340 research outputs found

    Optimal Estimation Inversion of Ionospheric Electron Density from GNSS-POD Limb Measurements: Part II-Validation and Comparison Using NmF2 and hmF2

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    A growing number of SmallSat/CubeSat constellations with high-rate (50–100 Hz) global navigation satellite system radio occultations (GNSS-RO) as well as low-rate (1 Hz) precise orbit determination (GNSS-POD) limb-viewing capabilities provide unprecedented spatial and temporal sampling rates for ionospheric studies. In the F-region electron density (Ne) retrieval process, instead of the conventional onion-peeling (OP) inversion, an optimal estimation (OE) inversion technique was recently developed using total electron content measurements acquired by GNSS-POD link. The new technique is applied to data acquired from the COSMIC-1, COSMIC-2, and Spire constellations. Although both OE and OP techniques use the Abel weighting function in Ne inversion, OE significantly differs in its performance, especially in the lower F- and E-regions. In this work, we evaluate and compare newly derived data sets using F2 peak properties with other space-based and ground-based observations. We determine the F2 peak Ne (NmF2) and its altitude (hmF2), and compare them with the OP-retrieved values. Good agreement is observed between the two techniques for both NmF2 and hmF2. In addition, we also utilize autoscaled F2 peak measurements from a number of worldwide Digisonde stations (∼30). The diurnal sensitivity and latitudinal variability of the F2 peak between the two techniques are carefully studied at these locations. Good agreement is observed between OE-retrieved NmF2 and Digisonde-measured NmF2. However, significant differences appear between OE-retrieved hmF2 and Digisonde-measured hmF2. During the daytime, Digisonde-measured hmF2 remains ∼25–45 km below the OE-retrieved hmF2, especially at mid and high latitudes. We also incorporate F-region Ne measurements from two incoherent scatter radar observations at high latitudes, located in the North American (Millstone Hill) and European (EISCAT at Tromso) sectors. The radar measurements show good agreement with OE-retrieved values. Although there are several possible sources of error in the ionogram-derived Ne profiles, our further analysis on F1 and F2 layers indicates that the low Digisonde hmF2 is caused by the autoscaled method, which tends to detect a height systematically below the F2 peak when the F1 layer is present

    Optimal Estimation Inversion of Ionospheric Electron Density from GNSS-POD Limb Measurements: Part I-Algorithm and Morphology

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    GNSS-LEO radio links from Precise Orbital Determination (POD) and Radio Occultation (RO) antennas have been used increasingly in characterizing the global 3D distribution and variability of ionospheric electron density (Ne). In this study, we developed an optimal estimation (OE) method to retrieve Ne profiles from the slant total electron content (hTEC) measurements acquired by the GNSS-POD links at negative elevation angles (ε \u3c 0°). Although both OE and onion-peeling (OP) methods use the Abel weighting function in the Ne inversion, they are significantly different in terms of performance in the lower ionosphere. The new OE results can overcome the large Ne oscillations, sometimes negative values, seen in the OP retrievals in the E-region ionosphere. In the companion paper in this Special Issue, the HmF2 and NmF2 from the OE retrieval are validated against ground-based ionosondes and radar observations, showing generally good agreements in NmF2 from all sites. Nighttime hmF2 measurements tend to agree better than the daytime when the ionosonde heights tend to be slightly lower. The OE algorithm has been applied to all GNSS-POD data acquired from the COSMIC-1 (2006–2019), COSMIC-2 (2019–present), and Spire (2019–present) constellations, showing a consistent ionospheric Ne morphology. The unprecedented spatiotemporal sampling of the ionosphere from these constellations now allows a detailed analysis of the frequency–wavenumber spectra for the Ne variability at different heights. In the lower ionosphere (~150 km), we found significant spectral power in DE1, DW6, DW4, SW5, and SE4 wave components, in addition to well-known DW1, SW2, and DE3 waves. In the upper ionosphere (~450 km), additional wave components are still present, including DE4, DW4, DW6, SE4, and SW4. The co-existence of eastward- and westward-propagating wave4 components implies the presence of a stationary wave4 (SPW4), as suggested by other earlier studies. Further improvements to the OE method are proposed, including a tomographic inversion technique that leverages the asymmetric sampling about the tangent point associated with GNSS-LEO links

    DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing

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    DNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Using methylation-sensitive restriction enzyme-based next generation sequencing (Canine DREAM), we obtained canine DNA methylation maps of 16 somatic tissues from two dogs. In total, we evaluated 130,861 CpG sites. The majority of CpG sites were either highly methylated (>70%, 52.5-64.6% of all CpG sites analyzed) or unmethylated (<30%, 22.5-28.0% of all CpG sites analyzed) which are methylation patterns similar to other species. The overall methylation status of CpG sites across the 32 methylomes were remarkably similar. However, the tissue types were clearly defined by principle component analysis and hierarchical clustering analysis with DNA methylome. We found 6416 CpG sites located closely at promoter region of genes and inverse correlation between DNA methylation and gene expression of these genes. Our study provides basic dataset for DNA methylation profiles in dogs

