Constructing computer virus phylogenies

There has been much recent algorithmic work on the problem of reconstructing the evolutionary history of biological species. Computer virus specialists are interested in finding the evolutionary history of computer viruses - a virus is often written using code fragments from one or more other viruses, which are its immediate ancestors. A phylogeny for a collection of computer viruses is a directed acyclic graph whose nodes are the viruses and whose edges map ancestors to descendants and satisfy the property that each code fragment is "invented" only once. To provide a simple explanation for the data, we consider the problem of constructing such a phylogeny with a minimum number of edges. In general this optimization problem is NP-complete; some associated approximation problems are also hard, but others are easy. When tree solutions exist, they can be constructed and randomly sampled in polynomial time

Social Category Diversity Promotes Premeeting Elaboration: The Role of Relationship Focus

A purported downside of social category diversity is decreased relationship focus (i.e., one’s focus on establishing a positive social bond with a coworker). However, we argue that this lack of relationship focus serves as a central mechanism that improves information processing even prior to interaction and, ultimately, decision-making performance in diverse settings. We introduce the construct of premeeting elaboration (i.e., the extent to which individuals consider their own and others’ perspectives in the anticipation of an interaction) and explore its link with social category diversity and relationship focus. Experiments 1 and 2 demonstrate that when disagreement occurs, social category diversity increases premeeting elaboration, with relationship focus as a central causal mechanism. Experiment 3 shows that premeeting elaboration has important implications for performance: disagreeing dyads with social category diversity elaborate more prior to meeting and, as a result, perform better on a decision-making task than those with social category homogeneity. We discuss the value of studying early-stage interaction and propose a reconsideration of the “downside” of social category diversity.Kellogg School of Managemen

Probing a Set of Trajectories to Maximize Captured Information

We study a trajectory analysis problem we call the Trajectory Capture Problem (TCP), in which, for a given input set T of trajectories in the plane, and an integer k? 2, we seek to compute a set of k points ("portals") to maximize the total weight of all subtrajectories of T between pairs of portals. This problem naturally arises in trajectory analysis and summarization. We show that the TCP is NP-hard (even in very special cases) and give some first approximation results. Our main focus is on attacking the TCP with practical algorithm-engineering approaches, including integer linear programming (to solve instances to provable optimality) and local search methods. We study the integrality gap arising from such approaches. We analyze our methods on different classes of data, including benchmark instances that we generate. Our goal is to understand the best performing heuristics, based on both solution time and solution quality. We demonstrate that we are able to compute provably optimal solutions for real-world instances

Improved Bounds on Relaxations of a Parallel Machine Scheduling Problem

We consider the problem of scheduling n jobs with release dates on m identical parallel machines to minimize the average completion time of the jobs. We prove that the ratio of the average completion time of the optimal nonpreemptive schedule to that of the optimal preemptive schedule is at most 7}{3}, improving a bound of (3- 1}{m}) due to Phillips, Stein and Wein. We then use our technique to give an improved bound on the quality of a linear programming relaxation of the problem considered by Hall, Schulz, Shmoys and Wein

Solid-Phase Microextraction and the Human Fecal VOC Metabolome

The diagnostic potential and health implications of volatile organic compounds (VOCs) present in human feces has begun to receive considerable attention. Headspace solid-phase microextraction (SPME) has greatly facilitated the isolation and analysis of VOCs from human feces. Pioneering human fecal VOC metabolomic investigations have utilized a single SPME fiber type for analyte extraction and analysis. However, we hypothesized that the multifarious nature of metabolites present in human feces dictates the use of several diverse SPME fiber coatings for more comprehensive metabolomic coverage. We report here an evaluation of eight different commercially available SPME fibers, in combination with both GC-MS and GC-FID, and identify the 50/30 µm CAR-DVB-PDMS, 85 µm CAR-PDMS, 65 µm DVB-PDMS, 7 µm PDMS, and 60 µm PEG SPME fibers as a minimal set of fibers appropriate for human fecal VOC metabolomics, collectively isolating approximately 90% of the total metabolites obtained when using all eight fibers. We also evaluate the effect of extraction duration on metabolite isolation and illustrate that ex vivo enteric microbial fermentation has no effect on metabolite composition during prolonged extractions if the SPME is performed as described herein

Storylines of family medicine V:ways of thinking-honing the therapeutic self

Storylines of Family Medicine is a 12-part series of thematically linked essays with accompanying illustrations that explore the many dimensions of family medicine, as interpreted by individual family physicians and medical educators in the USA and elsewhere around the world. In 'V: ways of thinking-honing the therapeutic self', authors present the following sections: 'Reflective practice in action', 'The doctor as drug-Balint groups', 'Cultivating compassion', 'Towards a humanistic approach to doctoring', 'Intimacy in family medicine', 'The many faces of suffering', 'Transcending suffering' and 'The power of listening to stories.' May readers feel a deeper sense of their own therapeutic agency by reflecting on these essays.</p

Processor allocation on Cplant: Achieving general processor locality using one-dimensional allocation strategies.

Abstract Follows 3 Abstract The Computational Plant or Cplant is a commodity-based supercomputer under development at Sandia National Laboratories. This paper describes resource-allocation strategies to achieve processor locality for parallel jobs in Cplant and other supercomputers. Users of Cplant and other Sandia supercomputers submit parallel jobs to a job queue. When a job is scheduled to run, it is assigned to a set of processors. To obtain maximum throughput, jobs should be allocated to localized clusters of processors to minimize communication costs and to avoid bandwidth contention caused by overlapping jobs. This paper introduces new allocation strategies and performance metrics based on space-filling curves and one dimensional allocation strategies. These algorithms are general and simple. Preliminary simulations and Cplant experiments indicate that both space-filling curves and one-dimensional packing improve processor locality compared to the sorted free list strategy previously used on Cplant. These new allocation strategies are implemented in the new release of the Cplant System Software, Version 2.0, phased into th

Randomized trial of neoadjuvant vaccination with tumor-cell lysate induces T cell response in low-grade gliomas

BACKGROUND. Long-term prognosis of WHO grade II low-grade gliomas (LGGs) is poor, with a high risk of recurrence and malignant transformation into high-grade gliomas. Given the relatively intact immune system of patients with LGGs and the slow tumor growth rate, vaccines are an attractive treatment strategy. METHODS. We conducted a pilot study to evaluate the safety and immunological effects of vaccination with GBM6-AD, lysate of an allogeneic glioblastoma stem cell line, with poly-ICLC in patients with LGGs. Patients were randomized to receive the vaccines before surgery (arm 1) or not (arm 2) and all patients received adjuvant vaccines. Coprimary outcomes were to evaluate safety and immune response in the tumor. RESULTS. A total of 17 eligible patients were enrolled — 9 in arm 1 and 8 in arm 2. This regimen was well tolerated with no regimen-limiting toxicity. Neoadjuvant vaccination induced upregulation of type-1 cytokines and chemokines and increased activated CD8+ T cells in peripheral blood. Single-cell RNA/T cell receptor sequencing detected CD8+ T cell clones that expanded with effector phenotype and migrated into the tumor microenvironment (TME) in response to neoadjuvant vaccination. Mass cytometric analyses detected increased tissue resident–like CD8+ T cells with effector memory phenotype in the TME after the neoadjuvant vaccination. CONCLUSION. The regimen induced effector CD8+ T cell response in peripheral blood and enabled vaccine-reactive CD8+ T cells to migrate into the TME. Further refinements of the regimen may have to be integrated into future strategies