01-01

    developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels......Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we...... paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future....

  16. An accurate clone-based haplotyping method by overlapping pool sequencing.

    Science.gov (United States)

    Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao

    2016-07-08

    Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

    Energy Technology Data Exchange (ETDEWEB)

    Drmanac, R.; Drmanac, S.; Labat, I.; Vicentic, A.; Gemmell, A.; Stavropoulos, N.; Jarvis, J.

    1992-01-01

    A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 [sup 32]P- or [sup 33]P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation.

  18. SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

    Energy Technology Data Exchange (ETDEWEB)

    Drmanac, R.; Drmanac, S.; Labat, I.; Vicentic, A.; Gemmell, A.; Stavropoulos, N.; Jarvis, J.

    1992-12-01

    A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 {sup 32}P- or {sup 33}P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation.

  19. SBH and the integration of complementary approaches in the mapping, sequencing, and understanding of complex genomes

    International Nuclear Information System (INIS)

    Drmanac, R.; Drmanac, S.; Labat, I.; Vicentic, A.; Gemmell, A.; Stavropoulos, N.; Jarvis, J.

    1992-01-01

    A variant of sequencing by hybridization (SBH) is being developed with a potential to inexpensively determine up to 100 million base pairs per year. The method comprises (1) arraying short clones in 864-well plates; (2) growth of the M13 clones or PCR of the inserts; (3) automated spotting of DNAs by corresponding pin-arrays; (4) hybridization of dotted samples with 200-3000 32 P- or 33 P-labeled 6- to 8-mer probes; and (5) scoring hybridization signals using storage phosphor plates. Some 200 7- to 8-mers can provide an inventory of the genes if CDNA clones are hybridized, or can define the order of 2-kb genomic clones, creating physical and structural maps with 100-bp resolution; the distribution of G+C, LINEs, SINEs, and gene families would be revealed. cDNAs that represent new genes and genomic clones in regions of interest selected by SBH can be sequenced by a gel method. Uniformly distributed clones from the previous step will be hybridized with 2000--3000 6- to 8-mers. As a result, approximately 50--60% of the genomic regions containing members of large repetitive and gene families and those families represented in GenBank would be completely sequenced. In the less redundant regions, every base pair is expected to be read with 3-4 probes, but the complete sequence can not be reconstructed. Such partial sequences allow the inference of similarity and the recognition of coding, regulatory, and repetitive sequences, as well as study of the evolutionary processes all the way up to the species delineation

  20. ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly

    Directory of Open Access Journals (Sweden)

    Spang Rainer

    2009-12-01

    Full Text Available Abstract Background The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis. Results We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/. Conclusions ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.

  1. Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.

    Science.gov (United States)

    Archer, John; Weber, Jan; Henry, Kenneth; Winner, Dane; Gibson, Richard; Lee, Lawrence; Paxinos, Ellen; Arts, Eric J; Robertson, David L; Mimms, Larry; Quiñones-Mateu, Miguel E

    2012-01-01

    HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile™, Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454™ Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile™ and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage.

  2. Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.

    Directory of Open Access Journals (Sweden)

    John Archer

    Full Text Available HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5 viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile™, Monogram Biosciences and genotypic (e.g., population sequencing linked to bioinformatic algorithms assays are the most widely used. Although several next-generation sequencing (NGS platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454™ Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences, Illumina®, and Ion Torrent™ (Life Technologies. Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile™ and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used, compared to Trofile (80% and population sequencing (70%. In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage.

  3. Detection of Hereditary 1,25-Hydroxyvitamin D-Resistant Rickets Caused by Uniparental Disomy of Chromosome 12 Using Genome-Wide Single Nucleotide Polymorphism Array.

    Directory of Open Access Journals (Sweden)

    Mayuko Tamura

    Full Text Available Hereditary 1,25-dihydroxyvitamin D-resistant rickets (HVDRR is an autosomal recessive disease caused by biallelic mutations in the vitamin D receptor (VDR gene. No patients have been reported with uniparental disomy (UPD.Using genome-wide single nucleotide polymorphism (SNP array to confirm whether HVDRR was caused by UPD of chromosome 12.A 2-year-old girl with alopecia and short stature and without any family history of consanguinity was diagnosed with HVDRR by typical laboratory data findings and clinical features of rickets. Sequence analysis of VDR was performed, and the origin of the homozygous mutation was investigated by target SNP sequencing, short tandem repeat analysis, and genome-wide SNP array.The patient had a homozygous p.Arg73Ter nonsense mutation. Her mother was heterozygous for the mutation, but her father was negative. We excluded gross deletion of the father's allele or paternal discordance. Genome-wide SNP array of the family (the patient and her parents showed complete maternal isodisomy of chromosome 12. She was successfully treated with high-dose oral calcium.This is the first report of HVDRR caused by UPD, and the third case of complete UPD of chromosome 12, in the published literature. Genome-wide SNP array was useful for detecting isodisomy and the parental origin of the allele. Comprehensive examination of the homozygous state is essential for accurate genetic counseling of recurrence risk and appropriate monitoring for other chromosome 12 related disorders. Furthermore, oral calcium therapy was effective as an initial treatment for rickets in this instance.

  4. Novel ring resonator-based integrated photonic beamformer for broadband phased array receive antennas - part 1: design and performance analysis

    NARCIS (Netherlands)

    Meijerink, Arjan; Roeloffzen, C.G.H.; Meijerink, Roland; Zhuang, L.; Marpaung, D.A.I.; Bentum, Marinus Jan; Burla, M.; Verpoorte, Jaco; Jorna, Pieter; Huizinga, Adriaan; van Etten, Wim

    2010-01-01

    A novel optical beamformer concept is introduced that can be used for seamless control of the reception angle in broadband wireless receivers employing a large phased array antenna (PAA). The core of this beamformer is an optical beamforming network (OBFN), using ring resonator-based broadband

  5. SCRLH-TL Based Sequential Rotation Feed Network for Broadband Circularly Polarized Antenna Array

    Directory of Open Access Journals (Sweden)

    B. F. Zong

    2016-04-01

    Full Text Available In this paper, a broadband circularly polarized (CP microstrip antenna array using composite right/left-handed transmission line (SCRLH-TL based sequential rotation (SR feed network is presented. The characteristics of a SCRLH-TL are initially investigated. Then, a broadband and low insertion loss 45º phase shifter is designed using the SCRLH-TL and the phase shifter is employed in constructing a SR feed network for CP antenna array. To validate the design method of the SR feed network, a 2×2 antenna array comprising sequentially rotated coupled stacked CP antenna elements is designed, fabricated and measured. Both the simulated and measured results indicate that the performances of the antenna element are further enhanced when the SR network is used. The antenna array exhibits the VSWR less than 1.8 dB from 4 GHz to 7 GHz and the 3 dB axial ratio (AR from 4.4 GHz to 6.8 GHz. Also, high peak gain of 13.7 dBic is obtained. Besides, the normalized radiation patterns at the operating frequencies are symmetrical and the side lobe levels are low at φ=0º and φ=90º.

  6. An IBM PC-based math model for space station solar array simulation

    Science.gov (United States)

    Emanuel, E. M.

    1986-01-01

    This report discusses and documents the design, development, and verification of a microcomputer-based solar cell math model for simulating the Space Station's solar array Initial Operational Capability (IOC) reference configuration. The array model is developed utilizing a linear solar cell dc math model requiring only five input parameters: short circuit current, open circuit voltage, maximum power voltage, maximum power current, and orbit inclination. The accuracy of this model is investigated using actual solar array on orbit electrical data derived from the Solar Array Flight Experiment/Dynamic Augmentation Experiment (SAFE/DAE), conducted during the STS-41D mission. This simulator provides real-time simulated performance data during the steady state portion of the Space Station orbit (i.e., array fully exposed to sunlight). Eclipse to sunlight transients and shadowing effects are not included in the analysis, but are discussed briefly. Integrating the Solar Array Simulator (SAS) into the Power Management and Distribution (PMAD) subsystem is also discussed.

  7. Complex programmable logic device based alarm sequencer for nuclear power plants

    International Nuclear Information System (INIS)

    Khedkar, Ravindra; Solomon, J. Selva; KrishnaKumar, B.

    2001-01-01

    Complex Programmable Logic Device based Alarm Sequencer is an instrument, which detects alarms, memorizes them and displays the sequences of occurrence of alarms. It caters to sixteen alarm signals and distinguishes the sequence among any two alarms with a time resolution of 1 ms. The system described has been designed for continuous operation in process plants, nuclear power plants etc. The system has been tested and found to be working satisfactorily. (author)

  8. Antibody repertoire profiling with mimotope arrays

    OpenAIRE

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

    2016-01-01

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

  9. Rocking convex array used for 3D synthetic aperture focusing

    DEFF Research Database (Denmark)

    Andresen, Henrik; Nikolov, Svetoslav; Pedersen, M M

    2008-01-01

    Volumetric imaging can be performed using 1D arrays in combination with mechanical motion. Outside the elevation focus of the array, the resolution and contrast quickly degrade compared to the azimuth plane, because of the fixed transducer focus. The purpose of this paper is to use synthetic...... aperture focusing (SAF) for enhancing the elevation focusing for a convex rocking array, to obtain a more isotropic point spread function. This paper presents further development of the SAF method, which can be used with curved array combined with a rocking motion. The method uses a virtual source (VS...... Kretztechnik, Zipf, Austria). The array has an elevation focus at 60 mm of depth, and the angular rocking velocity is up to 140deg/s. The scan sequence uses an fprf of 4500 - 7000 Hz allowing up to 15 cm of penetration. The full width at half max (FWHM) and main-lobe to side-lobe ratio (MLSL) is used...

  10. Haplotype-Based Genotyping in Polyploids

    Directory of Open Access Journals (Sweden)

    Josh P. Clevenger

    2018-04-01

    Full Text Available Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2 was developed for Arachis hypogaea (peanut, an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

  11. Development of the smartphone-based colorimetry for multi-analyte sensing arrays.

    Science.gov (United States)

    Hong, Jong Il; Chang, Byoung-Yong

    2014-05-21

    Here we report development of a smartphone app (application) that digitizes the colours of a colorimetric sensor array. A conventional colorimetric sensor array consists of multiple paper-based sensors, and reports the detection results in terms of colour change. Evaluation of the colour changes is normally done by the naked eye, which may cause uncertainties due to personal subjectivity and the surrounding conditions. Solutions have been particularly sought in smartphones as they are capable of spectrometric functions. Our report specifically focuses on development of a practical app for immediate point-of-care (POC) multi-analyte sensing without additional devices. First, the individual positions of the sensors are automatically identified by the smartphone; second, the colours measured at each sensor are digitized based on a correction algorithm; and third, the corrected colours are converted to concentration values by pre-loaded calibration curves. All through these sequential processes, the sensor array taken in a smartphone snapshot undergoes laboratory-level spectrometry. The advantages of inexpensive and convenient paper-based colorimetry and the ubiquitous smartphone are tied to achieve a ready-to-go POC diagnosis.

  12. From nonfinite to finite 1D arrays of origami tiles.

    Science.gov (United States)

    Wu, Tsai Chin; Rahman, Masudur; Norton, Michael L

    2014-06-17

    CONSPECTUS: DNA based nanotechnology provides a basis for high-resolution fabrication of objects almost without physical size limitations. However, the pathway to large-scale production of large objects is currently unclear. Operationally, one method forward is to use high information content, large building blocks, which can be generated with high yield and reproducibility. Although flat DNA origami naturally invites comparison to pixels in zero, one, and two dimensions and voxels in three dimensions and has provided an excellent mechanism for generating blocks of significant size and complexity and a multitude of shapes, the field is young enough that a single "brick" has not become the standard platform used by the majority of researchers in the field. In this Account, we highlight factors we considered that led to our adoption of a cross-shaped, non-space-filling origami species, designed by Dr. Liu of the Seeman laboratory, as the building block ideal for use in the fabrication of finite one-dimensional arrays. Three approaches that can be employed for uniquely coding origami-origami linkages are presented. Such coding not only provides the energetics for tethering the species but also uniquely designates the relative orientation of the origami building blocks. The strength of the coding approach implemented in our laboratory is demonstrated using examples of oligomers ranging from finite multimers composed of four, six, and eight origami structures to semi-infinite polymers (100mers). Two approaches to finite array design and the series of assembly steps that each requires are discussed. The process of AFM observation for array characterization is presented as a critical case study. For these soft species, the array images do not simply present the solution phase geometry projected onto a two-dimensional surface. There are additional perturbations associated with fluidic forces associated with sample preparation. At this time, reconstruction of the "true" or

  13. Model-based quality assessment and base-calling for second-generation sequencing data.

    Science.gov (United States)

    Bravo, Héctor Corrada; Irizarry, Rafael A

    2010-09-01

    Second-generation sequencing (sec-gen) technology can sequence millions of short fragments of DNA in parallel, making it capable of assembling complex genomes for a small fraction of the price and time of previous technologies. In fact, a recently formed international consortium, the 1000 Genomes Project, plans to fully sequence the genomes of approximately 1200 people. The prospect of comparative analysis at the sequence level of a large number of samples across multiple populations may be achieved within the next five years. These data present unprecedented challenges in statistical analysis. For instance, analysis operates on millions of short nucleotide sequences, or reads-strings of A,C,G, or T's, between 30 and 100 characters long-which are the result of complex processing of noisy continuous fluorescence intensity measurements known as base-calling. The complexity of the base-calling discretization process results in reads of widely varying quality within and across sequence samples. This variation in processing quality results in infrequent but systematic errors that we have found to mislead downstream analysis of the discretized sequence read data. For instance, a central goal of the 1000 Genomes Project is to quantify across-sample variation at the single nucleotide level. At this resolution, small error rates in sequencing prove significant, especially for rare variants. Sec-gen sequencing is a relatively new technology for which potential biases and sources of obscuring variation are not yet fully understood. Therefore, modeling and quantifying the uncertainty inherent in the generation of sequence reads is of utmost importance. In this article, we present a simple model to capture uncertainty arising in the base-calling procedure of the Illumina/Solexa GA platform. Model parameters have a straightforward interpretation in terms of the chemistry of base-calling allowing for informative and easily interpretable metrics that capture the variability in

  14. Nucleotide sequence of cloned cDNA for human sphingolipid activator protein 1 precursor

    International Nuclear Information System (INIS)

    Dewji, N.N.; Wenger, D.A.; O'Brien, J.S.

    1987-01-01

    Two cDNA clones encoding prepro-sphingolipid activator protein 1 (SAP-1) were isolated from a λ gt11 human hepatoma expression library using polyclonal antibodies. These had inserts of ≅ 2 kilobases (λ-S-1.2 and λ-S-1.3) and both were both homologous with a previously isolated clone (λ-S-1.1) for mature SAP-1. The authors report here the nucleotide sequence of the longer two EcoRI fragments of S-1.2 and S-1.3 that were not the same and the derived amino acid sequences of mature SAP-1 and its prepro form. The open reading frame encodes 19 amino acids, which are colinear with the amino-terminal sequence of mature SAP-1, and extends far beyond the predicted carboxyl terminus of mature SAP-1, indicating extensive carboxyl-terminal processing. The nucleotide sequence of cDNA encoding prepro-SAP-1 includes 1449 bases from the assigned initiation codon ATG at base-pair 472 to the stop codon TGA at base-pair 1921. The first 23 amino acids coded after the initiation ATG are characteristic of a signal peptide. The calculated molecular mass for a polypeptide encoded by 1449 bases is ≅ 53 kDa, in keeping with the reported value for pro-SAP-1. The data indicate that after removal of the signal peptide mature SAP-1 is generated by removing an additional 7 amino acids from the amino terminus and ≅ 373 amino acids from the carboxyl terminus. One potential glycosylation site was previously found in mature SAP-1. Three additional potential glycosylation sites are present in the processed carboxyl-terminal polypeptide, which they designate as P-2

  15. Investigating Multi-Array Antenna Signal Convergence using Wavelet Transform and Krylov Sequence

    Directory of Open Access Journals (Sweden)

    Muhammad Ahmed Sikander

    2018-01-01

    Full Text Available In the present world, wireless communication is becoming immensely popular for plethora of applications. Technology has been advancing at an accelerated rate leading to make communication reliable. Still, there are issues need to be address to minimize errors in the transmission. This research study expounds on the rapid convergence of the signal. Convergence is considered to be an important aspect in wireless communication. For rapid convergence, two ambiguities should be addressed; Eigenvalue spread and sparse identification or sparsity of the signal. Eigen value spread is defining as the ratio of minimum to maximum Eigenvalue, whereas sparsity is defining as the loosely bounded system. In this research, two of these attributes are investigated for MAA (Multi-Array Antenna signal using the cascading of Wavelet and Krylov processes. Specifically, the MAA signal is applied in the research because nowadays there are many physical hindrances in the communication path. These hurdles weaken the signal strength which in turn effects the quality of the reception. WT (Wavelet Transform is used to address the Eigenvalue problem and the Krylov sequence is used to attempt the sparse identification of the MAA signal. The results show that the convergence of the MMA signal is improved by applying Wavelet transform and Krylov Subspace.

  16. Investigating multi-array antenna signal convergence using wavelet transform and krylov sequence

    International Nuclear Information System (INIS)

    Sikander, M.A.; Hussain, R.; Hussain, R.

    2018-01-01

    In the present world, wireless communication is becoming immensely popular for plethora of applications. Technology has been advancing at an accelerated rate leading to make communication reliable. Still, there are issues need to be address to minimize errors in the transmission. This research study expounds on the rapid convergence of the signal. Convergence is considered to be an important aspect in wireless communication. For rapid convergence, two ambiguities should be addressed; Eigenvalue spread and sparse identification or sparsity of the signal. Eigen value spread is defining as the ratio of minimum to maximum Eigenvalue, whereas sparsity is defining as the loosely bounded system. In this research, two of these attributes are investigated for MAA (Multi-Array Antenna) signal using the cascading of Wavelet and Krylov processes. Specifically, the MAA signal is applied in the research because nowadays there are many physical hindrances in the communication path. These hurdles weaken the signal strength which in turn effects the quality of the reception. WT (Wavelet Transform) is used to address the Eigenvalue problem and the Krylov sequence is used to attempt the sparse identification of the MAA signal. The results show that the convergence of the MMA signal is improved by applying Wavelet transform and Krylov Subspace. (author)

  17. Abductive Inference using Array-Based Logic

    DEFF Research Database (Denmark)

    Frisvad, Jeppe Revall; Falster, Peter; Møller, Gert L.

    The notion of abduction has found its usage within a wide variety of AI fields. Computing abductive solutions has, however, shown to be highly intractable in logic programming. To avoid this intractability we present a new approach to logicbased abduction; through the geometrical view of data...... employed in array-based logic we embrace abduction in a simple structural operation. We argue that a theory of abduction on this form allows for an implementation which, at runtime, can perform abductive inference quite efficiently on arbitrary rules of logic representing knowledge of finite domains....

  18. An array-based study of increased system lifetime probability

    DEFF Research Database (Denmark)

    Nesgaard, Carsten

    2003-01-01

    Society's increased dependence on electronic systems calls for highly reliable power supplies comprised of multiple converters working in parallel. This paper describes a redundancy control scheme, based on the array technology that increases the overall reliability quite considerably and thereby...

  19. An array-based study of increased system lifetime probability

    DEFF Research Database (Denmark)

    Nesgaard, Carsten

    2002-01-01

    Society's increased dependence on electronic systems calls for highly reliable power supplies comprised of multiple converters working in parallel. This paper describes a redundancy control scheme, based on the array technology that increases the overall reliability quite considerably and thereby...

