Reducing the Effects of Unequal Number of Games on Rankings

Ranking is an important mathematical process in a variety of contexts such as information retrieval, sports and business. Sports ranking methods can be applied both in and beyond the context of athletics. In both settings, once the concept of a game has been defined, teams (or individuals) accumulate wins, losses, and ties, which are then factored into the ranking computation. Many settings involve an unequal number of games between competitors. This paper demonstrates how to adapt two sports rankings methods, the Colley and Massey ranking methods, to settings where an unequal number of games are played between the teams. In such settings, the standard derivations of the methods can produce nonsensical rankings. This paper introduces the idea of including a super-user into the rankings and considers the effect of this fictitious player on the ratings. We apply such techniques to rank batters and pitchers in Major League baseball, professional tennis players, and participants in a free online social game. The ideas introduced in this paper can further the scope that such methods are applied and the depth of insight they offer

Efficient hepatitis C virus particle formation requires diacylglycerol acyltransferase-1.

Hepatitis C virus (HCV) infection is closely tied to the lipid metabolism of liver cells. Here we identify the triglyceride-synthesizing enzyme diacylglycerol acyltransferase-1 (DGAT1) as a key host factor for HCV infection. DGAT1 interacts with the viral nucleocapsid core and is required for the trafficking of core to lipid droplets. Inhibition of DGAT1 activity or RNAi-mediated knockdown of DGAT1 severely impairs infectious virion production, implicating DGAT1 as a new target for antiviral therapy

Letter, 1926, August 20, from Charles R. Harris, to the Officers and Members of U.M.W. of A.

1 page, letter, 1926, August 20, to Officers and Members of U.M.W. of A. regarding himself as a candidate for nomination to International Secretary-Treasure

Coherent Population Trapping of Electron Spins in a Semiconductor

In high-purity n-type GaAs under strong magnetic field, we are able to isolate a lambda system composed of two Zeeman states of neutral-donor bound electrons and the lowest Zeeman state of bound excitons. When the two-photon detuning of this system is zero, we observe a pronounced dip in the excited-state photoluminescence indicating the creation of the coherent population-trapped state. Our data are consistent with a steady-state three-level density-matrix model. The observation of coherent population trapping in GaAs indicates that this and similar semiconductor systems could be used for various EIT-type experiments.Comment: 5 pages, 4 figures replaced 6/25/2007 with PRL versio

Tradition and Prudence in Locke's Exceptions to Toleration

Why did Locke exclude Catholics and atheists from toleration? Not, I contend, because he was trapped by his context, but because his prudential approach and practica ljudgments led him to traditiona ltexts. I make this argumentfirst by outlining the connections among prudential exceptionality, practical judgments, and traditional texts. I then describe important continuities betweenc onventional English understandings of the relationship between state and religion and Locke's writings on toleration, discuss Locke's conception of rights, and illustrate his use of prudential exceptions and distinctions. I conclude by arguing that Locke's problems are relevant to assessingc ontemporary liberal discussions of tolerationa nd the separation of state and religion that lean heavily on practical justification

Determining Transition State Geometries in Liquids Using 2D-IR

Many properties of chemical reactions are determined by the transition state connecting reactant and product, yet it is difficult to directly obtain any information about these short-lived structures in liquids. We show that two-dimensional infrared (2D-IR) spectroscopy can provide direct information about transition states by tracking the transformation of vibrational modes as a molecule crossed a transition state. We successfully monitored a simple chemical reaction, the fluxional rearrangement of Fe(CO)5, in which the exchange of axial and equatorial CO ligands causes an exchange of vibrational energy between the normal modes of the molecule. This energy transfer provides direct evidence regarding the time scale, transition state, and mechanism of the reaction

Bone Ingrowth into Porous Coated Canine Total Hip Replacements. Quantification by Backscattered Scanning Electron Microscopy and Image Analysis

Bone ingrowth into titanium fiber mesh porous-surfaced canine total hip replacement prostheses was evaluated and quantified using a computer assisted image analysis system attached to a scanning electron microscope equipped with a back scattered electron detector. Excellent contrast between the bone, the porous metal and the soft tissues resulted in the backscatter mode, allowing easy differentiation of these components in real time by the image analysis based on gray scales. By three weeks the mean (± standard deviation) amount of bone ingrowth expressed as a percentage of porous layer measured 7.2% (± 1.5%) for the acetabular components, and 3.9% (± 1.7%) for the femoral components. At six weeks the amount of bone ingrowth increased to 10.5% (± 1.3%) for the acetabular components and 8.5% (± 1.4%) for the femoral components. Cementless prosthetic fixation using porous surfaced prostheses holds great promise in joint replacement surgery, and the ability to quantitate the amount of bone ingrowth will permit the evaluation of the efficacy of various techniques to improve bone ingrowth

Multi-State RNA Design with Geometric Multi-Graph Neural Networks

Computational RNA design has broad applications across synthetic biology and therapeutic development. Fundamental to the diverse biological functions of RNA is its conformational flexibility, enabling single sequences to adopt a variety of distinct 3D states. Currently, computational biomolecule design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired structural conformation. In this work, we propose gRNAde, a geometric RNA design pipeline that operates on sets of 3D RNA backbone structures to explicitly account for and reflect RNA conformational diversity in its designs. We demonstrate the utility of gRNAde for improving native sequence recovery over single-state approaches on a new large-scale 3D RNA design dataset, especially for multi-state and structurally diverse RNAs. Our code is available at https://github.com/chaitjo/geometric-rna-desig

Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models?

Deep generative models for structure-based drug design (SBDD), where molecule generation is conditioned on a 3D protein pocket, have received considerable interest in recent years. These methods offer the promise of higher-quality molecule generation by explicitly modelling the 3D interaction between a potential drug and a protein receptor. However, previous work has primarily focused on the quality of the generated molecules themselves, with limited evaluation of the 3D molecule \emph{poses} that these methods produce, with most work simply discarding the generated pose and only reporting a "corrected" pose after redocking with traditional methods. Little is known about whether generated molecules satisfy known physical constraints for binding and the extent to which redocking alters the generated interactions. We introduce PoseCheck, an extensive analysis of multiple state-of-the-art methods and find that generated molecules have significantly more physical violations and fewer key interactions compared to baselines, calling into question the implicit assumption that providing rich 3D structure information improves molecule complementarity. We make recommendations for future research tackling identified failure modes and hope our benchmark can serve as a springboard for future SBDD generative modelling work to have a real-world impact