Phylogenomics is a field in which genome analysis and evolutionary reconstructions are integrated. This integration is important because genome data is of great value in evolutionary reconstructions, because evolutionary analysis is critical for understanding and interpreting genomic data, and because there are feedback loops between evolutionary and genome analysis such that they need to be done in an integrated manner. In this paper I describe how I developed my particular phylogenomic approach under the guidance of my Ph.D advisor Philip C. Hanawalt. Since I was the first to use the term phylogenomics in a publication, I have decided to rename the field (at least temporarily) Philogenomics.

Boyer’s framework of scholarship was published before significant growth in digital technology. As more digital products are produced by medical educators, determining their scholarly value is of increasing importance. This scoping systematic review developed a taxonomy of digital products and determined their fit within Boyer’s framework of scholarship. We conducted a broad literature search for descriptions of digital products in the medical literature in July 2013 using Medline, EMBASE, ERIC, PSYCHinfo, and Google Scholar. A framework analysis categorized each product using Boyer’s model of scholarship, while a thematic analysis defined a taxonomy of digital products. 7422 abstracts were found and 524 met inclusion criteria. Digital products mapped primarily to the scholarship of teaching (85.4%) followed by integration (7.6%), application (5.5%), and discovery (1.5%). A taxonomy of 19 categories was defined. Web-based or computer assisted learning (41%) was described most frequently. We found that digital products are well described in medical literature and fit into Boyer’s framework of scholarship and proposed a taxonomy of digital products that parallel traditional forms of the scholarship of teaching and learning. This research should inform the development of tools to examine the impact and quality of digital products.

A document by Gary S. McDowell. Click on the document to view its contents.

A new approach to reconciling General Relativity with Quantum Field Theory is Relativization, the act of making a physical model which obeys the principles of special relativity and General Relativity. This approach immediately yields results that no other approach has. I have established the foundations and fundamentals of relativization via a set of axioms. Expressions such as appear Pμ⁢|p>=kμ⁢|p>P^{\mu}\left|p\right\rangle\,=k^{\mu}\left|p\right\rangle, or ==kμ⁢=kμ\left\langle p\right|P^{\mu}\left|p\right\rangle\,=\,\left\langle p\right|k^{% \mu}\left|p\right\rangle\,=k^{\mu}\left\langle p\right.\left|p\right\rangle\,=% k^{\mu}. Such expressions appear in textbooks and papers but they are given a clearer interpretation in this model. Using this new approach to the problem, I will formulate the standard model as a relativized model in a curved space time with a locally valid graviton-Higgs interaction. This interaction will lead to a renormalized perturbation theory that can be summed up exactly to give the amplitude of graviton-graviton interaction as approximately C⁢o⁢s⁢h⁢(p)Cosh(p). I will solve a Schrodinger equation for a gravitationally bound system and get theoretical predictions relating to the thermodynamics of Planck scale black holes. Relativization has already provided a finite quantitative prediction for the quantum corrections to the local gravitational field, and gives results compatible with established black hole thermodynamics. Further research will certainly yield new insights.

A document by Erin McKiernan. Click on the document to view its contents.

Effective and accurate communication is of critical importance when transferring patients between healthcare providers. The accuracy of handover information transmission during these encounters has not been well studied. From August 2010 to April 2011, a pilot study was completed to examine physician satisfaction and physician accuracy regarding the performance of prehospital interventions by paramedics. Our findings suggest that physician overall satisfaction (3/5 Likert score) and accuracy (16-44%) were low in our local milieu, suggesting the need for improvement processes.

A document by Erin C. McKiernan. Click on the document to view its contents.

Correspondence re: Hung, C. M., et al. 2014. “Drastic population fluctuations explain the rapid extinction of the passenger pigeon.” Proc Natl Acad Sci U S A no. 111 (29):10636-41. doi: 10.1073/pnas.1401526111.

The question is how can we make quantum field theory part of General Relativity instead of how we can quantize gravity. Here it will be shown that a Hilbert space can be defined such that the bra-ket is a four vector in ℳ\mathcal{M}inkowski space-time, =va∈ℳ\langle\psi|\phi\rangle=v^{a}\in\mathcal{M}. Similar to a Hilbert space over the field of quarternions. Minkowski space is the tangent space at an arbitrary point on a Riemannian manifold. It will then be shown that the Riemann curvature connects these spaces by operating on the probability density 4-current jaj^{a} of the local QFT. Choosing the Klein-Gordon field as a simple example QFT, the quantized Einstein-Hilbert action will then be derived. From there the expected Feynman diagrams for General Relativity can be read off. In this way one may calculate the gravitational effect due to a quantum field theoretical event.

