Spatial structure increases the waiting time for cancer

Cancer results from a sequence of genetic and epigenetic changes which lead to a variety of abnormal phenotypes including increased proliferation and survival of somatic cells, and thus, to a selective advantage of pre-cancerous cells. The notion of cancer progression as an evolutionary process has been experiencing increasing interest in recent years. Many efforts have been made to better understand and predict the progression to cancer using mathematical models; these mostly consider the evolution of a well-mixed cell population, even though pre-cancerous cells often evolve in highly structured epithelial tissues. We propose a novel model of cancer progression that considers a spatially structured cell population where clones expand via adaptive waves. This model is used to asses two different paradigms of asexual evolution that have been suggested to delineate the process of cancer progression. The standard scenario of periodic selection assumes that driver mutations are accumulated strictly sequentially over time. However, when the mutation supply is sufficiently high, clones may arise simultaneously on distinct genetic backgrounds, and clonal adaptation waves interfere with each other. We find that in the presence of clonal interference, spatial structure increases the waiting time for cancer, leads to a patchwork structure of non-uniformly sized clones, decreases the survival probability of virtually neutral (passenger) mutations, and that genetic distance begins to increase over a characteristic length scale, determined here. These characteristic features of clonal interference may help to predict the onset of cancers with pronounced spatial structure and to interpret spatially-sampled genetic data obtained from biopsies. Our estimates suggest that clonal interference likely occurs in the progressing colon cancer, and possibly other cancers where spatial structure matters.Comment: 21 page

The Bolocam Galactic Plane Survey IV: 1.1 and 0.35 mm Dust Continuum Emission in the Galactic Center Region

The Bolocam Galactic Plane Survey (BGPS) data for a six square degree region of the Galactic plane containing the Galactic center is analyzed and compared to infrared and radio continuum data. The BGPS 1.1 mm emission consists of clumps interconnected by a network of fainter filaments surrounding cavities, a few of which are filled with diffuse near-IR emission indicating the presence of warm dust or with radio continuum characteristic of HII regions or supernova remnants. New 350 {\mu}m images of the environments of the two brightest regions, Sgr A and B, are presented. Sgr B2 is the brightest mm-emitting clump in the Central Molecular Zone and may be forming the closest analog to a super star cluster in the Galaxy. The Central Molecular Zone (CMZ) contains the highest concentration of mm and sub-mm emitting dense clumps in the Galaxy. Most 1.1 mm features at positive longitudes are seen in silhouette against the 3.6 to 24 {\mu}m background observed by the Spitzer Space Telescope. However, only a few clumps at negative longitudes are seen in absorption, confirming the hypothesis that positive longitude clumps in the CMZ tend to be on the near-side of the Galactic center, consistent with the suspected orientation of the central bar in our Galaxy. Some 1.1 mm cloud surfaces are seen in emission at 8 {\mu}m, presumably due to polycyclic aromatic hydrocarbons (PAHs). A ~0.2\degree (~30 pc) diameter cavity and infrared bubble between l \approx 0.0\degree and 0.2\degree surrounds the Arches and Quintuplet clusters and Sgr A. The bubble contains several clumpy dust filaments that point toward Sgr A\ast; its potential role in their formation is explored. [abstract truncated]Comment: 76 pages, 22 figures, published in ApJ: http://iopscience.iop.org/0004-637X/721/1/137

Gender Differences in Russian Colour Naming

In the present study we explored Russian colour naming in a web-based psycholinguistic experiment (http://www.colournaming.com). Colour singletons representing the Munsell Color Solid (N=600 in total) were presented on a computer monitor and named using an unconstrained colour-naming method. Respondents were Russian speakers (N=713). For gender-split equal-size samples (NF=333, NM=333) we estimated and compared (i) location of centroids of 12 Russian basic colour terms (BCTs); (ii) the number of words in colour descriptors; (iii) occurrences of BCTs most frequent non-BCTs. We found a close correspondence between females’ and males’ BCT centroids. Among individual BCTs, the highest inter-gender agreement was for seryj ‘grey’ and goluboj ‘light blue’, while the lowest was for sinij ‘dark blue’ and krasnyj ‘red’. Females revealed a significantly richer repertory of distinct colour descriptors, with great variety of monolexemic non-BCTs and “fancy” colour names; in comparison, males offered relatively more BCTs or their compounds. Along with these measures, we gauged denotata of most frequent CTs, reflected by linguistic segmentation of colour space, by employing a synthetic observer trained by gender-specific responses. This psycholinguistic representation revealed females’ more refined linguistic segmentation, compared to males, with higher linguistic density predominantly along the redgreen axis of colour space

