Simplicity of Completion Time Distributions for Common Complex Biochemical Processes

Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the precise construction of specific macromolecules. In this work, we study the transient properties of such systems and fully characterize their first passage (completion) time distributions. In particular, we provide explicit expressions for the mean and the variance of the completion time for a kinetic proofreading process and computational analyses for more complicated biochemical systems. We find that, for a wide range of parameters, as the system size grows, the completion time behavior simplifies: it becomes either deterministic or exponentially distributed, with a very narrow transition between the two regimes. In both regimes, the dynamical complexity of the full system is trivial compared to its apparent structural complexity. Similar simplicity is likely to arise in the dynamics of many complex multi-step biochemical processes. In particular, these findings suggest not only that one may not be able to understand individual elementary reactions from macroscopic observations, but also that such understanding may be unnecessary

Final State Interactions Effects in Neutrino-Nucleus Interactions

Final State Interactions effects are discussed in the context of Monte Carlo simulations of neutrino-nucleus interactions. A role of Formation Time is explained and several models describing this effect are compared. Various observables which are sensitive to FSI effects are reviewed including pion-nucleus interaction and hadron yields in backward hemisphere. NuWro Monte Carlo neutrino event generator is described and its ability to understand neutral current $\pi^0$ production data in $\sim 1$ GeV neutrino flux experiments is demonstrated.Comment: 13 pages, 16 figure

Fast Primal-Dual Gradient Method for Strongly Convex Minimization Problems with Linear Constraints

In this paper we consider a class of optimization problems with a strongly convex objective function and the feasible set given by an intersection of a simple convex set with a set given by a number of linear equality and inequality constraints. A number of optimization problems in applications can be stated in this form, examples being the entropy-linear programming, the ridge regression, the elastic net, the regularized optimal transport, etc. We extend the Fast Gradient Method applied to the dual problem in order to make it primal-dual so that it allows not only to solve the dual problem, but also to construct nearly optimal and nearly feasible solution of the primal problem. We also prove a theorem about the convergence rate for the proposed algorithm in terms of the objective function and the linear constraints infeasibility.Comment: Submitted for DOOR 201

Designing a physical activity parenting course : parental views on recruitment, content and delivery

Background Many children do not engage in sufficient levels of physical activity (PA) and spend too much time screen-viewing (SV). High levels of SV (e.g. watching TV, playing video games and surfing the internet) and low levels of PA have been associated with adverse health outcomes. Parenting courses may hold promise as an intervention medium to change children’s PA and SV. The current study was formative work conducted to design a new parenting programme to increase children’s PA and reduce their SV. Specifically, we focussed on interest in a course, desired content and delivery style, barriers and facilitators to participation and opinions on control group provision. Methods In-depth telephone interviews were conducted with thirty two parents (29 female) of 6–8 year olds. Data were analysed thematically. An anonymous online survey was also completed by 750 parents of 6–8 year old children and descriptive statistics calculated. Results Interview participants were interested in a parenting course because they wanted general parenting advice and ideas to help their children be physically active. Parents indicated that they would benefit from knowing how to quantify their child’s PA and SV levels. Parents wanted practical ideas of alternatives to SV. Most parents would be unable to attend unless childcare was provided. Schools were perceived to be a trusted source of information about parenting courses and the optimal recruitment location. In terms of delivery style, the majority of parents stated they would prefer a group-based approach that provided opportunities for peer learning and support with professional input. Survey participants reported the timing of classes and the provision of childcare were essential factors that would affect participation. In terms of designing an intervention, the most preferred control group option was the opportunity to attend the same course at a later date. Conclusions Parents are interested in PA/SV parenting courses but the provision of child care is essential for attendance. Recruitment is likely to be facilitated via trusted sources. Parents want practical advice on how to overcome barriers and suggest advice is provided in a mutually supportive group experience with expert input

Elevated physiological arousal is associated with larger but more variable neural responses to small acoustic change in children during a passive auditory attention task

Little is known of how autonomic arousal relates to neural responsiveness during auditory attention. We presented N = 21 5-7-year-old children with an oddball auditory mismatch paradigm, whilst concurrently measuring heart rate fluctuations. Children with higher mean autonomic arousal, as indexed by higher heart rate (HR) and decreased high-frequency (0.15-0.8 Hz) variability in HR, showed smaller amplitude N250 responses to frequently presented (70%), 500 Hz standard tones. Follow-up analyses showed that the modal evoked response was in fact similar, but accompanied by more large and small amplitude responses and greater variability in peak latency in the high HR group, causing lower averaged responses. Similar patterns were also observed when examining heart rate fluctuations within a testing session, in an analysis that controlled for between-participant differences in mean HR. In addition, we observed larger P150/P3a amplitudes in response to small acoustic contrasts (750 Hz tones) in the high HR group. Responses to large acoustic contrasts (bursts of white noise), however, evoked strong early P3a phase in all children and did not differ by high/low HR. Our findings suggest that elevated physiological arousal may be associated with high variability in auditory ERP responses in young children, along with increased responsiveness to small acoustic changes