  20. Reliability analysis of the solar array based on Fault Tree Analysis

    International Nuclear Information System (INIS)

    Wu Jianing; Yan Shaoze

    2011-01-01

    The solar array is an important device used in the spacecraft, which influences the quality of in-orbit operation of the spacecraft and even the launches. This paper analyzes the reliability of the mechanical system and certifies the most vital subsystem of the solar array. The fault tree analysis (FTA) model is established according to the operating process of the mechanical system based on DFH-3 satellite; the logical expression of the top event is obtained by Boolean algebra and the reliability of the solar array is calculated. The conclusion shows that the hinges are the most vital links between the solar arrays. By analyzing the structure importance(SI) of the hinge's FTA model, some fatal causes, including faults of the seal, insufficient torque of the locking spring, temperature in space, and friction force, can be identified. Damage is the initial stage of the fault, so limiting damage is significant to prevent faults. Furthermore, recommendations for improving reliability associated with damage limitation are discussed, which can be used for the redesigning of the solar array and the reliability growth planning.

  1. Reliability analysis of the solar array based on Fault Tree Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wu Jianing; Yan Shaoze, E-mail: yansz@mail.tsinghua.edu.cn [State Key Laboratory of Tribology, Department of Precision Instruments and Mechanology, Tsinghua University,Beijing 100084 (China)

    2011-07-19

    The solar array is an important device used in the spacecraft, which influences the quality of in-orbit operation of the spacecraft and even the launches. This paper analyzes the reliability of the mechanical system and certifies the most vital subsystem of the solar array. The fault tree analysis (FTA) model is established according to the operating process of the mechanical system based on DFH-3 satellite; the logical expression of the top event is obtained by Boolean algebra and the reliability of the solar array is calculated. The conclusion shows that the hinges are the most vital links between the solar arrays. By analyzing the structure importance(SI) of the hinge's FTA model, some fatal causes, including faults of the seal, insufficient torque of the locking spring, temperature in space, and friction force, can be identified. Damage is the initial stage of the fault, so limiting damage is significant to prevent faults. Furthermore, recommendations for improving reliability associated with damage limitation are discussed, which can be used for the redesigning of the solar array and the reliability growth planning.

  2. A new feedback image encryption scheme based on perturbation with dynamical compound chaotic sequence cipher generator

    Science.gov (United States)

    Tong, Xiaojun; Cui, Minggen; Wang, Zhu

    2009-07-01

    The design of the new compound two-dimensional chaotic function is presented by exploiting two one-dimensional chaotic functions which switch randomly, and the design is used as a chaotic sequence generator which is proved by Devaney's definition proof of chaos. The properties of compound chaotic functions are also proved rigorously. In order to improve the robustness against difference cryptanalysis and produce avalanche effect, a new feedback image encryption scheme is proposed using the new compound chaos by selecting one of the two one-dimensional chaotic functions randomly and a new image pixels method of permutation and substitution is designed in detail by array row and column random controlling based on the compound chaos. The results from entropy analysis, difference analysis, statistical analysis, sequence randomness analysis, cipher sensitivity analysis depending on key and plaintext have proven that the compound chaotic sequence cipher can resist cryptanalytic, statistical and brute-force attacks, and especially it accelerates encryption speed, and achieves higher level of security. By the dynamical compound chaos and perturbation technology, the paper solves the problem of computer low precision of one-dimensional chaotic function.

  3. Vibrotactile using micromachined electromagnetic actuators array

    International Nuclear Information System (INIS)

    Talbi, A; Ducloux, O; Tiercelin, N; Deblock, Y; Pernod, P; Preobrazhensky, V

    2006-01-01

    One motivating application of this technology is the development of a tactile display interface, where discrete mechanical actuators apply vibratory excitation at discrete locations on the skin. Specifically, this paper describes the development fabrication and characterization of a 4 x 4 micro-actuator array of vibrating pixels for fingertip tactile communication. The vibrting pixels are generated by using an electromagnetic microresonator. The fabrication sequence and the actuation performance of the array are also presented

  4. Telescope Array Control System Based on Wireless Touch Screen Platform

    Science.gov (United States)

    Fu, Xia-nan; Huang, Lei; Wei, Jian-yan

    2017-10-01

    Ground-based Wide Angle Cameras (GMAC) are the ground-based observational facility for the SVOM (Space Variable Object Monitor) astronomical satellite of Sino-French cooperation, and Mini-GWAC is the pathfinder and supplement of GWAC. In the context of the Mini-GWAC telescope array, this paper introduces the design and implementation of a kind of telescope array control system based on the wireless touch screen platform. We describe the development and implementation of the system in detail in terms of control system principle, system hardware structure, software design, experiment, and test etc. The system uses a touch-control PC which is based on the Windows CE system as the upper computer, while the wireless transceiver module and PLC (Programmable Logic Controller) are taken as the system kernel. It has the advantages of low cost, reliable data transmission, and simple operation. And the control system has been applied to the Mini-GWAC successfully.

  5. DNA-Catalytically Active Gold Nanoparticle Conjugates-Based Colorimetric Multidimensional Sensor Array for Protein Discrimination.

    Science.gov (United States)

    Wei, Xiangcong; Chen, Zhengbo; Tan, Lulu; Lou, Tianhong; Zhao, Yan

    2017-01-03

    A series of single-strand oligonucleotides functionalized catalytically active gold nanoparticle (AuNPs) as nonspecific receptors have been designed to build a protein sensing array. We take advantage of the correlation between the catalytic activity and the exposed surface area of AuNPs, i.e., DNA-proteins interactions mask the surface area of AuNPs, leading to poor catalytic performance of AuNPs. As the number of DNA-bound proteins increases, the surfaces of AuNPs become more masked; thus, the time of 4- nitrophenol/NaBH 4 reaction for color change (yellow → colorless) of the solution increases. Taking advantage of three nonspecific SH-labeled DNA sequences (A15, C15, and T15) as array sensing elements and the color-change time (CCT) of the solution as signal readout, colorimetric response patterns can be obtained on the array and identified via linear discriminant analysis (LDA). Eleven proteins have been completely distinguished with 100% accuracy with the naked eye at the 30 nM level. Remarkably, two similar proteins (bovine serum albumin and human serum albumin), two different proteins (bovine serum albumin and concanavalin) at the same concentration, and the mixtures of the two proteins with different molar ratios have been discriminated with 100%. The practicability of this sensor array is further validated by high accuracy (100%) identification of 11 proteins in human serum samples.

  6. Evaluation of MRI sequences for quantitative T1 brain mapping

    Science.gov (United States)

    Tsialios, P.; Thrippleton, M.; Glatz, A.; Pernet, C.

    2017-11-01

    T1 mapping constitutes a quantitative MRI technique finding significant application in brain imaging. It allows evaluation of contrast uptake, blood perfusion, volume, providing a more specific biomarker of disease progression compared to conventional T1-weighted images. While there are many techniques for T1-mapping there is a wide range of reported T1-values in tissues, raising the issue of protocols reproducibility and standardization. The gold standard for obtaining T1-maps is based on acquiring IR-SE sequence. Widely used alternative sequences are IR-SE-EPI, VFA (DESPOT), DESPOT-HIFI and MP2RAGE that speed up scanning and fitting procedures. A custom MRI phantom was used to assess the reproducibility and accuracy of the different methods. All scans were performed using a 3T Siemens Prisma scanner. The acquired data processed using two different codes. The main difference was observed for VFA (DESPOT) which grossly overestimated T1 relaxation time by 214 ms [126 270] compared to the IR-SE sequence. MP2RAGE and DESPOT-HIFI sequences gave slightly shorter time than IR-SE (~20 to 30ms) and can be considered as alternative and time-efficient methods for acquiring accurate T1 maps of the human brain, while IR-SE-EPI gave identical result, at a cost of a lower image quality.

  7. Next-generation sequencing identifies a novel compound heterozygous mutation in MYO7A in a Chinese patient with Usher Syndrome 1B.

    Science.gov (United States)

    Wei, Xiaoming; Sun, Yan; Xie, Jiansheng; Shi, Quan; Qu, Ning; Yang, Guanghui; Cai, Jun; Yang, Yi; Liang, Yu; Wang, Wei; Yi, Xin

    2012-11-20

    Targeted enrichment and next-generation sequencing (NGS) have been employed for detection of genetic diseases. The purpose of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection of hereditary hearing loss, and identify inherited mutations involved in human deafness accurately and economically. To make genetic diagnosis of hereditary hearing loss simple and timesaving, we designed a 0.60 MB array-based chip containing 69 nuclear genes and mitochondrial genome responsible for human deafness and conducted NGS toward ten patients with five known mutations and a Chinese family with hearing loss (never genetically investigated). Ten patients with five known mutations were sequenced using next-generation sequencing to validate the sensitivity of the method. We identified four known mutations in two nuclear deafness causing genes (GJB2 and SLC26A4), one in mitochondrial DNA. We then performed this method to analyze the variants in a Chinese family with hearing loss and identified compound heterozygosity for two novel mutations in gene MYO7A. The compound heterozygosity identified in gene MYO7A causes Usher Syndrome 1B with severe phenotypes. The results support that the combination of enrichment of targeted genes and next-generation sequencing is a valuable molecular diagnostic tool for hereditary deafness and suitable for clinical application. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Intelligent fault diagnosis of photovoltaic arrays based on optimized kernel extreme learning machine and I-V characteristics

    International Nuclear Information System (INIS)

    Chen, Zhicong; Wu, Lijun; Cheng, Shuying; Lin, Peijie; Wu, Yue; Lin, Wencheng

    2017-01-01

    Highlights: •An improved Simulink based modeling method is proposed for PV modules and arrays. •Key points of I-V curves and PV model parameters are used as the feature variables. •Kernel extreme learning machine (KELM) is explored for PV arrays fault diagnosis. •The parameters of KELM algorithm are optimized by the Nelder-Mead simplex method. •The optimized KELM fault diagnosis model achieves high accuracy and reliability. -- Abstract: Fault diagnosis of photovoltaic (PV) arrays is important for improving the reliability, efficiency and safety of PV power stations, because the PV arrays usually operate in harsh outdoor environment and tend to suffer various faults. Due to the nonlinear output characteristics and varying operating environment of PV arrays, many machine learning based fault diagnosis methods have been proposed. However, there still exist some issues: fault diagnosis performance is still limited due to insufficient monitored information; fault diagnosis models are not efficient to be trained and updated; labeled fault data samples are hard to obtain by field experiments. To address these issues, this paper makes contribution in the following three aspects: (1) based on the key points and model parameters extracted from monitored I-V characteristic curves and environment condition, an effective and efficient feature vector of seven dimensions is proposed as the input of the fault diagnosis model; (2) the emerging kernel based extreme learning machine (KELM), which features extremely fast learning speed and good generalization performance, is utilized to automatically establish the fault diagnosis model. Moreover, the Nelder-Mead Simplex (NMS) optimization method is employed to optimize the KELM parameters which affect the classification performance; (3) an improved accurate Simulink based PV modeling approach is proposed for a laboratory PV array to facilitate the fault simulation and data sample acquisition. Intensive fault experiments are

  9. 75 FR 51392 - Federal Management Regulation; Transportation Management

    Science.gov (United States)

    2010-08-20

    ...; Docket Number 2010-0011, sequence 1] RIN 3090-AJ03 Federal Management Regulation; Transportation Management AGENCY: Office of Governmentwide Policy, General Services Administration (GSA). ACTION: Final rule. SUMMARY: The General Services Administration (GSA) is amending the Federal Management Regulation (FMR) by...

  10. Massively Parallel Interrogation of Aptamer Sequence, Structure and Function

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, N O; Tok, J B; Tarasow, T M

    2008-02-08

    Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

  11. Massively parallel interrogation of aptamer sequence, structure and function.

    Directory of Open Access Journals (Sweden)

    Nicholas O Fischer

    Full Text Available BACKGROUND: Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. METHODOLOGY/PRINCIPAL FINDINGS: High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and inter-chip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. CONCLUSION AND SIGNIFICANCE: The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

  12. Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens.

    Science.gov (United States)

    de Groot, Reinoud; Lüthi, Joel; Lindsay, Helen; Holtackers, René; Pelkmans, Lucas

    2018-01-23

    High-content imaging using automated microscopy and computer vision allows multivariate profiling of single-cell phenotypes. Here, we present methods for the application of the CISPR-Cas9 system in large-scale, image-based, gene perturbation experiments. We show that CRISPR-Cas9-mediated gene perturbation can be achieved in human tissue culture cells in a timeframe that is compatible with image-based phenotyping. We developed a pipeline to construct a large-scale arrayed library of 2,281 sequence-verified CRISPR-Cas9 targeting plasmids and profiled this library for genes affecting cellular morphology and the subcellular localization of components of the nuclear pore complex (NPC). We conceived a machine-learning method that harnesses genetic heterogeneity to score gene perturbations and identify phenotypically perturbed cells for in-depth characterization of gene perturbation effects. This approach enables genome-scale image-based multivariate gene perturbation profiling using CRISPR-Cas9. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  13. Armillaria phylogeny based on tef-1α sequences suggests ongoing divergent speciation within the boreal floristic kingdom

    Science.gov (United States)

    Ned B. Klopfenstein; John W. Hanna; Amy L. Ross-Davis; Jane E. Stewart; Yuko Ota; Rosario Medel-Ortiz; Miguel Armando Lopez-Ramirez; Ruben Damian Elias-Roman; Dionicio Alvarado-Rosales; Mee-Sook Kim

    2013-01-01

    Armillaria plays diverse ecological roles in forests worldwide, which has inspired interest in understanding phylogenetic relationships within and among species of this genus. Previous rDNA sequence-based phylogenetic analyses of Armillaria have shown general relationships among widely divergent taxa, but rDNA sequences were not reliable for separating closely related...

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

    Science.gov (United States)

    Foster, G. H.

    1974-01-01

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

  15. Kalman filter-based tracking of moving objects using linear ultrasonic sensor array for road vehicles

    Science.gov (United States)

    Li, Shengbo Eben; Li, Guofa; Yu, Jiaying; Liu, Chang; Cheng, Bo; Wang, Jianqiang; Li, Keqiang

    2018-01-01

    Detection and tracking of objects in the side-near-field has attracted much attention for the development of advanced driver assistance systems. This paper presents a cost-effective approach to track moving objects around vehicles using linearly arrayed ultrasonic sensors. To understand the detection characteristics of a single sensor, an empirical detection model was developed considering the shapes and surface materials of various detected objects. Eight sensors were arrayed linearly to expand the detection range for further application in traffic environment recognition. Two types of tracking algorithms, including an Extended Kalman filter (EKF) and an Unscented Kalman filter (UKF), for the sensor array were designed for dynamic object tracking. The ultrasonic sensor array was designed to have two types of fire sequences: mutual firing or serial firing. The effectiveness of the designed algorithms were verified in two typical driving scenarios: passing intersections with traffic sign poles or street lights, and overtaking another vehicle. Experimental results showed that both EKF and UKF had more precise tracking position and smaller RMSE (root mean square error) than a traditional triangular positioning method. The effectiveness also encourages the application of cost-effective ultrasonic sensors in the near-field environment perception in autonomous driving systems.

  16. Rate-determining Step of Flap Endonuclease 1 (FEN1) Reflects a Kinetic Bias against Long Flaps and Trinucleotide Repeat Sequences.

    Science.gov (United States)

    Tarantino, Mary E; Bilotti, Katharina; Huang, Ji; Delaney, Sarah

    2015-08-21

    Flap endonuclease 1 (FEN1) is a structure-specific nuclease responsible for removing 5'-flaps formed during Okazaki fragment maturation and long patch base excision repair. In this work, we use rapid quench flow techniques to examine the rates of 5'-flap removal on DNA substrates of varying length and sequence. Of particular interest are flaps containing trinucleotide repeats (TNR), which have been proposed to affect FEN1 activity and cause genetic instability. We report that FEN1 processes substrates containing flaps of 30 nucleotides or fewer at comparable single-turnover rates. However, for flaps longer than 30 nucleotides, FEN1 kinetically discriminates substrates based on flap length and flap sequence. In particular, FEN1 removes flaps containing TNR sequences at a rate slower than mixed sequence flaps of the same length. Furthermore, multiple-turnover kinetic analysis reveals that the rate-determining step of FEN1 switches as a function of flap length from product release to chemistry (or a step prior to chemistry). These results provide a kinetic perspective on the role of FEN1 in DNA replication and repair and contribute to our understanding of FEN1 in mediating genetic instability of TNR sequences. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Comparative study of single-nucleotide polymorphism array and next generation sequencing based strategies on triploid identification in preimplantation genetic diagnosis and screen.

    Science.gov (United States)

    Xu, Jiawei; Niu, Wenbin; Peng, Zhaofeng; Bao, Xiao; Zhang, Meixiang; Wang, Linlin; Du, Linqing; Zhang, Nan; Sun, Yingpu

    2016-12-06

    Triploidy occurred about 2-3% in human pregnancies and contributed to approximately 15% of chromosomally caused human early miscarriage. It is essential for preimplantation genetic diagnosis and screen to distinct triploidy sensitively. Here, we performed comparative investigations between MALBAC-NGS and MDA-SNP array sensitivity on triploidy detection. Self-correction and reference-correction algorism were used to analyze the NGS data. We identified 5 triploid embryos in 1198 embryos of 218 PGD and PGS cycles using MDA-SNP array, the rate of tripoidy was 4.17‰ in PGS and PGD patients. Our results indicated that the MDA-SNP array was sensitive to digyny and diandry triploidy, MALBAC-NGS combined with self and reference genome correction strategies analyze were not sensitive to detect triploidy. Our study demonstrated that triploidy occurred at 4.17‰ in PGD and PGS, MDA-SNP array could successfully identify triploidy in PGD and PGS and genomic DNA. MALBAC-NGS combined with self and reference genome correction strategies were not sensitive to triploidy.

  18. A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome.

    Directory of Open Access Journals (Sweden)

    Ahmad M Khalil

    2008-01-01

    Full Text Available Several genome-wide transcriptomics efforts have shown that a large percentage of the mammalian genome is transcribed into RNAs, however, only a small percentage (1-2% of these RNAs is translated into proteins. Currently there is an intense interest in characterizing the function of the different classes of noncoding RNAs and their relevance to human disease. Using genomic approaches we discovered FMR4, a primate-specific noncoding RNA transcript (2.4 kb that resides upstream and likely shares a bidirectional promoter with FMR1. FMR4 is a product of RNA polymerase II and has a similar half-life to FMR1. The CGG expansion in the 5' UTR of FMR1 appears to affect transcription in both directions as we found FMR4, similar to FMR1, to be silenced in fragile X patients and up-regulated in premutation carriers. Knockdown of FMR4 by several siRNAs did not affect FMR1 expression, nor vice versa, suggesting that FMR4 is not a direct regulatory transcript for FMR1. However, FMR4 markedly affected human cell proliferation in vitro; siRNAs knockdown of FMR4 resulted in alterations in the cell cycle and increased apoptosis, while the overexpression of FMR4 caused an increase in cell proliferation. Collectively, our results demonstrate an antiapoptotic function of FMR4 and provide evidence that a well-studied genomic locus can show unexpected functional complexity. It cannot be excluded that altered FMR4 expression might contribute to aspects of the clinical presentation of fragile X syndrome and/or related disorders.

