Statistics of Solar Wind Electron Breakpoint Energies Using Machine Learning Techniques

Solar wind electron velocity distributions at 1 au consist of a thermal "core" population and two suprathermal populations: "halo" and "strahl". The core and halo are quasi-isotropic, whereas the strahl typically travels radially outwards along the parallel and/or anti-parallel direction with respect to the interplanetary magnetic field. With Cluster-PEACE data, we analyse energy and pitch angle distributions and use machine learning techniques to provide robust classifications of these solar wind populations. Initially, we use unsupervised algorithms to classify halo and strahl differential energy flux distributions to allow us to calculate relative number densities, which are of the same order as previous results. Subsequently, we apply unsupervised algorithms to phase space density distributions over ten years to study the variation of halo and strahl breakpoint energies with solar wind parameters. In our statistical study, we find both halo and strahl suprathermal breakpoint energies display a significant increase with core temperature, with the halo exhibiting a more positive correlation than the strahl. We conclude low energy strahl electrons are scattering into the core at perpendicular pitch angles. This increases the number of Coulomb collisions and extends the perpendicular core population to higher energies, resulting in a larger difference between halo and strahl breakpoint energies at higher core temperatures. Statistically, the locations of both suprathermal breakpoint energies decrease with increasing solar wind speed. In the case of halo breakpoint energy, we observe two distinct profiles above and below 500 km/s. We relate this to the difference in origin of fast and slow solar wind.Comment: Published in Astronomy & Astrophysics, 11 pages, 10 figure

High-resolution evidence for dynamic transitional geomagnetic field behaviour from a Miocene reversal, McMurdo Sound, Ross Sea, Antarctica

We report a high-resolution record of a Miocene polarity transition (probably the Chron C6r-C6n transition) from glacimarine sediments in McMurdo Sound, Ross Sea, Antarctica, which is the first transition record reported from high southern latitudes. The transition is recorded in two parallel cores through a 10.7 m stratigraphic thickness. The sediments are interpreted as having been deposited in a marine environment under the influence of floating ice or seaward of a glacier terminus from which a large sediment load was delivered to the drill site. The core was recovered using rotary drilling, which precludes azimuthal orientation of the core and determination of a vector record of the field during the transition. However, constraints on transitional field behaviour are provided by the exceptional resolution of this record. Large-scale paleomagnetic inclination fluctuations in the two cores can be independently correlated with each other using magnetic susceptibility data, which suggests that the sediments are reliable recorders of geomagnetic field variations. Agreement between the two parallel transition records provides evidence for highly dynamic field behaviour, as suggested by numerous large-scale inclination changes (∼90◦) throughout the transition. These large-scale changes occur across stratigraphically narrow intervals, which is consistent with the suggestion of rapid field changes during transitions. In one intact portion of the core, where there is no apparent relative core rotation between samples, declinations and inclinations are consistent with the presence of a stable cluster of virtual geomagnetic poles within the transition (although the possibility that this cluster represents a rapid depositional event cannot be precluded). These observations are consistent with those from other high-resolution records and provide a rare detailed view of transitional field behaviour compared to most sedimentary records, which are not as thick and which appear to have been smoothed by sedimentary remanence acquisition processes

Using Dimensionality Reduction and Clustering Techniques to Classify Space Plasma Regimes

Collisionless space plasma environments are typically characterized by distinct particle populations. Although moments of their velocity distribution functions help in distinguishing different plasma regimes, the distribution functions themselves provide more comprehensive information about the plasma state, especially at times when the distribution function includes non-thermal effects. Unlike moments, however, distribution functions are not easily characterized by a small number of parameters, making their classification more difficult to achieve. In order to perform this classification, we propose to distinguish between the different plasma regions by applying dimensionality reduction and clustering methods to electron distributions in pitch angle and energy space. We utilize four separate algorithms to achieve our plasma classifications: autoencoders, principal component analysis, mean shift, and agglomerative clustering. We test our classification algorithms by applying our scheme to data from the Cluster-Plasma Electron and Current Experiment instrument measured in the Earth’s magnetotail. Traditionally, it is thought that the Earth’s magnetotail is split into three different regions (the plasma sheet, the plasma sheet boundary layer, and the lobes), that are primarily defined by their plasma characteristics. Starting with the ECLAT database with associated classifications based on the plasma parameters, we identify eight distinct groups of distributions, that are dependent upon significantly more complex plasma and field dynamics. By comparing the average distributions as well as the plasma and magnetic field parameters for each region, we relate several of the groups to different plasma sheet populations, and the rest we attribute to the plasma sheet boundary layer and the lobes. We find clear distinctions between each of our classified regions and the ECLAT results. The automated classification of different regions in space plasma environments provides a useful tool to identify the physical processes governing particle populations in near-Earth space. These tools are model independent, providing reproducible results without requiring the placement of arbitrary thresholds, limits or expert judgment. Similar methods could be used onboard spacecraft to reduce the dimensionality of distributions in order to optimize data collection and downlink resources in future missions

