Emergence of order in selection-mutation dynamics

We characterize the time evolution of a d-dimensional probability distribution by the value of its final entropy. If it is near the maximally-possible value we call the evolution mixing, if it is near zero we say it is purifying. The evolution is determined by the simplest non-linear equation and contains a d times d matrix as input. Since we are not interested in a particular evolution but in the general features of evolutions of this type, we take the matrix elements as uniformly-distributed random numbers between zero and some specified upper bound. Computer simulations show how the final entropies are distributed over this field of random numbers. The result is that the distribution crowds at the maximum entropy, if the upper bound is unity. If we restrict the dynamical matrices to certain regions in matrix space, for instance to diagonal or triangular matrices, then the entropy distribution is maximal near zero, and the dynamics typically becomes purifying.Comment: 8 pages, 8 figure

Time-reversed symmetry and covariant Lyapunov vectors for simple particle models in and out of thermal equilibrium

Recently, a new algorithm for the computation of covariant Lyapunov vectors and of corresponding local Lyapunov exponents has become available. Here we study the properties of these still unfamiliar quantities for a number of simple models, including an harmonic oscillator coupled to a thermal gradient with a two-stage thermostat, which leaves the system ergodic and fully time reversible. We explicitly demonstrate how time-reversal invariance affects the perturbation vectors in tangent space and the associated local Lyapunov exponents. We also find that the local covariant exponents vary discontinuously along directions transverse to the phase flow.Comment: 13 pages, 11 figures submitted to Physical Review E, 201

The use of external controls: To what extent can it currently be recommended?

With more and better clinical data being captured outside of clinical studies and greater data sharing of clinical studies, external controls may become a more attractive alternative to randomized clinical trials. Both industry and regulators recognize that in situations where a randomized study cannot be performed, external controls can provide the needed contextualization to allow a better interpretation of studies without a randomized control. It is also agreed that external controls will not fully replace randomized clinical trials as the gold standard for formal proof of efficacy in drug development and the yardstick of clinical research. However, it remains unclear in which situations conclusions about efficacy and a positive benefit/risk can reliably be based on the use of an external control. This paper will provide an overview on types of external control, their applications and the different sources of bias their use may incur, and discuss potential mitigation steps. It will also give recommendations on how the use of external controls can be justified

Identifying rare chaotic and regular trajectories in dynamical systems with Lyapunov weighted path sampling

Depending on initial conditions, individual finite time trajectories of dynamical systems can have very different chaotic properties. Here we present a numerical method to identify trajectories with atypical chaoticity, pathways that are either more regular or more chaotic than average. The method is based on the definition of an ensemble of trajectories weighted according to their chaoticity, the Lyapunov weighted path ensemble. This ensemble of trajectories is sampled using algorithms borrowed from transition path sampling, a method originally developed to study rare transitions between long-lived states. We demonstrate our approach by applying it to several systems with numbers of degrees of freedom ranging from one to several hundred and in all cases the algorithm found rare pathways with atypical chaoticity. For a double-well dimer embedded in a solvent, which can be viewed as simple model for an isomerizing molecule, rare reactive pathways were found for parameters strongly favoring chaotic dynamics.Comment: 8 pages, 5 figure

The Evolutionary Conserved γ-Core Motif Influences the Anti-Candida Activity of the Penicillium chrysogenum Antifungal Protein PAF

Small, cysteine-rich and cationic antimicrobial proteins (AMPs) from filamentous ascomycetes represent ideal bio-molecules for the development of next generation antifungal therapeutics. They are promising candidates to counteract resistance development and may complement or even replace current small molecule-based antibiotics in the future. In this study, we show that a 14 amino acid (aa) long peptide (Pγ) spanning the highly conserved γ-core motif of the Penicillium chrysogenum antifungal protein PAF has antifungal activity against the opportunistic human pathogenic yeast Candida albicans. By substituting specific aa we elevated the positive net charge and the hydrophilicity of Pγ and created the peptide variants Pγvar and Pγopt with ten-fold higher antifungal activity than Pγ. Similarly, the antifungal efficacy of the PAF protein could be significantly improved by exchanging the respective aa in the γ-core of the protein by creating the protein variants PAFγvar and PAFγopt. The designed peptides and proteins were investigated in detail for their physicochemical features and mode of action, and were tested for cytotoxicity on mammalian cells. This study proves for the first time the important role of the γ-core motif in the biological function of an AMP from ascomycetes. Furthermore, we provide a detailed phylogenetic analysis that proves the presence and conservation of the γ-core motif in all AMP classes from Eurotiomycetes. We emphasize the potential of this common protein motif for the design of short antifungal peptides and as a protein motif in which targeted aa substitutions enhance antimicrobial activity

Patterns of Disease Progression and Outcome of Patients With Testicular Seminoma Who Relapse After Adjuvant or Curative Radiation Therapy.

PURPOSE Radiation therapy is a possible treatment strategy for patients with testicular seminoma after orchiectomy in clinical stage I or II disease. Little is known about the outcome of patients who experience a relapse after radiation therapy. METHODS AND MATERIALS Data from 61 patients who relapsed after adjuvant or curative radiation therapy from 17 centers in 11 countries were collected and retrospectively analyzed. Primary outcomes were disease-free and overall survival. Secondary outcomes were time to relapse, stage at relapse, treatment for relapse, and rate of febrile neutropenia during chemotherapy for relapse. RESULTS With a median follow-up of 9.9 years (95% confidence interval [CI], 7.5-10.9), we found a 5-year disease-free survival of 90% (95% CI, 79-95) and a 5-year overall survival of 98% (95% CI, 89-100). Sixty-six percent of patients had stage III disease at time of relapse and 93% of patients fell into the good prognosis group per the International Germ Cell Cancer Collaborative Group classification. The median time to relapse after radiation therapy was 15.6 months (95% CI, 12-23). Twenty-two (36%) patients relapsed more than 2 years after radiation therapy and 7 (11.5%) patients relapsed more than 5 years after radiation therapy. One-third of relapses was detected owing to patients' symptoms, whereas two-thirds of relapses were detected during routine follow-up. The majority (93%) of cases were treated with cisplatin-based chemotherapy. The rate of febrile neutropenia during chemotherapy was 35%. Five patients experienced a second relapse. At last follow-up, 55 patients (90%) were alive without disease. Only 1 patient died owing to disease progression. CONCLUSIONS Cisplatin-based chemotherapy for patients with seminoma who have relapsed after treatment with radiation therapy alone leads to excellent outcomes. Patients and physicians should be aware of possible late relapses after radiation therapy

Complement as an Endogenous Adjuvant for Dendritic Cell-Mediated Induction of Retrovirus-Specific CTLs

Previous studies have demonstrated the involvement of complement (C) in induction of efficient CTL responses against different viral infections, but the exact role of complement in this process has not been determined. We now show that C opsonization of retroviral particles enhances the ability of dendritic cells (DCs) to induce CTL responses both in vitro and in vivo. DCs exposed to C-opsonized HIV in vitro were able to stimulate CTLs to elicit antiviral activity significantly better than non-opsonized HIV. Furthermore, experiments using the Friend virus (FV) mouse model illustrated that the enhancing role of complement on DC-mediated CTL induction also occurred in vivo. Our results indicate that complement serves as natural adjuvant for DC-induced expansion and differentiation of specific CTLs against retroviruses