The Immunological Basis of Dry Eye Disease and Current Topical Treatment Options.

Homeostasis of the lacrimal functional unit is needed to ensure a well-regulated ocular immune response comprising innate and adaptive phases. When the ocular immune system is excessively stimulated and/or immunoregulatory mechanisms are disrupted, the balance between innate and adaptive phases is dysregulated and chronic ocular surface inflammation can result, leading to chronic dry eye disease (DED). According to the Tear Film and Ocular Surface Society Dry Eye Workshop II definition, DED is a multifactorial disorder of the ocular surface characterized by impairment and loss of tear homeostasis (hyperosmolarity), ocular discomfort or pain, and neurosensory abnormalities. Dysregulated ocular immune responses result in ocular surface damage, which is a further contributing factor to DED pathology. Several therapeutics are available to break the vicious circle of DED and prevent chronic disease and progression, including immunosuppressive agents (steroids) and immunomodulators (cyclosporine and lifitegrast). Given the chronic inflammatory nature of DED, each of these agents is commonly used in clinical practice. In this study, we review the immunopathology of DED and the molecular and cellular actions of current topical DED therapeutics to inform clinical decision making

Estimating conformational traits in dairy cattle with deepAPS : A two-step deep learning automated phenotyping and segmentation approach

Assessing conformation features in an accurate and rapid manner remains a challenge in the dairy industry. While recent developments in computer vision has greatly improved automated background removal, these methods have not been fully translated to biological studies. Here, we present a composite method (DeepAPS) that combines two readily available algorithms in order to create a precise mask for an animal image. This method performs accurately when compared with manual classification of proportion of coat color with an adjusted R2 = 0.926. Using the output mask, we are able to automatically extract useful phenotypic information for 14 additional morphological features. Using pedigree and image information from a web catalog (www.semex.com), we estimated high heritabilities (ranging from h2 = 0.18-0.82), indicating that meaningful biological information has been extracted automatically from imaging data. This method can be applied to other datasets and requires only a minimal number of image annotations (50) to train this partially supervised machinelearning approach. DeepAPS allows for the rapid and accurate quantification of multiple phenotypic measurements while minimizing study cost. The pipeline is available at https://github.com/lauzingaretti/deepaps

Study of second and third harmonic generation from an indium tin oxide nanolayer: Influence of nonlocal effects and hot electrons

We report comparative experimental and theoretical studies of the second and third harmonic generation from a 20 nm-thick indium tin oxide layer in proximity of the epsilon-near-zero condition. Using a tunable optical parametric amplifier, we record both spectral and angular dependence of the generated harmonic signals close to this particular point. In addition to the enhancement of the second harmonic efficiency close to the epsilon-near-zero wavelength, at oblique incidence, third harmonic generation displays an unusual behavior, predicted but not observed before. We implement a comprehensive, first-principles hydrodynamic approach able to simulate our experimental conditions. The model is unique, flexible, and able to capture all major physical mechanisms that drive the electrodynamic behavior of conductive oxide layers: nonlocal effects, which blueshift the epsilon-near-zero resonance by tens of nanometers; plasma frequency redshift due to variations of the effective mass of hot carriers; charge density distribution inside the layer, which determines the nonlinear surface and magnetic interactions; and the nonlinearity of the background medium triggered by bound electrons. We show that, by taking these contributions into account, our theoretical predictions are in very good qualitative and quantitative agreement with our experimental results. We expect that our results can be extended to other geometries where epsilon-near-zero nonlinearity plays an important role.Peer ReviewedPostprint (published version

SeqBreed : a python tool to evaluate genomic prediction in complex scenarios

Background: Genomic prediction (GP) is a method whereby DNA polymorphism information is used to predict breeding values for complex traits. Although GP can significantly enhance predictive accuracy, it can be expensive and difficult to implement. To help design optimum breeding programs and experiments, including genome-wide association studies and genomic selection experiments, we have developed SeqBreed, a generic and flexible forward simulator programmed in python3. Results: SeqBreed accommodates sex and mitochondrion chromosomes as well as autopolyploidy. It can simulate any number of complex phenotypes that are determined by any number of causal loci. SeqBreed implements several GP methods, including genomic best linear unbiased prediction (GBLUP), single-step GBLUP, pedigree-based BLUP, and mass selection. We illustrate its functionality with Drosophila genome reference panel (DGRP) sequence data and with tetraploid potato genotype data. Conclusions: SeqBreed is a flexible and easy to use tool that can be used to optimize GP or genome-wide association studies. It incorporates some of the most popular GP methods and includes several visualization tools. Code is open and can be freely modified. Software, documentation, and examples are available at https://github.com/miguelperezenciso/SeqBreed

Methanol Dehydrogenation on Pt Electrodes : Active Sites and Role of Adsorbed Spectators Revealed through Time-Resolved ATR-SEIRAS

ACKNOWLEDGMENT L.P.-M. acknowledges a doctoral scholarship within the Leverhulme Centre for Doctoral Training in Sustainable Production of Chemicals and Materials (Grant DS-2017-073).Peer reviewedPostprin

