Identifying translational science within the triangle of biomedicine

Background: The National Institutes of Health (NIH) Roadmap places special emphasis on “bench-to-bedside” research, or the “translation” of basic science research into practical clinical applications. The Clinical and Translational Science Awards (CTSA) Consortium is one example of the large investments being made to develop a national infrastructure to support translational science, which involves reducing regulatory burdens, launching new educational initiatives, and forming partnerships between academia and industry. However, while numerous definitions have been suggested for translational science, including the qualitative T1-T4 classification, a consensus has not yet been reached. This makes it challenging to tract the impact of these major policy changes. Methods: In this study, we use a bibliometric approach to map PubMed articles onto a graph, called the Triangle of Biomedicine. The corners of the triangle represent research related to animals, cells and molecules, and humans; and, the position of a publication on the graph is based on its topics, as determined by its Medical Subject Headings (MeSH). We define translation as movement of a collection of articles, or the articles that cite those articles, towards the human corner. Results: The Triangle of Biomedicine provides a quantitative way of determining if an individual scientist, research organization, funding agency, or scientific field is producing results that are relevant to clinical medicine. We validate our technique using examples that have been previously described in the literature and by comparing it to prior methods of measuring translational science. Conclusions: The Triangle of Biomedicine is a novel way to identify translational science and track changes over time. This is important to policy makers in evaluating the impact of the large investments being made to accelerate translation. The Triangle of Biomedicine also provides a simple visual way of depicting this impact, which can be far more powerful than numbers alone

Extracting Physician Group Intelligence from Electronic Health Records to Support Evidence Based Medicine

Evidence-based medicine employs expert opinion and clinical data to inform clinical decision making. The objective of this study is to determine whether it is possible to complement these sources of evidence with information about physician “group intelligence” that exists in electronic health records. Specifically, we measured laboratory test “repeat intervals”, defined as the amount of time it takes for a physician to repeat a test that was previously ordered for the same patient. Our assumption is that while the result of a test is a direct measure of one marker of a patient's health, the physician's decision to order the test is based on multiple factors including past experience, available treatment options, and information about the patient that might not be coded in the electronic health record. By examining repeat intervals in aggregate over large numbers of patients, we show that it is possible to 1) determine what laboratory test results physicians consider “normal”, 2) identify subpopulations of patients that deviate from the norm, and 3) identify situations where laboratory tests are over-ordered. We used laboratory tests as just one example of how physician group intelligence can be used to support evidence based medicine in a way that is automated and continually updated

The spectroscopic orbit of Capella revisited

Context. Capella is among the few binary stars with two evolved giant components. The hotter component is a chromospherically active star within the Hertzsprung gap, while the cooler star is possibly helium-core burning. Aims. The known inclination of the orbital plane from astrometry in combination with precise radial velocities will allow very accurate masses to be determined for the individual Capella stars. This will constrain their evolutionary stage and possibly the role of the active star's magnetic field on the dynamical evolution of the binary system. Methods. We obtained a total of 438 high-resolution \'echelle spectra during the years 2007-2010 and used the measured velocities to recompute the orbital elements. Our double-lined orbital solution yields average residuals of 64 m/s for the cool component and 297 m/s for the more rapidly rotating hotter component. Results. The semi-amplitude of the cool component is smaller by 0.045 km/s than the orbit determination of Torres et al. from data taken during 1996-1999 but more precise by a factor of 5.5, while for the hotter component it is larger by 0.580 km/s and more precise by a factor of 3.6. This corresponds to masses of 2.573\pm0.009 M_sun and 2.488\pm0.008 M_sun for the cool and hot component, respectively. Their relative errors of 0.34% and 0.30% are about half of the values given in Torres et al. for a combined literature- data solution but with absolute values different by 4% and 2% for the two components, respectively. The mass ratio of the system is therefore q = M_A/M_B = 0.9673 \pm 0.0020. Conclusions. Our orbit is the most precise and also likely to be the most accurate ever obtained for Capella

Representation in stochastic search for phylogenetictree reconstruction

Phylogenetic tree reconstruction is a process in which the ancestral relationships among a group of organisms are inferred from their DNA sequences. For all but trivial sized data sets, finding the optimal tree is computationally intractable. Many heuristic algorithms exist, but the branch-swapping algorithm used in the software package PAUP is the most popular. This method performs a stochastic search over the space of trees, using a branch-swapping operation to construct neighboring trees in the search space. This study introduces a new stochastic search algorithm that operates over an alternative representation of trees, namely as permutations of taxa giving the order in which they are processed during stepwise addition. Experiments on several data sets suggest that this algorithm for generating an initial tree, when followed by branch-swapping, can produce better trees for a given total amount of time.Engineering and Applied Science

