X-ray phase contrast imaging of biological specimens with tabletop synchrotron radiation

Since their discovery in 1896, x-rays have had a profound impact on science, medicine and technology. Here we show that the x-rays from a novel tabletop source of bright coherent synchrotron radiation can be applied to phase contrast imaging of biological specimens, yielding superior image quality and avoiding the need for scarce or expensive conventional sources

Fueling the gender gap? Oil and women's labor and marriage market outcomes

This paper analyzes the effect of resource-based economic specialization on women's labor market outcomes. Using information on the location and discovery of major oil fields in the Southern United States coupled with a county-level panel derived from US Census data for 1900-1940, we specifically test the hypothesis that the presence of mineral resources can induce changes in the sectoral composition of the local economy that are detrimental to women's labor market outcomes. We find evidence that the discovery of oil at the county level may constitute a substantial male biased demand shock to local labor markets, as it is associated with a higher gender pay gap. However, we find no evidence that oil wealth lowers female labor force participation or has any impact on local marriage and fertility patterns. While our results are consistent with oil shocks limiting female labor market opportunities in some sectors (mainly manufacturing), this effect tends to be compensated by the higher availability of service sector jobs for women who are therefore not driven out of the labor market

Economic Integration in the Euro-Mediterranean Region

This study evaluates the effects of the current Euro-Mediterranean Free Trade Agreement for the EU and the Mediterranean region, in order to assist policy makers in defining the next steps in the Euro-Mediterranean Road map till 2010 and beyond. It provides quantitative, qualitative and sectoral assessment of the impacts of the Euro-Mediterranean FTA on trade and investment, points out the partnerships’ strengths and weaknesses and provides policy recommendations with the view of realizing a goal of a well functioning free trade area in the future. The focus of the study is on Egypt, Israel, Jordan, Morocco, and Tunisia (MED5). [...

Community Structure and Market Outcomes: A Repeated Games in Networks Approach

Consider a large market with asymmetric information, in which sellers choose whether to cooperate or deviate and ‘cheat’ their buyers, and buyers decide whether to re-purchase from different sellers. We model active trade relationships as links in a buyer-seller network and suggest a framework for studying repeated games in such networks. In our framework, buyers and sellers have rich yet incomplete knowledge of the network structure; allowing us to derive meaningful conditions that determine whether a network is consistent with trade and cooperation between every buyer and seller that are connected. We show that three network features reduce the minimal discount factor necessary for sustaining cooperation: moderate competition, sparseness, and segregation. We find that the incentive constraints rule out networks that maximize the volume of trade and that the constrained trade maximizing networks are in between ‘old world’ segregated and sparse networks, and a ‘global market’

PieParty: Visualizing cells from scRNA-seq data as pie charts

Abstract Single cell RNA sequencing (scRNA-seq) has been a transformative technology in many research fields. Dimensional reduction techniques such as UMAP and tSNE are used to visualize scRNA-seq data in two or three dimensions in order for cells to be clustered in biologically meaningful ways. Subsequently, gene expression is frequently mapped onto these plots to show the distribution of gene expression across the plots, for instance to distinguish cell types. However, plotting each cell with only one color leads to repetitive and unintuitive representations. Here, we present Pie Party, which allows scRNA-seq data to be plotted such that every cell is represented as a pie chart, and every slice in the pie charts corresponds to the gene expression of individual genes. This allows for the simultaneous visualization of the expression of multiple genes and gene networks. The resulting figures are information dense, space efficient and highly intuitive. PieParty is publicly available on GitHub at https://github.com/harbourlab/PieParty. Competing Interest Statement The authors have declared no competing interest. Footnotes * ↵☩ Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center, Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA. * https://github.com/harbourlab/PiePart

Abstract 2764: Mechanisms of genomic-microenvironmental interactions in uveal melanoma

Abstract Uveal melanoma (UM) is the most common primary eye cancer and has a high rate of metastasis with liver tropism. UM can be stratified according to metastatic risk into low risk Class 1 and high risk Class 2 tumor. Biallelic mutational inactivation of the tumor suppressor BAP1 is the quintessential molecular feature of Class 2 UM, but the mechanism by which loss of BAP1 leads to metastasis is poorly understood. We recently showed using single-cell RNA sequencing that the tumor microenvironment of primary and metastatic Class 2 UM is characterized by large numbers of inhibitory T cells and macrophages. Taken together, these findings led us to hypothesize that loss of BAP1 triggers changes in tumor-immune cell interactions that lead to an immunosuppressive microenvironment. To test this hypothesis, we performed RNA-seq and proteomic mass spectrometry in uveal melanocytes and UM cells engineered to lack BAP1 expression. These experiments identified a small cassette of immune modulatory genes that are up-regulated at the mRNA and protein levels following BAP1 loss. These proteins are known to drive monocytes towards type 2 macrophage polarization, which secrete cytokines that can inhibit T cell activation. Our findings suggest that altered interaction between UM cells and monocytes may be key to the emergence of metastatic competence in UM, and we are exploring this possibility with function experiments that may open the door to targeted therapy to subvert this process. Citation Format: Christopher J. Kaler, James J. Dollar, Stefan Kurtenbach, Jeffim N. Kuznetsov, Michael A. Durante, J. William Harbour. Mechanisms of genomic-microenvironmental interactions in uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2764