From Protein Folding to Blood Coagulation: Menaquinone as a Metabolic Link between Bacteria and Mammals

Menaquinones have long played a central role in bacterial metabolism due to their solubility in membranes and their ability to mediate electron transfer reactions between a large variety of enzymes. In addition to acting as important nodes in fermentation and respiration, menaquinones are critical to the formation of disulphide bonds in the periplasm. Their utility as molecular wires has also led to their incorporation into redox reactions in higher‐order organisms, where they participate in numerous physiological processes, including blood coagulation. Through studying the menaquinone‐dependent pathways in organisms across the phylogenetic spectrum, researchers have begun to uncover intriguing metabolic links and have identified novel compounds for modulating these vital pathways

Generalized Ramanujan Primes

In 1845, Bertrand conjectured that for all integers $x\ge2$, there exists at least one prime in $(x/2, x]$. This was proved by Chebyshev in 1860, and then generalized by Ramanujan in 1919. He showed that for any $n\ge1$, there is a (smallest) prime $R_n$ such that $\pi(x)- \pi(x/2) \ge n$ for all $x \ge R_n$. In 2009 Sondow called $R_n$ the $n$th Ramanujan prime and proved the asymptotic behavior $R_n \sim p_{2n}$ (where $p_m$ is the $m$th prime). In the present paper, we generalize the interval of interest by introducing a parameter $c \in (0,1)$ and defining the $n$th $c$-Ramanujan prime as the smallest integer $R_{c,n}$ such that for all $x\ge R_{c,n}$, there are at least $n$ primes in $(cx,x]$. Using consequences of strengthened versions of the Prime Number Theorem, we prove that $R_{c,n}$ exists for all $n$ and all $c$, that $R_{c,n} \sim p_{\frac{n}{1-c}}$ as $n\to\infty$, and that the fraction of primes which are $c$-Ramanujan converges to $1-c$. We then study finer questions related to their distribution among the primes, and see that the $c$-Ramanujan primes display striking behavior, deviating significantly from a probabilistic model based on biased coin flipping; this was first observed by Sondow, Nicholson, and Noe in the case $c = 1/2$. This model is related to the Cramer model, which correctly predicts many properties of primes on large scales, but has been shown to fail in some instances on smaller scales.Comment: 13 pages, 2 tables, to appear in the CANT 2011 Conference Proceedings. This is version 2.0. Changes: fixed typos, added references to OEIS sequences, and cited Shevelev's preprin

Race, Genetics and Medicine: New Information, Enduring Questions

Final Report on Conference held on April 9, 2005 and its Sequelae The Conference, “Race, Genetics and Medicine: New Information, Enduring Questions,” was held on Saturday, April 9, 2005 in the Science Center, Lecture Hall D at Harvard University, Cambridge, MA. Approximately 150 people attended. The audience was composed mainly of college and graduate school science students and postdoctoral fellows, some science and medical school faculty, science teachers at various levels, journalists and interested members of the public. The keynote speaker and the panelists reflected different academic disciplines (genetics, medicine, anthropology, sociology) and a CEO of a biotechnology company with background in medicine and law. They also presented different perspectives on the utility of race concepts in medicine and even on the use of the word “race.” While the talks often involved descriptions of genetic approaches that were not simple to explain, the speakers did an effective job of getting across the gist of studies that have been carried out on these issues. Although no consensus was reached, the conference gave the audience the opportunity to understand the issues and to have the tools to follow the debates in the future. Our strongest feedback was from attendees who had heard of the race and genetics issues through various media, but did not have a sense of what they were really about. They reported to us that they now felt they understood the basis of these discussions. Our post-conference activities have been successfully completed. While we had proposed to make available transcripts of the talks to the public through a Website, some of the speakers would not agree to have their presentations available in this way. Therefore, we asked permission from the DOE to use the funds to prepare classroom lesson plans for high school students to discuss the issues. These were prepared over a year-long period by the Genetic Screening Study Group Members with an educator, Ms. Ronnee Yashon, who teaches at Tufts University and who had long experience as a high school biology teacher. The lesson plans were then distributed for free to high school teachers attending the annual Conferences of the National Association of Biology Teachers and the National Science Teachers Association. One of the participants in our Conference, Professor Evelynn Hammonds of Harvard University, subsequently initiated a study group comprising faculty from a number of different New England universities and colleges, who have been analyzing the issues raised at the conference. That group, of which I am a member, has published an article examining the issues in a recent issue of PLoS Medicine. In summary, the Conference was successful in directly communicating to the public an understanding of these controversial issues, providing materials for teaching about the subject in schools, and stimulated others to involve themselves more deeply in the issues. Included with this Report are a copy of the Program for the Conference and a copy of the prepared high school Lesson Plans

