The phase diagram of random threshold networks

Threshold networks are used as models for neural or gene regulatory networks. They show a rich dynamical behaviour with a transition between a frozen and a chaotic phase. We investigate the phase diagram of randomly connected threshold networks with real-valued thresholds h and a fixed number of inputs per node. The nodes are updated according to the same rules as in a model of the cell-cycle network of Saccharomyces cereviseae [PNAS 101, 4781 (2004)]. Using the annealed approximation, we derive expressions for the time evolution of the proportion of nodes in the "on" and "off" state, and for the sensitivity $\lambda$. The results are compared with simulations of quenched networks. We find that for integer values of h the simulations show marked deviations from the annealed approximation even for large networks. This can be attributed to the particular choice of the updating rule.Comment: 8 pages, 6 figure

Primjena autologne fibrinske membrane obogaćene trombocitima (PRF) u liječenju dubokih čireva rožnice u pasa

The aim of this study was to evaluate the clinical efficacy of a platelet-rich fibrin (PRF) membrane, which is considered to be a new alternative surgical method in the treatment of vision-threatening corneal ulcers in dogs. Fourteen dogs (17 eyes) of various breeds and ages with deep corneal ulcers were treated surgically with a PRF membrane transplantation. The corneal ulcer of all the patients was closed with an autologous platelet-rich fibrin membrane. In the first 10 days after the operation, it was observed that the fibrin membrane partially melted, and corneal epithelialization and granulation tissue occurred in and around the ulcer area due to the graft material. Pain was significantly relieved, and conjunctival inflammation was noticeably improved. From the 20th day after the surgery, the granulation tissue was gradually cleaned. It was determined that all the eyes had vision. The most common complications after surgery were corneal pigmentation and fibrosis of varying severity. The use of autologous fibrin membranes is a safe and effective surgical alternative for the closure and healing of corneal ulcers. Our findings show that the autologous platelet-rich fibrin membrane is useful and effective in treating canine corneal deep ulcers.Čirevi rožnice mogu oštetiti vid u pasa. Cilj je ovog istraživanja bio procijeniti kliničku učinkovitost fibrinske membrane obogaćene trombocitima (PRF), kao nove alternative kirurških metoda u liječenju čireva rožnice. Četrnaest pasa (17 očiju) različitih pasmina i dobi, s dubokim čirevima rožnice liječeno je kirurški transplantacijom. Čir na rožnici u svih je pacijenata bio zatvoren autolognom fibrinskom membranom obogaćenom trombocitima. Prvih 10 dana nakon kirurškog zahvata uočeno je da se fibrinska membrana parcijalno talila, dok se na čiru i oko njega pojavilo epitelizacijsko i granulacijsko tkivo zbog graft materijala. Bol je znatno ublažena, a upala konjunktive osjetno smanjena. Od 20. dana nakon kirurškog zahvata granulacijsko je tkivo postupno očišćeno. Pokazalo se da je svim psima vraćen vid. Najčešće su komplikacije nakon kirurškog zahvata bile pigmentacija rožnice i fibroza različita stupnja. Rezultati istraživanja pokazuju da je autologna fibrinska membrana obogaćena trombocitima sigurna, korisna i učinkovita kirurška alternativa u liječenju dubokih čireva rožnice u pasa

Self-optimization, community stability, and fluctuations in two individual-based models of biological coevolution

We compare and contrast the long-time dynamical properties of two individual-based models of biological coevolution. Selection occurs via multispecies, stochastic population dynamics with reproduction probabilities that depend nonlinearly on the population densities of all species resident in the community. New species are introduced through mutation. Both models are amenable to exact linear stability analysis, and we compare the analytic results with large-scale kinetic Monte Carlo simulations, obtaining the population size as a function of an average interspecies interaction strength. Over time, the models self-optimize through mutation and selection to approximately maximize a community fitness function, subject only to constraints internal to the particular model. If the interspecies interactions are randomly distributed on an interval including positive values, the system evolves toward self-sustaining, mutualistic communities. In contrast, for the predator-prey case the matrix of interactions is antisymmetric, and a nonzero population size must be sustained by an external resource. Time series of the diversity and population size for both models show approximate 1/f noise and power-law distributions for the lifetimes of communities and species. For the mutualistic model, these two lifetime distributions have the same exponent, while their exponents are different for the predator-prey model. The difference is probably due to greater resilience toward mass extinctions in the food-web like communities produced by the predator-prey model.Comment: 26 pages, 12 figures. Discussion of early-time dynamics added. J. Math. Biol., in pres

