Cell-type phylogenetics and the origin of endometrial stromal cells

SummaryA challenge of genome annotation is the identification of genes performing specific biological functions. Here, we propose a phylogenetic approach that utilizes RNA-seq data to infer the historical relationships among cell types and to trace the pattern of gene-expression changes on the tree. The hypothesis is that gene-expression changes coincidental with the origin of a cell type will be important for the function of the derived cell type. We apply this approach to the endometrial stromal cells (ESCs), which are critical for the initiation and maintenance of pregnancy. Our approach identified well-known regulators of ESCs, PGR and FOXO1, as well as genes not yet implicated in female fertility, including GATA2 and TFAP2C. Knockdown analysis confirmed that they are essential for ESC differentiation. We conclude that phylogenetic analysis of cell transcriptomes is a powerful tool for discovery of genes performing cell-type-specific functions

Can Ice-Like Structures Form on Non-Ice-Like Substrates? The Example of the K-feldspar Microcline

Feldspar minerals are the most common rock formers in Earth’s crust. As such they play an important role in subjects ranging from geology to climate science. An atomistic understanding of the feldspar structure and its interaction with water is therefore desirable, not least because feldspar has been shown to dominate ice nucleation by mineral dusts in Earth’s atmosphere. The complexity of the ice/feldspar interface arising from the numerous chemical motifs expressed on the surface makes it a challenging system. Here we report a comprehensive study of this challenging system with ab initio density functional theory calculations. We show that the distribution of Al atoms, which is crucial for the dissolution kinetics of tectosilicate minerals, differs significantly between the bulk environment and on the surface. Furthermore, we demonstrate that water does not form ice-like overlayers in the contact layer on the most easily cleaved (001) surface of K-feldspar. We do, however, identify contact layer structures of water that induce ice-like ordering in the second overlayer. This suggests that even substrates without an apparent match with the ice structure may still act as excellent ice nucleating agents

Stargardt disease: clinical features, molecular genetics, animal models and therapeutic options

Stargardt disease (STGD1; MIM 248200) is the most prevalent inherited macular dystrophy and is associated with disease-causing sequence variants in the gene ABCA4 Significant advances have been made over the last 10 years in our understanding of both the clinical and molecular features of STGD1, and also the underlying pathophysiology, which has culminated in ongoing and planned human clinical trials of novel therapies. The aims of this review are to describe the detailed phenotypic and genotypic characteristics of the disease, conventional and novel imaging findings, current knowledge of animal models and pathogenesis, and the multiple avenues of intervention being explored

Power system stability enhancement through the optimal, passivity-based, placement of SVCs

Over the last decades, several techniques have been proposed for the optimal placement of FACTS devices across power systems. Although these techniques were shown to improve \il{power system} operation, they are usually computationally intractable while having serious inherent limitations. In this paper, we present a novel approach to guide the SVC location identification in order to enhance power system stability. Specifically, the proposed method exploits findings in passivity-based control analysis and design in order to address the most vulnerable -in terms of passivity- buses of the system and consequently the optimal locations for SVC installation. We then show how the incorporation of SVCs at the aforementioned buses can passivate the system and provide \il{guarantees} for increased stability. Furthermore, we provide a brief discussion regarding the sizing and the number of required SVC devices in order to guarantee such stability improvement. Finally, we illustrate our results with simulations on the IEEE 68 bus system and show that both the dynamic response and the damping of the system are significantly improved

A machine learning potential for hexagonal boron nitride applied to thermally and mechanically induced rippling

We introduce an interatomic potential for hexagonal boron nitride (hBN) based on the Gaussian approximation potential (GAP) machine learning methodology. The potential is based on a training set of configurations collected from density functional theory (DFT) simulations and is capable of treating bulk and multilayer hBN as well as nanotubes of arbitrary chirality. The developed force field faithfully reproduces the potential energy surface predicted by DFT while improving the efficiency by several orders of magnitude. We test our potential by comparing formation energies, geometrical properties, phonon dispersion spectra, and mechanical properties with respect to benchmark DFT calculations and experiments. In addition, we use our model and a recently developed graphene-GAP to analyze and compare thermally and mechanically induced rippling in large scale two-dimensional (2D) hBN and graphene. Both materials show almost identical scaling behavior with an exponent of η ≈ 0.85 for the height fluctuations agreeing well with the theory of flexible membranes. On the basis of its lower resistance to bending, however, hBN experiences slightly larger out-of-plane deviations both at zero and finite applied external strain. Upon compression, a phase transition from incoherent ripple motion to soliton-ripples is observed for both materials. Our potential is freely available online at [http://www.libatoms.org]

