Genome3D: A Viewer-Model Framework for Integrating and Visualizing Multi-Scale Epigenomic Information within a Three-Dimensional Genome

Background New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation. Results We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order to integrate and visualize large volume of data, novel statistical and mathematical approaches have been developed to reduce the size of the data. To our knowledge, this is the first such tool developed that can visualize human genome in three-dimension. We describe here the major features of Genome3D and discuss our multi-scale data framework using a representative basic physical model. We then demonstrate many of the issues and benefits of multi-resolution data integration. Conclusions Genome3D is a software visualization tool that explores a wide range of structural genomic and epigenetic data. Data from various sources of differing scales can be integrated within a hierarchical framework that is easily adapted to new developments concerning the structure of the physical genome. In addition, our tool has a simple annotation mechanism to incorporate non-structural information. Genome3D is unique is its ability to manipulate large amounts of multi-resolution data from diverse sources to uncover complex and new structural relationships within the genome

Science and Film-making

The essay reviews the literature, mostly historical, on the relationship between science and film-making, with a focus on the science documentary. It then discusses the circumstances of the emergence of the wildlife making-of documentary genre. The thesis examined here is that since the early days of cinema, film-making has evolved from being subordinate to science, to being an equal partner in the production of knowledge, controlled by non-scientists

Fixing the BMS Frame of Numerical Relativity Waveforms with BMS Charges

The Bondi-van der Burg-Metzner-Sachs (BMS) group, which uniquely describes the symmetries of asymptotic infinity and therefore of the gravitational waves that propagate there, has become increasingly important for accurate modeling of waveforms. In particular, waveform models, such as post-Newtonian (PN) expressions, numerical relativity (NR), and black hole perturbation theory, produce results that are in different BMS frames. Consequently, to build a model for the waveforms produced during the merging of compact objects, which ideally would be a hybridization of PN, NR, and black hole perturbation theory, one needs a fast and robust method for fixing the BMS freedoms. In this work, we present the first means of fixing the entire BMS freedom of NR waveforms to match the frame of either PN waveforms or black hole perturbation theory. We achieve this by finding the BMS transformations that change certain charges in a prescribed way -- e.g., finding the center-of-mass transformation that maps the center-of-mass charge to a mean of zero. We find that this new method is 20 times faster, and more correct when mapping to the superrest frame, than previous methods that relied on optimization algorithms. Furthermore, in the course of developing this charge-based frame fixing method, we compute the PN expression for the Moreschi supermomentum to 3PN order without spins and 2PN order with spins. This Moreschi supermomentum is effectively equivalent to the energy flux or the null memory contribution at future null infinity $\mathscr{I}^{+}$. From this PN calculation, we also compute oscillatory ($m\not=0$ modes) and spin-dependent memory terms that have not been identified previously or have been missing from strain expressions in the post-Newtonian literature. <br

Adding Gravitational Memory to Waveform Catalogs using BMS Balance Laws

Accurate models of gravitational waves from merging binary black holes are crucial for detectors to measure events and extract new science. One important feature that is currently missing from the Simulating eXtreme Spacetimes (SXS) Collaboration's catalog of waveforms for merging black holes, and other waveform catalogs, is the gravitational memory effect: a persistent, physical change to spacetime that is induced by the passage of transient radiation. We find, however, that by exploiting the Bondi-Metzner-Sachs (BMS) balance laws, which come from the extended BMS transformations, we can correct the strain waveforms in the SXS catalog to include the missing displacement memory. Our results show that these corrected waveforms satisfy the BMS balance laws to a much higher degree of accuracy. Furthermore, we find that these corrected strain waveforms coincide especially well with the waveforms obtained from Cauchy-characteristic extraction (CCE) that already exhibit memory effects. These corrected strain waveforms also evade the transient junk effects that are currently present in CCE waveforms. Lastly, we make our code for computing these contributions to the BMS balance laws and memory publicly available as a part of the python package $\texttt{sxs}$, thus enabling anyone to evaluate the expected memory effects and violation of the BMS balance laws

Fixing the BMS Frame of Numerical Relativity Waveforms

Understanding the Bondi-Metzner-Sachs (BMS) frame of the gravitational waves produced by numerical relativity is crucial for ensuring that analyses on such waveforms are performed properly. It is also important that models are built from waveforms in the same BMS frame. Up until now, however, the BMS frame of numerical waveforms has not been thoroughly examined, largely because the necessary tools have not existed. In this paper, we show how to analyze and map to a suitable BMS frame for numerical waveforms calculated with the Spectral Einstein Code (SpEC). However, the methods and tools that we present are general and can be applied to any numerical waveforms. We present an extensive study of 13 binary black hole systems that broadly span parameter space. From these simulations, we extract the strain and also the Weyl scalars using both SpECTRE's Cauchy-characteristic extraction module and also the standard extrapolation procedure with a displacement memory correction applied during post-processing. First, we show that the current center-of-mass correction used to map these waveforms to the center-of-mass frame is not as effective as previously thought. Consequently, we also develop an improved correction that utilizes asymptotic Poincar\'e charges instead of a Newtonian center-of-mass trajectory. Next, we map our waveforms to the post-Newtonian (PN) BMS frame using a PN strain waveform. This helps us find the unique BMS transformation that minimizes the $L^{2}$ norm of the difference between the numerical and PN strain waveforms during the early inspiral phase. We find that once the waveforms are mapped to the PN BMS frame, they can be hybridized with a PN strain waveform much more effectively than if one used any of the previous alignment schemes, which only utilize the Poincar\'e transformations

