From fat droplets to floating forests: cross-domain transfer learning using a PatchGAN-based segmentation model

Many scientific domains gather sufficient labels to train machine algorithms through human-in-the-loop techniques provided by the Zooniverse.org citizen science platform. As the range of projects, task types and data rates increase, acceleration of model training is of paramount concern to focus volunteer effort where most needed. The application of Transfer Learning (TL) between Zooniverse projects holds promise as a solution. However, understanding the effectiveness of TL approaches that pretrain on large-scale generic image sets vs. images with similar characteristics possibly from similar tasks is an open challenge. We apply a generative segmentation model on two Zooniverse project-based data sets: (1) to identify fat droplets in liver cells (FatChecker; FC) and (2) the identification of kelp beds in satellite images (Floating Forests; FF) through transfer learning from the first project. We compare and contrast its performance with a TL model based on the COCO image set, and subsequently with baseline counterparts. We find that both the FC and COCO TL models perform better than the baseline cases when using >75% of the original training sample size. The COCO-based TL model generally performs better than the FC-based one, likely due to its generalized features. Our investigations provide important insights into usage of TL approaches on multi-domain data hosted across different Zooniverse projects, enabling future projects to accelerate task completion.Comment: 5 pages, 4 figures, accepted for publication at the Proceedings of the ACM/CIKM 2022 (Human-in-the-loop Data Curation Workshop

A spatially resolved analysis of star-formation burstiness by comparing UV and Hα\alpha in galaxies at z∼\sim1 with UVCANDELS

The UltraViolet imaging of the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey Fields (UVCANDELS) program provides HST/UVIS F275W imaging for four CANDELS fields. We combine this UV imaging with existing HST/near-IR grism spectroscopy from 3D-HST+AGHAST to directly compare the resolved rest-frame UV and H$\alpha$ emission for a sample of 979 galaxies at $0.7<z<1.5$ spanning a range in stellar mass of $10^{8-11.5}~M_\odot$. Since both rest-UV and H$\alpha$ are sensitive to on-going star-formation but over different timescales, their resolved comparison allows us to infer the burstiness in star-formation as a function of galaxy structural parameters. We generate homogenized maps of rest-UV and H$\alpha$ emission for all galaxies in our sample and stack them to compute the average UV-to-H$\alpha$ luminosity ratio as a function of galactocentric radius. We find that galaxies below stellar mass of $\sim10^{9.5}~M_\odot$, at all radii, have a UV-to-H$\alpha$ ratio higher than the equilibrium value expected from constant star-formation, indicating a significant contribution from bursty star-formation. Even for galaxies with stellar mass $\gtrsim10^{9.5} M_\odot$, the UV-to-H$\alpha$ ratio is elevated towards in their outskirts ($R/R_{eff}>1.5$), suggesting that bursty star-formation is likely prevalent in the outskirts of even the most massive galaxies but is likely over-shadowed by their brighter cores. Furthermore, we present the UV-to-H$\alpha$ ratio as a function of galaxy surface brightness, a proxy for stellar mass surface density, and find that regions below $\sim10^8~M_\odot~kpc^{-2}$ are consistent with bursty star-formation, regardless of their galaxy stellar mass, potentially suggesting that local star-formation is independent of global galaxy properties at the smallest scales.Comment: 19 pages, 8 figures; submitted to Ap

The Lyman Continuum Escape Fraction of Star-forming Galaxies at 2.4≲z≲3.72.4\lesssim z\lesssim3.7 from UVCANDELS

The UltraViolet Imaging of the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey Fields (UVCANDELS) survey is a Hubble Space Telescope (HST) Cycle-26 Treasury Program, allocated in total 164 orbits of primary Wide-Field Camera 3 Ultraviolet and Visible light F275W imaging with coordinated parallel Advanced Camera for Surveys F435W imaging, on four of the five premier extragalactic survey fields: GOODS-N, GOODS-S, EGS, and COSMOS. We introduce this survey by presenting a thorough search for galaxies at $z\gtrsim2.4$ that leak significant Lyman continuum (LyC) radiation, as well as a stringent constraint on the LyC escape fraction ($f_{\rm esc}$) from stacking the UV images of a population of star-forming galaxies with secure redshifts. Our extensive search for LyC emission and stacking analysis benefit from the catalogs of high-quality spectroscopic redshifts compiled from archival ground-based data and HST slitless spectroscopy, carefully vetted by dedicated visual inspection efforts. We report a sample of five galaxies as individual LyC leaker candidates, showing $f_{\rm esc}^{\rm rel}\gtrsim60\%$ estimated using detailed Monte Carlo analysis of intergalactic medium attenuation. We develop a robust stacking method to apply to five samples of in total 85 non-detection galaxies in the redshift range of $z\in[2.4,3.7]$. Most stacks give tight 2-$\sigma$ upper limits below $f_{\rm esc}^{\rm rel}<6\%$. A stack for a subset of 32 emission-line galaxies shows tentative LyC leakage detected at 2.9-$\sigma$, indicating $f_{\rm esc}^{\rm rel}=5.7\%$ at $z\sim2.65$, supporting the key role of such galaxies in contributing to the cosmic reionization and maintaining the UV ionization background. These new F275W and F435W imaging mosaics from UVCANDELS have been made publicly available on the Barbara A. Mikulski Archive for Space Telescopes.Comment: 33 pages, 21 figures, and 5 tables. Resubmitted after addressing the referee repor

Cancer therapy shapes the fitness landscape of clonal hematopoiesis.

Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies

Cancer therapy shapes the fitness landscape of clonal hematopoiesis.

Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies

The Ultraviolet Luminosity Function at 0.6 < z < 1 from UVCANDELS

UVCANDELS is a Hubble Space Telescope Cycle-26 Treasury Program awarded 164 orbits of primary ultraviolet (UV) F275W imaging and coordinated parallel optical F435W imaging in four CANDELS fields—GOODS-N, GOODS-S, EGS, and COSMOS—covering a total area of ∼426 arcmin2. This is ∼2.7 times larger than the area covered by previous deep-field space UV data combined, reaching a depth of about 27 and 28 ABmag (5σ in 0.”2 apertures) for F275W and F435W, respectively. Along with new photometric catalogs, we present an analysis of the rest-frame UV luminosity function (LF), relying on our UV-optimized aperture photometry method, yielding a factor of 1.5 increase over H-isophot aperture photometry in the signal-to-noise ratios of galaxies in our F275W imaging. Using well-tested photometric redshift measurements, we identify 5810 galaxies at redshifts 0.6 &lt; z &lt; 1, down to an absolute magnitude of M UV = −14.2. In order to minimize the effect of uncertainties in estimating the completeness function, especially at the faint end, we restrict our analysis to sources above 30% completeness, which provides a final sample of 4726 galaxies at −21.5 &lt; M UV &lt; −15.5. We performed a maximum likelihood estimate to derive the best-fit parameters of the UV LF. We report a best-fit faint-end slope of α=−1.359−0.041+0.041 at z ∼ 0.8. Creating subsamples at z ∼ 0.7 and z ∼ 0.9, we observe a possible evolution of α with redshift. The unobscured UV luminosity density at M UV &lt; −10 is derived as ρUV=1.339−0.030+0.027(×1026ergs−1Hz−1Mpc−3) using our best-fit LF parameters. The new F275W and F435 photometric catalogs from UVCANDELS have been made publicly available on the Barbara A. Mikulski Archive for Space Telescopes

Dose and Radioadaptive Response Analysis of Micronucleus Induction in Mouse Bone Marrow

Enhanced cellular DNA repair efficiency and suppression of genomic instability have been proposed as mechanisms underlying radio-adaptive responses following low-dose radiation exposures. We previously showed that low-dose γ irradiation does not generate radio-adaptation by lowering radiation-induced cytogenetic damage in mouse spleen. Since radiation may exert tissue-specific effects, we extended these results here by examining the effects of γ radiation on cytogenetic damage and proliferative index in bone marrow erythrocytes of C57BL/6 and BALB/c mice. In C57BL/6 mice, the induction of micronuclei in polychromatic erythrocytes (MN-PCE) was observed at radiation doses of 100 mGy and greater, and suppression of erythroblast maturation occurred at doses of &gt;500 mGy. A linear dose–response relationship for MN-PCE frequencies in C57BL/6 mice was established for radiation doses between 100 mGy and 1 Gy, with departure from linearity at doses of &gt;1 Gy. BALB/c mice exhibited increased MN-PCE frequencies above baseline following a 20 mGy radiation exposure but did not exhibit radio-sensitivity relative to C57BL/6 mice following 2 Gy exposure. Radio-adaptation of bone marrow erythrocytes was not observed in either strain of mice exposed to low-dose priming γ irradiation (single doses of 20 mGy or 100 mGy or multiple 20 mGy doses) administered at various times prior to acute 2 Gy irradiation, confirming the lack of radio-adaptive response for induction of cytogenetic damage or suppression or erythrocyte proliferation/maturation in bone marrow of these mouse strains

Risk of Lung Cancer Associated with COPD Phenotype Based on Quantitative Image Analysis

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a risk factor for lung cancer. This study evaluates alternative measures of COPD based on spirometry and quantitative image analysis to better define a phenotype that predicts lung cancer risk. METHODS: A total of 341 lung cancer cases and 752 volunteer controls, ages 21 to 89 years, participated in a structured interview, standardized CT scan, and spirometry. Logistic regression, adjusted for age, race, gender, pack-years, and inspiratory and expiratory total lung volume, was used to estimate the odds of lung cancer associated with FEV1/FVC, percent voxels less than -950 Hounsfield units on the inspiratory scan (HUI) and percent voxels less than -856 HU on expiratory scan (HUE). RESULTS: The odds of lung cancer were increased 1.4- to 3.1-fold among those with COPD compared with those without, regardless of assessment method; however, in multivariable modeling, only percent voxels \u3c-856 HUE as a continuous measure of air trapping [OR = 1.04; 95% confidence interval (CI), 1.03-1.06] and FEV1/FVC \u3c 0.70 (OR = 1.71; 95% CI, 1.21-2.41) were independent predictors of lung cancer risk. Nearly 10% of lung cancer cases were negative on all objective measures of COPD. CONCLUSION: Measures of air trapping using quantitative imaging, in addition to FEV1/FVC, can identify individuals at high risk of lung cancer and should be considered as supplementary measures at the time of screening for lung cancer. IMPACT: Quantitative measures of air trapping based on imaging provide additional information for the identification of high-risk groups who might benefit the most from lung cancer screening. Cancer Epidemiol Biomarkers Prev; 25(9); 1341-7. ©2016 AACR