  19. Similar star formation rate and metallicity variability time-scales drive the fundamental metallicity relation

    Science.gov (United States)

    Torrey, Paul; Vogelsberger, Mark; Hernquist, Lars; McKinnon, Ryan; Marinacci, Federico; Simcoe, Robert A.; Springel, Volker; Pillepich, Annalisa; Naiman, Jill; Pakmor, Rüdiger; Weinberger, Rainer; Nelson, Dylan; Genel, Shy

    2018-06-01

    The fundamental metallicity relation (FMR) is a postulated correlation between galaxy stellar mass, star formation rate (SFR), and gas-phase metallicity. At its core, this relation posits that offsets from the mass-metallicity relation (MZR) at a fixed stellar mass are correlated with galactic SFR. In this Letter, we use hydrodynamical simulations to quantify the time-scales over which populations of galaxies oscillate about the average SFR and metallicity values at fixed stellar mass. We find that Illustris and IllustrisTNG predict that galaxy offsets from the star formation main sequence and MZR oscillate over similar time-scales, are often anticorrelated in their evolution, evolve with the halo dynamical time, and produce a pronounced FMR. Our models indicate that galaxies oscillate about equilibrium SFR and metallicity values - set by the galaxy's stellar mass - and that SFR and metallicity offsets evolve in an anticorrelated fashion. This anticorrelated variability of the metallicity and SFR offsets drives the existence of the FMR in our models. In contrast to Illustris and IllustrisTNG, we speculate that the SFR and metallicity evolution tracks may become decoupled in galaxy formation models dominated by feedback-driven globally bursty SFR histories, which could weaken the FMR residual correlation strength. This opens the possibility of discriminating between bursty and non-bursty feedback models based on the strength and persistence of the FMR - especially at high redshift.

  20. ZnO nano-array-based EGFET biosensor for glucose detection

    Science.gov (United States)

    Qi, Junjie; Zhang, Huihui; Ji, Zhaoxia; Xu, Minxuan; Zhang, Yue

    2015-06-01

    Electrochemical biosensors are normally based on enzymatic catalysis of a reaction that produces or consumes electrons and the sensing membranes dominate the performance. In this work, ZnO nano-array-based EGFETs were fabricated for pH and glucose detection. The ZnO nano-arrays prepared via low-temperature hydrothermal method were well-aligned, with an average length of 2 μm and diameter of 100-150 nm, and have a typical hexagonal wurtzite structure. The sensor performed with a sensitivity of 45 mV/pH and response time of about 6-7 s from pH = 4-12. UV irradiation can improve the Vref response as a result of the formation of a depletion region at the surface of ZnO nanomaterials. Due to its high specific surface area, the ZnO nano-array EGFET sensor showed a sensitivity of -0.395 mV/μM to the glucose detection in a concentration range between 20 and 100 μM. These EGFET glucose biosensors demonstrate a low detectable concentration (20 μM) with good linearity, therefore may be used to detect glucose in saliva and tears at much lower concentrations than that in blood.

  1. Carcinogen-DNA interaction study by base sequence footprinting. Final report, July 1, 1983-June 30, 1986

    International Nuclear Information System (INIS)

    Bases, R.

    1986-01-01

    Our previous studies on acetylaminofluorene (AAF) modified DNA demonstrated three kinds of structural changes in DNA of defined base sequence. For example, adduct formation by N-Aco-AAF was found at each guanine. We studied the interaction of IgG specific for AAF guanosine in an in vitro system using AAF modified phi X-174 rf DNA. We had expected to find protection against DNAase I digestion. Instead, when the DNA was immunobound to an inert matrix via the IgG, DNAase I digestion was enhanced 20 fold without changing the base sequence pattern of digestion. DNAase I hypersensitive sites are a necessary but not a sufficient condition for transcription. Moreover, some hypersensitive sites are stably propagated, independent of the continued presence of the inducer. Stability of these hypersensitive sites in the absence of their inducer suggests that they can be propagated. It appeared likely that distortion of DNA by a carcinogen adduct such as AAF, and the interaction of this modified DNA with a specific protein such as IgG or cellular proteins might inappropriately enhance the transcription of specific genes. That hypothesis will be tested; surprisingly, little is known about the early action of carcinogens on expression of specific genes. 34 refs., 2 figs., 1 tab

  2. Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).

    Science.gov (United States)

    Bianco, Luca; Cestaro, Alessandro; Sargent, Daniel James; Banchi, Elisa; Derdak, Sophia; Di Guardo, Mario; Salvi, Silvio; Jansen, Johannes; Viola, Roberto; Gut, Ivo; Laurens, Francois; Chagné, David; Velasco, Riccardo; van de Weg, Eric; Troggio, Michela

    2014-01-01

    High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

  3. Development and validation of a 20K single nucleotide polymorphism (SNP whole genome genotyping array for apple (Malus × domestica Borkh.

    Directory of Open Access Journals (Sweden)

    Luca Bianco

    Full Text Available High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus. A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs. Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

  4. Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

    Science.gov (United States)

    Bianco, Luca; Cestaro, Alessandro; Sargent, Daniel James; Banchi, Elisa; Derdak, Sophia; Di Guardo, Mario; Salvi, Silvio; Jansen, Johannes; Viola, Roberto; Gut, Ivo; Laurens, Francois; Chagné, David; Velasco, Riccardo; van de Weg, Eric; Troggio, Michela

    2014-01-01

    High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs. PMID:25303088

  5. Towards local oscillators based on arrays of niobium Josephson junctions

    International Nuclear Information System (INIS)

    Galin, M A; Klushin, A M; Kurin, V V; Seliverstov, S V; Finkel, M I; Goltsman, G N; Müller, F; Scheller, T; Semenov, A D

    2015-01-01

    Various applications in the field of terahertz technology are in urgent need of compact, wide-tunable solid-state continuous wave radiation sources with a moderate power. However, satisfactory solutions for the THz frequency range are scarce yet. Here we report on coherent radiation from a large planar array of Josephson junctions (JJs) in the frequency range between 0.1 and 0.3 THz. The external resonator providing the synchronization of JJ array is identified as a straight fragment of a single-strip-line containing the junctions themselves. We demonstrate a prototype of the quasioptical heterodyne receiver with the JJ array as a local oscillator and a hot-electron bolometer mixer. (paper)

  6. Optimization of modal filters based on arrays of piezoelectric sensors

    International Nuclear Information System (INIS)

    Pagani, Carlos C Jr; Trindade, Marcelo A

    2009-01-01

    Modal filters may be obtained by a properly designed weighted sum of the output signals of an array of sensors distributed on the host structure. Although several research groups have been interested in techniques for designing and implementing modal filters based on a given array of sensors, the effect of the array topology on the effectiveness of the modal filter has received much less attention. In particular, it is known that some parameters, such as size, shape and location of a sensor, are very important in determining the observability of a vibration mode. Hence, this paper presents a methodology for the topological optimization of an array of sensors in order to maximize the effectiveness of a set of selected modal filters. This is done using a genetic algorithm optimization technique for the selection of 12 piezoceramic sensors from an array of 36 piezoceramic sensors regularly distributed on an aluminum plate, which maximize the filtering performance, over a given frequency range, of a set of modal filters, each one aiming to isolate one of the first vibration modes. The vectors of the weighting coefficients for each modal filter are evaluated using QR decomposition of the complex frequency response function matrix. Results show that the array topology is not very important for lower frequencies but it greatly affects the filter effectiveness for higher frequencies. Therefore, it is possible to improve the effectiveness and frequency range of a set of modal filters by optimizing the topology of an array of sensors. Indeed, using 12 properly located piezoceramic sensors bonded on an aluminum plate it is shown that the frequency range of a set of modal filters may be enlarged by 25–50%

  7. Array display tool ADT reference manual. Version 1.2

    International Nuclear Information System (INIS)

    Evans, K. Jr.

    1995-12-01

    Array Display Tool (ADT) is a Motif program to display arrays of process variables from the Advanced Photon Source control system. A typical use is to display the horizontal and vertical monitor readings. A picture of the ADT interface is here. The screen layout, apart from the menu bar, consists of two types of graphic areas in which the values for the arrays of process variables are shown: Display areas, which display one or more arrays as a function of index, and a zoom area. In the zoom area specified arrays only are displayed as a function of lattice position along with symbols for the major elements of the lattice. There can be several display areas, but at most one zoom area. When the screen is resized these areas change size proportionally. There are a number of options in the View Menu to change the way the values are displayed. It is also possible via the Options Menu to: (1) Store the current values internally. (2) Store the values from a snapshot file internally. (3) Display one of the stored sets of values along with the current values. (4) Display the difference of the current values with one of the stored sets of values. (5) Write the current values to a snapshot file. There are several (currently 5) slots in which you can store values internally. In addition you can display the values with specified reference values subtracted

  8. Fragile X syndrome and fragile X-associated disorders [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Akash Rajaratnam

    2017-12-01

    Full Text Available Fragile X syndrome (FXS is caused by a full mutation on the FMR1 gene and a subsequent lack of FMRP, the protein product of FMR1. FMRP plays a key role in regulating the translation of many proteins involved in maintaining neuronal synaptic connections; its deficiency may result in a range of intellectual disabilities, social deficits, psychiatric problems, and dysmorphic physical features. A range of clinical involvement is also associated with the FMR1 premutation, including fragile X-associated tremor ataxia syndrome, fragile X-associated primary ovarian insufficiency, psychiatric problems, hypertension, migraines, and autoimmune problems. Over the past few years, there have been a number of advances in our knowledge of FXS and fragile X-associated disorders, and each of these advances offers significant clinical implications. Among these developments are a better understanding of the clinical impact of the phenomenon known as mosaicism, the revelation that various types of mutations can cause FXS, and improvements in treatment for FXS.

  9. Novel environmental class 1 integrons and cassette arrays recovered from an on-farm bio-purification plant.

    Science.gov (United States)

    Martini, María Carla; Quiroga, María Paula; Pistorio, Mariano; Lagares, Antonio; Centrón, Daniela; Del Papa, María Florencia

    2018-03-01

    Rapid dissemination and emergence of novel antibiotic resistance genes among bacteria are rising problems worldwide. Since their discovery in clinical isolates in the late 1980s, class 1 integrons have been found in a wide range of bacterial genera and have been extensively studied as contributors to dissemination of antibiotic resistance. The present study aimed to investigate the presence and structure of class 1 integrons in plasmid-carrying bacterial isolates obtained from a biopurification system used for decontamination of pesticide-contaminated water as well as their possible role as reservoir of antimicrobial resistance gene cassettes. A total of 35 representative isolates were screened for the presence of class 1 integron integrase encoded by intI1. PCR and DNA sequencing revealed the presence of six class 1 integrons with four variable regions: 5΄CS-aadA1b-3΄CS, 5΄CS-aadA2-3΄CS, 5΄CS-aadA11cΔ-3΄CS and 5΄CS-dfrB3-aadA1di-catB2-aadA6k-3΄CS, the last two being unseen arrays of antimicrobial resistance gene cassettes associated with novel environmental alleles of intI1. These four class 1 integrons were identified as being present in four different genera, including Ochrobactrum, and Variovorax, where class 1 integrons have not been previously reported. The results provide evidence of the biopurification systems as a tank of class 1 integron carrying strains and novel environmental class 1 integron integrases associated with antimicrobial resistance gene cassette arrays. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Control of intravascular catheters using an array of active steering coils.

    Science.gov (United States)

    Gudino, N; Heilman, J A; Derakhshan, J J; Sunshine, J L; Duerk, J L; Griswold, M A

    2011-07-01

    To extend the concept of deflecting the tip of a catheter with the magnetic force created in an MRI system through the use of an array of independently controllable steering coils located in the catheter tip, and to present methods for visualization of the catheter and/or surrounding areas while the catheter is deflected. An array of steering coils made of 42-gauge wire was built over a 2.5 Fr (0.83 mm) fiber braided microcatheter. Two of the coils were 70 turn axial coils separated by 1 cm, and the third was a 15-turn square side coil that was 2 x 4 mm2. Each coil was driven independently by a pulse width modulation (PWM) current source controlled by a microprocessor that received commands from a MATLAB routine that dynamically set current amplitude and direction for each coil. The catheter was immersed in a water phantom containing 1% Gd-DTPA that was placed at the isocenter of a 1.5 T MRI scanner. Deflections of the catheter tip were measured from image-based data obtained with a real-time radio frequency (RF) spoiled gradient echo sequence (GRE). The small local magnetic fields generated by the steering coils were exploited to generate a hyperintense signal at the catheter tip by using a modified GRE sequence that did not include slice-select rewinding gradients. Imaging and excitation modes were implemented by synchronizing the excitation of the steering coil array with the scanner by ensuring that no current was driven through the coils during the data acquisition window; this allowed visualization of the surrounding tissue while not affecting the desired catheter position. Deflections as large as 2.5 cm were measured when exciting the steering coils sequentially with a 100 mA maximum current per coil. When exciting a single axial coil, the deflection was half this value with 30% higher current. A hyperintense catheter tip useful for catheter tracking was obtained by imaging with the modified GRE sequence. Clear visualization of the areas surrounding the

  11. Sequence Control System of 1-MW CW Klystron for the PEFP

    CERN Document Server

    Park, Byoung R; Chun Myung Hwan; Han Yeung Jin; Hyo Jeong Maeng; Kim Sung Chul; Yang Jae Seok; Yu In Ha

    2005-01-01

    Sequence control system of 1-MW CW klystron for the PEFP (Proton Engineering Frontier Project) has been developed in order to drive the 1-MW klystron amplifier. The system is able to control several power supplies and many environment conditions. The hardware of sequence control and the interlock system are based on the Allen-Bradley's SLC500 Program Logic Controller (PLC). Also the system can be controlled by a touch screen at local mode or Ethernet network with high level HMI at remote mode.

  12. Flat-plate solar array project. Volume 1: Executive summary

    Science.gov (United States)

    Callaghan, W.; Mcdonald, R.

    1986-01-01

    In 1975, the U.S. Government contracted the Jet Propulsion Lab. to develop, by 1985, in conjunction with industry, the photovoltaics (PV) module and array technology required for widespread use of photovoltaics as a significant terrestrial energy source. As a result, a project that eventually became known as the Flat Plate Solar Array (FSA) Project was formed to manage an industry, university, and Government team to perform the necessary research and development. The original goals were to achieve widespread commercial use of PV modules and arrays through the development of technology that would allow them to be profitably sold for $1.07/peak watts (1985 dollars). A 10% module conversion efficiency and a 20 year lifetime were also goals. It is intended that the executive summary provide the means by which one can gain a perspective on 11 years of terrestrial photovoltaic research and development conducted by the FSA Project.

  13. Computer-aided engineering system for design of sequence arrays and lithographic masks

    Science.gov (United States)

    Hubbell, Earl A.; Morris, MacDonald S.; Winkler, James L.

    1996-01-01

    An improved set of computer tools for forming arrays. According to one aspect of the invention, a computer system (100) is used to select probes and design the layout of an array of DNA or other polymers with certain beneficial characteristics. According to another aspect of the invention, a computer system uses chip design files (104) to design and/or generate lithographic masks (110).

  14. A SNP Genotyping Array for Hexaploid Oat

    Directory of Open Access Journals (Sweden)

    Nicholas A. Tinker

    2014-11-01

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

  15. Study of Implosion of Twisted Nested Arrays at the Angara-5-1 Facility

    Science.gov (United States)

    Mitrofanov, K. N.; Zukakishvili, G. G.; Aleksandrov, V. V.; Grabovski, E. V.; Frolov, I. N.; Gribov, A. N.

    2018-01-01

    Results are presented from experimental studies of the implosion of twisted nested arrays in which the wires of the outer and inner arrays are twisted about the array axis in opposite directions (clockwise and counterclockwise). Experiments with twisted arrays were carried out at the Angara-5-1 facility at currents of up to 4 MA. The currents through the arrays were switched either simultaneously or the current pulse through the outer array was delayed by 10-15 ns with the help of an anode spark gap. It is shown that, in such arrays, the currents flow along the inclined wires and, accordingly, there are both the azimuthal and axial components of the discharge current. The process of plasma implosion in twisted arrays depends substantially on the value of the axial (longitudinal) magnetic field generated inside the array by the azimuthal currents. Two-dimensional simulations of the magnetic field in twisted nested arrays were performed in the ( r, z) geometry with allowance for the skin effect in the discharge electrodes. It is shown that, depending on the geometry of the discharge electrodes, different configurations of the magnetic field can be implemented inside twisted nested arrays. The calculated magnetic configurations are compared with the results of measurements of the magnetic field inside such arrays. It is shown that the configuration of the axial magnetic field inside a twisted nested array depends substantially on the distribution of the azimuthal currents between the inner and outer arrays.

  16. Large Scale Plasmonic nanoCones array For Spectroscopy Detection

    KAUST Repository

    Das, Gobind

    2015-09-24

    Advanced optical materials or interfaces are gaining attention for diagnostic applications. However, the achievement of large device interface as well as facile surface functionalization largely impairs their wide use. The present work is aimed to address different innovative aspects related to the fabrication of large area 3D plasmonic arrays, their direct and easy functionalization with capture elements and their spectroscopic verifications through enhanced Raman and enhanced fluorescence techniques. In detail we have investigated the effect of Au-based nanoCones array, fabricated by means of direct nanoimprint technique over large area (mm2), on protein capturing and on the enhancement in optical signal. A selective functionalization of gold surfaces was proposed by using a peptide (AuPi3) previously selected by phage display. In this regard, two different sequences, labeled with fluorescein and biotin, were chemisorbed on metallic surfaces. The presence of Au nanoCones array consents an enhancement in electric field on the apex of cone, enabling the detection of molecules. We have witnessed around 12-fold increase in fluorescence intensity and SERS enhancement factor around 1.75 ×105 with respect to the flat gold surface. Furthermore, a sharp decrease in fluorescence lifetime over nanoCones confirms the increase in radiative emission (i.e. an increase in photonics density at the apex of cones).

  17. Large Scale Plasmonic nanoCones array For Spectroscopy Detection

    KAUST Repository

    Das, Gobind; Battista, Edmondo; Manzo, Gianluigi; Causa, Filippo; Netti, Paolo; Di Fabrizio, Enzo M.

    2015-01-01

    Advanced optical materials or interfaces are gaining attention for diagnostic applications. However, the achievement of large device interface as well as facile surface functionalization largely impairs their wide use. The present work is aimed to address different innovative aspects related to the fabrication of large area 3D plasmonic arrays, their direct and easy functionalization with capture elements and their spectroscopic verifications through enhanced Raman and enhanced fluorescence techniques. In detail we have investigated the effect of Au-based nanoCones array, fabricated by means of direct nanoimprint technique over large area (mm2), on protein capturing and on the enhancement in optical signal. A selective functionalization of gold surfaces was proposed by using a peptide (AuPi3) previously selected by phage display. In this regard, two different sequences, labeled with fluorescein and biotin, were chemisorbed on metallic surfaces. The presence of Au nanoCones array consents an enhancement in electric field on the apex of cone, enabling the detection of molecules. We have witnessed around 12-fold increase in fluorescence intensity and SERS enhancement factor around 1.75 ×105 with respect to the flat gold surface. Furthermore, a sharp decrease in fluorescence lifetime over nanoCones confirms the increase in radiative emission (i.e. an increase in photonics density at the apex of cones).

  18. A rapid compression technique for 4-D functional MRI images using data rearrangement and modified binary array techniques.

