Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.

Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute-funded cancer centers. Although each of the participating cancer centers is structured differently, and leaders' titles vary, we know firsthand there are similarities in both the issues we face and the solutions we achieve. As a consortium, we have initiated a dedicated listserv, an open-initiatives program, and targeted biannual face-to-face meetings. These meetings are a place to review our priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues we, as informatics leaders, individually face at our respective institutions and cancer centers. Here we provide a brief history of the CI4CC organization and meeting highlights from the latest CI4CC meeting that took place in Napa, California from October 14-16, 2019. The focus of this meeting was "intersections between informatics, data science, and population science." We conclude with a discussion on "hot topics" on the horizon for cancer informatics

Co-evolution of density and topology in a simple model of city formation

We study the influence that population density and the road network have on each others' growth and evolution. We use a simple model of formation and evolution of city roads which reproduces the most important empirical features of street networks in cities. Within this framework, we explicitely introduce the topology of the road network and analyze how it evolves and interact with the evolution of population density. We show that accessibility issues -pushing individuals to get closer to high centrality nodes- lead to high density regions and the appearance of densely populated centers. In particular, this model reproduces the empirical fact that the density profile decreases exponentially from a core district. In this simplified model, the size of the core district depends on the relative importance of transportation and rent costs.Comment: 13 pages, 13 figure

Ultra Long Period Cepheids: a primary standard candle out to the Hubble flow

The cosmological distance ladder crucially depends on classical Cepheids (with P=3-80 days), which are primary distance indicators up to 33 Mpc. Within this volume, very few SNe Ia have been calibrated through classical Cepheids, with uncertainty related to the non-linearity and the metallicity dependence of their period-luminosity (PL) relation. Although a general consensus on these effects is still not achieved, classical Cepheids remain the most used primary distance indicators. A possible extension of these standard candles to further distances would be important. In this context, a very promising new tool is represented by the ultra-long period (ULP) Cepheids (P \geq 80 days), recently identified in star-forming galaxies. Only a small number of ULP Cepheids have been discovered so far. Here we present and analyse the properties of an updated sample of 37 ULP Cepheids observed in galaxies within a very large metallicity range of 12+log(O/H) from ~7.2 to 9.2 dex. We find that their location in the colour(V-I)-magnitude diagram as well as their Wesenheit (V-I) index-period (WP) relation suggests that they are the counterparts at high luminosity of the shorter-period (P \leq 80 days) classical Cepheids. However, a complete pulsation and evolutionary theoretical scenario is needed to properly interpret the true nature of these objects. We do not confirm the flattening in the studied WP relation suggested by Bird et al. (2009). Using the whole sample, we find that ULP Cepheids lie around a relation similar to that of the LMC, although with a large spread (~0.4 mag).Comment: 8 pages, 4 figures, accepted for publication in Astrophysics & Space Scienc

Observational constraint on generalized Chaplygin gas model

We investigate observational constraints on the generalized Chaplygin gas (GCG) model as the unification of dark matter and dark energy from the latest observational data: the Union SNe Ia data, the observational Hubble data, the SDSS baryon acoustic peak and the five-year WMAP shift parameter. It is obtained that the best fit values of the GCG model parameters with their confidence level are $A_{s}=0.73^{+0.06}_{-0.06}$ ($1\sigma$) $^{+0.09}_{-0.09}$ $(2\sigma)$, $\alpha=-0.09^{+0.15}_{-0.12}$ ($1\sigma$) $^{+0.26}_{-0.19}$ $(2\sigma)$. Furthermore in this model, we can see that the evolution of equation of state (EOS) for dark energy is similar to quiessence, and its current best-fit value is $w_{0de}=-0.96$ with the $1\sigma$ confidence level $-0.91\geq w_{0de}\geq-1.00$.Comment: 9 pages, 5 figure

Genetic Incompatibility Dampens Hybrid Fertility More Than Hybrid Viability: Yeast as a Case Study

