Epidemics on contact networks: a general stochastic approach

Dynamics on networks is considered from the perspective of Markov stochastic processes. We partially describe the state of the system through network motifs and infer any missing data using the available information. This versatile approach is especially well adapted for modelling spreading processes and/or population dynamics. In particular, the generality of our systematic framework and the fact that its assumptions are explicitly stated suggests that it could be used as a common ground for comparing existing epidemics models too complex for direct comparison, such as agent-based computer simulations. We provide many examples for the special cases of susceptible-infectious-susceptible (SIS) and susceptible-infectious-removed (SIR) dynamics (e.g., epidemics propagation) and we observe multiple situations where accurate results may be obtained at low computational cost. Our perspective reveals a subtle balance between the complex requirements of a realistic model and its basic assumptions.Comment: Main document: 16 pages, 7 figures. Electronic Supplementary Material (included): 6 pages, 1 tabl

Continuous image distortion by astrophysical thick lenses

Image distortion due to weak gravitational lensing is examined using a non-perturbative method of integrating the geodesic deviation and optical scalar equations along the null geodesics connecting the observer to a distant source. The method we develop continuously changes the shape of the pencil of rays from the source to the observer with no reference to lens planes in astrophysically relevant scenarios. We compare the projected area and the ratio of semi-major to semi-minor axes of the observed elliptical image shape for circular sources from the continuous, thick-lens method with the commonly assumed thin-lens approximation. We find that for truncated singular isothermal sphere and NFW models of realistic galaxy clusters, the commonly used thin-lens approximation is accurate to better than 1 part in 10^4 in predicting the image area and axes ratios. For asymmetric thick lenses consisting of two massive clusters separated along the line of sight in redshift up to \Delta z = 0.2, we find that modeling the image distortion as two clusters in a single lens plane does not produce relative errors in image area or axes ratio more than 0.5%Comment: accepted to GR

Randomized Comparison of Everolimus- and Paclitaxel-Eluting Stents 2-Year Follow-Up From the SPIRIT (Clinical Evaluation of the XIENCE V Everolimus Eluting Coronary Stent System) IV Trial

ObjectivesWe sought to determine whether the differences in outcomes present between everolimus-eluting stents (EES) and paclitaxel-eluting stents (PES) in the SPIRIT (Clinical Evaluation of the XIENCE V Everolimus Eluting Coronary Stent System) IV trial at 1 year were sustained with longer-term follow-up.BackgroundIn the SPIRIT IV trial, patients undergoing percutaneous coronary intervention who were randomized to EES compared with PES experienced lower 1-year rates of target lesion failure (cardiac death, target vessel myocardial infarction [MI], or ischemia-driven target lesion revascularization [TLR]), with significant reductions in the individual rates of MI, TLR, and stent thrombosis.MethodsWe prospectively randomized 3,687 patients with up to 3 noncomplex previously untreated native coronary artery lesions to EES versus PES at 66 U.S. sites. Follow-up through 2 years is complete in 3,578 patents (97.0%).ResultsTreatment with EES compared with PES reduced the 2-year rates of TLF (6.9% vs. 9.9%, p = 0.003), all MI (2.5% vs. 3.9%, p = 0.02), Q-wave MI (0.1% vs. 0.8%, p = 0.002), stent thrombosis (0.4% vs. 1.2%, p = 0.008), and ischemia-driven TLR (4.5% vs. 6.9%, p = 0.004), with nonsignificantly different rates of all-cause and cardiac mortality. Between 1 year and 2 years, there were no significant differences in adverse event rates between the 2 stent types.ConclusionsIn the large-scale, prospective, multicenter, randomized SPIRIT IV trial, the benefits of EES compared with those of PES present at 1 year were sustained at 2 years. (Clinical Evaluation of the XIENCE V Everolimus Eluting Coronary Stent System; NCT01016041

Using the Wigner-Ibach Surmise to Analyze Terrace-Width Distributions: History, User's Guide, and Advances

A history is given of the applications of the simple expression generalized from the surmise by Wigner and also by Ibach to extract the strength of the interaction between steps on a vicinal surface, via the terrace width distribution (TWD). A concise guide for use with experiments and a summary of some recent extensions are provided.Comment: 11 pages, 4 figures, reformatted (with revtex) version of refereed paper for special issue of Applied Physics A entitled "From Surface Science to Device Physics", in honor of the retirements of Prof. H. Ibach and Prof. H. L\"ut