Topological Semimetal features in the Multiferroic Hexagonal Manganites

Using first-principles calculations we examine the band structures of ferromagnetic hexagonal manganites $\mathrm{YXO_3}$ (X=V, Cr, Mn, Fe and Co) in the nonpolar nonsymmorphic $P6_3/mmc$ space group. For $\mathrm{YVO_3}$ and $\mathrm{YCrO_3}$ we find a band inversion near the Fermi energy that generates a nodal ring in the $k_z=0$ mirror plane. We perform a more detailed analysis for these compounds and predict the existence of the topological "drumhead" surface states. Finally, we briefly discuss the low-symmetry polar phases (space group $P6_3cm$) of these systems, and show they can undergo a $P6_3/mmc \rightarrow P6_3cm$ transition by condensation of soft $K_3$ and $\Gamma_2^-$ phonons. Based on our findings, stabilizing these compounds in the hexagonal phase could offer a promising platform for studying the interplay of topology and multiferroicity, and the coexistence of real-space and reciprocal-space topological protection in the same phase

BioNumbers—the database of key numbers in molecular and cell biology

BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology—the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. While always of importance to biologists, having numbers in hand is becoming increasingly critical for experimenting, modeling, and analyzing biological systems. BioNumbers was motivated by an appreciation of how long it can take to find even the simplest number in the vast biological literature. All numbers are taken directly from a literature source and that reference is provided with the number. BioNumbers is designed to be highly searchable and queries can be performed by keywords or browsed by menus. BioNumbers is a collaborative community platform where registered users can add content and make comments on existing data. All new entries and commentary are curated to maintain high quality. Here we describe the database characteristics and implementation, demonstrate its use, and discuss future directions for its development

Rotation, activity, and lithium abundance in cool binary stars

We have used two robotic telescopes to obtain time-series high-resolution spectroscopy and V I and/or by photometry for a sample of 60 active stars. Orbital solutions are presented for 26 SB2 and 19 SB1 systems with unprecedented phase coverage and accuracy. The total of 6,609 R=55,000 echelle spectra are also used to systematically determine effective temperatures, gravities, metallicities, rotational velocities, lithium abundances and absolute H{\alpha}-core fluxes as a function of time. The photometry is used to infer unspotted brightness, V - I and/or b - y colors, spot-induced brightness amplitudes and precise rotation periods. Our data are complemented by literature data and are used to determine rotation-temperature-activity relations for active binary components. We also relate lithium abundance to rotation and surface temperature. We find that 74% of all known rapidly-rotating active binary stars are synchronized and in circular orbits but 26% are rotating asynchronously of which half have Prot > Porb and e > 0. Because rotational synchronization is predicted to occur before orbital circularization active binaries should undergo an extra spin-down besides tidal dissipation. We suspect this to be due to a magnetically channeled wind with its subsequent braking torque. We find a steep increase of rotation period with decreasing effective temperature for active stars. For inactive, single giants with Prot > 100 d, the relation is much weaker. Our data also indicate a period-activity relation for H{\alpha} of the form RH{\alpha} \propto P - 0.24 for binaries and RH{\alpha} \propto P -0.14 for singles. Lithium abundances in our sample increase with effective temperature. On average, binaries of comparable effective temperature appear to exhibit 0.25 dex less surface lithium than singles. We also find a trend of increased Li abundance with rotational period of form log n(Li) \propto - 0.6 log Prot

Panentheism and the undoing of disenchantment

In this article I draw on historical and conceptual arguments to show, first, that disenchantment and the influential view of the relationship between science and religion to which disenchantment gives rise are rooted in the metaphysics of theism. I then introduce the alternative metaphysical position of panentheism and identify Jungian psychology as an important, if implicit, mid-twentieth-century instance of panentheistic thought. Using the example of Jungian psychology, I demonstrate how the viewpoint of panentheism undoes the implications of disenchantment for the relationship between science and religion, promoting greater opportunities for dialogue and reconciliation between science and religion. I note, however, that these closer relations may depend on understanding science and religion differently from how they are understood under disenchantment. While the original tension between science and religion is eased, another tension – between panentheistic and disenchanted understandings of science and religion – is exposed. I conclude by reflecting on some implications of this discussion for sociology