The three species monomer-monomer model in the reaction-controlled limit

We study the one dimensional three species monomer-monomer reaction model in the reaction controlled limit using mean-field theory and dynamic Monte Carlo simulations. The phase diagram consists of a reactive steady state bordered by three equivalent adsorbing phases where the surface is saturated with one monomer species. The transitions from the reactive phase are all continuous, while the transitions between adsorbing phases are first-order. Bicritical points occur where the reactive phase simultaneously meets two adsorbing phases. The transitions from the reactive to an adsorbing phase show directed percolation critical behaviour, while the universal behaviour at the bicritical points is in the even branching annihilating random walk class. The results are contrasted and compared to previous results for the adsorption-controlled limit of the same model.Comment: 12 pages using RevTeX, plus 4 postscript figures. Uses psfig.sty. accepted to Journal of Physics

Nonequilibrium Critical Dynamics of a Three Species Monomer-Monomer Model

We study a three species monomer-monomer catalytic surface reaction model with a reactive steady state bordered by three equivalent unreactive phases where the surface is saturated with one species. The transition from the reactive to a saturated phase shows directed percolation critical behavior. Each pair of these reactive-saturated phase boundaries join at a bicritical point where the universal behavior is in the even branching annihilating random walk class. We find the crossover exponent from bicritical to critical behavior and a new exponent associated with the bicritical interface dynamics.Comment: 4 pages RevTex. 4 eps figures included with psfig.sty. Uses multicol.sty. Accepted for publication in PR

The three species monomer-monomer model: A mean-field analysis and Monte Carlo study

We study the phase diagram and critical behavior of a one dimensional three species monomer-monomer surface reaction model. Static Monte Carlo simulations show a phase diagram consisting of a reactive steady state bordered by three equivalent unreactive phases where the surface is saturated with one monomer species. The transitions from the reactive to saturated phases are all continuous, while the transitions between poisoned phases are first-order, with bicritical points where the reactive phase meets two poisoned phases. A mean-field cluster analysis predicts all of the qualitative features of the phase diagram only when correlations up to triplets of adjacent sites are included. Dynamic Monte Carlo simulations show that the transition from the reactive to a saturated phase show critical behavior in the directed percolation universality class, while the bicritical point shows critical behavior in the even branching annihilating random walk class. The crossover from bicritical to critical behavior is also studied.Comment: 16 pages using RevTeX, plus 10 figures. Uses psfig.st

Spontaneous clearance of Chlamydia trachomatis accounting for bacterial viability in vaginally or rectally infected women (FemCure)

Objectives: Spontaneous clearance of Chlamydia trachomatis (CT) infections can occur between diagnosis and treatment. We followed CT patien

The Discrepancy between Patient and Clinician Reported Function in Extremity Bone Metastases

Background:. The Musculoskeletal Tumor Society (MSTS) scoring system measures function and is commonly used but criticized because it was developed to be completed by the clinician and not by the patient. We therefore evaluated if there is a difference between patient and clinician reported function using the MSTS score. Methods. 128 patients with bone metastasis of the lower (n = 100) and upper (n = 28) extremity completed the MSTS score. The MSTS score consists of six domains, scored on a 0 to 5 scale and transformed into an overall score ranging from 0 to 100% with a higher score indicating better function. The MSTS score was also derived from clinicians' reports in the medical record. Results. The median age was 63 years (interquartile range [IQR]: 55–71) and the study included 74 (58%) women. We found that the clinicians' MSTS score (median: 65, IQR: 49–83) overestimated the function as compared to the patient perceived score (median: 57, IQR: 40–70) by 8 points (p < 0.001). Conclusion. Clinician reports overestimate function as compared to the patient perceived score. This is important for acknowledging when informing patients about the expected outcome of treatment and for understanding patients' perceptions

Design of the FemCure study: prospective multicentre study on the transmission of genital and extra-genital Chlamydia trachomatis infections in women receiving routine care