An accurate and transferable machine learning potential for carbon

We present an accurate machine learning (ML) model for atomistic simulations of carbon, constructed using the Gaussian approximation potential (GAP) methodology. The potential, named GAP-20, describes the properties of the bulk crystalline and amorphous phases, crystal surfaces, and defect structures with an accuracy approaching that of direct ab initio simulation, but at a significantly reduced cost. We combine structural databases for amorphous carbon and graphene, which we extend substantially by adding suitable configurations, for example, for defects in graphene and other nanostructures. The final potential is fitted to reference data computed using the optB88-vdW density functional theory (DFT) functional. Dispersion interactions, which are crucial to describe multilayer carbonaceous materials, are therefore implicitly included. We additionally account for long-range dispersion interactions using a semianalytical two-body term and show that an improved model can be obtained through an optimization of the many-body smooth overlap of atomic positions descriptor. We rigorously test the potential on lattice parameters, bond lengths, formation energies, and phonon dispersions of numerous carbon allotropes. We compare the formation energies of an extensive set of defect structures, surfaces, and surface reconstructions to DFT reference calculations. The present work demonstrates the ability to combine, in the same ML model, the previously attained flexibility required for amorphous carbon [V. L. Deringer and G. Csányi, Phys. Rev. B 95, 094203 (2017)] with the high numerical accuracy necessary for crystalline graphene [Rowe et al., Phys. Rev. B 97, 054303 (2018)], thereby providing an interatomic potential that will be applicable to a wide range of applications concerning diverse forms of bulk and nanostructured carbon

The New Pretender: A Large UK Case Series of Retinal Injuries in Children Secondary to Handheld Lasers

Purpose: To characterize a large single-center series of retinal injuries in children secondary to handheld laser devices, with emphasis on potential prognostic factors. / Design: Retrospective case series. / Methods: Sixteen children (24 eyes) with retinal injuries secondary to handheld lasers were identified from our electronic patient record system. Case notes, digital fundus photography, and spectral-domain optical coherence tomography images were reviewed. / Results: The mean age of affected children was 12.7 years (range 9–16 years), with 12 male and 4 female subjects. Mean follow up was 5.4 months (range 1–23 months). Five children (31%) were referred as suspected retinal dystrophies. The mean logMAR visual acuity at presentation was 0.30 (20/40) (range −0.20 [20/12.5] to 1.6 [20/800]). Eleven children (69%; 15 eyes) had “mild” injuries with focal retinal disruption confined to the photoreceptor and ellipsoid layers; such injuries were associated with a better prognosis, the mean visual acuity at presentation being 0.10 (20/25). “Moderate” injuries were seen in 3 eyes of 2 children, with retinal disruption confined to the outer retinal layer but diffuse rather than focal in nature. Three patients (4 eyes) had “severe” injuries, with subfoveal outer retinal architecture loss and overlying hyperreflective material in inner retinal layers. / Conclusion: Retinal injuries secondary to handheld laser devices may be difficult to diagnose and are likely underreported. It is important that such data are in the public domain, so regulatory authorities recognize the importance of laser retinopathy as an avoidable cause of childhood visual impairment and take steps to minimize the incidence and impact of laser injuries

The impact of an upper tropospheric teleconnection pattern on precipitation extremes over Cyprus

International audienceThe objective of this study is to estimate the duration, frequency and intensity of precipitation extreme episodes in Cyprus, in relation with the two phases of the Eastern Mediterranean teleconnection Pattern (EMP), during winter for the period 1958?2005. A standardised teleconnection index was employed to determine the phases (positive and negative) and the strength of the EMP. The identification of the precipitation extremes was performed with the aid of four climatic indices. It was found that during the positive phase of the pattern, the length of dry periods reduces while that of wet periods increases, being followed by increase of frequency of extreme wet days and precipitation intensity. On the contrary, during the negative phase, the dry spells become longer in accordance with shortening of the wet spells, decrease of the number of extreme wet days and precipitation intensity

Ice formation on kaolinite: Insights from molecular dynamics simulations

The formation of ice affects many aspects of our everyday life as well as important technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing through heterogeneous ice nucleation, but the molecular details of this process remain largely unknown. In fact, insight into the microscopic mechanism of ice formation on different substrates is difficult to obtain even if state-of-the-art experimental techniques are used. At the same time, atomistic simulations of heterogeneous ice nucleation frequently face extraordinary challenges due to the complexity of the water-substrate interaction and the long time scales that characterize nucleation events. Here, we have investigated several aspects of molecular dynamics simulations of heterogeneous ice nucleation considering as a prototypical ice nucleating material the clay mineral kaolinite, which is of relevance in atmospheric science. We show via seeded molecular dynamics simulations that ice nucleation on the hydroxylated (001) face of kaolinite proceeds exclusively via the formation of the hexagonal ice polytype. The critical nucleus size is two times smaller than that obtained for homogeneous nucleation at the same supercooling. Previous findings suggested that the flexibility of the kaolinite surface can alter the time scale for ice nucleation within molecular dynamics simulations. However, we here demonstrate that equally flexible (or non flexible) kaolinite surfaces can lead to very different outcomes in terms of ice formation, according to whether or not the surface relaxation of the clay is taken into account. We show that very small structural changes upon relaxation dramatically alter the ability of kaolinite to provide a template for the formation of a hexagonal overlayer of water molecules at the water-kaolinite interface, and that this relaxation therefore determines the nucleation ability of this mineral

Preliminary verification results of the DWD limited area model LME and evaluation of its storm forecasting skill over the area of Cyprus

A preliminary verification and evaluation is made of the forecast fields of the non-hydrostatic limited area model LME of the German Weather Service (DWD), for a recent three month period. For this purpose, observations from two synoptic stations in Cyprus are utilized. In addition, days with depressions over the area were selected in order to evaluate the model's forecast skill in storm forecasting