Confluence and Convergence in Probabilistically Terminating Reduction Systems

Convergence of an abstract reduction system (ARS) is the property that any derivation from an initial state will end in the same final state, a.k.a. normal form. We generalize this for probabilistic ARS as almost-sure convergence, meaning that the normal form is reached with probability one, even if diverging derivations may exist. We show and exemplify properties that can be used for proving almost-sure convergence of probabilistic ARS, generalizing known results from ARS.Comment: Pre-proceedings paper presented at the 27th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR 2017), Namur, Belgium, 10-12 October 2017 (arXiv:1708.07854

Conditional Gene Expression in Mycobacterium abscessus

Mycobacterium abscessus is an emerging human pathogen responsible for lung infections, skin and soft-tissue infections and disseminated infections in immunocompromised patients. It may exist either as a smooth (S) or rough (R) morphotype, the latter being associated with increased pathogenicity in various models. Genetic tools for homologous recombination and conditional gene expression are desperately needed to allow the study of M. abscessus virulence. However, descriptions of knock-out (KO) mutants in M. abscessus are rare, with only one KO mutant from an S strain described so far. Moreover, of the three major tools developed for homologous recombination in mycobacteria, only the one based on expression of phage recombinases is working. Several conditional gene expression tools have recently been engineered for Mycobacterium tuberculosis and Mycobacterium smegmatis, but none have been tested yet in M. abscessus. Based on previous experience with genetic tools allowing homologous recombination and their failure in M. abscessus, we evaluated the potential interest of a conditional gene expression approach using a system derived from the two repressors system, TetR/PipOFF. After several steps necessary to adapt TetR/PipOFF for M. abscessus, we have shown the efficiency of this system for conditional expression of an essential mycobacterial gene, fadD32. Inhibition of fadD32 was demonstrated for both the S and R isotypes, with marginally better efficiency for the R isotype. Conditional gene expression using the dedicated TetR/PipOFF system vectors developed here is effective in S and R M. abscessus, and may constitute an interesting approach for future genetic studies in this pathogen

Evaluation of a novel magneto-optical method for the detection of malaria parasites

Improving the efficiency of malaria diagnosis is one of the main goals of current malaria research. We have recently developed a magneto-optical (MO) method which allows high-sensitivity detection of malaria pigment (hemozoin crystals) in blood via the magnetically induced rotational motion of the hemozoin crystals. Here, we evaluate this MO technique for the detection of Plasmodium falciparum in infected erythrocytes using in-vitro parasite cultures covering the entire intraerythrocytic life cycle. Our novel method detected parasite densities as low as approximately 40 parasites per microliter of blood (0.0008% parasitemia) at the ring stage and less than 10 parasites/microL (0.0002% parasitemia) in the case of the later stages. These limits of detection, corresponding to approximately 20 pg/microL of hemozoin produced by the parasites, exceed that of rapid diagnostic tests and compete with the threshold achievable by light microscopic observation of blood smears. The MO diagnosis requires no special training of the operator or specific reagents for parasite detection, except for an inexpensive lysis solution to release intracellular hemozoin. The devices can be designed to a portable format for clinical and in-field tests. Besides testing its diagnostic performance, we also applied the MO technique to investigate the change in hemozoin concentration during parasite maturation. Our preliminary data indicate that this method may offer an efficient tool to determine the amount of hemozoin produced by the different parasite stages in synchronized cultures. Hence, it could eventually be used for testing the susceptibility of parasites to antimalarial drugs

Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait

The genetic control of common traits is rarely deterministic, with many genes contributing only to the chance of developing a given phenotype. This incomplete penetrance is poorly understood and is usually attributed to interactions between genes or interactions between genes and environmental conditions. Because many traits such as cancer can emerge from rare events happening in one or very few cells, we speculate an alternative and complementary possibility where some genotypes could facilitate these events by increasing stochastic cell-to-cell variations (or ‘noise’). As a very first step towards investigating this possibility, we studied how natural genetic variation influences the level of noise in the expression of a single gene using the yeast S. cerevisiae as a model system. Reproducible differences in noise were observed between divergent genetic backgrounds. We found that noise was highly heritable and placed under a complex genetic control. Scanning the genome, we mapped three Quantitative Trait Loci (QTL) of noise, one locus being explained by an increase in noise when transcriptional elongation was impaired. Our results suggest that the level of stochasticity in particular molecular regulations may differ between multicellular individuals depending on their genotypic background. The complex genetic architecture of noise buffering couples genetic to non-genetic robustness and provides a molecular basis to the probabilistic nature of complex traits