BACKGROUND: In women, anorectal infections with Chlamydia trachomatis (CT) are about as common as genital CT, yet the anorectal site remains largely untested in routine care. Anorectal CT frequently co-occurs with genital CT and may thus often be treated co-incidentally. Nevertheless, post-treatment detection of CT at both anatomic sites has been demonstrated. It is unknown whether anorectal CT may play a role in post-treatment transmission. This study, called FemCure, in women who receive routine treatment (either azithromycin or doxycycline) aims to understand the post-treatment transmission of anorectal CT infections, i.e., from their male sexual partner(s) and from and to the genital region of the same woman. The secondary objective is to evaluate other reasons for CT detection by nucleic acid amplification techniques (NAAT) such as treatment failure, in order to inform guidelines to optimize CT control. METHODS: A multicentre prospective cohort study (FemCure) is set up in which genital and/or anorectal CT positive women (n = 400) will be recruited at three large Dutch STI clinics located in South Limburg, Amsterdam and Rotterdam. The women self-collect anorectal and vaginal swabs before treatment, and at the end of weeks 1, 2, 4, 6, 8, 10, and 12. Samples are tested for presence of CT-DNA (by NAAT), load (by quantitative polymerase chain reaction -PCR), viability (by culture and viability PCR) and CT type (by multilocus sequence typing). Sexual exposure is assessed by online self-administered questionnaires and by testing samples for Y chromosomal DNA. Using logistic regression models, the impact of two key factors (i.e., sexual exposure and alternate anatomic site of infection) on detection of anorectal and genital CT will be assessed. DISCUSSION: The FemCure study will provide insight in the role of anorectal chlamydia infection in maintaining the CT burden in the context of treatment, and it will provide practical recommendations to reduce avoidable transmission. Implications will improve care strategies that take account of anorectal CT. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02694497

Network 'small-world-ness': a quantitative method for determining canonical network equivalence

Background: Many technological, biological, social, and information networks fall into the broad class of 'small-world' networks: they have tightly interconnected clusters of nodes, and a shortest mean path length that is similar to a matched random graph (same number of nodes and edges). This semi-quantitative definition leads to a categorical distinction ('small/not-small') rather than a quantitative, continuous grading of networks, and can lead to uncertainty about a network's small-world status. Moreover, systems described by small-world networks are often studied using an equivalent canonical network model-the Watts-Strogatz (WS) model. However, the process of establishing an equivalent WS model is imprecise and there is a pressing need to discover ways in which this equivalence may be quantified. Methodology/Principal Findings: We defined a precise measure of 'small-world-ness' S based on the trade off between high local clustering and short path length. A network is now deemed a 'small-world' if S. 1-an assertion which may be tested statistically. We then examined the behavior of S on a large data-set of real-world systems. We found that all these systems were linked by a linear relationship between their S values and the network size n. Moreover, we show a method for assigning a unique Watts-Strogatz (WS) model to any real-world network, and show analytically that the WS models associated with our sample of networks also show linearity between S and n. Linearity between S and n is not, however, inevitable, and neither is S maximal for an arbitrary network of given size. Linearity may, however, be explained by a common limiting growth process. Conclusions/Significance: We have shown how the notion of a small-world network may be quantified. Several key properties of the metric are described and the use of WS canonical models is placed on a more secure footing

Halide homogenization for low energy loss in 2-eV-bandgap perovskites and increased efficiency in all-perovskite triple-junction solar cells

Monolithic all-perovskite triple-junction solar cells have the potential to deliver power conversion efficiencies beyond those of state-of-art double-junction tandems and well beyond the detailed-balance limit for single junctions. Today, however, their performance is limited by large deficits in open-circuit voltage and unfulfilled potential in both short-circuit current density and fill factor in the wide-bandgap perovskite sub cell. Here we find that halide heterogeneity—present even immediately following materials synthesis—plays a key role in interfacial non-radiative recombination and collection efficiency losses under prolonged illumination for Br-rich perovskites. We find that a diammonium halide salt, propane-1,3-diammonium iodide, introduced during film fabrication, improves halide homogenization in Br-rich perovskites, leading to enhanced operating stability and a record open-circuit voltage of 1.44 V in an inverted (p–i–n) device; ~86% of the detailed-balance limit for a bandgap of 1.97 eV. The efficient wide-bandgap sub cell enables the fabrication of monolithic all-perovskite triple-junction solar cells with an open-circuit voltage of 3.33 V and a champion PCE of 25.1% (23.87% certified quasi-steady-state efficiency)

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts