Taking responsibilities seriously: The role of the state in preventing transmission of HIV from mother to child

No Abstract

A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements, and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.Comment: Documents version 3 of the forma

A wide scalar neutrino resonance and b\bar{b} production at LEP

In supersymmetric models with R-parity violation, scalar neutrinos may be produced as s-channel resonances in e^+e^- colliders. We note that within current constraints, the scalar neutrino may have a width of several GeV into b\bar{b} and be produced with large cross section, leading to a novel supersymmetry discovery signal at LEP II. In addition, if the scalar neutrino mass approximately equals m_Z, such a resonance necessarily increases R_b and reduces A_{FB}(b), significantly improving the fit to electroweak data. Bounds from B meson and top quark decays are leading constraints, and we stress the importance of future measurements.Comment: 8 pages. LaTex + RevTex. Revised to include a discussion of ISR effects. Version to appear in Phys. Rev. Let

Adaptive Mesh Refinement for Characteristic Grids

I consider techniques for Berger-Oliger adaptive mesh refinement (AMR) when numerically solving partial differential equations with wave-like solutions, using characteristic (double-null) grids. Such AMR algorithms are naturally recursive, and the best-known past Berger-Oliger characteristic AMR algorithm, that of Pretorius & Lehner (J. Comp. Phys. 198 (2004), 10), recurses on individual "diamond" characteristic grid cells. This leads to the use of fine-grained memory management, with individual grid cells kept in 2-dimensional linked lists at each refinement level. This complicates the implementation and adds overhead in both space and time. Here I describe a Berger-Oliger characteristic AMR algorithm which instead recurses on null \emph{slices}. This algorithm is very similar to the usual Cauchy Berger-Oliger algorithm, and uses relatively coarse-grained memory management, allowing entire null slices to be stored in contiguous arrays in memory. The algorithm is very efficient in both space and time. I describe discretizations yielding both 2nd and 4th order global accuracy. My code implementing the algorithm described here is included in the electronic supplementary materials accompanying this paper, and is freely available to other researchers under the terms of the GNU general public license.Comment: 37 pages, 15 figures (40 eps figure files, 8 of them color; all are viewable ok in black-and-white), 1 mpeg movie, uses Springer-Verlag svjour3 document class, includes C++ source code. Changes from v1: revised in response to referee comments: many references added, new figure added to better explain the algorithm, other small changes, C++ code updated to latest versio

In Situ Probes of the First Galaxies and Reionization: Gamma-ray Bursts

The first structures in the Universe formed at z>7, at higher redshift than all currently known galaxies. Since GRBs are brighter than other cosmological sources at high redshift and exhibit simple power-law afterglow spectra that is ideal for absorption studies, they serve as powerful tools for studying the early universe. New facilities planned for the coming decade will be able to obtain a large sample of high-redshift GRBs. Such a sample would constrain the nature of the first stars, galaxies, and the reionization history of the Universe.Comment: 8 pages, 3 figures, science white paper submitted to the US Astro2010 Decadal Surve

Kentucky Labor Supply and Demand Surveys

Excerpt from the executive summary: The Center for Business and Economic Research at the University of Kentucky (CBER), along with its partners, the Survey Research Center at the University of Kentucky (UK-SRC), the Survey Research Center in the Urban Studies Institute at the University of Louisville (UL-SRC), and the Department of Economics at the University of Louisville, is pleased to present this final report on the findings of the Kentucky labor supply and demand surveys sponsored by the Kentucky Cabinet for Workforce Development. The two universities have put together a consortium including some of the best scholars in the region in the areas of labor economics, local economic development, and survey design and administration