What’s past (and present) is prologue : interactions between justice levels and trajectories predicting behavioral reciprocity

Much of organizational justice research has tended to take a static approach, linking employees’ contemporaneous justice levels to outcomes of interest. In the present study, we tested a dynamic model emphasizing the interactive influences of both justice levels and trajectories for predicting behavioral social exchange outcomes. Specifically, our model posited both main effects and interactions between present justice levels and past justice changes over time in predicting helping behavior and voluntary turnover behavior. Data over four yearly measurement periods from 4,348 employees of a banking organization generally supported the notion that justice trajectories interact with absolute levels to predict both outcomes. Together, the findings highlight how employees invoke present fairness evaluations within the context of past fairness trends—rather than either in isolation—to inform decisions about behaviorally reciprocating at work

Dichorionic twin trajectories: the NICHD Fetal Growth Studies

BACKGROUND: Systematic evaluation and estimation of growth trajectories in twins require ultrasound measurements across gestation, performed in controlled clinical settings. Currently there are few such data for contemporary populations. There is also controversy about whether twin fetal growth should be evaluated using the same benchmarks as singleton growth. OBJECTIVES: Our objective was to empirically define the trajectory of fetal growth in dichorionic twins using longitudinal two-dimensional ultrasonography and to compare the fetal growth trajectories for dichorionic twins with those based on a growth standard developed by our group for singletons. STUDY DESIGN: A prospective cohort of 171 women with twin gestations was recruited from eight U.S. sites from 2012 to 2013. After an initial sonogram at 11w0d–13w6d where dichorionicity was confirmed, women were randomized to one of two serial ultrasonology schedules. Growth curves and percentiles were estimated using linear mixed models with cubic splines. Percentiles were compared statistically at each gestational week between the twins and 1,731 singletons, after adjustment for maternal age, race/ethnicity, height, weight, parity, employment, marital status, insurance, income, education and infant sex. Linear mixed models were used to test for overall differences between the twin and singleton trajectories using likelihood ratio tests of interaction terms between spline mean structure terms and twin-singleton indicator variables. Singleton standards were weighted to correspond to the distribution of maternal race in twins. For those ultrasound measurements where there were significant global tests for differences between twins and singletons, we tested for week-specific differences using Wald tests computed at each gestational age. In a separate analysis, we evaluated the degree of reclassification in small for gestational age, defined as below the 10(th) percentile that would be introduced if fetal growth estimation for twins was based upon an unweighted singleton standard. RESULTS: Women underwent a median of 5 ultrasounds. The 50(th) percentile abdominal circumference and estimated fetal weight trajectories of twin fetuses diverged significantly beginning at 32 weeks, while biparietal diameter in twins was smaller from 34 through 36 weeks. There were no differences in head circumference or femur length. The mean head circumference/abdominal circumference ratio was progressively larger for twins compared with singletons beginning at 33 weeks, indicating a comparatively asymmetric growth pattern. At 35 weeks, the average gestational age at delivery for twins, the estimated fetal weights for the 10(th), 50(th) and 90(th) percentiles were 1960, 2376, and 2879 g for dichorionic twins and 2180, 2567, and 3022 g for the singletons. At 32 weeks, the initial week when the mean estimated fetal weight for twins was smaller than that of singletons, 34% of twins would be classified as small for gestational age using a singleton, non-Hispanic white standard. By 35 weeks, 38% of twins would be classified as small for gestational age. CONCLUSIONS: The comparatively asymmetric growth pattern in twin gestations, initially evident at 32 weeks, is consistent with the concept that the intrauterine environment becomes constrained in its ability to sustain growth in twin fetuses. Near term, nearly 40% of twins would be classified as small for gestational age based on a singleton growth standard