Fast Witness Extraction Using a Decision Oracle

The gist of many (NP-)hard combinatorial problems is to decide whether a universe of $n$ elements contains a witness consisting of $k$ elements that match some prescribed pattern. For some of these problems there are known advanced algebra-based FPT algorithms which solve the decision problem but do not return the witness. We investigate techniques for turning such a YES/NO-decision oracle into an algorithm for extracting a single witness, with an objective to obtain practical scalability for large values of $n$. By relying on techniques from combinatorial group testing, we demonstrate that a witness may be extracted with $O(k\log n)$ queries to either a deterministic or a randomized set inclusion oracle with one-sided probability of error. Furthermore, we demonstrate through implementation and experiments that the algebra-based FPT algorithms are practical, in particular in the setting of the $k$-path problem. Also discussed are engineering issues such as optimizing finite field arithmetic.Comment: Journal version, 16 pages. Extended abstract presented at ESA'1

Randomized controlled trial to evaluate screening and brief intervention for drug-using multiethnic emergency and trauma department patients

BACKGROUND: Screening and brief intervention (SBI) is a comprehensive, integrated public health approach to identify and deliver a spectrum of early detection and intervention services for substance use in general medical care settings. Although the SBI approach has shown promise for alcohol use, relatively little is known about its effectiveness for illicit drug use. We are evaluating the SBI approach for drug use using a rigorous randomized controlled trial. The purpose of the report is to describe the overall trial and its programmatic and methodological strengths with a focus on health educator (HE) selection and training. In addition, the baseline characteristics of the recently enrolled multiethnic cohort are described. METHODS/DESIGN: A randomized two-group repeated measures design is being used in which drug-related outcomes of an intervention group will be compared with those of an attention-placebo control group. Selection of bicultural paraprofessional HEs—their training in research concepts, comorbid mental health issues, special treatment of marijuana use, and nonscripted enhanced motivational interviewing as well as their ongoing monitoring and evaluation—are among the features described. The HEs enrolled, consented, and conducted an intervention among 700 illicit drug users in two large hospital emergency departments/trauma units. To be eligible, a participant needed to be an adult (age ≥18 years), an English or Spanish speaker, awake and able to give consent, and reachable by telephone to schedule a six-month follow-up interview. DISCUSSION: A comprehensive HE training protocol combined with rigorous, ongoing process measurement resulted in skill mastery in many areas and a successful participant recruitment period. Strengths and limitations of the study protocol are discussed as well as the characteristics of those recruited. This trial will be among the first to provide information about the effectiveness of SBI for illicit drug use. Outcome analysis has not yet been completed, but demonstrated programming and design successes have implications for future research and service delivery. TRIAL REGISTRATION: http://NCT0168322

Polarization of interacting bosons with spin

We demonstrate rigorously that in the absence of explicit spin-dependent forces one of the ground states of interacting bosons with spin is always fully polarized -- however complicated the many-body interaction potential might be. Depending on the particle spin, the polarized ground state will generally be degenerate with other states, but one can specify the exact degeneracy. For T>0 the magnetization and susceptibility necessarily exceed that of a pure paramagnet. These results are relevant to recent experiments exploring the relation between triplet superconductivity and ferromagnetism, and the Bose-Einstein condensation of atoms with spin. They eliminate the possibility, raised in some theoretical speculations, that the ground state or positive temperature state might be antiferromagnetic.Comment: v4: as published in PR

Stochastic dynamics of remote knock-on permeation in biological ion channels

Brownian dynamics simulations provide evidence for a remote knock-on mechanism facilitating the permeation of a biological ion channel by an ion that is initially trapped at the selectivity filter (SF). Unlike the case of conventional direct knock-on, the second ion that instigates permeation does not need to enter the channel. Nor does it necessarily take the place of the permeating ion at the SF, and it can even be of a different ionic species. The study is based on the simultaneous, self-consistent, solution of the coupled Poisson and Langevin equations for a simple generic model, taking account of all the charges present. The new permeation mechanism involves electrostatic amplification attributable to the permittivity mismatch between water and protein: the arrival of the instigating ion at the channel entrance reduces the exit barrier for the ion trapped at the SF, facilitating escape

Self-organized enhancement of conductivity in biological ion channels

We discuss an example of self-organization in a biological system. It arises from long-range ion–ion interactions, and it leads us to propose a new kind of enhanced conduction in ion channels. The underlying mechanism involves charge fluctuations near the channel mouth, amplified by the mismatch between the relative permittivities of water and the protein of the channel walls. We use Brownian dynamics simulations to show that, as in conventional 'knock on' permeation, these interactions can strongly enhance the channel current; but unlike the conventional mechanism, the enhancement occurs without the instigating bath ion entering the channel. The transition between these two mechanisms is clearly demonstrated, emphasizing their distinction. A simple model accurately reproduces the observed phenomena. We point out that electrolyte plus protein of low relative permittivity are universal in living systems, so that long-range ion–ion correlations of the kind considered must be common

Bleeding changes after levonorgestrel 52-mg intrauterine system insertion for contraception in women with self-reported heavy menstrual bleeding.