Genetic incompatibility is believed to be the major cause of postzygotic reproductive isolation. Despite huge efforts seeking for speciation-related incompatibilities in the past several decades, a general understanding of how genetic incompatibility evolves in affecting hybrid fitness is not available, primarily due to the fact that the number of known incompatibilities is small. Instead of further mapping specific incompatible genes, in this paper we aimed to know the overall effects of incompatibility on fertility and viability, the two aspects of fitness, by examining 89 gametes produced by yeast S. cerevisiae - S. paradoxus F1 hybrids. Homozygous F2 hybrids formed by autodiploidization of F1 gametes were subject to tests for growth rate and sporulation efficiency. We observed much stronger defects in sporulation than in clonal growth for every single F2 hybrid strain, indicating that genetic incompatibility affects hybrid fertility more than hybrid viability in yeast. We related this finding in part to the fast-evolving nature of meiosis-related genes, and proposed that the generally low expression levels of these genes might be a cause of the observation

High Yield Production Process for Shigella Outer Membrane Particles

Gram-negative bacteria naturally shed particles that consist of outer membrane lipids, outer membrane proteins, and soluble periplasmic components. These particles have been proposed for use as vaccines but the yield has been problematic. We developed a high yielding production process of genetically derived outer membrane particles from the human pathogen Shigella sonnei. Yields of approximately 100 milligrams of membrane-associated proteins per liter of fermentation were obtained from cultures of S. sonnei ΔtolR ΔgalU at optical densities of 30–45 in a 5 L fermenter. Proteomic analysis of the purified particles showed the preparation to primarily contain predicted outer membrane and periplasmic proteins. These were highly immunogenic in mice. The production of these outer membrane particles from high density cultivation of bacteria supports the feasibility of scaling up this approach as an affordable manufacturing process. Furthermore, we demonstrate the feasibility of using this process with other genetic manipulations e.g. abolition of O antigen synthesis and modification of the lipopolysaccharide structure in order to modify the immunogenicity or reactogenicity of the particles. This work provides the basis for a large scale manufacturing process of Generalized Modules of Membrane Antigens (GMMA) for production of vaccines from Gram-negative bacteria

Annexin II represents metastatic potential in clear-cell renal cell carcinoma

BACKGROUND: Annexin II (ANX2) is a multi-functional protein involved in cell proliferation and membrane physiology and is related to cancer progression. The purpose of this study was to assess ANX2 expression in clear-cell (cc) renal cell carcinoma (RCC)

Network Structure of Vertebrate Scavenger Assemblages at the Global Scale: Drivers and Ecosystem Functioning Implications

The organization of ecological assemblages has important implications for ecosystem functioning, but little is known about how scavenger communities organize at the global scale. Here, we test four hypotheses on the factors affecting the network structure of terrestrial vertebrate scavenger assemblages and its implications on ecosystem functioning. We expect scavenger assemblages to be more nested (i.e. structured): 1) in species‐rich and productive regions, as nestedness has been linked to high competition for carrion resources, and 2) regions with low human impact, because the most efficient carrion consumers that promote nestedness are large vertebrate scavengers, which are especially sensitive to human persecution. 3) We also expect climatic conditions to affect assemblage structure, because some scavenger assemblages have been shown to be more nested in colder months. Finally, 4) we expect more organized assemblages to be more efficient in the consumption of the resource. We first analyzed the relationship between the nestedness of the scavenger assemblages and climatic variables (i.e. temperature, precipitation, temperature variability and precipitation variability), ecosystem productivity and biomass (i.e. NDVI) and degree of human impact (i.e. human footprint) using 53 study sites in 22 countries across five continents. Then, we related structure (i.e. nestedness) with its function (i.e. carrion consumption rate). We found a more nested structure for scavenger assemblages in regions with higher NDVI values and lower human footprint. Moreover, more organized assemblages were more efficient in the consumption of carrion. However, our results did not support the prediction that the structure of the scavenger assemblages is directly related to climate. Our findings suggest that the nested structure of vertebrate scavenger assemblages affects its functionality and is driven by anthropogenic disturbance and ecosystem productivity worldwide. Disarray of scavenger assemblage structure by anthropogenic disturbance may lead to decreases in functionality of the terrestrial ecosystems via loss of key species and trophic facilitation processes