One Solution to the Mass Budget Problem for Planet Formation: Optically Thick Disks with Dust Scattering

Atacama Large Millimeter Array (ALMA) surveys have suggested that the dust in Class II disks may not be enough to explain the averaged solid mass in exoplanets, under the assumption that the mm disk continuum emission is optically thin. This optically thin assumption seems to be supported by recent Disk Substructures at High Angular Resolution Project (DSHARP) observations where the measured optical depths are mostly less than one. However, we point out that dust scattering can considerably reduce the emission from an optically thick region. If that scattering is ignored, an optically thick disk with scattering can be misidentified as an optically thin disk. Dust scattering in more inclined disks can reduce the intensity even further, making the disk look even fainter. The measured optical depth of ~0.6 in several DSHARP disks can be naturally explained by optically thick dust with an albedo of ~0.9 at 1.25 mm. Using the DSHARP opacity, this albedo corresponds to a dust population with the maximum grain size (s max) of 0.1–1 mm. For optically thick scattering disks, the measured spectral index α can be either larger or smaller than 2 depending on whether the dust albedo increases or decreases with wavelength. We describe how this optically thick scattering scenario could explain the observed scaling between submm continuum sizes and luminosities, and might help ease the tension between the dust size constraints from polarization and dust continuum measurements. We suggest that a significant amount of disk mass can be hidden from ALMA observations and longer wavelength observations (e.g., Very Large Array or Square Kilometre Array) are desired to probe the dust mass in disks

A century of Shope Papillomavirus in museum rabbit specimens

Sylvilagus floridanus Papillomavirus (SfPV) causes growth of large horn-like tumors on rabbits. SfPV was described in cottontail rabbits (probably Sylvilagus floridanus) from Kansa and Iowa by Richard Shope in 1933, and detected in S. audubonii in 2011. It is known almost exclusively from the US Midwest. We explored the University of Kansas Natural History Museum for historical museum specimens infected with SfPV, using molecular techniques, to assess if additional wild species host SfPV, and whether SfPV occurs throughout the host range, or just in the Midwest. Secondary aims were to detect distinct strains, and evidence for strain spatio-temporal specificity. We found 20 of 1395 rabbits in the KU collection SfPV symptomatic. Three of 17 lagomorph species (S. nuttallii, and the two known hosts) were symptomatic, while Brachylagus, Lepus and eight additional Sylvilagus species were not. 13 symptomatic individuals were positive by molecular testing, including the first S. nuttallii detection. Prevalence of symptomatic individuals was significantly higher in Sylvilagus (1.8%) than Lepus. Half of these specimens came from Kansas, though new molecular detections were obtained from Jalisco—Mexico’s first—and Nebraska, Nevada, New Mexico, and Texas, USA. We document the oldest lab-confirmed case (Kansas, 1915), predating Shope’s first case. SfPV amplification was possible from 63.2% of symptomatic museum specimens. Using multiple methodologies, rolling circle amplification and, multiple isothermal displacement amplification in addition to PCR, greatly improved detection rates. Short sequences were obtained from six individuals for two genes. L1 gene sequences were identical to all previously detected sequences; E7 gene sequences, were more variable, yielding five distinct SfPV1 strains that differing by less than 2% from strains circulating in the Midwest and Mexico, between 1915 and 2005. Our results do not clarify whether strains are host species specific, though they are consistent with SfPV specificity to genus Sylvilagus.Costs of lab work were funded by the Spanish Ministry of Science and Innovation, (Ref CGL2010-15734/BOS) awarded to JPT. RW was supported by the Programa Internacional de Captación de Talento (PICATA) de Moncloa Campus de Excelencia Internacional(http://www.campusmoncloa.es/en/calls/picata.php) while writing the manuscript. The authors thank The One University Open Access Author Fund at The University of Kansas for funding this publication. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

High Resolution 8 mm and 1 cm Polarization of IRAS 4A from the VLA Nascent Disk and Multiplicity (VANDAM) Survey

Magnetic fields can regulate disk formation, accretion and jet launching. Until recently, it has been difficult to obtain high resolution observations of the magnetic fields of the youngest protostars in the critical region near the protostar. The VANDAM survey is observing all known protostars in the Perseus Molecular Cloud. Here we present the polarization data of IRAS 4A. We find that with ~ 0.2'' (50 AU) resolution at {\lambda} = 8.1 and 10.3 mm, the inferred magnetic field is consistent with a circular morphology, in marked contrast with the hourglass morphology seen on larger scales. This morphology is consistent with frozen-in field lines that were dragged in by rotating material entering the infall region. The field morphology is reminiscent of rotating circumstellar material near the protostar. This is the first polarization detection of a protostar at these wavelengths. We conclude from our observations that the dust emission is optically thin with {\beta} ~ 1.3, suggesting that mm/cm-sized grains have grown and survived in the short lifetime of the protostar.Comment: Accepted to ApJL. 13 pages, 4 figure