    Biochemical identification of nonmethylated DNA by BioCAP-Seq

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    CpG islands are regions of vertebrate genomes that often function as gene regulatory elements and are associated with most gene promoters. CpG island elements usually contain nonmethylated CpG dinucleotides, while the remainder of the genome is pervasively methylated. We developed a biochemical approach called biotinylated CxxC affinity purification (BioCAP) to unbiasedly isolate regions of the genome that contain nonmethylated CpG dinucleotides. The resulting highly pure nonmethylated DNA is easily analyzed by quantitative PCR to interrogate specific loci or via massively parallel sequencing to yield genome-wide profiles

    Observations and modeling of traveling ionospheric disturbance signatures from an Australian network of oblique angle-of-arrival sounders

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    A network of oblique angle‐of‐arrival (AoA) ionosondes was installed as part of the Elevation‐scanned Oblique Incidence Sounder Experiment (ELOISE) in September 2015. The ELOISE experimental campaign was designed to study the spatial and temporal structure of ionospheric variability at midlatitudes, of which traveling ionospheric disturbances are a key component. The new AoA sounder makes use of Defence Science and Technology Group's direct‐digital high‐frequency transmitter and receiver technology, to enable multichannel collection of both ionograms and channel scattering functions (Doppler spectra) on a common 2‐D array. In this paper, the array design and onboard signal processing for the AoA sounder is described, along with a sample of results showing typical disturbance signatures across the delay, Doppler frequency, bearing, and elevation measurements. Realistic parameterized models of electron density perturbations, along with geometric ray tracing, were used to synthesize the effects of medium‐ to large‐scale traveling ionospheric disturbances on the sounder observables and aid in interpreting the measured signatures.Andrew J. Heitmann, Manuel A. Cervera, Robert S. Gardiner‐Garden, David A. Holdsworth, Andrew D. MacKinnon, Iain M. Reid, Bruce D. War

    The legacy of racism and Indigenous Australian identity within education

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    © 2014 Taylor & Francis. It may be argued that the emerging discourses focusing on the social, emotional, educational, and economic disadvantages identified for Australia’s First Peoples (when compared to their non-Indigenous counterparts) are becoming increasingly dissociated with an understanding of the interplay between historical and current trends in racism. Additionally, and if not somewhat related to this critique, it can be suggested that the very construction of research from a Western perspective of Indigenous identity (as opposed to identities) and ways of being are deeply entwined within the undertones of epistemological racism still prevalent today. It is the purpose of this article to move beyond the overreliance of outside-based understanding Western epistemologies, and to explore not only the complex nature of both racism and identity from Aboriginal and Torres Strait Islander perspectives, but to also explore the role of education and research in perpetuating varying levels of racism and resistance to Indigenous identity(ies) from a contemporary insider-based standpoint. It is hoped this article will shed some light on the pervasive nature of racism directed at Indigenous Australians, and highlight the need for the continual acceptance, respect, and promotion of Indigenous voices and identities within the educational environment and beyond

    Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a

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    Gains and losses in DNA methylation are prominent features of mammalian cell types. To gain insight into the mechanisms that promote shifts in DNA methylation and contribute to changes in cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine and 5-hydroxymethylcytosine in purified mouse hematopoietic stem cells. We discovered extended regions of low methylation (canyons) that span conserved domains frequently containing transcription factors and are distinct from CpG islands and shores. About half of the genes in these methylation canyons are coated with repressive histone marks, whereas the remainder are covered by activating histone marks and are highly expressed in hematopoietic stem cells (HSCs). Canyon borders are demarked by 5-hydroxymethylcytosine and become eroded in the absence of DNA methyltransferase 3a (Dnmt3a). Genes dysregulated in human leukemias are enriched for canyon-associated genes. The new epigenetic landscape we describe may provide a mechanism for the regulation of hematopoiesis and may contribute to leukemia development. &amp;#169; 2014 Nature America, Inc.close585

    Impact of sperm DNA chromatin in the clinic

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    The paternal contribution to fertilization and embryogenesis is frequently overlooked as the spermatozoon is often considered to be a silent vessel whose only function is to safely deliver the paternal genome to the maternal oocyte. In this article, we hope to demonstrate that this perception is far from the truth. Typically, infertile men have been unable to conceive naturally (or through regular IVF), and therefore, a perturbation of the genetic integrity of sperm heads in infertile males has been under-considered. The advent of intracytoplasmic sperm injection (ICSI) however has led to very successful treatment of male factor infertility and subsequent widespread use in IVF clinics worldwide. Until recently, little concern has been raised about the genetic quality of sperm in ICSI patients or the impact genetic aberrations could have on fertility and embryogenesis. This review highlights the importance of chromatin packaging in the sperm nucleus as essential for the establishment and maintenance of a viable pregnancy