Three temperate Neptunes orbiting nearby stars

We present the discovery of three modestly irradiated, roughly Neptune-mass planets orbiting three nearby Solartype stars. HD 42618 b has a minimum mass of 15.4±2.4 M⊕, a semimajor axis of 0.55 au, an equilibrium temperature of 337 K, and is the first planet discovered to orbit the solar analogue host star, HD 42618. We also discover new planets orbiting the known exoplanet host stars HD 164922 and HD 143761 (p CrB). The new planet orbiting HD 164922 has a minimum mass of 12.9±1.6 M⊕ and orbits interior to the previously known Jovian mass planet orbiting at 2.1 au. HD 164922 c has a semimajor axis of 0.34 au and an equilibrium temperature of 418 K. HD 143761 c orbits with a semimajor axis of 0.44 au, has a minimum mass of 25±2 M⊕, and is the warmest of the three new planets with an equilibrium temperature of 445 K. It orbits exterior to the previously known warm Jupiter in the system. A transit search using space-based CoRoT data and ground-based photometry from the Automated Photometric Telescopes (APTs) at Fairborn Observatory failed to detect any transits, but the precise, high-cadence APT photometry helped to disentangle planetary-reflex motion from stellar activity. These planets were discovered as part of an ongoing radial velocity survey of bright, nearby, chromospherically inactive stars using the Automated Planet Finder (APF) telescope at Lick Observatory. The high-cadence APF data combined with nearly two decades of radial velocity data from Keck Observatory and gives unprecedented sensitivity to both short-period low-mass, and long-period intermediate-mass planets

The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes

Nitrogen-fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2 -fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades. We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen-fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane-bound symbiosomes (SYMs). Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs. We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species-rich pantropical legume clade

astroplan: An Open Source Observation Planning Package in Python

We present astroplan - an open source, open development, Astropy affiliated package for ground-based observation planning and scheduling in Python. astroplan is designed to provide efficient access to common observational quantities such as celestial rise, set, and meridian transit times and simple transformations from sky coordinates to altitude-azimuth coordinates without requiring a detailed understanding of astropy's implementation of coordinate systems. astroplan provides convenience functions to generate common observational plots such as airmass and parallactic angle as a function of time, along with basic sky (finder) charts. Users can determine whether or not a target is observable given a variety of observing constraints, such as airmass limits, time ranges, Moon illumination/separation ranges, and more. A selection of observation schedulers are included which divide observing time among a list of targets, given observing constraints on those targets. Contributions to the source code from the community are welcome

Leaf Trait-Environment Relationships in a Subtropical Broadleaved Forest in South-East China

Although trait analyses have become more important in community ecology, trait-environment correlations have rarely been studied along successional gradients. We asked which environmental variables had the strongest impact on intraspecific and interspecific trait variation in the community and which traits were most responsive to the environment. We established a series of plots in a secondary forest in the Chinese subtropics, stratified by successional stages that were defined by the time elapsed since the last logging activities. On a total of 27 plots all woody plants were recorded and a set of individuals of every species was analysed for leaf traits, resulting in a trait matrix of 26 leaf traits for 122 species. A Fourth Corner Analysis revealed that the mean values of many leaf traits were tightly related to the successional gradient. Most shifts in traits followed the leaf economics spectrum with decreasing specific leaf area and leaf nutrient contents with successional time. Beside succession, few additional environmental variables resulted in significant trait relationships, such as soil moisture and soil C and N content as well as topographical variables. Not all traits were related to the leaf economics spectrum, and thus, to the successional gradient, such as stomata size and density. By comparing different permutation models in the Fourth Corner Analysis, we found that the trait-environment link was based more on the association of species with the environment than of the communities with species traits. The strong species-environment association was brought about by a clear gradient in species composition along the succession series, while communities were not well differentiated in mean trait composition. In contrast, intraspecific trait variation did not show close environmental relationships. The study confirmed the role of environmental trait filtering in subtropical forests, with traits associated with the leaf economics spectrum being the most responsive ones

Impact of sex on response to neoadjuvant chemotherapy in patients with bladder cancer

© 2020 Elsevier Ltd. All rights reserved. This manuscript is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence http://creativecommons.org/licenses/by-nc-nd/4.0/.Objective: To assess the effect of patient's sex on response to neoadjuvant chemotherapy (NAC) in patients with clinically nonmetastatic muscle-invasive bladder cancer (MIBC). Methods: Complete pathologic response, defined as ypT0N0 at radical cystectomy, and downstaging were evaluated using sex-adjusted univariable and multivariable logistic regression modeling. We used interaction terms to account for age of menopause and smoking status. The association of sex with overall survival and cancer-specific survival was evaluated using Cox regression analyses. Results: A total of 1,031 patients were included in the analysis, 227 (22%) of whom were female. Female patients had a higher rate of extravesical disease extension (P = 0.01). After the administration of NAC, ypT stage was equally distributed between sexes (P = 0.39). On multivariable logistic regression analyses, there was no difference between the sexes or age of menopause with regards to ypT0N0 rates or downstaging (all P > 0.5). On Cox regression analyses, sex was associated with neither overall survival (hazard ratio 1.04, 95% confidence interval 0.75–1.45, P = 0.81) nor cancer-specific survival (hazard ratio 1.06, 95% confidence interval 0.71–1.58, P = 0.77). Conclusion: Our study generates the hypothesis that NAC equalizes the preoperative disparity in pathologic stage between males and females suggesting a possible differential response between sexes. This might be the explanation underlying the comparable survival outcomes between sexes despite females presenting with more advanced tumor stage.Peer reviewedFinal Accepted Versio