| 1. |
- Anney, Richard, et al.
(author)
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A genome-wide scan for common alleles affecting risk for autism.
- 2010
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 19:20, s. 4072-4082
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Journal article (peer-reviewed)abstract
- Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
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| 2. |
- Anney, Richard, et al.
(author)
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Individual common variants exert weak effects on the risk for autism spectrum disorders.
- 2012
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:21, s. 4781-92
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Journal article (peer-reviewed)abstract
- While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASD), the contribution of common variation to ASD risk is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating association of individual SNPs, we also sought evidence that common variants, en masse, might affect risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest p-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. By contrast, allele-scores derived from the transmission of common alleles to Stage 1 cases significantly predict case-status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele-score results, it is reasonable to conclude that common variants affect ASD risk but their individual effects are modest.
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| 3. |
- Casey, Jillian P, et al.
(author)
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A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder.
- 2012
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In: Human Genetics. - : Springer Science and Business Media LLC. - 0340-6717 .- 1432-1203. ; 131:4, s. 565-579
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Journal article (peer-reviewed)abstract
- Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.
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| 4. |
- Garcia-Ruiz, Andres, et al.
(author)
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Hermetic Carbon Coatings for Electro-Thermal All-Fiber Phase Modulators
- 2019
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In: Journal of Lightwave Technology. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 0733-8724 .- 1558-2213. ; 37:18, s. 4567-4572
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Journal article (peer-reviewed)abstract
- Joule effect and thermal response of several carbon-coated fibers are modeled and analyzed. An electro-thermally driven all-fiber phase modulator based on these principles is proposed and a proof of concept of it is characterized. This kind of fiber could be the basis for developing all-fiber components aimed to operate in environments where the strength increase and impermeability to hydrogen diffusion guaranteed by the carbon coating is crucial.
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| 5. |
- Householder, John Ethan, et al.
(author)
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One sixth of Amazonian tree diversity is dependent on river floodplains
- 2024
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In: NATURE ECOLOGY & EVOLUTION. - 2397-334X. ; 8, s. 901-911
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Journal article (peer-reviewed)abstract
- Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.
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| 6. |
- Luize, Bruno Garcia, et al.
(author)
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Geography and ecology shape the phylogenetic composition of Amazonian tree communities
- 2024
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In: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699. ; 51:7, s. 1163-1184
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Journal article (peer-reviewed)abstract
- Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and v & aacute;rzea forest types, the phylogenetic composition varies by geographic region, but the igap & oacute; and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R-2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R-2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.
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| 7. |
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| 8. |
- Magalhães, Regina, et al.
(author)
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Distributed detection of quadratic Kerr effect in silica fibers using chirped-pulse φoTDR
- 2019
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In: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 9781510631236 - 9781510631243
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Conference paper (peer-reviewed)abstract
- Monitoring the presence of external electric fields over large distances and detecting losses along power transmission networks, is of extreme importance nowadays due to concerns with environment, efficiency, cost and safety. In this work, we evaluate a method to achieve distributed measurements of the quadratic electro-optic Kerr effect in silica fibers in a distributed way. For this purpose, we integrate a twin-hole fiber filled with BiSn alloy electrodes and monitor its electric-field induced refractive index (RI) change Δn by using a chirped-pulse phase-sensitive OTDR (CP-ΦOTDR). By exploiting its high sensitivity (RI changes of the order of 10-9), we demonstrate that the proposed system is able to detect the intrinsic quadratic electrooptic nonlinearity (the electric Kerr effect) in the fiber, an effect that is usually considered to be too weak to be exploited for practical applications. Additionally, we show that the CP-ΦOTDR is sufficiently sensitive to measure the electric Kerr effect with untreated standard telecommunication fibers under realistic fields.
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| 9. |
- Magalhaes, Regina, et al.
(author)
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Fiber-based distributed bolometry
- 2019
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In: Optics Express. - : Optical Society of America. - 1094-4087. ; 27:4, s. 4317-4328
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Journal article (peer-reviewed)abstract
- Optical fibers are inherently designed to allow no interaction between the guided light and the surrounding optical radiation. Thus, very few optical fiber-based technologies exist in the field of optical radiation sensing. Accomplishing fully-distributed optical radiation sensing appears then as even more challenging since, on top of the lack of sensitivity explained above, we should add the need of addressing thousands of measurement points in a single, continuous optical cable. Nevertheless, it is clear that there exist a number of applications which could benefit from such a distributed sensing scheme, particularly if the sensitivity was sufficiently high to be able to measure correctly variations in optical radiation levels compatible with the earth surface. Distributed optical radiation sensing over large distances could be employed in applications such as Dynamic Line Rating (DLR), where it is known that solar radiation can be an important limiting factor in energy transmission through overhead power cables, and also in other applications such as thermo-solar energy. In this work, we present the proof-of-concept of the first distributed bolometer based on optical fiber technology and capable of detecting absolute changes of irradiance. The core idea of the system is the use of a special fiber coating with high emissivity (e.g., carbon coating or black paint). The high absorption of these coatings translates into a temperature change that can be read with sufficiently high sensitivity using phase-sensitive reflectometry. To demonstrate the concept, we interrogate distinct black-coated optical fibers using a chirped-pulse ÖOTDR, and we readily demonstrate the detection of light with resolutions in the order of 1% of the reference solar irradiance, offering a high-potential technology for integration in the aforementioned applications.
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| 10. |
- Magalhães, Regina, et al.
(author)
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Towards Distributed Measurements of Electric Fields Using Optical Fibers : Proposal and Proof-Of-Concept Experiment.
- 2020
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In: Sensors. - : MDPI AG. - 1424-8220. ; 20:16
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Journal article (peer-reviewed)abstract
- Nowadays there is an increasing demand for the cost-effective monitoring of potential threats to the integrity of high-voltage networks and electric power infrastructures. Optical fiber sensors are a particularly interesting solution for applications in these environments, due to their low cost and positive intrinsic features, including small size and weight, dielectric properties, and invulnerability to electromagnetic interference (EMI). However, due precisely to their intrinsic EMI-immune nature, the development of a distributed optical fiber sensing solution for the detection of partial discharges and external electrical fields is in principle very challenging. Here, we propose a method to exploit the third-order and second-order nonlinear effects in silica fibers, as a means to achieve highly sensitive distributed measurements of external electrical fields in real time. By monitoring the electric-field-induced variations in the refractive index using a highly sensitive Rayleigh-based CP-φOTDR scheme, we demonstrate the distributed detection of Kerr and Pockels electro-optic effects, and how those can assign a new sensing dimension to optical fibers, transducing external electric fields into visible minute disturbances in the guided light. The proposed sensing configuration, electro-optical time domain reflectometry, is validated both theoretically and experimentally, showing experimental second-order and third-order nonlinear coefficients, respectively, of χ(2) ~ 0.27 × 10-12 m/V and χ(3) ~ 2.5 × 10-22 m2/V2 for silica fibers.
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