Large-scale identification of genetic design strategies using local search

In the past decade, computational methods have been shown to be well suited to unraveling the complex web of metabolic reactions in biological systems. Methods based on flux–balance analysis (FBA) and bi-level optimization have been used to great effect in aiding metabolic engineering. These methods predict the result of genetic manipulations and allow for the best set of manipulations to be found computationally. Bi-level FBA is, however, limited in applicability because the required computational time and resources scale poorly as the size of the metabolic system and the number of genetic manipulations increase. To overcome these limitations, we have developed Genetic Design through Local Search (GDLS), a scalable, heuristic, algorithmic method that employs an approach based on local search with multiple search paths, which results in effective, low-complexity search of the space of genetic manipulations. Thus, GDLS is able to find genetic designs with greater in silico production of desired metabolites than can feasibly be found using a globally optimal search and performs favorably in comparison with heuristic searches based on evolutionary algorithms and simulated annealing.Hertz Foundatio

A Plan for a Long-Term, Automated, Broadband Seismic Monitoring Network on the Global Seafloor

Establishing an extensive and highly durable, long‐term, seafloor network of autonomous broadband seismic stations to complement the land‐based Global Seismographic Network has been a goal of seismologists for decades. Seismic signals, chiefly the vibrations from earthquakes but also signals generated by storms and other environmental processes, have been processed from land‐based seismic stations to build intriguing but incomplete images of the Earth’s interior. Seismologists have mapped structures such as tectonic plates and other crustal remnants sinking deep into the mantle to obtain information on their chemical composition and physical state; but resolution of these structures from land stations is not globally uniform. Because the global surface is two‐thirds ocean, increasing the number of seismic stations located in the oceans is critical for better resolution of the Earth’s interior and tectonic structures. A recommendation for a long‐term seafloor seismic station pilot experiment is presented here. The overarching instrumentation goal of a pilot experiment is performance that will lead to the installation of a large number of long‐term autonomous ocean‐bottom seismic stations. The payoff of a network of stations separated from one another by a few hundred kilometers under the global oceans would be greatly refined resolution of the Earth’s interior at all depths. A second prime result would be enriched understanding of large‐earthquake rupture processes in both oceanic and continental plates. The experiment would take advantage of newly available technologies such as robotic wave gliders that put an affordable autonomous prototype within reach. These technologies would allow data to be relayed to satellites from seismometers that are deployed on the seafloor with long‐lasting, rechargeable batteries. Two regions are presented as promising arenas for such a prototype seafloor seismic station. One site is the central North Atlantic Ocean, and the other high‐interest locale is the central South Pacific Ocean

Opicapone, a Novel Catechol-O-methyl Transferase Inhibitor, for Treatment of Parkinson\u27s Disease Off Episodes

Parkinson\u27s Disease (PD) is a common neurodegenerative disorder and the leading cause of disability. It causes significant morbidity and disability through a plethora of symptoms, including movement disorders, sleep disturbances, and cognitive and psychiatric symptoms. The traditional pathogenesis theory of PD involves the loss of dopaminergic neurons in the substantia nigra (SN). Classically, treatment is pursued with an assortment of medications that are directed at overcoming this deficiency with levodopa being central to most treatment plans. Patients taking levodopa tend to experience off episodes with decreasing medication levels, causing large fluctuations in their symptoms. These off episodes are disturbing and a source of morbidity for these patients. Opicapone is a novel, peripherally acting Catechol-O-methyl transferase (COMT) inhibitor that is used as adjunctive therapy to carbidopa/levodopa for treatment and prevention of off episodes. It has been approved for use as an adjunct to levodopa since 2016 in Europe and has recently (April 2020) gained FDA approval for use in the USA. By inhibiting COMT, opicapone slows levodopa metabolism and increases its availability. Several clinical studies demonstrated significant improvement in treatment efficacy and reduction in duration of off episodes. The main side effect demonstrated was dyskinesia, mostly with the 100mg dose, which is higher than the approved, effective dose of 50mg. Post-marketing surveillance and analysis are required to further elucidate its safety profile and contribute to patient selection. This paper reviews the seminal and latest evidence in the treatment of PD off episodes with the novel drug Opicapone, including efficacy, safety, and clinical indications