An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life

Comprehensive, time‐scaled phylogenies provide a critical resource for many questions in ecology, evolution and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging.We introduce the Fish Tree of Life website and associated r package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations and diversification rate estimates for the most diverse group of vertebrate organisms, the ray‐finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by the r package, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyse the data.We demonstrate functionality with an overview of the website, and show three examples of advanced usage through the r package. First, we test for the presence of long branch attraction artefacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package.This resource makes a large comparative vertebrate dataset easily accessible via the website, while the r package enables the rapid reuse and reproducibility of research results via its ability to easily integrate with other r packages and software for molecular biology and comparative methods.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/1/mee313182-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/2/mee313182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/3/mee313182.pd

Extracting Zero-Gravity Surface Figure of a Mirror

The technical innovation involves refinement of the classic optical technique of averaging surface measurements made in different orientations with respect to gravity, so the effects of gravity cancel in the averaged image. Particularly for large, thin mirrors subject to substantial deformation, the further requirement is that mount forces must also cancel when averaged over measurement orientations. The zerogravity surface figure of a mirror in a hexapod mount is obtained by analyzing the summation of mount forces in the frame of the optic as surface metrology is averaged over multiple clockings. This is illustrated with measurements taken from the Space Interferometry Mission (SIM) PT-Ml mirror for both twofold and threefold clocking. The positive results of these measurements and analyses indicate that, from this perspective, a lighter mirror could be used; that is, one might place less reliance on the damping effects of the elliptic partial differential equations that describe the propagation of forces through glass. The advantage over prior art is relaxing the need for an otherwise substantial thickness of glass that might be needed to ensure accurate metrology in the absence of a detailed understanding and analysis of the mount forces. The general insights developed here are new, and provide the basic design principles on which mirror mount geometry may be chosen

FDTD Simulation of Thermal Noise in Open Cavities

A numerical model based on the finite-difference time-domain (FDTD) method is developed to simulate thermal noise in open cavities owing to output coupling. The absorbing boundary of the FDTD grid is treated as a blackbody, whose thermal radiation penetrates the cavity in the grid. The calculated amount of thermal noise in a one-dimensional dielectric cavity recovers the standard result of the quantum Langevin equation in the Markovian regime. Our FDTD simulation also demonstrates that in the non-Markovian regime the buildup of the intracavity noise field depends on the ratio of the cavity photon lifetime to the coherence time of thermal radiation. The advantage of our numerical method is that the thermal noise is introduced in the time domain without prior knowledge of cavity modes.Comment: 8 pages, 7 figure

A quantitative workflow for modeling diversification in material culture.

Questions about the evolution of material culture are widespread in the humanities and social sciences. Statistical modeling of long-term changes in material culture is less common due to a lack of appropriate frameworks. Our goal is to close this gap and provide robust statistical methods for examining changes in the diversity of material culture. We provide an open-source and quantitative workflow for estimating rates of origination, extinction, and preservation, as well as identifying key shift points in the diversification histories of material culture. We demonstrate our approach using two distinct kinds of data: age ranges for the production of American car models, and radiocarbon dates associated with archaeological cultures of the European Neolithic. Our approach improves on existing frameworks by disentangling the relative contributions of origination and extinction to diversification. Our method also permits rigorous statistical testing of competing hypotheses to explain changes in diversity. Finally, we stress the value of a flexible approach that can be applied to data in various forms; this flexibility allows scholars to explore commonalities between forms of material culture and ask questions about the general properties of cultural change

Association of social support during emergency department evaluation for acute coronary syndrome with subsequent posttraumatic stress symptoms

We examined the associations of different aspects of social support during emergency department (ED) evaluation for an acute cardiac event with perceptions of threat in the ED and subsequent posttraumatic stress symptoms (PSS) in 484 patients. Participants were enrolled in the ED where they reported on their perceptions of threat in the ED. Social support in the ED and PSS were assessed at inpatient bedside or by telephone a median of 3 days later. Positive aspects of social support were not associated with subsequent PSS. Anxiety-provoking social support was significantly associated with increased PSS at follow-up. Greater ED threat perception partially mediated that relationship

Restoring Ureagenesis in Hepatocytes by CRISPR/Cas9-mediated Genomic Addition to Arginase-deficient Induced Pluripotent Stem Cells.

Urea cycle disorders are incurable enzymopathies that affect nitrogen metabolism and typically lead to hyperammonemia. Arginase deficiency results from a mutation in Arg1, the enzyme regulating the final step of ureagenesis and typically results in developmental disabilities, seizures, spastic diplegia, and sometimes death. Current medical treatments for urea cycle disorders are only marginally effective, and for proximal disorders, liver transplantation is effective but limited by graft availability. Advances in human induced pluripotent stem cell research has allowed for the genetic modification of stem cells for potential cellular replacement therapies. In this study, we demonstrate a universally-applicable CRISPR/Cas9-based strategy utilizing exon 1 of the hypoxanthine-guanine phosphoribosyltransferase locus to genetically modify and restore arginase activity, and thus ureagenesis, in genetically distinct patient-specific human induced pluripotent stem cells and hepatocyte-like derivatives. Successful strategies restoring gene function in patient-specific human induced pluripotent stem cells may advance applications of genetically modified cell therapy to treat urea cycle and other inborn errors of metabolism