    Science.gov (United States)

    Uma Vetri Selvi, G; Nadarajan, R

    2015-12-01

    Compression techniques are vital for efficient storage and fast transfer of medical image data. The existing compression techniques take significant amount of time for performing encoding and decoding and hence the purpose of compression is not fully satisfied. In this paper a rapid 4-D lossy compression method constructed using data rearrangement, wavelet-based contourlet transformation and a modified binary array technique has been proposed for functional magnetic resonance imaging (fMRI) images. In the proposed method, the image slices of fMRI data are rearranged so that the redundant slices form a sequence. The image sequence is then divided into slices and transformed using wavelet-based contourlet transform (WBCT). In WBCT, the high frequency sub-band obtained from wavelet transform is further decomposed into multiple directional sub-bands by directional filter bank to obtain more directional information. The relationship between the coefficients has been changed in WBCT as it has more directions. The differences in parent–child relationships are handled by a repositioning algorithm. The repositioned coefficients are then subjected to quantization. The quantized coefficients are further compressed by modified binary array technique where the most frequently occurring value of a sequence is coded only once. The proposed method has been experimented with fMRI images the results indicated that the processing time of the proposed method is less compared to existing wavelet-based set partitioning in hierarchical trees and set partitioning embedded block coder (SPECK) compression schemes [1]. The proposed method could also yield a better compression performance compared to wavelet-based SPECK coder. The objective results showed that the proposed method could gain good compression ratio in maintaining a peak signal noise ratio value of above 70 for all the experimented sequences. The SSIM value is equal to 1 and the value of CC is greater than 0.9 for all

  19. An Analysis of Delay-based and Integrator-based Sequence Detectors for Grid-Connected Converters

    DEFF Research Database (Denmark)

    Khazraj, Hesam; Silva, Filipe Miguel Faria da; Bak, Claus Leth

    2017-01-01

    -signal cancellation operators are the main members of the delay-based sequence detectors. The aim of this paper is to provide a theoretical and experimental comparative study between integrator and delay based sequence detectors. The theoretical analysis is conducted based on the small-signal modelling......Detecting and separating positive and negative sequence components of the grid voltage or current is of vital importance in the control of grid-connected power converters, HVDC systems, etc. To this end, several techniques have been proposed in recent years. These techniques can be broadly...... classified into two main classes: The integrator-based techniques and Delay-based techniques. The complex-coefficient filter-based technique, dual second-order generalized integrator-based method, multiple reference frame approach are the main members of the integrator-based sequence detector and the delay...

  20. Left-handed compact MIMO antenna array based on wire spiral resonator for 5-GHz wireless applications

    Science.gov (United States)

    Alqadami, Abdulrahman Shueai Mohsen; Jamlos, Mohd Faizal; Soh, Ping Jack; Rahim, Sharul Kamal Abdul; Narbudowicz, Adam

    2017-01-01

    A compact coplanar waveguide-fed multiple-input multiple-output antenna array based on the left-handed wire loaded spiral resonators (SR) is presented. The proposed antenna consists of a 2 × 2 wire SR with two symmetrical microstrip feed lines, each line exciting a 1 × 2 wire SR. Left-handed metamaterial unit cells are placed on its reverse side and arranged in a 2 × 3 array. A reflection coefficient of less than -16 dB and mutual coupling of less than -28 dB are achieved at 5.15 GHz WLAN band.

  1. BRDF-dependent accuracy of array-projection-based 3D sensors.

    Science.gov (United States)

    Heist, Stefan; Kühmstedt, Peter; Tünnermann, Andreas; Notni, Gunther

    2017-03-10

    In order to perform high-speed three-dimensional (3D) shape measurements with structured light systems, high-speed projectors are required. One possibility is an array projector, which allows pattern projection at several tens of kilohertz by switching on and off the LEDs of various slide projectors. The different projection centers require a separate analysis, as the intensity received by the cameras depends on the projection direction and the object's bidirectional reflectance distribution function (BRDF). In this contribution, we investigate the BRDF-dependent errors of array-projection-based 3D sensors and propose an error compensation process.

  2. HKUST-1 Membranes Anchored on Porous Substrate by Hetero MIL-110 Nanorod Array Seeds.

    Science.gov (United States)

    Mao, Yiyin; Cao, Wei; Li, Junwei; Sun, Luwei; Peng, Xinsheng

    2013-09-02

    Great anchors and seeds: Hetero-seeding growth processes and anchored nanorod arrays were successfully utilized in the synthesis of HKUST-1 membranes. These arrays were firmly anchored on porous substrates by using a MIL-110 nanorod array as both the anchor and seed. The resulting HKUST-1 membranes demonstrated good separation factors for binary gases exceeding the Knudson selectivity. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Aluminum-based one- and two-dimensional micro fin array structures: high-throughput fabrication and heat transfer testing

    International Nuclear Information System (INIS)

    Primeaux, Philip A; Zhang, Bin; Zhang, Xiaoman; Miller, Jacob; Meng, W J; KC, Pratik; Moore, Arden L

    2017-01-01

    Microscale fin array structures were replicated onto surfaces of aluminum 1100 and aluminum 6061 alloy (Al1100/Al6061) sheet metals through room-temperature instrumented roll molding. Aluminum-based micro fin arrays were replicated at room temperature, and the fabrication process is one with high throughput and low cost. One-dimensional (1D) micro fin arrays were made through one-pass rolling, while two-dimensional (2D) micro fin arrays were made by sequential 90° cross rolling with the same roller sleeve. For roll molding of 1D micro fins, fin heights greater than 600 µ m were achieved and were shown to be proportional to the normal load force per feature width. At a given normal load force, the fin height was further shown to scale inversely with the hardness of the sheet metal. For sequential 90° cross rolling, morphologies of roll molded 2D micro fin arrays were examined, which provided clues to understand how plastic deformation occurred under cross rolling conditions. A series of pool boiling experiments on low profile Al micro fin array structures were performed within Novec 7100, a widely used commercial dielectric coolant. Results for both horizontal and vertical surface orientations show that roll molded Al micro fin arrays can increase heat flux at fixed surface temperature as compared to un-patterned Al sheet. The present results further suggest that many factors beyond just increased surface area can influence heat transfer performance, including surface finish and the important multiphase transport mechanisms in and around the fin geometry. These factors must also be considered when designing and optimizing micro fin array structures for heat transfer applications. (paper)

  4. Biaxially stretchable supercapacitors based on the buckled hybrid fiber electrode array

    Science.gov (United States)

    Zhang, Nan; Zhou, Weiya; Zhang, Qiang; Luan, Pingshan; Cai, Le; Yang, Feng; Zhang, Xiao; Fan, Qingxia; Zhou, Wenbin; Xiao, Zhuojian; Gu, Xiaogang; Chen, Huiliang; Li, Kewei; Xiao, Shiqi; Wang, Yanchun; Liu, Huaping; Xie, Sishen

    2015-07-01

    In order to meet the growing need for smart bionic devices and epidermal electronic systems, biaxial stretchability is essential for energy storage units. Based on porous single-walled carbon nanotube/poly(3,4-ethylenedioxythiophene) (SWCNT/PEDOT) hybrid fiber, we designed and fabricated a biaxially stretchable supercapacitor, which possesses a unique configuration of the parallel buckled hybrid fiber array. Owing to the reticulate SWCNT film and the improved fabrication technique, the hybrid fiber retained its porous architecture both outwardly and inwardly, manifesting a superior capacity of 215 F g-1. H3PO4-polyvinyl alcohol gel with an optimized component ratio was introduced as both binder and stretchable electrolyte, which contributed to the regularity and stability of the buckled fiber array. The buckled structure and the quasi one-dimensional character of the fibers endow the supercapacitor with 100% stretchability along all directions. In addition, the supercapacitor exhibited good transparency, as well as excellent electrochemical properties and stability after being stretched 5000 times.In order to meet the growing need for smart bionic devices and epidermal electronic systems, biaxial stretchability is essential for energy storage units. Based on porous single-walled carbon nanotube/poly(3,4-ethylenedioxythiophene) (SWCNT/PEDOT) hybrid fiber, we designed and fabricated a biaxially stretchable supercapacitor, which possesses a unique configuration of the parallel buckled hybrid fiber array. Owing to the reticulate SWCNT film and the improved fabrication technique, the hybrid fiber retained its porous architecture both outwardly and inwardly, manifesting a superior capacity of 215 F g-1. H3PO4-polyvinyl alcohol gel with an optimized component ratio was introduced as both binder and stretchable electrolyte, which contributed to the regularity and stability of the buckled fiber array. The buckled structure and the quasi one-dimensional character of the

  5. Multidirectional flexible force sensors based on confined, self-adjusting carbon nanotube arrays

    Science.gov (United States)

    Lee, J.-I.; Pyo, Soonjae; Kim, Min-Ook; Kim, Jongbaeg

    2018-02-01

    We demonstrate a highly sensitive force sensor based on self-adjusting carbon nanotube (CNT) arrays. Aligned CNT arrays are directly synthesized on silicon microstructures by a space-confined growth technique which enables a facile self-adjusting contact. To afford flexibility and softness, the patterned microstructures with the integrated CNTs are embedded in polydimethylsiloxane structures. The sensing mechanism is based on variations in the contact resistance between the facing CNT arrays under the applied force. By finite element analysis, proper dimensions and positions for each component are determined. Further, high sensitivities up to 15.05%/mN of the proposed sensors were confirmed experimentally. Multidirectional sensing capability could also be achieved by designing multiple sets of sensing elements in a single sensor. The sensors show long-term operational stability, owing to the unique properties of the constituent CNTs, such as outstanding mechanical durability and elasticity.

  6. Characterization of Dnmt1 Binding and DNA Methylation on Nucleosomes and Nucleosomal Arrays.

    Directory of Open Access Journals (Sweden)

    Anna Schrader

    Full Text Available The packaging of DNA into nucleosomes and the organisation into higher order structures of chromatin limits the access of sequence specific DNA binding factors to DNA. In cells, DNA methylation is preferentially occuring in the linker region of nucleosomes, suggesting a structural impact of chromatin on DNA methylation. These observations raise the question whether DNA methyltransferases are capable to recognize the nucleosomal substrates and to modify the packaged DNA. Here, we performed a detailed analysis of nucleosome binding and nucleosomal DNA methylation by the maintenance DNA methyltransferase Dnmt1. Our binding studies show that Dnmt1 has a DNA length sensing activity, binding cooperatively to DNA, and requiring a minimal DNA length of 20 bp. Dnmt1 needs linker DNA to bind to nucleosomes and most efficiently recognizes nucleosomes with symmetric DNA linkers. Footprinting experiments reveal that Dnmt1 binds to both DNA linkers exiting the nucleosome core. The binding pattern correlates with the efficient methylation of DNA linkers. However, the enzyme lacks the ability to methylate nucleosomal CpG sites on mononucleosomes and nucleosomal arrays, unless chromatin remodeling enzymes create a dynamic chromatin state. In addition, our results show that Dnmt1 functionally interacts with specific chromatin remodeling enzymes to enable complete methylation of hemi-methylated DNA in chromatin.

  7. An accurate projection algorithm for array processor based SPECT systems

    International Nuclear Information System (INIS)

    King, M.A.; Schwinger, R.B.; Cool, S.L.

    1985-01-01

    A data re-projection algorithm has been developed for use in single photon emission computed tomography (SPECT) on an array processor based computer system. The algorithm makes use of an accurate representation of pixel activity (uniform square pixel model of intensity distribution), and is rapidly performed due to the efficient handling of an array based algorithm and the Fast Fourier Transform (FFT) on parallel processing hardware. The algorithm consists of using a pixel driven nearest neighbour projection operation to an array of subdivided projection bins. This result is then convolved with the projected uniform square pixel distribution before being compressed to original bin size. This distribution varies with projection angle and is explicitly calculated. The FFT combined with a frequency space multiplication is used instead of a spatial convolution for more rapid execution. The new algorithm was tested against other commonly used projection algorithms by comparing the accuracy of projections of a simulated transverse section of the abdomen against analytically determined projections of that transverse section. The new algorithm was found to yield comparable or better standard error and yet result in easier and more efficient implementation on parallel hardware. Applications of the algorithm include iterative reconstruction and attenuation correction schemes and evaluation of regions of interest in dynamic and gated SPECT

  8. Centroid based clustering of high throughput sequencing reads based on n-mer counts.

    Science.gov (United States)

    Solovyov, Alexander; Lipkin, W Ian

    2013-09-08

    Many problems in computational biology require alignment-free sequence comparisons. One of the common tasks involving sequence comparison is sequence clustering. Here we apply methods of alignment-free comparison (in particular, comparison using sequence composition) to the challenge of sequence clustering. We study several centroid based algorithms for clustering sequences based on word counts. Study of their performance shows that using k-means algorithm with or without the data whitening is efficient from the computational point of view. A higher clustering accuracy can be achieved using the soft expectation maximization method, whereby each sequence is attributed to each cluster with a specific probability. We implement an open source tool for alignment-free clustering. It is publicly available from github: https://github.com/luscinius/afcluster. We show the utility of alignment-free sequence clustering for high throughput sequencing analysis despite its limitations. In particular, it allows one to perform assembly with reduced resources and a minimal loss of quality. The major factor affecting performance of alignment-free read clustering is the length of the read.

  9. A novel fabrication of MEH-PPV/Al:ZnO nanorod arrays based ordered bulk heterojunction hybrid solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Malek, M.F., E-mail: firz_solarzelle@yahoo.com [NANO-ElecTronic Centre (NET), Faculty of Electrical Engineering, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor (Malaysia); Sahdan, M.Z.; Mamat, M.H.; Musa, M.Z. [NANO-ElecTronic Centre (NET), Faculty of Electrical Engineering, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor (Malaysia); Khusaimi, Z.; Husairi, S.S. [NANO-SciTech Centre (NST), Institute of Science (IOS), Universiti Teknologi MARA -UiTM, 40450 Shah Alam, Selangor (Malaysia); Md Sin, N.D. [NANO-ElecTronic Centre (NET), Faculty of Electrical Engineering, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor (Malaysia); Rusop, M. [NANO-ElecTronic Centre (NET), Faculty of Electrical Engineering, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor (Malaysia); NANO-SciTech Centre (NST), Institute of Science (IOS), Universiti Teknologi MARA - UiTM, 40450 Shah Alam, Selangor (Malaysia)

    2013-06-15

    Vertically aligned Al:ZnO nanorod arrays has been used as window layer in the fabrication of ordered bulk heterojuction hybrid solar cells. The utilization of the nanorod arrays will enhance the electron transport in vertical direction and also for light harvesting applications for high performance devices. The performance of this hybrid polymer/metal oxide photovoltaic devices based on MEH-PPV [poly(2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene)] and oriented Al:ZnO nanorod arrays is studied. The Al:ZnO nanorod arrays with a diameter of about 70–80 nm and thickness of approximately 500 nm were successfully grown on Al:ZnO-coated ITO substrate by sonicated sol–gel immersion technique. The photovoltaic performance of a short-circuit current density of 5.320 mA/cm{sup 2}, an open-circuit voltage of 195 mV and a fill factor of 27.71%, with a power conversion efficiency of about 0.287% under AM 1.5 illumination (100 mW/cm{sup 2}). To the best of our knowledge, preparation of aligned Al:ZnO nanorod arrays for this type of solar cell fabrication has not been reported by any research group.

  10. A Paper-Based Electrochromic Array for Visualized Electrochemical Sensing

    OpenAIRE

    Fengling Zhang; Tianyi Cai; Liang Ma; Liyuan Zhan; Hong Liu

    2017-01-01

    We report a battery-powered, paper-based electrochromic array for visualized electrochemical sensing. The paper-based sensing system consists of six parallel electrochemical cells, which are powered by an aluminum-air battery. Each single electrochemical cell uses a Prussian Blue spot electrodeposited on an indium-doped tin oxide thin film as the electrochromic indicator. Each electrochemical cell is preloaded with increasing amounts of analyte. The sample activates the battery for the sensin...

  11. Crash sequence based risk matrix for motorcycle crashes.

    Science.gov (United States)

    Wu, Kun-Feng; Sasidharan, Lekshmi; Thor, Craig P; Chen, Sheng-Yin

    2018-04-05

    Considerable research has been conducted related to motorcycle and other powered-two-wheeler (PTW) crashes; however, it always has been controversial among practitioners concerning with types of crashes should be first targeted and how to prioritize resources for the implementation of mitigating actions. Therefore, there is a need to identify types of motorcycle crashes that constitute the greatest safety risk to riders - most frequent and most severe crashes. This pilot study seeks exhibit the efficacy of a new approach for prioritizing PTW crash causation sequences as they relate to injury severity to better inform the application of mitigating countermeasures. To accomplish this, the present study constructed a crash sequence-based risk matrix to identify most frequent and most severe motorcycle crashes in an attempt to better connect causes and countermeasures of PTW crashes. Although the frequency of each crash sequence can be computed from crash data, a crash severity model is needed to compare the levels of crash severity among different crash sequences, while controlling for other factors that also have effects on crash severity such drivers' age, use of helmet, etc. The construction of risk matrix based on crash sequences involve two tasks: formulation of crash sequence and the estimation of a mixed-effects (ME) model to adjust the levels of severities for each crash sequence to account for other crash contributing factors that would have an effect on the maximum level of crash severity in a crash. Three data elements from the National Automotive Sampling System - General Estimating System (NASS-GES) data were utilized to form a crash sequence: critical event, crash types, and sequence of events. A mixed-effects model was constructed to model the severity levels for each crash sequence while accounting for the effects of those crash contributing factors on crash severity. A total of 8039 crashes involving 8208 motorcycles occurred during 2011 and 2013 were

  12. Assessment of low-cost manufacturing process sequences. [photovoltaic solar arrays

    Science.gov (United States)

    Chamberlain, R. G.

    1979-01-01

    An extensive research and development activity to reduce the cost of manufacturing photovoltaic solar arrays by a factor of approximately one hundred is discussed. Proposed and actual manufacturing process descriptions were compared to manufacturing costs. An overview of this methodology is presented.

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

    Science.gov (United States)

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

    2016-07-01

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

  14. Sweet Spot Control of 1:2 Array Antenna using A Modified Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Kyo-Hwan HYUN

    2007-10-01

    Full Text Available This paper presents a novel scheme that quickly searches for the sweet spot of 1:2 array antennas, and locks on to it for high-speed millimeter wavelength transmissions, when communications to another antenna array are disconnected. The proposed method utilizes a modified genetic algorithm, which selects a superior initial group through preprocessing in order to solve the local solution in a genetic algorithm. TDD (Time Division Duplex is utilized as the transfer method and data controller for the antenna. Once the initial communication is completed for the specific number of individuals, no longer antenna's data will be transmitted until each station processes GA in order to produce the next generation. After reproduction, individuals of the next generation become the data, and communication between each station is made again. The simulation results of 1:1, 1:2 array antennas, and experiment results of 1:1 array antenna confirmed the efficiency of the proposed method. The bit of gene is each 8bit, 16bit and 16bit split gene. 16bit split has similar performance as 16bit gene, but the gene of antenna is 8bit.

  15. Note: A resonating reflector-based optical system for motion measurement in micro-cantilever arrays

    International Nuclear Information System (INIS)

    Sathishkumar, P.; Punyabrahma, P.; Sri Muthu Mrinalini, R.; Jayanth, G. R.

    2015-01-01

    A robust, compact optical measurement unit for motion measurement in micro-cantilever arrays enables development of portable micro-cantilever sensors. This paper reports on an optical beam deflection-based system to measure the deflection of micro-cantilevers in an array that employs a single laser source, a single detector, and a resonating reflector to scan the measurement laser across the array. A strategy is also proposed to extract the deflection of individual cantilevers from the acquired data. The proposed system and measurement strategy are experimentally evaluated and demonstrated to measure motion of multiple cantilevers in an array

  16. Cloning and sequencing of phenol oxidase 1 (pox1) gene from ...

    African Journals Online (AJOL)

    The gene (pox1) encoding a phenol oxidase 1 from Pleurotus ostreatus was sequenced and the corresponding pox1-cDNA was also synthesized, cloned and sequenced. The isolated gene is flanked by an upstream region called the promoter (399 bp) prior to the start codon (ATG). The putative metalresponsive elements ...