Correspondence re: Stringer, C. 2014. “Why we are not all multiregionalists now.” Trends Ecol Evol no. 29 (5):248-251

This article examines the U.S. Army’s Comprehensive Soldier Fitness (CSF) program from a scientific, ethical, and pragmatic viewpoint. CSF is one of the largest single applications of psychological research in history, intended to develop “resilience” in every U.S. Army soldier. I highlight several areas where the available information about the program either suggests the likelihood of specific problems, or is insufficient to allow the research community to evaluate the effectiveness of CSF independently of the claims made by its originators and assurances given by other non-disinterested parties. In particular, I question (a) whether a program based on resiliency training for school-aged children can hope to address the serious mental trauma, including PTSD, faced by soldiers deployed to war zones; (b) whether the instruments used to measure the performance of the program are reliable, valid, and appropriate for the circumstances in which they are being used, and (c) whether the design and delivery of the program takes sufficient account of the conflicting real-world demands placed on the individuals involved. I conclude that the program appears to have a number of potentially problematic aspects that require wider scrutiny from psychological researchers and practitioners.

The aim of this paper is to model the level of volcanic activity on Earth-like planets over time. We consider the level of volcanic activity on a planet to be a function of the planet’s thermodynamic state. A planet is considered to become volcanically inactive once it has reached a thermodynamic steady state. We first model the heat flow in the planet’s interior by the heat equation, which we reduce to a one-dimensional Laplace equation. We then calculate the temperature field of the planet by numerically solving a spherically symmetric boundary value problem. Finally, we relate discrete time-steps in our simulation to real-time via an empirically-informed mapping. Our results indicate that Earth will remain volcanically active for a total of ∼6.0\sim 6.0 billion years since its formation, while Earth-like planets of 0.50.5 and 2.02.0 Earth masses will be active for ∼5.5\sim 5.5 and ∼7.7\sim 7.7 billion years respectively. Our model incorrectly predicts that Earth-like planets above 2.02.0 Earth masses continually increase their internal temperatures if their conductivity and density profiles are assumed to be identical to that of Earth, which suggests some limitations of the model.

A document by Jonathan P. Tennant. Click on the document to view its contents.

Correspondence re: Zimonjic et al. 2001. “Derivation of human tumor cells in vitro without widespread genomic instability.” Cancer Res no. 61 (24):8838-44. Submitted to Cancer Research 8/19/2002, rejected 8/29/2002

Correspondence re: Villeda et al. 2014.“Young blood reverses age-related impairments in cognitive function and synaptic plasticity in mice.” Nat Med no. 20 (6):659-63. doi: 10.1038/nm.3569.

Big science is on the rise. Recent endeavors, such as the Large Hadron Collider and the Human Genome Project, illustrate the rise in large-scale scientific inquiries. To assess whether big science is part of a general trend towards increased authorship, we queried the publicly available database Pubmed and measured the trend in number of authors per paper over the last century. Here we show that authorship has increased five-fold since 1913 and predict that by 2034, publications will boast an average of 8 authors.

The following are pre-publication peer reviews received on the manuscript: Will we cure cancer by sequencing thousands of genomes (Nicholson 2013), which was initially rejected and later resubmitted and published in Molecular Cytogenetics

This report summarizes the presentations and discussions on the research activities presented at XP 2014, the 15th International Conference on Agile Processes in Software Engineering and Extreme Programming, which was held May 26-30, 2014 in Rome, Italy. XP conferences are major supporters of the agile vision of software developers, the related multidisciplinary research, and bridging industrial practitioners with academia. XP 2014 continued this trend, hosting research papers divided in the topics of agile development, agile challenges and contracting, lessons learned and agile maturity, how to evolve software engineering teaching, methods and metrics, testing and beyond, and lean development.

Correspondence re: Forsberg, L. A., et al. 2014. “Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer.” Nat Genet 46 (6):624-8. doi: 10.1038/ng.2966.

Novel software development approaches are embracing abstraction and automation techniques. It is claimed that abstraction and automation techniques increase the productivity, improve the reusability and lower the complexity of the projects. In this study we address these new frontiers of software development by investigating on one novel proposal, namely the Ball. The Ball is an information ecosystem for authorised information containing web content, digital content as well as service development and integration. It is claimed to improve the reusability, productivity and security of software development while lowering the complexity. While improving the software developer's productivity it should produce smaller and more reasonable software systems, leading to a better reusability and a shorter learning phase for new developers. Up to now there exists no evidence to support these claims. In this study we analyse the Ball ecosystem from multiple perspectives. We compare it to related approaches in order to find its advantages and disadvantages. In order to provide empirical data we replicated a study where a mobile information system was developed using three different technologies. The results of this study show that the Ball ecosystem has the potential to improve the productivity of software development. However, it still needs further development and improvements before being competitive with traditional ways of developing software.

A document by Holly Dunsworth. Click on the document to view its contents.

A brief account of the Medical Hypotheses Affair may be found here: http://medicalhypotheses.blogspot.com/2010/05/medical-hypotheses-affair-times-higher.html But there is one general aspect which I learned from the experience, and which is - I think - worth further emphasis.

The Journal of Open Research Software (JORS) is an open access journal, which publishes peer reviewed software papers. Software papers describe open source software for research with high reuse potential. The authors publishing in the journal are awarded for opening up software with a peer reviewed journal article. This article is an author-based review of JORS and an experience report of the submission process of one now published paper there.

Why would anyone thank a publisher for his permission to reprint an article as part of a dissertation, instead of thanking the publisher for printing it in the first place?