Characteristics of Antiphospholipid Antibody Positive Patients in AntiPhospholipid Syndrome Alliance for Clinical Trials and InternatiOnal Networking

OBJECTIVE: To describe baseline characteristics of antiphospholipid antibody (aPL)-positive patients, overall and by clinical and laboratory subtypes, enrolled in an international registry. METHODS: AntiPhospholipid Syndrome Alliance for Clinical Trials and InternatiOnal Networking Registry includes persistently aPL-positive adults. We evaluated baseline sociodemographic and aPL-related (APS classification criteria and "non-criteria") characteristics of patients overall and in subgroups (aPL-positive without APS, APS overall, thrombotic APS [TAPS] only, obstetric APS [OAPS] only, and both TAPS/OAPS). We assessed baseline characteristics of patients tested for three aPL (lupus anticoagulant test [LA], anticardiolipin antibody [aCL], and anti-β2 -Glycoprotein-I [aβ2 GPI]) by aPL profiles (LA only, single, double, and triple aPL positivity). RESULTS: Of 804 aPL-positive patients (mean age: 45 ± 13y; female: 74%; white 68%; other systemic autoimmune diseases: 36%), 80% were classified as APS (55% TAPS, 9% OAPS, and 15% TAPS/OAPS). In the overall cohort, 71% had vascular thrombosis, 50% with pregnancy history had obstetric morbidity, and 56% had at least one non-criteria manifestation. Among those with three aPL tested (n: 660), 42% were triple aPL positive. While single, double and triple aPL positive subgroups had similar frequencies of vascular, obstetric, and non-criteria events, these events were lowest in the single aPL subgroup consisting of aCL or aβ2 GPI only. CONCLUSION: Our study demonstrates the heterogeneity of aPL-related clinical manifestations and laboratory profiles in a multicenter, international cohort. Within single aPL-positivity, LA may be a major contributor to clinical events. Future prospective analyses, using standardized core laboratory aPL tests, will help clarify aPL risk profiles and improve risk stratification

Standardized Treatment of Active Tuberculosis in Patients with Previous Treatment and/or with Mono-resistance to Isoniazid: A Systematic Review and Meta-analysis

Performing a systematic review of studies evaluating retreatment of tuberculosis or treatment of isoniazid mono-resistant infection, Dick Menzies and colleagues find a paucity of evidence to support the WHO-recommended regimen

Most Networks in Wagner's Model Are Cycling

In this paper we study a model of gene networks introduced by Andreas Wagner in the 1990s that has been used extensively to study the evolution of mutational robustness. We investigate a range of model features and parameters and evaluate the extent to which they influence the probability that a random gene network will produce a fixed point steady state expression pattern. There are many different types of models used in the literature, (discrete/continuous, sparse/dense, small/large network) and we attempt to put some order into this diversity, motivated by the fact that many properties are qualitatively the same in all the models. Our main result is that random networks in all models give rise to cyclic behavior more often than fixed points. And although periodic orbits seem to dominate network dynamics, they are usually considered unstable and not allowed to survive in previous evolutionary studies. Defining stability as the probability of fixed points, we show that the stability distribution of these networks is highly robust to changes in its parameters. We also find sparser networks to be more stable, which may help to explain why they seem to be favored by evolution. We have unified several disconnected previous studies of this class of models under the framework of stability, in a way that had not been systematically explored before

Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm

In mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3′ untranslated region (UTR) of many short-lived mRNAs. AREs cause mRNAs to be degraded rapidly and thereby suppress gene expression at the posttranscriptional level. Based on the number of AUUUA pentamers, their proximity, and surrounding AU-rich regions, we generated an algorithm termed AREScore that identifies AREs and provides a numerical assessment of their strength. By analyzing the AREScore distribution in the transcriptomes of 14 metazoan species, we provide evidence that AREs were selected for in several vertebrates and Drosophila melanogaster. We then measured mRNA expression levels genome-wide to address the importance of AREs in SL2 cells derived from D. melanogaster hemocytes. Tis11, a zinc finger RNA–binding protein homologous to mammalian tristetraprolin, was found to target ARE–containing reporter mRNAs for rapid degradation in SL2 cells. Drosophila mRNAs whose expression is elevated upon knock down of Tis11 were found to have higher AREScores. Moreover high AREScores correlate with reduced mRNA expression levels on a genome-wide scale. The precise measurement of degradation rates for 26 Drosophila mRNAs revealed that the AREScore is a very good predictor of short-lived mRNAs. Taken together, this study introduces AREScore as a simple tool to identify ARE–containing mRNAs and provides compelling evidence that AREs are widespread regulatory elements in Drosophila

Multi-ancestry meta-analysis of tobacco use disorder prioritizes novel candidate risk genes and reveals associations with numerous health outcomes

Tobacco use disorder (TUD) is the most prevalent substance use disorder in the world. Genetic factors influence smoking behaviors, and although strides have been made using genome-wide association studies (GWAS) to identify risk variants, the majority of variants identified have been for nicotine consumption, rather than TUD. We leveraged five biobanks to perform a multi-ancestral meta-analysis of TUD (derived via electronic health records, EHR) in 898,680 individuals (739,895 European, 114,420 African American, 44,365 Latin American). We identified 88 independent risk loci; integration with functional genomic tools uncovered 461 potential risk genes, primarily expressed in the brain. TUD was genetically correlated with smoking and psychiatric traits from traditionally ascertained cohorts, externalizing behaviors in children, and hundreds of medical outcomes, including HIV infection, heart disease, and pain. This work furthers our biological understanding of TUD and establishes EHR as a source of phenotypic information for studying the genetics of TUD

Adverse effects of extra-articular corticosteroid injections: a systematic review

<p>Abstract</p> <p>Background</p> <p>To estimate the occurrence and type of adverse effects after application of an extra-articular (soft tissue) corticosteroid injection.</p> <p>Methods</p> <p>A systematic review of the literature was made based on a PubMed and Embase search covering the period 1956 to January 2010. Case reports were included, as were prospective and retrospective studies that reported adverse events of corticosteroid injection. All clinical trials which used extra-articular corticosteroid injections were examined. We divided the reported adverse events into major (defined as those needing intervention or not disappearing) and minor ones (transient, not requiring intervention).</p> <p>Results</p> <p>The search yielded 87 relevant studies:44 case reports, 37 prospective studies and 6 retrospective studies. The major adverse events included osteomyelitis and protothecosis; one fatal necrotizing fasciitis; cellulitis and ecchymosis; tendon ruptures; atrophy of the plantar fat was described after injecting a neuroma; and local skin effects appeared as atrophy, hypopigmentation or as skin defect. The minor adverse events effects ranged from skin rash to flushing and disturbed menstrual pattern. Increased pain or steroid flare after injection was reported in 19 studies. After extra-articular injection, the incidence of major adverse events ranged from 0-5.8% and that of minor adverse events from 0-81%. It was not feasible to pool the risk for adverse effects due to heterogeneity of study populations and difference in interventions and variance in reporting.</p> <p>Conclusion</p> <p>In this literature review it was difficult to accurately quantify the incidence of adverse effects after extra-articular corticosteroid injection. The reported adverse events were relatively mild, although one fatal reaction was reported.</p