  17. Electrostatic Discharge Test of Multi-Junction Solar Array Coupons After Combined Space Environmental Exposures

    Science.gov (United States)

    Wright, Kenneth H.; Schneider, Todd; Vaughn, Jason; Hoang, Bao; Funderburk, Victor V.; Wong, Frankie; Gardiner, George

    2010-01-01

    A set of multi-junction GaAs/Ge solar array test coupons were subjected to a sequence of 5-year increments of combined environmental exposure tests. The test coupons capture an integrated design intended for use in a geosynchronous (GEO) space environment. A key component of this test campaign is conducting electrostatic discharge (ESD) tests in the inverted gradient mode. The protocol of the ESD tests is based on the ISO/CD 11221, the ISO standard for ESD testing on solar array panels. This standard is currently in its final review with expected approval in 2010. The test schematic in the ISO reference has been modified with Space System/Loral designed circuitry to better simulate the on-orbit operational conditions of its solar array design. Part of the modified circuitry is to simulate a solar array panel coverglass flashover discharge. All solar array coupons used in the test campaign consist of 4 cells. The ESD tests are performed at the beginning of life (BOL) and at each 5-year environment exposure point. The environmental exposure sequence consists of UV radiation, electron/proton particle radiation, thermal cycling, and ion thruster plume. This paper discusses the coverglass flashover simulation, ESD test setup, and the importance of the electrical test design in simulating the on-orbit operational conditions. Results from 5th-year testing are compared to the baseline ESD characteristics determined at the BOL condition.

  18. Boronate-Modified Interdigitated Electrode Array for Selective Impedance-Based Sensing of Glycated Hemoglobin

    DEFF Research Database (Denmark)

    Boonyasit, Yuwadee; Laiwattanapaisal, Wanida; Chailapakul, Orawon

    2016-01-01

    An impedance-based label-free affinity sensor was developed for the recognition of glycated hemoglobin (HbA1c). Interdigitated gold microelectrode arrays (IDA) were first modified with a self-assembled monolayer of cysteamine followed by cross-linking with glutaraldehyde and subsequent binding of 3......-aminophenylboronic acid (APBA), which selectively binds HbA1c via cis-diol interactions. Impedance sensing was demonstrated to be highly responsive to the clinically relevant HbA1c levels (0.1%-8.36%) with a detection limit of 0.024% (3σ). The specificity of the assay was evaluated with non-glycated hemoglobin (Hb...

  19. Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.

    Science.gov (United States)

    Humble, Emily; Thorne, Michael A S; Forcada, Jaume; Hoffman, Joseph I

    2016-08-26

    Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be

  20. Optically Controlled Reconfigurable Antenna Array Based on E-Shaped Elements

    Directory of Open Access Journals (Sweden)

    Arismar Cerqueira Sodré Junior

    2014-01-01

    Full Text Available This work presents the development of optically controlled reconfigurable antenna arrays. They are based on two patch elements with E-shaped slots, a printed probe, and a photoconductive switch made from an intrinsic silicon die. Numerical simulations and experiments have been shown to be in agreement, and both demonstrate that the frequency response of the antenna arrays can be efficiently reconfigured over two different frequency ISM bands, namely, 2.4 and 5 GHz. A measured gain of 12.5 dBi has been obtained through the use of two radiating elements printed in a low-cost substrate and a dihedral corner reflector.

  1. Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana

    Science.gov (United States)

    Richardson, Dale N.; Wiehe, Thomas

    Whole genome duplication (WGD) has catalyzed the formation of new species, genes with novel functions, altered expression patterns, complexified signaling pathways and has provided organisms a level of genetic robustness. We studied the long-term evolution and interrelationships of 5’ upstream regulatory sequences (URSs), protein coding sequences (CDSs) and expression correlations (EC) of duplicated gene pairs in Arabidopsis. Three distinct methods revealed significant evolutionary conservation between paralogous URSs and were highly correlated with microarray-based expression correlation of the respective gene pairs. Positional information on exact matches between sequences unveiled the contribution of micro-chromosomal rearrangements on expression divergence. A three-way rank analysis of URS similarity, CDS divergence and EC uncovered specific gene functional biases. Transcription factor activity was associated with gene pairs exhibiting conserved URSs and divergent CDSs, whereas a broad array of metabolic enzymes was found to be associated with gene pairs showing diverged URSs but conserved CDSs.

  2. Principal component analysis for predicting transcription-factor binding motifs from array-derived data

    Directory of Open Access Journals (Sweden)

    Vincenti Matthew P

    2005-11-01

    Full Text Available Abstract Background The responses to interleukin 1 (IL-1 in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBMs. In order to select a critical set of TFBMs from genomic DNA information and an array-derived data, an efficient algorithm to solve a combinatorial optimization problem is required. Although computational approaches based on evolutionary algorithms are commonly employed, an analytical algorithm would be useful to predict TFBMs at nearly no computational cost and evaluate varying modelling conditions. Singular value decomposition (SVD is a powerful method to derive primary components of a given matrix. Applying SVD to a promoter matrix defined from regulatory DNA sequences, we derived a novel method to predict the critical set of TFBMs. Results The promoter matrix was defined to establish a quantitative relationship between the IL-1-driven mRNA alteration and genomic DNA sequences of the IL-1 responsive genes. The matrix was decomposed with SVD, and the effects of 8 potential TFBMs (5'-CAGGC-3', 5'-CGCCC-3', 5'-CCGCC-3', 5'-ATGGG-3', 5'-GGGAA-3', 5'-CGTCC-3', 5'-AAAGG-3', and 5'-ACCCA-3' were predicted from a pool of 512 random DNA sequences. The prediction included matches to the core binding motifs of biologically known TFBMs such as AP2, SP1, EGR1, KROX, GC-BOX, ABI4, ETF, E2F, SRF, STAT, IK-1, PPARγ, STAF, ROAZ, and NFκB, and their significance was evaluated numerically using Monte Carlo simulation and genetic algorithm. Conclusion The described SVD-based prediction is an analytical method to provide a set of potential TFBMs involved in transcriptional regulation. The results would be useful to evaluate analytically a contribution of individual DNA sequences.

  3. 1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling.

    Science.gov (United States)

    Liang, Feng; Lindsay, Stuart; Zhang, Peiming

    2012-11-21

    With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A : T and G : C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.

  4. Growth of ZnO nanotube arrays and nanotube based piezoelectric nanogenerators

    KAUST Repository

    Xi, Yi; Song, Jinhui; Xu, Sheng; Yang, Rusen; Gao, Zhiyuan; Hu, Chenguo; Wang, Zhong Lin

    2009-01-01

    We present a systematic study of the growth of hexagonal ZnO nanotube arrays using a solution chemical method by varying the growth temperature (<100 °C), time and solution concentration. A piezoelectric nanogenerator using the as-grown ZnO nanotube arrays has been demonstrated for the first time. The nanogenerator gives an output voltage up to 35 mV. The detailed profile of the observed electric output is understood based on the calculated piezoelectric potential in the nanotube with consideration of the Schottky contact formed between the metal tip and the nanotube; and the mechanism agrees with that proposed for nanowire based nanogenerator. Our study shows that ZnO nanotubes can also be used for harvesting mechanical energy. © 2009 The Royal Society of Chemistry.

  5. Pseudo-Coherence-Based MVDR Beamformer for Speech Enhancement with Ad Hoc Microphone Arrays

    DEFF Research Database (Denmark)

    Tavakoli, Vincent Mohammad; Jensen, Jesper Rindom; Christensen, Mads Græsbøll

    2015-01-01

    Speech enhancement with distributed arrays has been met with various methods. On the one hand, data independent methods require information about the position of sensors, so they are not suitable for dynamic geometries. On the other hand, Wiener-based methods cannot assure a distortionless output....... This paper proposes minimum variance distortionless response filtering based on multichannel pseudo-coherence for speech enhancement with ad hoc microphone arrays. This method requires neither position information nor control of the trade-off used in the distortion weighted methods. Furthermore, certain...

  6. Hydrodynamic prediction of multidimensional single- and two-phase flow in rod arrays. Progress report, January 1-December 31, 1983

    International Nuclear Information System (INIS)

    Ebeling-Koning, D.B.; Robinson, J.T.; Todreas, N.E.

    1984-01-01

    The objective of this research is to develop comprehensive constitutive models for multidimensional two-phase flow in rod arrays. The constitutive parameters are the solid-fluid flow resistance and the gas-liquid interfacial momentum exchange force. This report covers work in four areas: (1) a correlation for flow resistance across banks of tubes which is independent of rod arrangement has been developed. The correlation was developed from data from three rod arrangements covering a Reynolds number range (based on superficial velocity) of 1 to 40,000; (2) complete pressure drop data for water flows in the laminar region in crossflow and 45 0 inclined rod arrays were taken; (3) the development of a model for the interfacial momentum exchange force in bubbly flows has been completed. This model has been validated against single bubble velocity data in inclined rod arrays. The model has been cast in a form suitable for implementation to two-fluid computer codes; and (4) rise velocities of bubbles in 0 0 , 45 0 , and 90 0 inclined rod arrays have been measured. This data should prove useful for the development of a bubble drag coefficient model for rod arrays

  7. Limits in point to point resolution of MOS based pixels detector arrays

    Science.gov (United States)

    Fourches, N.; Desforge, D.; Kebbiri, M.; Kumar, V.; Serruys, Y.; Gutierrez, G.; Leprêtre, F.; Jomard, F.

    2018-01-01

    In high energy physics point-to-point resolution is a key prerequisite for particle detector pixel arrays. Current and future experiments require the development of inner-detectors able to resolve the tracks of particles down to the micron range. Present-day technologies, although not fully implemented in actual detectors, can reach a 5-μm limit, this limit being based on statistical measurements, with a pixel-pitch in the 10 μm range. This paper is devoted to the evaluation of the building blocks for use in pixel arrays enabling accurate tracking of charged particles. Basing us on simulations we will make here a quantitative evaluation of the physical and technological limits in pixel size. Attempts to design small pixels based on SOI technology will be briefly recalled here. A design based on CMOS compatible technologies that allow a reduction of the pixel size below the micrometer is introduced here. Its physical principle relies on a buried carrier-localizing collecting gate. The fabrication process needed by this pixel design can be based on existing process steps used in silicon microelectronics. The pixel characteristics will be discussed as well as the design of pixel arrays. The existing bottlenecks and how to overcome them will be discussed in the light of recent ion implantation and material characterization experiments.

  8. Detection system of capillary array electrophoresis microchip based on optical fiber

    Science.gov (United States)

    Yang, Xiaobo; Bai, Haiming; Yan, Weiping

    2009-11-01

    To meet the demands of the post-genomic era study and the large parallel detections of epidemic diseases and drug screening, the high throughput micro-fluidic detection system is needed urgently. A scanning laser induced fluorescence detection system based on optical fiber has been established by using a green laser diode double-pumped solid-state laser as excitation source. It includes laser induced fluorescence detection subsystem, capillary array electrophoresis micro-chip, channel identification unit and fluorescent signal processing subsystem. V-shaped detecting probe composed with two optical fibers for transmitting the excitation light and detecting induced fluorescence were constructed. Parallel four-channel signal analysis of capillary electrophoresis was performed on this system by using Rhodamine B as the sample. The distinction of different samples and separation of samples were achieved with the constructed detection system. The lowest detected concentration is 1×10-5 mol/L for Rhodamine B. The results show that the detection system possesses some advantages, such as compact structure, better stability and higher sensitivity, which are beneficial to the development of microminiaturization and integration of capillary array electrophoresis chip.

  9. Sensor array signal processing

    CERN Document Server

    Naidu, Prabhakar S

    2009-01-01

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

  10. Exome sequencing identifies mutations in ABCD1 and DACH2 in two brothers with a distinct phenotype.

    Science.gov (United States)

    Zhang, Yanliang; Liu, Yanhui; Li, Ya; Duan, Yong; Zhang, Keyun; Wang, Junwang; Dai, Yong

    2014-09-19

    We report on two brothers with a distinct syndromic phenotype and explore the potential pathogenic cause. Cytogenetic tests and exome sequencing were performed on the two brothers and their parents. Variants detected by exome sequencing were validated by Sanger sequencing. The main phenotype of the two brothers included congenital language disorder, growth retardation, intellectual disability, difficulty in standing and walking, and urinary and fecal incontinence. To the best of our knowledge, no similar phenotype has been reported previously. No abnormalities were detected by G-banding chromosome analysis or array comparative genomic hybridization. However, exome sequencing revealed novel mutations in the ATP-binding cassette, sub-family D member 1 (ABCD1) and Dachshund homolog 2 (DACH2) genes in both brothers. The ABCD1 mutation was a missense mutation c.1126G > C in exon 3 leading to a p.E376Q substitution. The DACH2 mutation was also a missense mutation c.1069A > T in exon 6, leading to a p.S357C substitution. The mother was an asymptomatic heterozygous carrier. Plasma levels of very-long-chain fatty acids were increased in both brothers, suggesting a diagnosis of adrenoleukodystrophy (ALD); however, their phenotype was not compatible with any reported forms of ALD. DACH2 plays an important role in the regulation of brain and limb development, suggesting that this mutation may be involved in the phenotype of the two brothers. The distinct phenotype demonstrated by these two brothers might represent a new form of ALD or a new syndrome. The combination of mutations in ABCD1 and DACH2 provides a plausible mechanism for this phenotype.

  11. Digital Sequences and a Time Reversal-Based Impact Region Imaging and Localization Method

    Science.gov (United States)

    Qiu, Lei; Yuan, Shenfang; Mei, Hanfei; Qian, Weifeng

    2013-01-01

    To reduce time and cost of damage inspection, on-line impact monitoring of aircraft composite structures is needed. A digital monitor based on an array of piezoelectric transducers (PZTs) is developed to record the impact region of impacts on-line. It is small in size, lightweight and has low power consumption, but there are two problems with the impact alarm region localization method of the digital monitor at the current stage. The first one is that the accuracy rate of the impact alarm region localization is low, especially on complex composite structures. The second problem is that the area of impact alarm region is large when a large scale structure is monitored and the number of PZTs is limited which increases the time and cost of damage inspections. To solve the two problems, an impact alarm region imaging and localization method based on digital sequences and time reversal is proposed. In this method, the frequency band of impact response signals is estimated based on the digital sequences first. Then, characteristic signals of impact response signals are constructed by sinusoidal modulation signals. Finally, the phase synthesis time reversal impact imaging method is adopted to obtain the impact region image. Depending on the image, an error ellipse is generated to give out the final impact alarm region. A validation experiment is implemented on a complex composite wing box of a real aircraft. The validation results show that the accuracy rate of impact alarm region localization is approximately 100%. The area of impact alarm region can be reduced and the number of PZTs needed to cover the same impact monitoring region is reduced by more than a half. PMID:24084123

  12. Enhanced Sensitivity of Surface Acoustic Wave-Based Rate Sensors Incorporating Metallic Dot Arrays

    Directory of Open Access Journals (Sweden)

    Wen Wang

    2014-02-01

    Full Text Available A new surface acoustic wave (SAW-based rate sensor pattern incorporating metallic dot arrays was developed in this paper. Two parallel SAW delay lines with a reverse direction and an operation frequency of 80 MHz on a same X-112°Y LiTaO3 wafer are fabricated as the feedback of two SAW oscillators, and mixed oscillation frequency was used to characterize the external rotation. To enhance the Coriolis force effect acting on the SAW propagation, a copper (Cu dot array was deposited along the SAW propagation path of the SAW devices. The approach of partial-wave analysis in layered media was referred to analyze the response mechanisms of the SAW based rate sensor, resulting in determination of the optimal design parameters. To improve the frequency stability of the oscillator, the single phase unidirectional transducers (SPUDTs and combed transducer were used to form the SAW device to minimize the insertion loss and accomplish the single mode selection, respectively. Excellent long-term (measured in hours frequency stability of 0.1 ppm/h was obtained. Using the rate table with high precision, the performance of the developed SAW rate sensor was evaluated experimentally; satisfactory detection sensitivity (16.7 Hz∙deg∙s−1 and good linearity were observed.

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  14. Discrimination learning and attentional set formation in a mouse model of Fragile X.

    Science.gov (United States)

    Casten, Kimberly S; Gray, Annette C; Burwell, Rebecca D

    2011-06-01

    Fragile X Syndrome is the most prevalent genetic cause of mental retardation. Selective deficits in executive function, including inhibitory control and attention, are core features of the disorder. In humans, Fragile X results from a trinucleotide repeat in the Fmr1 gene that renders it functionally silent and has been modeled in mice by targeted deletion of the Fmr1 gene. Fmr1 knockout (KO) mice recapitulate many features of Fragile X syndrome, but evidence for deficits in executive function is inconsistent. To address this issue, we trained wild-type and Fmr1 KO mice on an experimental paradigm that assesses attentional set-shifting. Mice learned to discriminate between stimuli differing in two of three perceptual dimensions. Successful discrimination required attending only to the relevant dimension, while ignoring irrelevant dimensions. Mice were trained on three discriminations in the same perceptual dimension, each followed by a reversal. This procedure normally results in the formation of an attentional set to the relevant dimension. Mice were then required to shift attention and discriminate based on a previously irrelevant perceptual dimension. Wild-type mice exhibited the increase in trials to criterion expected when shifting attention from one perceptual dimension to another. In contrast, the Fmr1 KO group failed to show the expected increase, suggesting impairment in forming an attentional set. Fmr1 KO mice also exhibited a general impairment in learning discriminations and reversals. This is the first demonstration that Fmr1 KO mice show a deficit in attentional set formation.

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

    Science.gov (United States)

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

    2006-12-22

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

  16. Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

    KAUST Repository

    Teng, Haotian; Cao, Minh Duc; Hall, Michael B; Duarte, Tania; Wang, Sheng; Coin, Lachlan J M

    2018-01-01

    Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

  17. Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

    KAUST Repository

    Teng, Haotian

    2018-04-10

    Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

  18. 76 FR 31545 - Federal Management Regulation; Motor Vehicle Management

    Science.gov (United States)

    2011-06-01

    ...; Sequence 1] RIN 3090-AJ14 Federal Management Regulation; Motor Vehicle Management AGENCY: Office of... Services Administration is proposing to amend the Federal Management Regulation (FMR) by revising current....C. 553(a)(2) because it applies to agency management. However, this proposed rule is being published...

  19. Anlægsbærere for fragilt X-syndrom kan udvise et bredt spektrum af kliniske manifestationer

    DEFF Research Database (Denmark)

    Jønch, Aia Elise; Grønskov, Karen; Lunding, Jytte

    2014-01-01

    Fragile X syndrome, fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X-associated primary ovarian insufficiency (FXPOI) are three clinically distinct disorders caused by expansions of a CGG repeat sequence in the non-coding part of the FMR1. FXTAS and FXPOI are seen in carriers...