Accurate Liability Estimation Improves Power in Ascertained Case Control Studies

Linear mixed models (LMMs) have emerged as the method of choice for confounded genome-wide association studies. However, the performance of LMMs in non-randomly ascertained case-control studies deteriorates with increasing sample size. We propose a framework called LEAP (Liability Estimator As a Phenotype, https://github.com/omerwe/LEAP) that tests for association with estimated latent values corresponding to severity of phenotype, and demonstrate that this can lead to a substantial power increase

Cyclic projectors and separation theorems in idempotent convex geometry

Semimodules over idempotent semirings like the max-plus or tropical semiring have much in common with convex cones. This analogy is particularly apparent in the case of subsemimodules of the n-fold cartesian product of the max-plus semiring it is known that one can separate a vector from a closed subsemimodule that does not contain it. We establish here a more general separation theorem, which applies to any finite collection of closed semimodules with a trivial intersection. In order to prove this theorem, we investigate the spectral properties of certain nonlinear operators called here idempotent cyclic projectors. These are idempotent analogues of the cyclic nearest-point projections known in convex analysis. The spectrum of idempotent cyclic projectors is characterized in terms of a suitable extension of Hilbert's projective metric. We deduce as a corollary of our main results the idempotent analogue of Helly's theorem.Comment: 20 pages, 1 figur

Somatostatin treatment attenuates proteinuria and prevents weight loss in NZB/W F1 mice

Somatostatin, a naturally occurring neuropeptide, is an immunomodulator which inhibits humoral and cell mediated immunity as well as secretion of proinflammatory cytokines. The objective of this study was to examine the effects of a somatostatin analogue on the severity of glomerulonephritis in the female NZB/W F1 murine model of systemic lupus erythematosus (SLE). Twenty female NZB/W F1 mice were treated at 23 weeks of age with 10 mg/kg of the somatostatin analogue Sandostatin-LAR, IM every four weeks. Ten control mice received IM injection of vehicle. Mice were assessed at fourweek intervals for weight change, proteinuria, anti-DNA antibodies and splenocyte cytokine profile. The mice were sacrificed at age 34.5 weeks. Kidneys were collected and evaluated by light and immunofluorescence (IF) microscopy. Spleens were collected and splenocyte intracellular cytokines were measured by FACS analysis. In the treatment group significantly less proteinuria was observed four weeks after the second somatostatin analogue injection (dipstik scale: ϩ2.07 Ϯ 0.95 versus. ϩ3.5 Ϯ 1.08, P ϭ 0.0002). The treated mice did not lose weight while the control group lost weight over time (P ϭ 0.016). No differences were noted between the groups in anti-DNA antibody titres, cytokine profile or the severity of lupus nephritis as assessed by light and IF microscopy. Somatostatin analogue treatment attenuated proteinuria and prevented weight loss in NZB/W F1 mice, suggesting a possible beneficial effect on renal parameters and systemic manifestations of the disease. Further studies will be needed to assess the value of somatostatin analogue treatment in lupus nephritis, utilizing higher doses, at different stages of the disease, for longer periods. Lupus (2006) 15, 526-531

Semiring and semimodule issues in MV-algebras

In this paper we propose a semiring-theoretic approach to MV-algebras based on the connection between such algebras and idempotent semirings - such an approach naturally imposing the introduction and study of a suitable corresponding class of semimodules, called MV-semimodules. We present several results addressed toward a semiring theory for MV-algebras. In particular we show a representation of MV-algebras as a subsemiring of the endomorphism semiring of a semilattice, the construction of the Grothendieck group of a semiring and its functorial nature, and the effect of Mundici categorical equivalence between MV-algebras and lattice-ordered Abelian groups with a distinguished strong order unit upon the relationship between MV-semimodules and semimodules over idempotent semifields.Comment: This version contains some corrections to some results at the end of Section

Studying Paths of Participation in Viral Diffusion Process

Authors propose a conceptual model of participation in viral diffusion process composed of four stages: awareness, infection, engagement and action. To verify the model it has been applied and studied in the virtual social chat environment settings. The study investigates the behavioral paths of actions that reflect the stages of participation in the diffusion and presents shortcuts, that lead to the final action, i.e. the attendance in a virtual event. The results show that the participation in each stage of the process increases the probability of reaching the final action. Nevertheless, the majority of users involved in the virtual event did not go through each stage of the process but followed the shortcuts. That suggests that the viral diffusion process is not necessarily a linear sequence of human actions but rather a dynamic system.Comment: In proceedings of the 4th International Conference on Social Informatics, SocInfo 201