Three-Dimensional Simulations of Magnetized Thin Accretion Disks around Black Holes: Stress in the Plunging Region

We describe three-dimensional general relativistic magnetohydrodynamic simulations of a geometrically thin accretion disk around a non-spinning black hole. The disk has a thickness $h/r\sim0.05-0.1$ over the radial range $(2-20)GM/c^2$. In steady state, the specific angular momentum profile of the inflowing magnetized gas deviates by less than 2% from that of the standard thin disk model of Novikov & Thorne (1973). Also, the magnetic torque at the radius of the innermost stable circular orbit (ISCO) is only $\sim2$ of the inward flux of angular momentum at this radius. Both results indicate that magnetic coupling across the ISCO is relatively unimportant for geometrically thin disks.Comment: 4 pages, 4 figures, ApJL accepte

Numerical Simulations of Driven Relativistic MHD Turbulence

A wide variety of astrophysical phenomena involve the flow of turbulent magnetized gas with relativistic velocity or energy density. Examples include gamma-ray bursts, active galactic nuclei, pulsars, magnetars, micro-quasars, merging neutron stars, X-ray binaries, some supernovae, and the early universe. In order to elucidate the basic properties of the relativistic magnetohydrodynamical (RMHD) turbulence present in these systems, we present results from numerical simulations of fully developed driven turbulence in a relativistically warm, weakly magnetized and mildly compressible ideal fluid. We have evolved the RMHD equations for many dynamical times on a uniform grid with 1024^3 zones using a high order Godunov code. We observe the growth of magnetic energy from a seed field through saturation at about 1% of the total fluid energy. We compute the power spectrum of velocity and density-weighted velocity and conclude that the inertial scaling is consistent with a slope of -5/3. We compute the longitudinal and transverse velocity structure functions of order p up to 11, and discuss their possible deviation from the expected scaling for non-relativistic media. We also compute the scale-dependent distortion of coherent velocity structures with respect to the local magnetic field, finding a weaker scale dependence than is expected for incompressible non-relativistic flows with a strong mean field.Comment: Accepted to Ap

Setting Priorities for Space Research: Opportunities and Imperatives

This report represents the first phase of a study by a task group convened by the Space Studies Board to ascertain whether it should attempt to develop a methodology for recommending priorities among the various initiatives in space research (that is, scientific activities concerned with phenomena in space or utilizing observations from space). The report argues that such priority statements by the space research community are both necessary and desirable and would contribute to the formulation and implementation of public policy. The report advocates the establishment of priorities to enhance effective management of the nation's scientific research program in space. It argues that scientific objectives and purposes should determine how and under what circumstances scientific research should be done. The report does not take a position on the controversy between advocates of manned space exploration and those who favor the exclusive use of unmanned space vehicles. Nor does the report address questions about the value or appropriateness of Space Station Freedom or proposals to establish a permanent manned Moon base or to undertake a manned mission to Mars. These issues lie beyond the charge to the task group

Automatic detection of protected health information from clinic narratives

This paper presents a natural language processing (NLP) system that was designed to participate in the 2014 i2b2 de-identification challenge. The challenge task aims to identify and classify seven main Protected Health Information (PHI) categories and 25 associated sub categories. A hybrid model was proposed which combines machine learning techniques with keyword-based and rule based approaches to deal with the complexity inherent in PHI categories. Our proposed approaches exploit a rich set of linguistic features, both syntactic and word surface-oriented, which are further enriched by task specific features and regular expression template patterns to characterize the semantics of various PHI categories. Our system achieved promising accuracy on the challenge test data with an overall micro-averaged F measure of 93.6%, which was the winner of this de-identification challenge

