Rotational properties of the Haumea family members and candidates: Short-term variability

Haumea is one of the most interesting and intriguing transneptunian objects (TNOs). It is a large, bright, fast rotator, and its spectrum indicates nearly pure water ice on the surface. It has at least two satellites and a dynamically related family of more than ten TNOs with very similar proper orbital parameters and similar surface properties. The Haumean family is the only one currently known in the transneptunian belt. Various models have been proposed but the formation of the family remains poorly understood. In this work, we have investigated the rotational properties of the family members and unconfirmed family candidates with short-term variability studies, and report the most complete review to date. We present results based on five years of observations and report the short-term variability of five family members, and seven candidates. The mean rotational periods, from Maxwellian fits to the frequency distributions, are 6.27+/-1.19 h for the confirmed family members, 6.44+/-1.16 h for the candidates, and 7.65+/-0.54 h for other TNOs (without relation to the family). According to our study, there is a suggestion that Haumea family members rotate faster than other TNOs, however, the sample of family member is still too limited for a secure conclusion. We also highlight the fast rotation of 2002 GH32. This object has a 0.36+/-0.02 mag amplitude lightcurve and a rotational period of about 3.98 h. Assuming 2002 GH32 is a triaxial object in hydrostatic equilibrium, we derive a lower limit to the density of 2.56 g cm^-3. This density is similar to Haumea's and much more dense than other small TNO densities.Comment: Accepted for publication, A

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

<p>Abstract</p> <p>Background</p> <p>High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs) in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs.</p> <p>Results</p> <p>We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO) probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno) that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a <it>Mus </it>species tree and local haplotype assignment in laboratory mouse strains.</p> <p>Conclusion</p> <p>The problems of ascertainment bias and missing information due to genotyping errors are widely recognized as limiting factors in genetic studies. We have conducted the first formal analysis of the effect of novel variants on genotyping arrays, and we have shown that these variants account for a large portion of miscalled and uncalled genotypes. Genetic studies will benefit from substantial improvements in the accuracy of their results by incorporating VINOs in their analyses.</p

Stride-level analysis of mouse open field behavior using deep-learning-based pose estimation.

Gait and posture are often perturbed in many neurological, neuromuscular, and neuropsychiatric conditions. Rodents provide a tractable model for elucidating disease mechanisms and interventions. Here, we develop a neural-network-based assay that adopts the commonly used open field apparatus for mouse gait and posture analysis. We quantitate both with high precision across 62 strains of mice. We characterize four mutants with known gait deficits and demonstrate that multiple autism spectrum disorder (ASD) models show gait and posture deficits, implying this is a general feature of ASD. Mouse gait and posture measures are highly heritable and fall into three distinct classes. We conduct a genome-wide association study to define the genetic architecture of stride-level mouse movement in the open field. We provide a method for gait and posture extraction from the open field and one of the largest laboratory mouse gait and posture data resources for the research community

A minimal limit-cycle model to profile movement patterns of individuals during agility drill performance : effects of skill level

Identification of control strategies during agility performance is significant in understanding movement behavior. This study aimed at providing a fundamental mathematical model for describing the motion of participants during an agility drill and to determine whether skill level constrained model components. Motion patterns of two groups of skilled and unskilled participants (n = 8 in each) during performance of a forward/backward agility drill modeled as limit-cycles. Participant movements were recorded by motion capture of a reflective marker attached to the sacrum of each individual. Graphical and regression analyses of movement kinematics in Hooke’s plane, phase plane and velocity profile were performed to determine components of the models. Results showed that the models of both skilled and unskilled groups had terms from Duffing stiffness as well as Van der Pol damping oscillators. Data also indicated that the proposed models captured on average 97% of the variance for both skilled and unskilled groups. Findings from this study revealed the movement patterning associated with skilled and unskilled performance in a typical forward/backward agility drill which might be helpful for trainers and physiotherapists in enhancing agility

Changes in corneal collagen architecture during mouse postnatal development

Purpose. To characterize changes in corneal collagen arrangement during mouse postnatal development. Methods. Small-angle X-ray scatter patterns were gathered from the centers of 32 excised mice corneas aged between postnatal days 10 (before eye opening) and 28 (onset of sexual maturity). These were analyzed to produce measurements of the average separation distance between corneal collagen fibrils. Changes in the predominant orientation of corneal collagen and its relative distribution during the same developmental period were determined using wide-angle X-ray scatter data collected at 0.2-mm intervals over the entire cornea and limbal region of each specimen. Results. Collagen interfibrillar spacing decreased in the days leading up to eye opening (61.3 ± 2.9 nm at day 10 to 45.5 ± 4.5 nm at day 14), after which it remained constant. However, changes in collagen orientation and distribution occurred throughout the entire developmental period. After eye opening at day 12, collagen alignment gradually increased in the peripheral cornea and limbus. By day 28, an annulus of highly aligned collagen surrounded the cornea. Conclusions. Changes in corneal thickness before and after eye opening are not caused by widespread alterations in the collagen fibrillar array but are more likely caused by expansion and contraction of regions devoid of regularly arranged collagen. The postnatal development of a corneal annulus of collagen, thought to play a role in stabilizing the curvature of the cornea, may be triggered by visual factors

An Exploration of Communities of Practice in the STEM Teacher Context: What Predicts Ties of Retention?

The STEM teacher workforce in the United States has faced a host of pressing challenges, including teacher shortages, pervasive job dissatisfaction, and high turnover, problems largely attributable to working conditions within schools and districts. These problems have been exacerbated in high-needs districts with fewer resources and more students from low-income communities. Since social network research has shown that workplace relationships are vital for retention, this study investigates the demographic and relational antecedents to what we dub ties of retention. We explore how demographic and relational properties affect the likelihood that teachers have “retention-friendly” networks, characterized by connections important for retention. Our analysis of data from a sample of 120 STEM teachers across five geographic regions identifies key demographics (i.e., site, gender, career changer, and prior teaching experience) and relational properties (network size, positive affect, and perceptions of bridging) associated with ties of retention. We discuss the implications of our findings for the STEM teacher workforce and for teacher education programs