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A people's future of the United States : speculative fiction from 25 extraordinary writers
\"For many Americans, imagining a bright future has always been an act of resistance. A People's Future of the United States presents twenty never-before-published stories by a diverse group of writers, featuring voices both new and well-established. These stories imagine their characters fighting everything from government surveillance, to corporate cities, to climate change disasters, to nuclear wars. But fear not: A People's Future also invites readers into visionary futures in which the country is shaped by justice, equity, and joy. Edited by Victor LaValle and John Joseph Adams, this collection features a glittering landscape of moving, visionary stories written from the perspective of people of color, indigenous writers, women, queer & trans people, Muslims and other people whose lives are often at risk\" -- Provided by publisher.
Book
A method for analysis of phenotypic change for phenotypes described by high-dimensional data
The analysis of phenotypic change is important for several evolutionary biology disciplines, including phenotypic plasticity, evolutionary developmental biology, morphological evolution, physiological evolution, evolutionary ecology and behavioral evolution. It is common for researchers in these disciplines to work with multivariate phenotypic data. When phenotypic variables exceed the number of research subjects--data called 'high-dimensional data'--researchers are confronted with analytical challenges. Parametric tests that require high observation to variable ratios present a paradox for researchers, as eliminating variables potentially reduces effect sizes for comparative analyses, yet test statistics require more observations than variables. This problem is exacerbated with data that describe 'multidimensional' phenotypes, whereby a description of phenotype requires high-dimensional data. For example, landmark-based geometric morphometric data use the Cartesian coordinates of (potentially) many anatomical landmarks to describe organismal shape. Collectively such shape variables describe organism shape, although the analysis of each variable, independently, offers little benefit for addressing biological questions. Here we present a nonparametric method of evaluating effect size that is not constrained by the number of phenotypic variables, and motivate its use with example analyses of phenotypic change using geometric morphometric data. Our examples contrast different characterizations of body shape for a desert fish species, associated with measuring and comparing sexual dimorphism between two populations. We demonstrate that using more phenotypic variables can increase effect sizes, and allow for stronger inferences.
Journal Article
Global field observations of tree die-off reveal hotter-drought fingerprint for Earth’s forests
Earth’s forests face grave challenges in the Anthropocene, including hotter droughts increasingly associated with widespread forest die-off events. But despite the vital importance of forests to global ecosystem services, their fates in a warming world remain highly uncertain. Lacking is quantitative determination of commonality in climate anomalies associated with pulses of tree mortality—from published, field-documented mortality events—required for understanding the role of extreme climate events in overall global tree die-off patterns. Here we established a geo-referenced global database documenting climate-induced mortality events spanning all tree-supporting biomes and continents, from 154 peer-reviewed studies since 1970. Our analysis quantifies a global “hotter-drought fingerprint” from these tree-mortality sites—effectively a hotter and drier climate signal for tree mortality—across 675 locations encompassing 1,303 plots. Frequency of these observed mortality-year climate conditions strongly increases nonlinearly under projected warming. Our database also provides initial footing for further community-developed, quantitative, ground-based monitoring of global tree mortality.
Tree mortality is increasing due to droughts and other climate change-related stressors, but isolating climate signals for tree mortality is challenging. Here, the authors assemble a geo-referenced global database that quantifies how drought and hotter climate drive tree mortality events.
Journal Article
Capsule carbohydrate structure determines virulence in Acinetobacter baumannii
Acinetobacter baumannii is a highly antibiotic-resistant bacterial pathogen for which novel therapeutic approaches are needed. Unfortunately, the drivers of virulence in A . baumannii remain uncertain. By comparing genomes among a panel of A . baumannii strains we identified a specific gene variation in the capsule locus that correlated with altered virulence. While less virulent strains possessed the intact gene gtr6 , a hypervirulent clinical isolate contained a spontaneous transposon insertion in the same gene, resulting in the loss of a branchpoint in capsular carbohydrate structure. By constructing isogenic gtr6 mutants, we confirmed that gtr6- disrupted strains were protected from phagocytosis in vitro and displayed higher bacterial burden and lethality in vivo . Gtr6 + strains were phagocytized more readily and caused lower bacterial burden and no clinical illness in vivo . We found that the CR3 receptor mediated phagocytosis of gtr6+ , but not gtr6 -, strains in a complement-dependent manner. Furthermore, hypovirulent gtr6+ strains demonstrated increased virulence in vivo when CR3 function was abrogated. In summary, loss-of-function in a single capsule assembly gene dramatically altered virulence by inhibiting complement deposition and recognition by phagocytes across multiple A . baumannii strains. Thus, capsular structure can determine virulence among A . baumannii strains by altering bacterial interactions with host complement-mediated opsonophagocytosis.
Journal Article
The Sensitivity of Eclipse Mapping to Planetary Rotation
Mapping exoplanets across phases and during secondary eclipse is a powerful technique for characterizing Hot Jupiters in emission. Since these planets are expected to rotate about axes normal to their orbital planes, with rotation periods synchronized with their orbital periods, mapping provides a direct correspondence between the orbital phase and planetary longitude. We develop a framework to understand the information content of planets where their rotation states are not well constrained, by constructing bases of light curves across different rotation rates and obliquities that are orthogonal in integrated flux across the secondary eclipse. These demonstrate that brightness variation during eclipse may arise from a variety of rotation rates, obliquities, and map structures, requiring priors to properly disentangle each of these components. By modeling eclipse observations of the Warm Jupiter HAT-P-18b we demonstrate that, at a signal-to-noise equivalent to ∼10 orbits with JWST, confusion about map structure is likely a concern only at the upper physical limits of possible rotation rates. Even without priors, one may nevertheless be able to put an order-of-magnitude constraint on rotation rate by determining at what rates the fitted map complexity is minimized, a prescription whose efficacy increases if out-of-eclipse data are available to isolate the effects of rotation. Finally, in the limit of maps with longitudinal symmetry, the projected obliquity in the plane of the sky determines the information available during eclipse, ranging from nondetections of structure to a basic constraint on hemispherical asymmetry and orientation depending on the obliquity angle.
Journal Article
في جوف النكتة : الفكاهة لعكس هندسة العقل
الفكاهة تقف خلف أسئلة حول ما نضحك لأجله لماذا نرى الطرفة القديمة وكأنها موضة قديمة ؟ كيف تاثرت الفكاهة بالتطور ؟ النكتة لها جوف، وفي كل مرة ستخدم غرضا ما، إذ تتعدد أغراضها وبالطبع لن تنجح النكتة المغشوشة ! فإما أن تضحك لها، أو أن لا تتفاعل معها. يفكك هذا الكتاب الفكاهة وعلاقتها بالأدراك ويكشف أدوارا تلعبها الفكاهة في حياتنا اليومية ربما لم ننتبه لها بالاصل، وربما لم لكن نعرف أنها نابعة من الفكاهة الضحك المعدي والفكاهة الإدراكية، كلها مواضيع ساخنة ترتبط بالتطور والنظرية الداروينية التي انطلقت كسفينة لا يمكن إيقافها طالما توفرت رياح المعرفة وتوفر السؤال الصحيح.
Book
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
The fit of atomic models of protein structures to high-resolution cryo-electron microscopy maps can be assessed with a validation tool, EMRinger.
Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report EMRinger, a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (
https://github.com/fraser-lab/EMRinger
) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.
Journal Article