  20. Manycore Performance-Portability: Kokkos Multidimensional Array Library

    Directory of Open Access Journals (Sweden)

    H. Carter Edwards

    2012-01-01

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

  1. Template-based fabrication of nanowire-nanotube hybrid arrays

    International Nuclear Information System (INIS)

    Ye Zuxin; Liu Haidong; Schultz, Isabel; Wu Wenhao; Naugle, D G; Lyuksyutov, I

    2008-01-01

    The fabrication and structure characterization of ordered nanowire-nanotube hybrid arrays embedded in porous anodic aluminum oxide (AAO) membranes are reported. Arrays of TiO 2 nanotubes were first deposited into the pores of AAO membranes by a sol-gel technique. Co nanowires were then electrochemically deposited into the TiO 2 nanotubes to form the nanowire-nanotube hybrid arrays. Scanning electron microscopy and transmission electron microscopy measurements showed a high nanowire filling factor and a clean interface between the Co nanowire and the TiO 2 nanotube. Application of these hybrids to the fabrication of ordered nanowire arrays with highly controllable geometric parameters is discussed

  2. Sequence variation in mitochondrial cox1 and nad1 genes of ascaridoid nematodes in cats and dogs from Iran.

    Science.gov (United States)

    Mikaeili, F; Mirhendi, H; Mohebali, M; Hosseini, M; Sharbatkhori, M; Zarei, Z; Kia, E B

    2015-07-01

    The study was conducted to determine the sequence variation in two mitochondrial genes, namely cytochrome c oxidase 1 (pcox1) and NADH dehydrogenase 1 (pnad1) within and among isolates of Toxocara cati, Toxocara canis and Toxascaris leonina. Genomic DNA was extracted from 32 isolates of T. cati, 9 isolates of T. canis and 19 isolates of T. leonina collected from cats and dogs in different geographical areas of Iran. Mitochondrial genes were amplified by polymerase chain reaction (PCR) and sequenced. Sequence data were aligned using the BioEdit software and compared with published sequences in GenBank. Phylogenetic analysis was performed using Bayesian inference and maximum likelihood methods. Based on pairwise comparison, intra-species genetic diversity within Iranian isolates of T. cati, T. canis and T. leonina amounted to 0-2.3%, 0-1.3% and 0-1.0% for pcox1 and 0-2.0%, 0-1.7% and 0-2.6% for pnad1, respectively. Inter-species sequence variation among the three ascaridoid nematodes was significantly higher, being 9.5-16.6% for pcox1 and 11.9-26.7% for pnad1. Sequence and phylogenetic analysis of the pcox1 and pnad1 genes indicated that there is significant genetic diversity within and among isolates of T. cati, T. canis and T. leonina from different areas of Iran, and these genes can be used for studying genetic variation of ascaridoid nematodes.

  3. Simulation Based Investigation of Focusing Phased Array Ultrasound in Dissimilar Metal Welds

    Directory of Open Access Journals (Sweden)

    Hun-Hee Kim

    2016-02-01

    Full Text Available Flaws at dissimilar metal welds (DMWs, such as reactor coolant systems components, Control Rod Drive Mechanism (CRDM, Bottom Mounted Instrumentation (BMI etc., in nuclear power plants have been found. Notably, primary water stress corrosion cracking (PWSCC in the DMWs could cause significant reliability problems at nuclear power plants. Therefore, phased array ultrasound is widely used for inspecting surface break cracks and stress corrosion cracks in DMWs. However, inspection of DMWs using phased array ultrasound has a relatively low probability of detection of cracks, because the crystalline structure of welds causes distortion and splitting of the ultrasonic beams which propagates anisotropic medium. Therefore, advanced evaluation techniques of phased array ultrasound are needed for improvement in the probability of detection of flaws in DMWs. Thus, in this study, an investigation of focusing and steering phased array ultrasound in DMWs was carried out using a time reversal technique, and an adaptive focusing technique based on finite element method (FEM simulation. Also, evaluation of focusing performance of three different focusing techniques was performed by comparing amplitude of phased array ultrasonic signals scattered from the targeted flaw with three different time delays.

  4. Application of high resolution SNP arrays in patients with congenital ...

    Indian Academy of Sciences (India)

    TING-YING LEI

    lent oligonucleotide-based array-CGH to determine the exact breakpoints in 14 patients with partial deletions of chromo- some 13q21.1-qter. They were able to refine the smallest deletion region linked to cleft lip/palate (13q31.3–13q33.1). Except for the arrays that measure DNA copy number differ- ences only, SNP arrays, ...

  5. Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM

    Directory of Open Access Journals (Sweden)

    Yunyun Liang

    2015-01-01

    Full Text Available Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM. Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS, segmented PsePSSM, and segmented autocovariance transformation (ACT based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640 are adopted in this paper. Then a 700-dimensional (700D feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA. To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences.

  6. Mutated and Bacteriophage T4 Nanoparticle Arrayed F1-V Immunogens from Yersinia pestis as Next Generation Plague Vaccines

    Science.gov (United States)

    Tao, Pan; Mahalingam, Marthandan; Kirtley, Michelle L.; van Lier, Christina J.; Sha, Jian; Yeager, Linsey A.; Chopra, Ashok K.; Rao, Venigalla B.

    2013-01-01

    Pneumonic plague is a highly virulent infectious disease with 100% mortality rate, and its causative organism Yersinia pestis poses a serious threat for deliberate use as a bioterror agent. Currently, there is no FDA approved vaccine against plague. The polymeric bacterial capsular protein F1, a key component of the currently tested bivalent subunit vaccine consisting, in addition, of low calcium response V antigen, has high propensity to aggregate, thus affecting its purification and vaccine efficacy. We used two basic approaches, structure-based immunogen design and phage T4 nanoparticle delivery, to construct new plague vaccines that provided complete protection against pneumonic plague. The NH2-terminal β-strand of F1 was transplanted to the COOH-terminus and the sequence flanking the β-strand was duplicated to eliminate polymerization but to retain the T cell epitopes. The mutated F1 was fused to the V antigen, a key virulence factor that forms the tip of the type three secretion system (T3SS). The F1mut-V protein showed a dramatic switch in solubility, producing a completely soluble monomer. The F1mut-V was then arrayed on phage T4 nanoparticle via the small outer capsid protein, Soc. The F1mut-V monomer was robustly immunogenic and the T4-decorated F1mut-V without any adjuvant induced balanced TH1 and TH2 responses in mice. Inclusion of an oligomerization-deficient YscF, another component of the T3SS, showed a slight enhancement in the potency of F1-V vaccine, while deletion of the putative immunomodulatory sequence of the V antigen did not improve the vaccine efficacy. Both the soluble (purified F1mut-V mixed with alhydrogel) and T4 decorated F1mut-V (no adjuvant) provided 100% protection to mice and rats against pneumonic plague evoked by high doses of Y. pestis CO92. These novel platforms might lead to efficacious and easily manufacturable next generation plague vaccines. PMID:23853602

  7. Mutated and bacteriophage T4 nanoparticle arrayed F1-V immunogens from Yersinia pestis as next generation plague vaccines.

    Directory of Open Access Journals (Sweden)

    Pan Tao

    Full Text Available Pneumonic plague is a highly virulent infectious disease with 100% mortality rate, and its causative organism Yersinia pestis poses a serious threat for deliberate use as a bioterror agent. Currently, there is no FDA approved vaccine against plague. The polymeric bacterial capsular protein F1, a key component of the currently tested bivalent subunit vaccine consisting, in addition, of low calcium response V antigen, has high propensity to aggregate, thus affecting its purification and vaccine efficacy. We used two basic approaches, structure-based immunogen design and phage T4 nanoparticle delivery, to construct new plague vaccines that provided complete protection against pneumonic plague. The NH₂-terminal β-strand of F1 was transplanted to the COOH-terminus and the sequence flanking the β-strand was duplicated to eliminate polymerization but to retain the T cell epitopes. The mutated F1 was fused to the V antigen, a key virulence factor that forms the tip of the type three secretion system (T3SS. The F1mut-V protein showed a dramatic switch in solubility, producing a completely soluble monomer. The F1mut-V was then arrayed on phage T4 nanoparticle via the small outer capsid protein, Soc. The F1mut-V monomer was robustly immunogenic and the T4-decorated F1mut-V without any adjuvant induced balanced TH1 and TH2 responses in mice. Inclusion of an oligomerization-deficient YscF, another component of the T3SS, showed a slight enhancement in the potency of F1-V vaccine, while deletion of the putative immunomodulatory sequence of the V antigen did not improve the vaccine efficacy. Both the soluble (purified F1mut-V mixed with alhydrogel and T4 decorated F1mut-V (no adjuvant provided 100% protection to mice and rats against pneumonic plague evoked by high doses of Y. pestis CO92. These novel platforms might lead to efficacious and easily manufacturable next generation plague vaccines.

  8. One dimensional FexCo1-x nanowires; ferromagnetic resonance and magnetization dynamics

    Directory of Open Access Journals (Sweden)

    Shehreen Aslam

    2017-05-01

    Full Text Available Soft magnetic nanowires (NWs are widely used for microwave and mm-wave components. The investigation of magnetization damping behavior of NWs have attracted great interest due to large influence of loss to the device, like integrated microwave device, magnetic sensors, and magnetic random access memory. With increasing operational frequency and degree of integration, the requirements to characterize 1-dimensional NWs become increasingly high. The purpose of this work is to study the magnetization dynamics in FexCo1-x NWs. A series of FexCo1-x (x=0, 0.25, 0.5, 0.75, 1 NWs were grown by controlled electro-deposition. By adjusting FexCo1-x concentration (x=0 to 1, the saturation magnetization, increased more than 20%. Ferromagnetic resonance (FMR both in field and frequency sweep mode are employed to characterize the NWs in flip-chip geometry. It is observed that FMR field (Hr increases with increase in applied frequency. At a fixed frequency, Fe NWs resonate at a lower field than the Co substituted NWs. FMR field linewidth (ΔH as well as frequency width (Δf are largest for Co NWs and decreased for Fe NWs. Whereas ΔH and Δf decreased further for FexCo1-x nanowires with increasing x.

  9. Microshutter Array Development for the Multi-Object Spectrograph for the New Generation Space Telescope, and Its Ground-based Demonstrator

    Science.gov (United States)

    Woodgate, Bruce E.; Moseley, Harvey; Fettig, Rainer; Kutyrev, Alexander; Ge, Jian; Fisher, Richard R. (Technical Monitor)

    2001-01-01

    The 6.5-m NASA/ESA/Canada New Generation Space Telescope to be operated at the L2 Lagrangian point will require a multi-object spectrograph (MOS) operating from 1 to 5 microns. Up to 3000 targets will be selected for simultaneous spectroscopy using a programmable cryogenic (approx. 35K) aperture array, consisting of a mosaic of arrays of micromirrors or microshutters. We describe the current status of the GSFC microshutter array development. The 100 micron square shutters are opened magnetically and latched open or closed electrostatically. Selection will be by two crossed one-dimensional addressing circuits. We will demonstrate the use of a 512 x 512 unit array on a ground-based IR MOS which will cover 0.6 to 5 microns, and operate rapidly to include spectroscopy of gamma ray burst afterglows.

  10. In vitro and in vivo comparison of wrist MR imaging at 3.0 and 7.0 tesla using a gradient echo sequence and identical eight-channel coil array designs.

    Science.gov (United States)

    Nordmeyer-Massner, Jurek A; Wyss, Michael; Andreisek, Gustav; Pruessmann, Klaas P; Hodler, Juerg

    2011-03-01

    To evaluate in vivo MR imaging of the wrist at 3.0 Tesla (T) and 7.0T quantitatively and qualitatively. To enable unbiased signal-to-noise ratio (SNR) comparisons, geometrically identical eight-channel receiver arrays were used at both field strengths. First, in vitro images of a phantom bottle were acquired at 3.0T and 7.0T to obtain an estimate of the maximum SNR gain that can be expected. MR images of the dominant wrist of 10 healthy volunteers were acquired at both field strengths. All measurements were done using the same sequence parameters. Quantitative SNR maps were calculated on a pixel-by-pixel basis and analyzed in several regions-of-interest. Furthermore, the images were qualitatively evaluated by two independent radiologists. The quantitative analysis showed SNR increases of up to 100% at 7.0T compared with 3.0T, with considerable variation between different anatomical structures. The qualitative analysis revealed no significant difference in the visualization of anatomical structures comparing 3.0T and 7.0T MR images (P>0.05). The presented results establish the SNR benefits of the transition from 3.0T to 7.0T for wrist imaging without bias by different array designs and based on exact, algebraic SNR quantification. The observed SNR increase nearly reaches expected values but varies greatly between different tissues. It does not necessarily improve the visibility of anatomic structures but adds valuable latitude for sequence optimization. Copyright © 2011 Wiley-Liss, Inc.

  11. Pharmacological rescue of Ras signaling, GluA1-dependent synaptic plasticity, and learning deficits in a fragile X model

    OpenAIRE

    Lim, Chae-Seok; Hoang, Elizabeth T.; Viar, Kenneth E.; Stornetta, Ruth L.; Scott, Michael M.; Zhu, J. Julius

    2014-01-01

    Fragile X syndrome, caused by the loss of Fmr1 gene function, is the most common form of inherited mental retardation. Lim et al. find that compounds activating serotonin (5HT) subtype 2B receptors or dopamine (DA) subtype 1-like receptors and those inhibiting 5HT2A-Rs or D2-Rs enhance Ras signaling, GluA1-dependent synaptic plasticity, and learning in Fmr1 knockout mice. Combining 5HT and DA compounds at low doses synergistically restored normal learning. This suggests that properly dosed an...

  12. Two-Slotted Surface Coil Array for Magnetic Resonance Imaging at 4 Tesla

    International Nuclear Information System (INIS)

    Solis, S. E.; Hernandez, J. A.; Rodriguez, A. O.; Tomasi, D.

    2008-01-01

    Arrays of antennas have been widely accepted for magnetic resonance imaging applications due to their high signal-to-noise ratio (SNR) over large volumes of interest. A new surface coil based on the magnetron tube and called slotted surface coil, has been recently introduced by our group. This coil design experimentally demonstrated a significant improvement over the circular-shaped coil when used in the receive-only mode. The slotted coils formed a two-sheet structure with a 90 deg. separation and each coil had 6 circular slots. Numerical simulations were performed using the finite element method for this coil design to study the behaviour of the array magnetic field. Then, we developed a two-coil array for brain magnetic resonance imaging to be operated at the resonant frequency of 170 MHz in the transceiver mode. Phantom images were acquired with our coil array and standard pulse sequences on a research-dedicated 4 Tesla scanner. Numerical simulations demonstrated that electromagnetic interaction between the coil elements is negligible, and that the magnetic field showed a good uniformity. In vitro images showed the feasibility of this coil array for standard pulses for high field magnetic resonance imaging

  13. Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome

    NARCIS (Netherlands)

    Santen, G.W.; Aten, E.; Sun, Y; Almomani, R.; Gilissen, C.F.; Nielsen, M.; Kant, S.G.; Snoeck, I.N.; Peeters, E.A.; Hilhorst-Hofstee, Y.; Wessels, M.W.; Hollander, N.S. den; Ruivenkamp, C.A.; van Ommen, G.J.; Breuning, M.H.; den Dunnen, J.T.; van Haeringen, A.; Kriek, M.

    2012-01-01

    We identified de novo truncating mutations in ARID1B in three individuals with Coffin-Siris syndrome (CSS) by exome sequencing. Array-based copy-number variation (CNV) analysis in 2,000 individuals with intellectual disability revealed deletions encompassing ARID1B in 3 subjects with phenotypes

  14. Soft X-ray radiation parameters of nested tungsten wire array

    International Nuclear Information System (INIS)

    Ning Jiamin; Jiang Shilun; Xu Rongkun; Xu Zeping; Li Zhenghong; Yang Jianlun

    2011-01-01

    Implosions with nested tungsten wire array were performed at the Angara-5-1 facility in Russian Research Centre. The experimental results of nested tungsten wire array are compared with those of single array. Radiation parameters of nested array are discussed based on four different dynamic models. When the implosions of outer and inner wire arrays are synchronized,the relatively uniform distribution of inner layer plasma will improve the uniformity of outer layer plasma. As compared with single array, nested array has an increase of 32% in X-ray radiation power. (authors)

  15. Accommodating Thickness in Origami-Based Deployable Arrays

    Science.gov (United States)

    Zirbel, Shannon A.; Magleby, Spencer P.; Howell, Larry L.; Lang, Robert J.; Thomson, Mark W.; Sigel, Deborah A.; Walkemeyer, Phillip E.; Trease, Brian P.

    2013-01-01

    The purpose of this work is to create deployment systems with a large ratio of stowed-to-deployed diameter. Deployment from a compact form to a final flat state can be achieved through origami-inspired folding of panels. There are many models capable of this motion when folded in a material with negligible thickness; however, when the application requires the folding of thick, rigid panels, attention must be paid to the effect of material thickness not only on the final folded state, but also during the folding motion (i.e., the panels must not be required to flex to attain the final folded form). The objective is to develop new methods for deployment from a compact folded form to a large circular array (or other final form). This paper describes a mathematical model for modifying the pattern to accommodate material thickness in the context of the design, modeling, and testing of a deployable system inspired by an origami six-sided flasher model. The model is demonstrated in hardware as a 1/20th scale prototype of a deployable solar array for space applications. The resulting prototype has a ratio of stowed-to-deployed diameter of 9.2 (or 1.25 m deployed outer diameter to 0.136 m stowed outer diameter).

  16. DOA and Polarization Estimation Using an Electromagnetic Vector Sensor Uniform Circular Array Based on the ESPRIT Algorithm.

    Science.gov (United States)

    Wu, Na; Qu, Zhiyu; Si, Weijian; Jiao, Shuhong

    2016-12-13

    In array signal processing systems, the direction of arrival (DOA) and polarization of signals based on uniform linear or rectangular sensor arrays are generally obtained by rotational invariance techniques (ESPRIT). However, since the ESPRIT algorithm relies on the rotational invariant structure of the received data, it cannot be applied to electromagnetic vector sensor arrays (EVSAs) featuring uniform circular patterns. To overcome this limitation, a fourth-order cumulant-based ESPRIT algorithm is proposed in this paper, for joint estimation of DOA and polarization based on a uniform circular EVSA. The proposed algorithm utilizes the fourth-order cumulant to obtain a virtual extended array of a uniform circular EVSA, from which the pairs of rotation invariant sub-arrays are obtained. The ESPRIT algorithm and parameter pair matching are then utilized to estimate the DOA and polarization of the incident signals. The closed-form parameter estimation algorithm can effectively reduce the computational complexity of the joint estimation, which has been demonstrated by numerical simulations.

  17. PV Array Driven Adjustable Speed Drive for a Lunar Base Heat Pump

    Science.gov (United States)

    Domijan, Alexander, Jr.; Buchh, Tariq Aslam

    1995-01-01

    A study of various aspects of Adjustable Speed Drives (ASD) is presented. A summary of the relative merits of different ASD systems presently in vogue is discussed. The advantages of using microcomputer based ASDs is now widely understood and accepted. Of the three most popular drive systems, namely the Induction Motor Drive, Switched Reluctance Motor Drive and Brushless DC Motor Drive, any one may be chosen. The choice would depend on the nature of the application and its requirements. The suitability of the above mentioned drive systems for a photovoltaic array driven ASD for an aerospace application are discussed. The discussion is based on the experience of the authors, various researchers and industry. In chapter 2 a PV array power supply scheme has been proposed, this scheme will have an enhanced reliability in addition to the other known advantages of the case where a stand alone PV array is feeding the heat pump. In chapter 3 the results of computer simulation of PV array driven induction motor drive system have been included. A discussion on these preliminary simulation results have also been included in this chapter. Chapter 4 includes a brief discussion on various control techniques for three phase induction motors. A discussion on different power devices and their various performance characteristics is given in Chapter 5.

  18. Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools.

    Science.gov (United States)

    Michael Dunne, W; Pouseele, Hannes; Monecke, Stefan; Ehricht, Ralf; van Belkum, Alex

    2017-09-21

    The magnitude of interest in the epidemiology of transmissible human diseases is reflected in the vast number of tools and methods developed recently with the expressed purpose to characterize and track evolutionary changes that occur in agents of these diseases over time. Within the past decade a new suite of such tools has become available with the emergence of the so-called "omics" technologies. Among these, two are exponents of the ongoing genomic revolution. Firstly, high-density nucleic acid probe arrays have been proposed and developed using various chemical and physical approaches. Via hybridization-mediated detection of entire genes or genetic polymorphisms in such genes and intergenic regions these so called "DNA chips" have been successfully applied for distinguishing very closely related microbial species and strains. Second and even more phenomenal, next generation sequencing (NGS) has facilitated the assessment of the complete nucleotide sequence of entire microbial genomes. This technology currently provides the most detailed level of bacterial genotyping and hence allows for the resolution of microbial spread and short-term evolution in minute detail. We will here review the very recent history of these two technologies, sketch their usefulness in the elucidation of the spread and epidemiology of mostly hospital-acquired infections and discuss future developments. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Multi-Array Back-Projections of The 2015 Gorkha Earthquake With Physics-Based Aftershock Calibrations

    Science.gov (United States)

    Meng, L.; Zhang, A.; Yagi, Y.