Gender Differences in Head Impacts Sustained by Collegiate Ice Hockey Players

Purpose—This study aims to quantify the frequency, magnitude, and location of head impacts sustained by male and female collegiate ice hockey players over two seasons of play. Methods—Over two seasons, 88 collegiate athletes (51 female, 37 male) on two female and male NCAA varsity ice hockey teams wore instrumented helmets. Each helmet was equipped with 6 single-axis accelerometers and a miniature data acquisition system to capture and record head impacts sustained during play. Data collected from the helmets were post-processed to compute linear and rotational acceleration of the head as well as impact location. The head impact exposure data (frequency, location, and magnitude) were then compared across gender. Results—Female hockey players experienced a significantly lower (p \u3c 0.001) number of impacts per athlete exposure than males (female: 1.7 ± 0.7; male: 2.9 ± 1.2). The frequency of impacts by location was the same between gender (p \u3e 0.278) for all locations except the right side of the head, where males received fewer impacts than females (p = 0.031). Female hockey players were 1.1 times more likely than males to sustain an impact less than 50 g while males were 1.3 times more likely to sustain an impact greater than 100 g. Similarly, males were 1.9 times more likely to sustain an impact with peak rotational acceleration greater than 5,000 rad/s2 and 3.5 times more likely to sustain an impact greater than 10,000 rad/s2. Conclusions—Although the incidence of concussion has typically been higher for female hockey players than male hockey players, female players sustain fewer impacts and impacts resulting in lower head acceleration than males. Further study is required to better understand th

Prograde and Retrograde Black Holes: Whose Jet is More Powerful?

The outflow efficiency (eta) from black hole (BH) accretion disc systems is known to depend upon both the BH spin (a) and the amount of large-scale magnetic flux threading the BH and disc. Semi-analytical flux-trapping models suggest retrograde BHs should trap much more large-scale magnetic flux near the BH leading to much higher eta than for prograde BHs. We self-consistently determine the amount of large-scale magnetic flux trapped by rapidly spinning (a = -0.9 and 0.9) BHs using global 3D time-dependent non-radiative general relativistic magnetohydrodynamic simulations of thick (h/r ~ 0.3-0.6) discs. We find that BH-trapped flux builds up until it is strong enough to disrupt the inner accretion disc. Contrary to prior flux-trapping models, which do not include the back-reaction of magnetic flux on the disc, our simulations show prograde BHs trap more magnetic flux, leading to about 3 times higher eta than retrograde BHs for |a| = 0.9. Both spin orientations can produce highly efficient jets, eta ~ 100%, with increasing eta for increasing disc thickness. The similarity of eta for prograde and retrograde BHs makes it challenging to infer the sign of BH spin based on jet energetics alone.Comment: 5 pages, 3 figures. Accepted to MNRAS. For associated movies see http://youtu.be/yNZLjsrz0Wo and http://youtu.be/bQE69wti3a

Efficient Generation of Jets from Magnetically Arrested Accretion on a Rapidly Spinning Black Hole

We describe global, 3D, time-dependent, non-radiative, general-relativistic, magnetohydrodynamic simulations of accreting black holes (BHs). The simulations are designed to transport a large amount of magnetic flux to the center, more than the accreting gas can force into the BH. The excess magnetic flux remains outside the BH, impedes accretion, and leads to a magnetically arrested disc. We find powerful outflows. For a BH with spin parameter a = 0.5, the efficiency with which the accretion system generates outflowing energy in jets and winds is eta ~ 30%. For a = 0.99, we find eta ~ 140%, which means that more energy flows out of the BH than flows in. The only way this can happen is by extracting spin energy from the BH. Thus the a = 0.99 simulation represents an unambiguous demonstration, within an astrophysically plausible scenario, of the extraction of net energy from a spinning BH via the Penrose-Blandford-Znajek mechanism. We suggest that magnetically arrested accretion might explain observations of active galactic nuclei with apparent eta ~ few x 100%.Comment: 5 pages, 2 figures, MNRAS, accepte