Constraining suprathermal electron evolution in a Parker spiral field with Cassini observations

Suprathermal electrons in the solar wind consist of the ‘halo’, present at all pitch angles, and the ‘strahl’ which is a field‐aligned, beam‐like population. Examining the heliospheric evolution of strahl beams is key to understanding the in‐transit processing of solar wind suprathermal electrons, in particular, to identify electron scattering mechanisms and to establish the origin of the halo population. Not only does this have significant implications with regard to the kinetic processes occurring within the solar wind but also its thermodynamic evolution, as the the suprathermal electrons carry the majority of the solar wind heat flux. In this investigation, an established model for suprathermal electron evolution in a Parker spiral interplanetary magnetic field (IMF) is adapted from its original use. The model is constrained using solar wind strahl observed by the Cassini mission on its interplanetary journey to Saturn. The effects of large scale IMF geometry due to different solar wind velocities and application of different electron scattering factors are examined. It is found that that slow solar wind speeds provide the closest match to the strahl width observations, both in terms of radial distance and electron energy trends, and that predominantly slower solar wind speeds were therefore likely observed by the Cassini mission en‐route to Saturn. It is necessary to include a strahl scattering factor which increases with electron energy in order to match observations, indicating that the strahl scattering mechanism must have an inherent energy dependence

Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances

Twin and family studies indicate that the timing of primary tooth eruption is highly heritable, with estimates typically exceeding 80%. To identify variants involved in primary tooth eruption we performed a population based genome-wide association study of ‘age at first tooth’ and ‘number of teeth’ using 5998 and 6609 individuals respectively from the Avon Longitudinal Study of Parents and Children (ALSPAC) and 5403 individuals from the 1966 Northern Finland Birth Cohort (NFBC1966). We tested 2,446,724 SNPs imputed in both studies. Analyses were controlled for the effect of gestational age, sex and age of measurement. Results from the two studies were combined using fixed effects inverse variance meta-analysis. We identified a total of fifteen independent loci, with ten loci reaching genome-wide significance (p<5x10−8) for ‘age at first tooth’ and eleven loci for ‘number of teeth’. Together these associations explain 6.06% of the variation in ‘age of first tooth’ and 4.76% of the variation in ‘number of teeth’. The identified loci included eight previously unidentified loci, some containing genes known to play a role in tooth and other developmental pathways, including a SNP in the protein-coding region of BMP4 (rs17563, P= 9.080x10−17). Three of these loci, containing the genes HMGA2, AJUBA and ADK, also showed evidence of association with craniofacial distances, particularly those indexing facial width. Our results suggest that the genome-wide association approach is a powerful strategy for detecting variants involved in tooth eruption, and potentially craniofacial growth and more generally organ development

Targeted 'Next-Generation' sequencing in anophthalmia and microphthalmia patients confirms SOX2, OTX2 and FOXE3 mutations

<p>Abstract</p> <p>Background</p> <p>Anophthalmia/microphthalmia (A/M) is caused by mutations in several different transcription factors, but mutations in each causative gene are relatively rare, emphasizing the need for a testing approach that screens multiple genes simultaneously. We used next-generation sequencing to screen 15 A/M patients for mutations in 9 pathogenic genes to evaluate this technology for screening in A/M.</p> <p>Methods</p> <p>We used a pooled sequencing design, together with custom single nucleotide polymorphism (SNP) calling software. We verified predicted sequence alterations using Sanger sequencing.</p> <p>Results</p> <p>We verified three mutations - c.542delC in S<it>OX2</it>, resulting in p.Pro181Argfs*22, p.Glu105X in <it>OTX2 </it>and p.Cys240X in <it>FOXE3</it>. We found several novel sequence alterations and SNPs that were likely to be non-pathogenic - p.Glu42Lys in <it>CRYBA4</it>, p.Val201Met in <it>FOXE3 </it>and p.Asp291Asn in <it>VSX2</it>. Our analysis methodology gave one false positive result comprising a mutation in <it>PAX6 </it>(c.1268A > T, predicting p.X423LeuextX*15) that was not verified by Sanger sequencing. We also failed to detect one 20 base pair (bp) deletion and one 3 bp duplication in <it>SOX2</it>.</p> <p>Conclusions</p> <p>Our results demonstrated the power of next-generation sequencing with pooled sample groups for the rapid screening of candidate genes for A/M as we were correctly able to identify disease-causing mutations. However, next-generation sequencing was less useful for small, intragenic deletions and duplications. We did not find mutations in 10/15 patients and conclude that there is a need for further gene discovery in A/M.</p