    2015-12-01

    The 2015 Mw 7.8 Nepal-Gorkha earthquake with casualties of over 9,000 people is the most devastating disaster to strike Nepal since the 1934 Nepal-Bihar earthquake. Its rupture process is well imaged by the teleseismic MUSIC back-projections (BP). Here, we perform independent back-projections of high-frequency recordings (0.5-2 Hz) from the Australian seismic network (AU), the North America network (NA) and the European seismic network (EU), located in complementary orientations. Our results of all three arrays show unilateral linear rupture path to the east of the hypocenter. But the propagating directions and the inferred rupture speeds differ significantly among different arrays. To understand the spatial uncertainties of the BP analysis, we image four moderate-size (M5~6) aftershocks based on the timing correction derived from the alignment of the initial P-wave of the mainshock. We find that the apparent source locations inferred from BP are systematically biased along the source-array orientation, which can be explained by the uncertainty of the 3D velocity structure deviated from the 1D reference model (e.g. IASP91). We introduced a slowness error term in travel time as a first-order calibration that successfully mitigates the source location discrepancies of different arrays. The calibrated BP results of three arrays are mutually consistent and reveal a unilateral rupture propagating eastward at a speed of 2.7 km/s along the down-dip edge of the locked Himalaya thrust zone over ~ 150 km, in agreement with a narrow slip distribution inferred from finite source inversions.

  20. Signal Processing for a Lunar Array: Minimizing Power Consumption

    Science.gov (United States)

    D'Addario, Larry; Simmons, Samuel

    2011-01-01

    Motivation for the study is: (1) Lunar Radio Array for low frequency, high redshift Dark Ages/Epoch of Reionization observations (z =6-50, f=30-200 MHz) (2) High precision cosmological measurements of 21 cm H I line fluctuations (3) Probe universe before first star formation and provide information about the Intergalactic Medium and evolution of large scale structures (5) Does the current cosmological model accurately describe the Universe before reionization? Lunar Radio Array is for (1) Radio interferometer based on the far side of the moon (1a) Necessary for precision measurements, (1b) Shielding from earth-based and solar RFI (12) No permanent ionosphere, (2) Minimum collecting area of approximately 1 square km and brightness sensitivity 10 mK (3)Several technologies must be developed before deployment The power needed to process signals from a large array of nonsteerable elements is not prohibitive, even for the Moon, and even in current technology. Two different concepts have been proposed: (1) Dark Ages Radio Interferometer (DALI) (2)( Lunar Array for Radio Cosmology (LARC)

  1. HLA class I sequence-based typing using DNA recovered from frozen plasma.

    Science.gov (United States)

    Cotton, Laura A; Abdur Rahman, Manal; Ng, Carmond; Le, Anh Q; Milloy, M-J; Mo, Theresa; Brumme, Zabrina L

    2012-08-31

    We describe a rapid, reliable and cost-effective method for intermediate-to-high-resolution sequence-based HLA class I typing using frozen plasma as a source of genomic DNA. The plasma samples investigated had a median age of 8.5 years. Total nucleic acids were isolated from matched frozen PBMC (~2.5 million) and plasma (500 μl) samples from a panel of 25 individuals using commercial silica-based kits. Extractions yielded median [IQR] nucleic acid concentrations of 85.7 [47.0-130.0]ng/μl and 2.2 [1.7-2.6]ng/μl from PBMC and plasma, respectively. Following extraction, ~1000 base pair regions spanning exons 2 and 3 of HLA-A, -B and -C were amplified independently via nested PCR using universal, locus-specific primers and sequenced directly. Chromatogram analysis was performed using commercial DNA sequence analysis software and allele interpretation was performed using a free web-based tool. HLA-A, -B and -C amplification rates were 100% and chromatograms were of uniformly high quality with clearly distinguishable mixed bases regardless of DNA source. Concordance between PBMC and plasma-derived HLA types was 100% at the allele and protein levels. At the nucleotide level, a single partially discordant base (resulting from a failure to call both peaks in a mixed base) was observed out of >46,975 bases sequenced (>99.9% concordance). This protocol has previously been used to perform HLA class I typing from a variety of genomic DNA sources including PBMC, whole blood, granulocyte pellets and serum, from specimens up to 30 years old. This method provides comparable specificity to conventional sequence-based approaches and could be applied in situations where cell samples are unavailable or DNA quantities are limiting. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. AUDIOME: a tiered exome sequencing-based comprehensive gene panel for the diagnosis of heterogeneous nonsyndromic sensorineural hearing loss.

    Science.gov (United States)

    Guan, Qiaoning; Balciuniene, Jorune; Cao, Kajia; Fan, Zhiqian; Biswas, Sawona; Wilkens, Alisha; Gallo, Daniel J; Bedoukian, Emma; Tarpinian, Jennifer; Jayaraman, Pushkala; Sarmady, Mahdi; Dulik, Matthew; Santani, Avni; Spinner, Nancy; Abou Tayoun, Ahmad N; Krantz, Ian D; Conlin, Laura K; Luo, Minjie

    2018-03-29

    PurposeHereditary hearing loss is highly heterogeneous. To keep up with rapidly emerging disease-causing genes, we developed the AUDIOME test for nonsyndromic hearing loss (NSHL) using an exome sequencing (ES) platform and targeted analysis for the curated genes.MethodsA tiered strategy was implemented for this test. Tier 1 includes combined Sanger and targeted deletion analyses of the two most common NSHL genes and two mitochondrial genes. Nondiagnostic tier 1 cases are subjected to ES and array followed by targeted analysis of the remaining AUDIOME genes.ResultsES resulted in good coverage of the selected genes with 98.24% of targeted bases at >15 ×. A fill-in strategy was developed for the poorly covered regions, which generally fell within GC-rich or highly homologous regions. Prospective testing of 33 patients with NSHL revealed a diagnosis in 11 (33%) and a possible diagnosis in 8 cases (24.2%). Among those, 10 individuals had variants in tier 1 genes. The ES data in the remaining nondiagnostic cases are readily available for further analysis.ConclusionThe tiered and ES-based test provides an efficient and cost-effective diagnostic strategy for NSHL, with the potential to reflex to full exome to identify causal changes outside of the AUDIOME test.Genetics in Medicine advance online publication, 29 March 2018; doi:10.1038/gim.2018.48.

  3. A Complementary Resistive Switch-based Crossbar Array Adder

    OpenAIRE

    Siemon, A.; Menzel, S.; Waser, R.; Linn, E.

    2014-01-01

    Redox-based resistive switching devices (ReRAM) are an emerging class of non-volatile storage elements suited for nanoscale memory applications. In terms of logic operations, ReRAM devices were suggested to be used as programmable interconnects, large-scale look-up tables or for sequential logic operations. However, without additional selector devices these approaches are not suited for use in large scale nanocrossbar memory arrays, which is the preferred architecture for ReRAM devices due to...

  4. Functionalization and Self-Assembly of DNA Bidimensional Arrays

    Directory of Open Access Journals (Sweden)

    Ramon Eritja

    2011-09-01

    Full Text Available Oligonucleotides carrying amino, thiol groups, as well as fluorescein, c-myc peptide sequence and nanogold at internal positions were prepared and used for the assembly of bidimensional DNA arrays.

  5. Mapping Base Modifications in DNA by Transverse-Current Sequencing

    Science.gov (United States)

    Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

    2018-02-01

    Sequencing DNA modifications and lesions, such as methylation of cytosine and oxidation of guanine, is even more important and challenging than sequencing the genome itself. The traditional methods for detecting DNA modifications are either insensitive to these modifications or require additional processing steps to identify a particular type of modification. Transverse-current sequencing in nanopores can potentially identify the canonical bases and base modifications in the same run. In this work, we demonstrate that the most common DNA epigenetic modifications and lesions can be detected with any predefined accuracy based on their tunneling current signature. Our results are based on simulations of the nanopore tunneling current through DNA molecules, calculated using nonequilibrium electron-transport methodology within an effective multiorbital model derived from first-principles calculations, followed by a base-calling algorithm accounting for neighbor current-current correlations. This methodology can be integrated with existing experimental techniques to improve base-calling fidelity.

  6. T1 Gd-enhanced compared with CISS sequences in retinoblastoma: superiority of T1 sequences in evaluation of tumour extension

    Energy Technology Data Exchange (ETDEWEB)

    Gizewski, Elke R.; Wanke, Isabel; Guengoer, Ali-Riza; Forsting, Michael [University Hospital, Department of Diagnostic and Interventional Neuroradiology, Essen (Germany); Jurklies, Christine [University Hospital Essen, Department of Ophthalmology (Germany)

    2005-01-01

    Background As adequate therapy for retinoblastoma in young children depends on infiltration of extra-retinal structures, diagnostic modalities play an essential role. Methods: In this widely extended study, 80 children with retinoblastoma were studied with MRI (standard fat-suppressed Gd-enhanced T1, T2 thin-slice sequences (additionally with small loop surface coil), constructive interference in steady state (CISS) sequence covering the orbita). The images were analysed by two blinded neuroradiologists. Histology was used as the gold standard. MRI assumed infiltration of extra-retinal structures in 13 of 80 patients of which ten were confirmed by histology. Affected extra-retinal structures were: optic nerve (five, of which two were on CISS and three on T1 with higher image resolution using the surface coil), scleral infiltration (five, of which four on CISS and T1) and ciliary body infiltration (one on CISS and T1). Another 61 enucleated patients did not have any extra-retinal infiltration in histology. The CISS sequence with multiplanar reconstruction was mainly helpful in revealing exact three-dimensional tumour extension with excellent clinical acceptance and pre-surgical planning but T1 fat-suppressed Gd-enhanced images were superior in revealing exact tumour extension. CISS sequences allow to produce excellent anatomical images and to perform multiplanar reconstruction to better demonstrate tumour extension. However, T1-weighted sequences after contrast application are more sensitive (60 versus 40%) in detecting infiltration of the optic nerve but equal in detecting scleral infiltration. (orig.)

  7. Pharmacological rescue of Ras signaling, GluA1-dependent synaptic plasticity, and learning deficits in a fragile X model.

    Science.gov (United States)

    Lim, Chae-Seok; Hoang, Elizabeth T; Viar, Kenneth E; Stornetta, Ruth L; Scott, Michael M; Zhu, J Julius

    2014-02-01

    Fragile X syndrome, caused by the loss of Fmr1 gene function, is the most common form of inherited mental retardation, with no effective treatment. Using a tractable animal model, we investigated mechanisms of action of a few FDA-approved psychoactive drugs that modestly benefit the cognitive performance in fragile X patients. Here we report that compounds activating serotonin (5HT) subtype 2B receptors (5HT2B-Rs) or dopamine (DA) subtype 1-like receptors (D1-Rs) and/or those inhibiting 5HT2A-Rs or D2-Rs moderately enhance Ras-PI3K/PKB signaling input, GluA1-dependent synaptic plasticity, and learning in Fmr1 knockout mice. Unexpectedly, combinations of these 5HT and DA compounds at low doses synergistically stimulate Ras-PI3K/PKB signal transduction and GluA1-dependent synaptic plasticity and remarkably restore normal learning in Fmr1 knockout mice without causing anxiety-related side effects. These findings suggest that properly dosed and combined FDA-approved psychoactive drugs may effectively treat the cognitive impairment associated with fragile X syndrome.

  8. 16 channel 200 GHz arrayed waveguide grating based on Si nanowire waveguides

    International Nuclear Information System (INIS)

    Zhao Lei; An Junming; Zhang Jiashun; Song Shijiao; Wu Yuanda; Hu Xiongwei

    2011-01-01

    A 16 channel arrayed waveguide grating demultiplexer with 200 GHz channel spacing based on Si nanowire waveguides is designed. The transmission spectra response simulated by transmission function method shows that the device has channel spacing of 1.6 nm and crosstalk of 31 dB. The device is fabricated by 193 nm deep UV lithography in silicon-on-substrate. The demultiplexing characteristics are observed with crosstalk of 5-8 dB, central channel's insertion loss of 2.2 dB, free spectral range of 24.7 nm and average channel spacing of 1.475 nm. The cause of the spectral distortion is analyzed specifically. (semiconductor devices)

  9. A dual-band planar array of connected dipoles: Experimental validation based on bistatic RCS measurements

    NARCIS (Netherlands)

    Cavallo, D.; Neto, A.; Gerini, G.; Morello, D.

    2010-01-01

    Rigorous equivalent networks representing connected arrays in transmission and reception are derived in this paper. These equivalent networks are not based on reciprocity but on Green's functions. Thus, all components have well identified and physically meaningful roles. A dual-band connected array

  10. Environmental Assessment for the Solar Photovoltaic Array at Eglin Air Force Base, Florida

    Science.gov (United States)

    2014-01-24

    fire hazard to solar panel array. ● Where applicable, reduce erosion using rough grade slopes or terrace slopes. ● Identify areas of existing...method would entail the installation of numerous smaller solar PV systems on the roofs of various buildings on the base. This alternative was...panel array.  Where applicable, reduce erosion using rough grade slopes or terrace slopes.  Identify areas of existing vegetation that the proponent

  11. APE1 incision activity at abasic sites in tandem repeat sequences.

    Science.gov (United States)

    Li, Mengxia; Völker, Jens; Breslauer, Kenneth J; Wilson, David M

    2014-05-29

    Repetitive DNA sequences, such as those present in microsatellites and minisatellites, telomeres, and trinucleotide repeats (linked to fragile X syndrome, Huntington disease, etc.), account for nearly 30% of the human genome. These domains exhibit enhanced susceptibility to oxidative attack to yield base modifications, strand breaks, and abasic sites; have a propensity to adopt non-canonical DNA forms modulated by the positions of the lesions; and, when not properly processed, can contribute to genome instability that underlies aging and disease development. Knowledge on the repair efficiencies of DNA damage within such repetitive sequences is therefore crucial for understanding the impact of such domains on genomic integrity. In the present study, using strategically designed oligonucleotide substrates, we determined the ability of human apurinic/apyrimidinic endonuclease 1 (APE1) to cleave at apurinic/apyrimidinic (AP) sites in a collection of tandem DNA repeat landscapes involving telomeric and CAG/CTG repeat sequences. Our studies reveal the differential influence of domain sequence, conformation, and AP site location/relative positioning on the efficiency of APE1 binding and strand incision. Intriguingly, our data demonstrate that APE1 endonuclease efficiency correlates with the thermodynamic stability of the DNA substrate. We discuss how these results have both predictive and mechanistic consequences for understanding the success and failure of repair protein activity associated with such oxidatively sensitive, conformationally plastic/dynamic repetitive DNA domains. Published by Elsevier Ltd.

  12. Enhanced immunization via dissolving microneedle array-based delivery system incorporating subunit vaccine and saponin adjuvant.

    Science.gov (United States)

    Zhao, Ji-Hui; Zhang, Qi-Bo; Liu, Bao; Piao, Xiang-Hua; Yan, Yu-Lu; Hu, Xiao-Ge; Zhou, Kuan; Zhang, Yong-Tai; Feng, Nian-Ping

    2017-01-01

    To enhance the immunogenicity of the model subunit vaccine, ovalbumin (OVA) was combined with platycodin (PD), a saponin adjuvant. To reduce the toxicity of PD, OVA, and adjuvant were loaded together into liposomes before being incorporated into a dissolving microneedle array. OVA- and PD-loaded liposomes (OVA-PD-Lipos) were prepared using the film dispersion method. Their uptake behavior, toxicity to mouse bone marrow dendritic cells (BMDCs), and hemolytic activity to rabbit red blood cells (RBCs) were evaluated. The OVA-PD-Lipos were incorporated into a dissolving microneedle array. The chemical stability of OVA and the physical stability of OVA-PD-Lipos in microneedle arrays were investigated. The immune response of Institute of Cancer Research mice and potential skin irritation reaction of rabbits to OVA-PD-Lipos-MNs were evaluated. The uptake of OVA by mouse BMDCs was greatly enhanced when OVA was prepared as OVA-PD-Lipos, and in this form, the toxicity of PD was dramatically reduced. OVA was chemically stable as OVA-PD-Lipos, when OVA-PD-Lipos was incorporated into a dissolving microneedle array. Institute of Cancer Research mice treated with OVA-PD-Lipos-MNs showed a significantly enhanced immune response. PD combined with OVA elicited a balanced Th1 and Th2 humoral immune response in mice, with minimal irritation in rabbit skin. The dissolving microneedle array-based system is a promising delivery vehicle for subunit vaccine and its adjuvant.

  13. Rational Design of QCM-D Virtual Sensor Arrays Based on Film Thickness, Viscoelasticity, and Harmonics for Vapor Discrimination.

    Science.gov (United States)

    Speller, Nicholas C; Siraj, Noureen; Regmi, Bishnu P; Marzoughi, Hassan; Neal, Courtney; Warner, Isiah M

    2015-01-01

    Herein, we demonstrate an alternative strategy for creating QCM-based sensor arrays by use of a single sensor to provide multiple responses per analyte. The sensor, which simulates a virtual sensor array (VSA), was developed by depositing a thin film of ionic liquid, either 1-octyl-3-methylimidazolium bromide ([OMIm][Br]) or 1-octyl-3-methylimidazolium thiocyanate ([OMIm][SCN]), onto the surface of a QCM-D transducer. The sensor was exposed to 18 different organic vapors (alcohols, hydrocarbons, chlorohydrocarbons, nitriles) belonging to the same or different homologous series. The resulting frequency shifts (Δf) were measured at multiple harmonics and evaluated using principal component analysis (PCA) and discriminant analysis (DA) which revealed that analytes can be classified with extremely high accuracy. In almost all cases, the accuracy for identification of a member of the same class, that is, intraclass discrimination, was 100% as determined by use of quadratic discriminant analysis (QDA). Impressively, some VSAs allowed classification of all 18 analytes tested with nearly 100% accuracy. Such results underscore the importance of utilizing lesser exploited properties that influence signal transduction. Overall, these results demonstrate excellent potential of the virtual sensor array strategy for detection and discrimination of vapor phase analytes utilizing the QCM. To the best of our knowledge, this is the first report on QCM VSAs, as well as an experimental sensor array, that is based primarily on viscoelasticity, film thickness, and harmonics.

  14. Single nucleotide polymorphism array lesions, TET2, DNMT3A, ASXL1 and CBL mutations are present in systemic mastocytosis.

    Directory of Open Access Journals (Sweden)

    Fabiola Traina

    Full Text Available We hypothesized that analysis of single nucleotide polymorphism arrays (SNP-A and new molecular defects may provide new insight in the pathogenesis of systemic mastocytosis (SM. SNP-A karyotyping was applied to identify recurrent areas of loss of heterozygosity and bidirectional sequencing was performed to evaluate the mutational status of TET2, DNMT3A, ASXL1, EZH2, IDH1/IDH2 and the CBL gene family. Overall survival (OS was analyzed using the Kaplan-Meier method. We studied a total of 26 patients with SM. In 67% of SM patients, SNP-A karyotyping showed new chromosomal abnormalities including uniparental disomy of 4q and 2p spanning TET2/KIT and DNMT3A. Mutations in TET2, DNMT3A, ASXL1 and CBL were found in 23%, 12%, 12%, and 4% of SM patients, respectively. No mutations were observed in EZH2 and IDH1/IDH2. Significant differences in OS were observed for SM mutated patients grouped based on the presence of combined TET2/DNMT3A/ASXL1 mutations independent of KIT (P = 0.04 and sole TET2 mutations (P<0.001. In conclusion, TET2, DNMT3A and ASXL1 mutations are also present in mastocytosis and these mutations may affect prognosis, as demonstrated by worse OS in mutated patients.

