Automated identification of multinucleated germ cells with U-Net.

Phthalic acid esters (phthalates) are male reproductive toxicants, which exert their most potent toxicity during fetal development. In the fetal rat, exposure to phthalates reduces testosterone biosynthesis, alters the development of seminiferous cords and other male reproductive tissues, and induces the formation of abnormal multinucleated germ cells (MNGs). Identification of MNGs is a time-intensive process, and it requires specialized training to identify MNGs in histological sections. As a result, MNGs are not routinely quantified in phthalate toxicity experiments. In order to speed up and standardize this process, we have developed an improved method for automated detection of MNGs. Using hand-labeled histological section images with human-identified MNGs, we trained a convolutional neural network with a U-Net architecture to identify MNGs on unlabeled images. With unseen hand-labeled images not used in model training, we assessed the performance of the model, using five different configurations of the data. On average, the model reached near human accuracy, and in the best model, it exceeded it. The use of automated image analysis will allow data on this histopathological endpoint to be more readily collected for analysis of phthalate toxicity. Our trained model application code is available for download at github.com/brown-ccv/mngcount.

Automated data extraction from historical city directories: The rise and fall of mid-century gas stations in Providence, RI.

The location of defunct environmentally hazardous businesses like gas stations has many implications for modern American cities. To track down these locations, we present the directoreadr code (github.com/brown-ccv/directoreadr). Using scans of Polk city directories from Providence, RI, directoreadr extracts and parses business location data with a high degree of accuracy. The image processing pipeline ran without any human input for 94.4% of the pages we examined. For the remaining 5.6%, we processed them with some human input. Through hand-checking a sample of three years, we estimate that ~94.6% of historical gas stations are correctly identified and located, with historical street changes and non-standard address formats being the main drivers of errors. As an example use, we look at gas stations, finding that gas stations were most common early in the study period in 1936, beginning a sharp and steady decline around 1950. We are making the dataset produced by directoreadr publicly available. We hope it will be used to explore a range of important questions about socioeconomic patterns in Providence and cities like it during the transformations of the mid-1900s.

The step-like evolution of Arctic open water.

September open water fraction in the Arctic is analyzed using the satellite era record of ice concentration (1979-2017). Evidence is presented that three breakpoints (shifts in the mean) occurred in the Pacific sector, with higher amounts of open water starting in 1989, 2002, and 2007. Breakpoints in the Atlantic sector record of open water are evident in 1971 in longer records, and around 2000 and 2011. Multiple breakpoints are also evident in the Canadian and Russian halves. Statistical models that use detected breakpoints of the Pacific and Atlantic sectors, as well as models with breakpoints in the Canadian and Russian halves and the Arctic as a whole, outperform linear trend models in fitting the data. From a physical standpoint, the results support the thesis that Arctic sea ice may have critical points beyond which a return to the previous state is less likely. From an analysis standpoint, the findings imply that de-meaning the data using the breakpoint means is less likely to cause spurious signals than employing a linear detrend.

Photosynthesis in hydrogen-dominated atmospheres.

The diversity of extrasolar planets discovered in the last decade shows that we should not be constrained to look for life in environments similar to early or present-day Earth. Super-Earth exoplanets are being discovered with increasing frequency, and some will be able to retain a stable, hydrogen-dominated atmosphere. We explore the possibilities for photosynthesis on a rocky planet with a thin H2-dominated atmosphere. If a rocky, H2-dominated planet harbors life, then that life is likely to convert atmospheric carbon into methane. Outgassing may also build an atmosphere in which methane is the principal carbon species. We describe the possible chemical routes for photosynthesis starting from methane and show that less energy and lower energy photons could drive CH4-based photosynthesis as compared with CO2-based photosynthesis. We find that a by-product biosignature gas is likely to be H2, which is not distinct from the hydrogen already present in the environment. Ammonia is a potential biosignature gas of hydrogenic photosynthesis that is unlikely to be generated abiologically. We suggest that the evolution of methane-based photosynthesis is at least as likely as the evolution of anoxygenic photosynthesis on Earth and may support the evolution of complex life.

Spectral fingerprints of Earth-like planets around FGK stars.

We present model atmospheres for an Earth-like planet orbiting the entire grid of main sequence FGK stars with effective temperatures ranging from Teff=4250 K to Teff=7000 K in 250 K intervals. We have modeled the remotely detectable spectra of Earth-like planets for clear and cloudy atmospheres at the 1 AU equivalent distance from the VIS to IR (0.4 to 20 µm) to compare detectability of features in different wavelength ranges in accordance with the James Webb Space Telescope and future design concepts to characterize exo-Earths. We have also explored the effect of the stellar UV levels as well as spectral energy distribution on a terrestrial atmosphere, concentrating on detectable atmospheric features that indicate habitability on Earth, namely, H2O, O3, CH4, N2O, and CH3Cl. The increase in UV dominates changes of O3, OH, CH4, N2O, and CH3Cl, whereas the increase in stellar temperature dominates changes in H2O. The overall effect as stellar effective temperatures and corresponding UV increase is a lower surface temperature of the planet due to a bigger part of the stellar flux being reflected at short wavelengths, as well as increased photolysis. Earth-like atmosphere models show more O3 and OH but less stratospheric CH4, N2O, CH3Cl, and tropospheric H2O (but more stratospheric H2O) with increasing effective temperature of main sequence stars. The corresponding detectable spectral features, on the other hand, show different detectability depending on the wavelength observed. We concentrate on directly imaged planets here as a framework to interpret future light curves, direct imaging, and secondary eclipse measurements of atmospheres of terrestrial planets in the habitable zone at varying orbital positions.