Loss of the BMP Antagonist, SMOC-1, Causes Ophthalmo-Acromelic (Waardenburg Anophthalmia) Syndrome in Humans and Mice

Ophthalmo-acromelic syndrome (OAS), also known as Waardenburg Anophthalmia syndrome, is defined by the combination of eye malformations, most commonly bilateral anophthalmia, with post-axial oligosyndactyly. Homozygosity mapping and subsequent targeted mutation analysis of a locus on 14q24.2 identified homozygous mutations in SMOC1 (SPARC-related modular calcium binding 1) in eight unrelated families. Four of these mutations are nonsense, two frame-shift, and two missense. The missense mutations are both in the second Thyroglobulin Type-1 (Tg1) domain of the protein. The orthologous gene in the mouse, Smoc1, shows site- and stage-specific expression during eye, limb, craniofacial, and somite development. We also report a targeted pre-conditional gene-trap mutation of Smoc1 (Smoc1tm1a) that reduces mRNA to ∼10% of wild-type levels. This gene-trap results in highly penetrant hindlimb post-axial oligosyndactyly in homozygous mutant animals (Smoc1tm1a/tm1a). Eye malformations, most commonly coloboma, and cleft palate occur in a significant proportion of Smoc1tm1a/tm1a embryos and pups. Thus partial loss of Smoc-1 results in a convincing phenocopy of the human disease. SMOC-1 is one of the two mammalian paralogs of Drosophila Pentagone, an inhibitor of decapentaplegic. The orthologous gene in Xenopus laevis, Smoc-1, also functions as a Bone Morphogenic Protein (BMP) antagonist in early embryogenesis. Loss of BMP antagonism during mammalian development provides a plausible explanation for both the limb and eye phenotype in humans and mice

Pleiotropic Effects of Sox2 during the Development of the Zebrafish Epithalamus

The zebrafish epithalamus is part of the diencephalon and encompasses three major components: the pineal, the parapineal and the habenular nuclei. Using sox2 knockdown, we show here that this key transcriptional regulator has pleiotropic effects during the development of these structures. Sox2 negatively regulates pineal neurogenesis. Also, Sox2 is identified as the unknown factor responsible for pineal photoreceptor prepatterning and performs this function independently of the BMP signaling. The correct levels of sox2 are critical for the functionally important asymmetrical positioning of the parapineal organ and for the migration of parapineal cells as a coherent structure. Deviations from this strict control result in defects associated with abnormal habenular laterality, which we have documented and quantified in sox2 morphants

The Endothelin Type A Receptor as a Potential Therapeutic Target in Preeclampsia

Preeclampsia (PE) is a disorder of pregnancy typically characterized by new onset hypertension after gestational week 20 and proteinuria. Although PE is one of the leading causes of maternal and perinatal morbidity and death worldwide, the mechanisms of the pathogenesis of the disease remain unclear and treatment options are limited. However, there is increasing evidence to suggest that endothelin-1 (ET-1) plays a critical role in the pathophysiology of PE. Multiple studies report that ET-1 is increased in PE and some studies report a positive correlation between ET-1 and the severity of symptoms. A number of experimental models of PE are also associated with elevated tissue levels of prepro ET-1 mRNA. Moreover, experimental models of PE (placental ischemia, sFlt-1 infusion, Tumor necrosis factor (TNF) -α infusion, and Angiotensin II type 1 receptor autoantibody (AT1-AA) infusion) have proven to be susceptible to Endothelin Type A (ETA) receptor antagonism. While the results are promising, further work is needed to determine whether ET antagonists could provide an effective therapy for the management of preeclampsia