A Species Tree for the Australo-Papuan Fairy-Wrens and Allies (Aves: Maluridae)

We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that incomplete lineage sorting (ILS) of neutrally evolving loci could be substantial, a situation that could compromise traditional methods of combining loci in phylogenetic analysis. Using 18 molecular markers (5 anonymous loci, 7 exons, 5 introns, and 1 mitochondrial DNA locus), we show that gene tree monophyly across species could be rejected for 16 of 18 loci, suggesting substantial ILS at the family level in these birds. Using the software Concaterpillar, we also detect three statistically distinct clusters of gene trees among the 18 loci. Despite substantial variation in gene trees, species trees constructed using four different species tree estimation methods (BEST, BUCKy, and STAR) were generally well supported and similar to each other and to the concatenation tree, with a few mild discordances at nodes that could be explained by rapid and recent speciation events. By contrast, minimizing deep coalescences produced a species tree that was topologically more divergent from those of the other methods as measured by multidimensional scaling of trees. Additionally, gene and species trees were topologically more similar in the BEST analysis, presumably because of the species tree prior employed in BEST which appropriately assumes that gene trees are correlated with each other and with the species tree. Among the 18 loci, we also discovered 102 independent indel markers, which also proved phylogenetically informative, primarily among genera, and displayed a $\sim4$-fold bias towards deletions. As suggested in earlier work, the grasswrens (Amytornis) are sister to the rest of the family and the emu-wrens (Stipiturus) are sister to fairy-wrens (Malurus, Clytomyias). Our study shows that ILS is common at the family level in birds yet, despite this, species tree methods converge on broadly similar results for this family.Organismic and Evolutionary Biolog

DeepCut: Object Segmentation from Bounding Box Annotations using Convolutional Neural Networks

In this paper, we propose DeepCut, a method to obtain pixelwise object segmentations given an image dataset labelled with bounding box annotations. It extends the approach of the well-known GrabCut method to include machine learning by training a neural network classifier from bounding box annotations. We formulate the problem as an energy minimisation problem over a densely-connected conditional random field and iteratively update the training targets to obtain pixelwise object segmentations. Additionally, we propose variants of the DeepCut method and compare those to a naive approach to CNN training under weak supervision. We test its applicability to solve brain and lung segmentation problems on a challenging fetal magnetic resonance dataset and obtain encouraging results in terms of accuracy

Spectrometer Scan Mechanism for Encountering Jovian Orbit Trojan Asteroids

This paper describes the design, testing, and lessons learned during the development of the Lucy Ralph (L'Ralph) Scan Mirror System (SMS), composed of the Scan Mirror Mechanism (SMM), Differential Position Sensor System (DPSS) and Mechanism Control Electronics (MCE). The L'Ralph SMS evolved from the Advanced Topographic Laser Altimeter System (ATLAS) Beam Steering Mechanism (BSM), so design comparisons will be made. Lucy is scheduled to launch in October 2021, embarking upon a 12-year mission to make close range encounters in 2025 and 2033 with seven Trojan asteroids and one main belt asteroid that are within the Jovian orbit. The L'Ralph instrument is based upon the New Horizons Ralph instrument, which is a panchromatic and color visible imager and infrared spectroscopic mapper that slewed the spacecraft for imaging. The L'Ralph SMM is to provide scanning for imaging to eliminate the need to slew the spacecraft. One purpose of this paper is to gain understanding of the reasoning behind some of the design features as compared with the ATLAS BSM. We will identify similarities and differences between the ATLAS BSM and the L'Ralph SMM that resulted from the latter's unique requirements. Another purpose of this paper is to focus upon "Lessons Learned" that came about during the development of the L'Ralph SMM and its MCE, both mechanism engineering issues and solutions as well as Ground Support Equipment (GSE) issues and solutions that came about during the validation of requirements process. At the time of this writing, the L'Ralph SMM has been flight qualified and delivered to the project

Sorting live stem cells based on Sox2 mRNA expression.

PMCID: PMC3507951This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.While cell sorting usually relies on cell-surface protein markers, molecular beacons (MBs) offer the potential to sort cells based on the presence of any expressed mRNA and in principle could be extremely useful to sort rare cell populations from primary isolates. We show here how stem cells can be purified from mixed cell populations by sorting based on MBs. Specifically, we designed molecular beacons targeting Sox2, a well-known stem cell marker for murine embryonic (mES) and neural stem cells (NSC). One of our designed molecular beacons displayed an increase in fluorescence compared to a nonspecific molecular beacon both in vitro and in vivo when tested in mES and NSCs. We sorted Sox2-MB(+)SSEA1(+) cells from a mixed population of 4-day retinoic acid-treated mES cells and effectively isolated live undifferentiated stem cells. Additionally, Sox2-MB(+) cells isolated from primary mouse brains were sorted and generated neurospheres with higher efficiency than Sox2-MB(-) cells. These results demonstrate the utility of MBs for stem cell sorting in an mRNA-specific manner

Effects of Growth Hormone Treatment in Adults with Prader-Willi Syndrome

OBJECTIVE: Since limited data exist on adults with Prader-Willi syndrome (PWS) and growth hormone (GH) treatment, we report our experience on the effects of treatment for one year on body composition, physical activity, strength and energy expenditure, diet, general chemistry and endocrine data with quality of life measures. DESIGN: We studied 11 adults with PWS (6F:5M; average age = 32 yrs) over a 2 year period with GH treatment during the first year only. Electrolytes, IGF-I, glucose, thyroid, insulin, lipids, body composition, physical activity and strength, diet, energy expenditure and quality of life data were collected and analyzed statistically using linear modeling at baseline, at 12 months following GH therapy and at 24 months after treatment cessation for 12 months. RESULTS: Total lean muscle mass was significantly increased (p < 0.05) during GH treatment along with moderate-vigorous physical activity and plasma IGF-I and HDL levels, but returned to near baseline after treatment. Percent body fat decreased during the 12 months of GH treatment but increased after treatment. CONCLUSIONS: Previously reported beneficial effects of GH treatment in children with PWS were found in our adults regarding body composition, physical activity and plasma HDL and IGF-I levels. Several beneficial effects diminished to near baseline after cessation of GH treatment for 12 months supporting the continuation of treatment in PWS into adulthood and possibly adults not previously treated during childhood