  15. Fabrication and characterization of nano-gas sensor arrays

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  16. Fabrication and characterization of nano-gas sensor arrays

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-30

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

  17. Heads or tails: L1 insertion-associated 5' homopolymeric sequences

    Directory of Open Access Journals (Sweden)

    Meyer Thomas J

    2010-02-01

    Full Text Available Abstract Background L1s are one of the most successful autonomous mobile elements in primate genomes. These elements comprise as much as 17% of primate genomes with the majority of insertions occurring via target primed reverse transcription (TPRT. Twin priming, a variant of TPRT, can result in unusual DNA sequence architecture. These insertions appear to be inverted, truncated L1s flanked by target site duplications. Results We report on loci with sequence architecture consistent with variants of the twin priming mechanism and introduce dual priming, a mechanism that could generate similar sequence characteristics. These insertions take the form of truncated L1s with hallmarks of classical TPRT insertions but having a poly(T simple repeat at the 5' end of the insertion. We identified loci using computational analyses of the human, chimpanzee, orangutan, rhesus macaque and marmoset genomes. Insertion site characteristics for all putative loci were experimentally verified. Conclusions The 39 loci that passed our computational and experimental screens probably represent inversion-deletion events which resulted in a 5' inverted poly(A tail. Based on our observations of these loci and their local sequence properties, we conclude that they most probably represent twin priming events with unusually short non-inverted portions. We postulate that dual priming could, theoretically, produce the same patterns. The resulting homopolymeric stretches associated with these insertion events may promote genomic instability and create potential target sites for future retrotransposition events.

  18. A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology.

    Science.gov (United States)

    Ustek, Duran; Sirma, Sema; Gumus, Ergun; Arikan, Muzaffer; Cakiris, Aris; Abaci, Neslihan; Mathew, Jaicy; Emrence, Zeliha; Azakli, Hulya; Cosan, Fulya; Cakar, Atilla; Parlak, Mahmut; Kursun, Olcay

    2012-10-01

    One application of next-generation sequencing (NGS) is the targeted resequencing of interested genes which has not been used in viral integration site analysis of gene therapy applications. Here, we combined targeted sequence capture array and next generation sequencing to address the whole genome profiling of viral integration sites. Human 293T and K562 cells were transduced with a HIV-1 derived vector. A custom made DNA probe sets targeted pLVTHM vector used to capture lentiviral vector/human genome junctions. The captured DNA was sequenced using GS FLX platform. Seven thousand four hundred and eighty four human genome sequences flanking the long terminal repeats (LTR) of pLVTHM fragment sequences matched with an identity of at least 98% and minimum 50 bp criteria in both cells. In total, 203 unique integration sites were identified. The integrations in both cell lines were totally distant from the CpG islands and from the transcription start sites and preferentially located in introns. A comparison between the two cell lines showed that the lentiviral-transduced DNA does not have the same preferred regions in the two different cell lines. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. 32 x 16 CMOS smart pixel array for optical interconnects

    Science.gov (United States)

    Kim, Jongwoo; Guilfoyle, Peter S.; Stone, Richard V.; Hessenbruch, John M.; Choquette, Kent D.; Kiamilev, Fouad E.

    2000-05-01

    Free space optical interconnects can increase throughput capacities and eliminate much of the energy consumption required for `all electronic' systems. High speed optical interconnects can be achieved by integrating optoelectronic devices with conventional electronics. Smart pixel arrays have been developed which use optical interconnects. An individual smart pixel cell is composed of a vertical cavity surface emitting laser (VCSEL), a photodetector, an optical receiver, a laser driver, and digital logic circuitry. Oxide-confined VCSELs are being developed to operate at 850 nm with a threshold current of approximately 1 mA. Multiple quantum well photodetectors are being fabricated from AlGaAs for use with the 850 nm VCSELs. The VCSELs and photodetectors are being integrated with complementary metal oxide semiconductor (CMOS) circuitry using flip-chip bonding. CMOS circuitry is being integrated with a 32 X 16 smart pixel array. The 512 smart pixels are serially linked. Thus, an entire data stream may be clocked through the chip and output electrically by the last pixel. Electrical testing is being performed on the CMOS smart pixel array. Using an on-chip pseudo random number generator, a digital data sequence was cycled through the chip verifying operation of the digital circuitry. Although, the prototype chip was fabricated in 1.2 micrometers technology, simulations have demonstrated that the array can operate at 1 Gb/s per pixel using 0.5 micrometers technology.

  20. Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

    Directory of Open Access Journals (Sweden)

    Gillings Michael R

    2006-01-01

    Full Text Available Abstract Background Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be. Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains. Results The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes. It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons. Conclusion Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene

  1. Analysis of measurements on wind turbine arrays. Vol. 1

    International Nuclear Information System (INIS)

    Hoeg, E.

    1990-12-01

    In 1989 a Danish electric power company initiated an analysis of eight wind turbine arrays. Data from this project is presented together with the explained results of the analyses and the output variations for individual arrays and for systems within the arrays. The models for prognosis are compared and evaluated in order to find that which is most effective. (AB)

  2. A drone detection with aircraft classification based on a camera array

    Science.gov (United States)

    Liu, Hao; Qu, Fangchao; Liu, Yingjian; Zhao, Wei; Chen, Yitong

    2018-03-01

    In recent years, because of the rapid popularity of drones, many people have begun to operate drones, bringing a range of security issues to sensitive areas such as airports and military locus. It is one of the important ways to solve these problems by realizing fine-grained classification and providing the fast and accurate detection of different models of drone. The main challenges of fine-grained classification are that: (1) there are various types of drones, and the models are more complex and diverse. (2) the recognition test is fast and accurate, in addition, the existing methods are not efficient. In this paper, we propose a fine-grained drone detection system based on the high resolution camera array. The system can quickly and accurately recognize the detection of fine grained drone based on hd camera.

  3. HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes

    Energy Technology Data Exchange (ETDEWEB)

    Tu, Q.; Deng, Ye; Lin, Lu; Hemme, Chris L.; He, Zhili; Zhou, Jizhong

    2010-05-17

    Microbiomes play very important roles in terms of nutrition, health and disease by interacting with their hosts. Based on sequence data currently available in public domains, we have developed a functional gene array to monitor both organismal and functional gene profiles of normal microbiota in human and mouse hosts, and such an array is called human and mouse microbiota array, HMM-Chip. First, seed sequences were identified from KEGG databases, and used to construct a seed database (seedDB) containing 136 gene families in 19 metabolic pathways closely related to human and mouse microbiomes. Second, a mother database (motherDB) was constructed with 81 genomes of bacterial strains with 54 from gut and 27 from oral environments, and 16 metagenomes, and used for selection of genes and probe design. Gene prediction was performed by Glimmer3 for bacterial genomes, and by the Metagene program for metagenomes. In total, 228,240 and 801,599 genes were identified for bacterial genomes and metagenomes, respectively. Then the motherDB was searched against the seedDB using the HMMer program, and gene sequences in the motherDB that were highly homologous with seed sequences in the seedDB were used for probe design by the CommOligo software. Different degrees of specific probes, including gene-specific, inclusive and exclusive group-specific probes were selected. All candidate probes were checked against the motherDB and NCBI databases for specificity. Finally, 7,763 probes covering 91.2percent (12,601 out of 13,814) HMMer confirmed sequences from 75 bacterial genomes and 16 metagenomes were selected. This developed HMM-Chip is able to detect the diversity and abundance of functional genes, the gene expression of microbial communities, and potentially, the interactions of microorganisms and their hosts.

  4. Fragile X-associated primary ovarian insufficiency: evidence for additional genetic contributions to severity.

    Science.gov (United States)

    Hunter, Jessica Ezzell; Epstein, Michael P; Tinker, Stuart W; Charen, Krista H; Sherman, Stephanie L

    2008-09-01

    The fragile X mental retardation gene (FMR1) contains a CGG repeat sequence in its 5' untranslated region that can become unstable and expand in length from generation to generation. Alleles with expanded repeats in the range of approximately 55-199, termed premutation alleles, are associated with an increased risk for fragile-X-associated primary ovarian insufficiency (FXPOI). However, not all women who carry the premutation develop FXPOI. To determine if additional genes could explain variability in onset and severity, we used a random-effects Cox proportional hazards model to analyze age at menopause on 680 women from 225 families who have a history of fragile X syndrome and 321 women from 219 families from the general population. We tested for the presence of a residual additive genetic effect after adjustment for FMR1 repeat length, race, smoking, body mass index, and method of ascertainment. Results showed significant familial aggregation of age at menopause with an estimated additive genetic variance of 0.55-0.96 depending on the parameterization of FMR1 repeat size and definition of age at menopause (P-values ranging between 0.0002 and 0.0027). This is the first study to analyze familial aggregation of FXPOI. This result is important for proper counseling of women who carry FMR1 premutation alleles and for guidance of future studies to identify additional genes that influence ovarian insufficiency. (c) 2008 Wiley-Liss, Inc.

  5. A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon

    Energy Technology Data Exchange (ETDEWEB)

    Mockler, Todd [Oregon State Univ., Corvallis, OR (United States)

    2017-04-17

    Brachypodium distachyon is the premier experimental model grass platform and is related to candidate feedstock crops for bioethanol production. Based on the DOE-JGI Brachypodium Bd21 genome sequence and annotation we designed a whole genome DNA microarray platform. The quality of this array platform is unprecedented due to the exceptional quality of the Brachypodium genome assembly and annotation and the stringent probe selection criteria employed in the design. We worked with members of the international community and the bioinformatics/design team at Affymetrix at all stages in the development of the array. We used the Brachypodium arrays to interrogate the transcriptomes of plants grown in a variety of environmental conditions including diurnal and circadian light/temperature conditions and under a variety of environmental conditions. We examined the transciptional responses of Brachypodium seedlings subjected to various abiotic stresses including heat, cold, salt, and high intensity light. We generated a gene expression atlas representing various organs and developmental stages. The results of these efforts including all microarray datasets are published and available at online public databases.

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

    Directory of Open Access Journals (Sweden)

    Krogh Anders

    2006-05-01

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

  7. Ontology-based, Tissue MicroArray oriented, image centered tissue bank

    Directory of Open Access Journals (Sweden)

    Viti Federica

    2008-04-01

    Full Text Available Abstract Background Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly managed, if possible with an infrastructure able to support tissue sharing between institutes. Moreover, the available frameworks oriented to Tissue MicroArray provide good storage for clinical patient, sample treatment and block construction information, but their utility is limited by the lack of data integration with biomolecular information. Results In this work we propose a Tissue MicroArray web oriented system to support researchers in managing bio-samples and, through the use of ontologies, enables tissue sharing aimed at the design of Tissue MicroArray experiments and results evaluation. Indeed, our system provides ontological description both for pre-analysis tissue images and for post-process analysis image results, which is crucial for information exchange. Moreover, working on well-defined terms it is then possible to query web resources for literature articles to integrate both pathology and bioinformatics data. Conclusions Using this system, users associate an ontology-based description to each image uploaded into the database and also integrate results with the ontological description of biosequences identified in every tissue. Moreover, it is possible to integrate the ontological description provided by the user with a full compliant gene ontology definition, enabling statistical studies about correlation between the analyzed pathology and the most commonly related biological processes.

  8. Single-base resolution and long-coverage sequencing based on single-molecule nanomanipulation

    International Nuclear Information System (INIS)

    An Hongjie; Huang Jiehuan; Lue Ming; Li Xueling; Lue Junhong; Li Haikuo; Zhang Yi; Li Minqian; Hu Jun

    2007-01-01

    We show new approaches towards a novel single-molecule sequencing strategy which consists of high-resolution positioning isolation of overlapping DNA fragments with atomic force microscopy (AFM), subsequent single-molecule PCR amplification and conventional Sanger sequencing. In this study, a DNA labelling technique was used to guarantee the accuracy in positioning the target DNA. Single-molecule multiplex PCR was carried out to test the contamination. The results showed that the two overlapping DNA fragments isolated by AFM could be successfully sequenced with high quality and perfect contiguity, indicating that single-base resolution and long-coverage sequencing have been achieved simultaneously

  9. In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing

    Science.gov (United States)

    Stuhlmüller, M.; Schwarz-Finsterle, J.; Fey, E.; Lux, J.; Bach, M.; Cremer, C.; Hinderhofer, K.; Hausmann, M.; Hildenbrand, G.

    2015-10-01

    Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.

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

    NARCIS (Netherlands)

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

    2012-01-01

    Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for

  11. Studies of base pair sequence effects on DNA solvation based on all

    Indian Academy of Sciences (India)

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization ...

  12. Recent advances in nanopore-based nucleic acid analysis and sequencing

    International Nuclear Information System (INIS)

    Shi, Jidong; Fang, Ying; Hou, Junfeng

    2016-01-01

    Nanopore-based sequencing platforms are transforming the field of genomic science. This review (containing 116 references) highlights some recent progress on nanopore-based nucleic acid analysis and sequencing. These studies are classified into three categories, biological, solid-state, and hybrid nanopores, according to their nanoporous materials. We begin with a brief description of the translocation-based detection mechanism of nanopores. Next, specific examples are given in nanopore-based nucleic acid analysis and sequencing, with an emphasis on identifying strategies that can improve the resolution of nanopores. This review concludes with a discussion of future research directions that will advance the practical applications of nanopore technology. (author)

  13. A Window Into Clinical Next-Generation Sequencing-Based Oncology Testing Practices.

    Science.gov (United States)

    Nagarajan, Rakesh; Bartley, Angela N; Bridge, Julia A; Jennings, Lawrence J; Kamel-Reid, Suzanne; Kim, Annette; Lazar, Alexander J; Lindeman, Neal I; Moncur, Joel; Rai, Alex J; Routbort, Mark J; Vasalos, Patricia; Merker, Jason D

    2017-12-01

    - Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. - To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. - College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. - These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. - This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

  14. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  15. Low-frequency synthesis array in earth orbit

    International Nuclear Information System (INIS)

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

    1987-01-01

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

  16. A Type-2 Block-Component-Decomposition Based 2D AOA Estimation Algorithm for an Electromagnetic Vector Sensor Array

    Directory of Open Access Journals (Sweden)

    Yu-Fei Gao

    2017-04-01

    Full Text Available This paper investigates a two-dimensional angle of arrival (2D AOA estimation algorithm for the electromagnetic vector sensor (EMVS array based on Type-2 block component decomposition (BCD tensor modeling. Such a tensor decomposition method can take full advantage of the multidimensional structural information of electromagnetic signals to accomplish blind estimation for array parameters with higher resolution. However, existing tensor decomposition methods encounter many restrictions in applications of the EMVS array, such as the strict requirement for uniqueness conditions of decomposition, the inability to handle partially-polarized signals, etc. To solve these problems, this paper investigates tensor modeling for partially-polarized signals of an L-shaped EMVS array. The 2D AOA estimation algorithm based on rank- ( L 1 , L 2 , · BCD is developed, and the uniqueness condition of decomposition is analyzed. By means of the estimated steering matrix, the proposed algorithm can automatically achieve angle pair-matching. Numerical experiments demonstrate that the present algorithm has the advantages of both accuracy and robustness of parameter estimation. Even under the conditions of lower SNR, small angular separation and limited snapshots, the proposed algorithm still possesses better performance than subspace methods and the canonical polyadic decomposition (CPD method.

  17. Discussion paper for a highly parallel array processor-based machine

    International Nuclear Information System (INIS)

    Hagstrom, R.; Bolotin, G.; Dawson, J.

    1984-01-01

    The architectural plant for a quickly realizable implementation of a highly parallel special-purpose computer system with peak performance in the range of 6 billion floating point operations per second is discussed. The architecture is suitable to Lattice Gauge theoretical computations of fundamental physics interest and may be applicable to a range of other problems which deal with numerically intensive computational problems. The plan is quickly realizable because it employs a maximum of commercially available hardware subsystems and because the architecture is software-transparent to the individual processors, allowing straightforward re-use of whatever commercially available operating-systems and support software that is suitable to run on the commercially-produced processors. A tiny prototype instrument, designed along this architecture has already operated. A few elementary examples of programs which can run efficiently are presented. The large machine which the authors would propose to build would be based upon a highly competent array-processor, the ST-100 Array Processor, and specific design possibilities are discussed. The first step toward realizing this plan practically is to install a single ST-100 to allow algorithm development to proceed while a demonstration unit is built using two of the ST-100 Array Processors

  18. Characterization of electronic structures from CdS/Si nanoheterostructure array based on silicon nanoporous pillar array

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yong, E-mail: liyong@pdsu.edu.cn [Department of Physics and Solar Energy Research Center, Pingdingshan University, Pingdingshan 467000 (China); Song, Xiao Yan [Department of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou 450045 (China); Song, Yue Li; Ji, Peng Fei; Zhou, Feng Qun; Tian, Ming Li; Huang, Hong Chun [Department of Physics and Solar Energy Research Center, Pingdingshan University, Pingdingshan 467000 (China); Li, Xin Jian [Department of Physics and Laboratory of Material Physics, Zhengzhou University, Zhengzhou 450052 (China)

    2016-02-15

    Highlights: • CdS/Si nanoheterostructure array has been fabricated through a CBD method. • The electronic properties have been investigated by the I–V and C–V techniques. • The onset voltages, characteristic frequency and built-in potential are investigated. • The electronic structures can be tuned through the annealing treatments. - Abstract: The electronic properties of heterostructures are very important to its applications in the field of optoelectronic devices. Understanding and control of electronic properties are very necessary. CdS/Si nanoheterostructure array have been fabricated through growing CdS nanocrystals on the silicon nanoporous pillar array using a chemical bath deposition method. The electronic properties of CdS nanoheterostructure array have been investigated by the current–voltage, complex impedance spectroscopy and capacitance–voltage techniques. The onset voltages, characteristic frequency and built-in potential are gradually increased with increasing the annealing temperature. It is indicated that the electronic structures of CdS/Si nanoheterostructure array can be tuned through the annealing treatments.

  19. Characterization of electronic structures from CdS/Si nanoheterostructure array based on silicon nanoporous pillar array

    International Nuclear Information System (INIS)

    Li, Yong; Song, Xiao Yan; Song, Yue Li; Ji, Peng Fei; Zhou, Feng Qun; Tian, Ming Li; Huang, Hong Chun; Li, Xin Jian

    2016-01-01

    Highlights: • CdS/Si nanoheterostructure array has been fabricated through a CBD method. • The electronic properties have been investigated by the I–V and C–V techniques. • The onset voltages, characteristic frequency and built-in potential are investigated. • The electronic structures can be tuned through the annealing treatments. - Abstract: The electronic properties of heterostructures are very important to its applications in the field of optoelectronic devices. Understanding and control of electronic properties are very necessary. CdS/Si nanoheterostructure array have been fabricated through growing CdS nanocrystals on the silicon nanoporous pillar array using a chemical bath deposition method. The electronic properties of CdS nanoheterostructure array have been investigated by the current–voltage, complex impedance spectroscopy and capacitance–voltage techniques. The onset voltages, characteristic frequency and built-in potential are gradually increased with increasing the annealing temperature. It is indicated that the electronic structures of CdS/Si nanoheterostructure array can be tuned through the annealing treatments.

  20. High Dynamic Range adaptive ΔΣ-based Focal Plane Array architecture

    KAUST Repository

    Yao, Shun; Kavusi, Sam; Salama, Khaled N.

    2012-01-01

    In this paper, an Adaptive Delta-Sigma based architecture for High Dynamic Range (HDR) Focal Plane Arrays is presented. The noise shaping effect of the Delta-Sigma modulation in the low end, and the distortion noise induced in the high end of Photo