BackgroundThe levonorgestrel 52-mg intrauterine system has proven efficacy for heavy menstrual bleeding treatment in clinical trials, but few data exist to demonstrate how rapidly the effects occur and the effects in women with self-reported heavy bleeding, as seen commonly in clinical practice.ObjectiveEvaluate changes in bleeding patterns in women with self-reported heavy menstrual bleeding before levonorgestrel 52-mg intrauterine system insertion.Study designA total of 1714 women aged 16-45 years old received a levonorgestrel 52-mg intrauterine system in a multicenter trial evaluating contraceptive efficacy and safety for up to 10 years. At screening, participants described their baseline menstrual bleeding patterns for the previous 3 months. Participants completed daily diaries with subjective evaluation of bleeding information for the first 2 years. For this analysis, we included women with at least 1 complete 28-day cycle of intrauterine system use and excluded women using a hormonal or copper intrauterine contraception in the month prior to study enrollment. We evaluated changes in menstrual bleeding and discontinuation for bleeding complaints per 28-day cycle over 26 cycles (2 years) in women who self-reported their baseline pattern as heavy. We also compared rates of amenorrhea, defined as no bleeding or spotting, within the entire study population in women with subjective heavy menstrual bleeding at baseline compared with those who did not complain of heavy menstrual bleeding.ResultsOf the 1513 women in this analysis, 150 (9.9%) reported baseline heavy menstrual bleeding. The majority of women reported no longer experiencing heavy menstrual bleeding by the end of cycle 1 (112/150, 74.7%) with even greater rates by cycle 2 (124/148, 83.8%). At the end of cycles 6, 13, and 26, 129 of 140 (92.1%; 95% confidence interval, 87.7%-96.6%), 114 of 123 (92.7%; 95% confidence interval, 88.1%-97.3%), and 100 of 103 (97.1%; 95% confidence interval, 93.8%-100%) women reported no heavy menstrual bleeding, respectively. After cycles 13 and 26, 63 of 123 (51.2%; 95% confidence interval, 42.4%-60.1%) and 66 of 103 (64.1%; 95% confidence interval, 54.8%-73.3%), respectively, reported their bleeding as amenorrhea or spotting only. A lower proportion of women with baseline self-reported heavy menstrual bleeding reported amenorrhea as compared with women in the overall study cohort without heavy menstrual bleeding at the end of 6 cycles (319 [25.5%] vs 21 [15.0%], P=.005) and 13 cycles (382 [34.4%] vs 26 [21.1%], P=.003); differences were not significant after 19 cycles (367 [37.2%] vs 36 [31.0%], P=.022) and 26 cycles (383 [43.5%] vs 38 [36.9%], P=.21). Only 4 (2.7%) women with baseline heavy menstrual bleeding discontinued for bleeding complaints (2 for heavy menstrual bleeding and 2 for irregular bleeding), all within the first year.ConclusionMost women who self-report heavy menstrual bleeding experience significant improvement quickly after levonorgestrel 52-mg intrauterine system insertion. Discontinuation for bleeding complaints among women with baseline heavy menstrual bleeding is very low

Pair creation in transport equations using the equal-time Wigner function

Based on the equal-time Wigner function for the Klein-Gordon field, we discuss analytically the mechanism of pair creation in a classical electromagnetic field including back-reaction. It is shown that the equations of motion for the Wigner function can be reduced to a variable-frequency oscillator. The pair-creation rate results then from a calculation analogous to barrier penetration in nonrelativistic quantum mechanics. The Wigner function allows one to utilize this treatment for the formulation of an effective transport theory for the back-reaction problem with a pair-creation source term including Bose enhancement.Comment: 19 pages, LaTeX, UFTP 316/199

A simple physical model for scaling in protein-protein interaction networks

It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been reproduced by evolutionary models. Here we consider the network of protein-protein interactions and demonstrate that two published independent measurements of these interactions produce graphs that are only weakly correlated with one another despite their strikingly similar topology. We then propose a physical model based on the fundamental principle that (de)solvation is a major physical factor in protein-protein interactions. This model reproduces not only the scale-free nature of such graphs but also a number of higher-order correlations in these networks. A key support of the model is provided by the discovery of a significant correlation between number of interactions made by a protein and the fraction of hydrophobic residues on its surface. The model presented in this paper represents the first physical model for experimentally determined protein-protein interactions that comprehensively reproduces the topological features of interaction networks. These results have profound implications for understanding not only protein-protein interactions but also other types of scale-free networks.Comment: 50 pages, 17 figure