High Precision Ringdown Modeling: Multimode Fits and BMS Frames

Quasi-normal mode (QNM) modeling is an invaluable tool for studying strong gravity, characterizing remnant black holes, and testing general relativity. To date, most studies have focused on the dominant $(2, 2)$ mode, and have fit to standard strain waveforms from numerical relativity. But, as gravitational wave observatories become more sensitive, they can resolve higher-order modes. Multimode fits will be critically important, and in turn require a more thorough treatment of the asymptotic frame at $\mathscr{I}^+$. The first main result of this work is a method for systematically fitting a QNM model containing many modes to a numerical waveform produced using Cauchy-characteristic extraction, which is known to exhibit memory effects. We choose the modes to model based on their power contribution to the residual between numerical and model waveforms. We show that the all-angles mismatch improves by a factor of $\sim 10^5$ when using multimode fitting as opposed to only fitting $(2, \pm2, n)$ modes. Our second main result addresses a critical point that has been overlooked in the literature: the importance of matching the Bondi-van der Burg-Metzner-Sachs (BMS) frame of the simulated gravitational wave to that of the QNM model. We show that by mapping the numerical relativity waveforms to the super rest frame, there is an improvement of $\sim 10^5$ in the all-angles strain mismatch, compared to using the strain whose BMS frame is not fixed. We illustrate the effectiveness of these modeling enhancements by applying them to families of waveforms produced by numerical relativity, and comparing our results to previous studies

The Social and Political Dimensions of the Ebola Response: Global Inequality, Climate Change, and Infectious Disease

The 2014 Ebola crisis has highlighted public-health vulnerabilities in Liberia, Sierra Leone, and Guinea – countries ravaged by extreme poverty, deforestation and mining-related disruption of livelihoods and ecosystems, and bloody civil wars in the cases of Liberia and Sierra Leone. Ebola’s emergence and impact are grounded in the legacy of colonialism and its creation of enduring inequalities within African nations and globally, via neoliberalism and the Washington Consensus. Recent experiences with new and emerging diseases such as SARS and various strains of HN influenzas have demonstrated the effectiveness of a coordinated local and global public health and education-oriented response to contain epidemics. To what extent is international assistance to fight Ebola strengthening local public health and medical capacity in a sustainable way, so that other emerging disease threats, which are accelerating with climate change, may be met successfully? This chapter considers the wide-ranging socio-political, medical, legal and environmental factors that have contributed to the rapid spread of Ebola, with particular emphasis on the politics of the global and public health response and the role of gender, social inequality, colonialism and racism as they relate to the mobilization and establishment of the public health infrastructure required to combat Ebola and other emerging diseases in times of climate change

'Tipping the Balance': Karl Friedrich Meyer, Latent Infections, and the Birth of Modern Ideas of Disease Ecology

The Swiss-born medical researcher Karl Friedrich Meyer (1884–1974) is best known as a ‘microbe hunter’ who pioneered investigations into diseases at the intersection of animal and human health in California in the 1920s and 1930s. In particular, historians have singled out Meyer’s 1931 Ludwig Hektoen Lecture in which he described the animal kingdom as a ‘reservoir of disease’ as a forerunner of ‘one medicine’ approaches to emerging zoonoses. In so doing, however, historians risk overlooking Meyer’s other intellectual contributions. Developed in a series of papers from the mid-1930s onwards, these were ordered around the concept of latent infections and sought to link microbial behavior to broader bio-ecological, environmental, and social factors that impact hostpathogen interactions. In this respect Meyer—like the comparative pathologist Theobald Smith and the immunologist Frank Macfarlane Burnet—can be seen as a pioneer of modern ideas of disease ecology. However, while Burnet’s and Smith’s contributions to this scientific field have been widely acknowledged, Meyer’s have been largely ignored. Drawing on Meyer’s published writings and private correspondence, this paper aims to correct that lacuna while contributing to a reorientation of the historiography of bacteriological epidemiology. In particular I trace Meyer’s intellectual exchanges with Smith, Burnet and the animal ecologist Charles Elton, over brucellosis, psittacosis and plague—exchanges that not only showed how environmental and ecological conditions could ‘tip the balance’ in favor of parasites but which transformed Meyer thinking about resistance to infection and disease