Risk stratification for the development of chronic postsurgical pain

Chronic postsurgical pain (CPSP) is a common complication of surgery with important consequences for the individual patient and society as a whole. Risk stratification is best defined as the grouping of patients based on factors measured at baseline (in this context before surgery), to determine an individual's risk of suffering a particular condition and thereby the likely level of need for preventive interventions. Risk factors for CPSP have been identified in the preoperative, intraoperative, and postoperative periods and cover 6 broad domains: genetic, demographic, psychosocial, pain, clinical, and surgical factors. Risk stratification for CPSP enables clinicians to address these risk factors before surgery, to discuss the necessity of surgery or to change the surgical and anaesthetic/analgesic planning

Cancer metabolism at a glance

A defining hallmark of cancer is uncontrolled cell proliferation. This is initiated once cells have accumulated alterations in signaling pathways that control metabolism and proliferation, wherein the metabolic alterations provide the energetic and anabolic demands of enhanced cell proliferation. How these metabolic requirements are satisfied depends, in part, on the tumor microenvironment, which determines the availability of nutrients and oxygen. In this Cell Science at a Glance paper and the accompanying poster, we summarize our current understanding of cancer metabolism, emphasizing pathways of nutrient utilization and metabolism that either appear or have been proven essential for cancer cells. We also review how this knowledge has contributed to the development of anticancer therapies that target cancer metabolism

Simulation of guiding of multiply charged projectiles through insulating capillaries

Recent experiments have demonstrated that highly charged ions can be guided through insulating nanocapillaries along the direction of the capillary axis for a surprisingly wide range of injection angles. Even more surprisingly, the transmitted particles remain predominantly in their initial charge state, thus opening the pathway to the construction of novel ion-optical elements without electric feedthroughs. We present a theoretical treatment of this self-organized guiding process. We develop a classical trajectory transport theory that relates the microscopic charge-up with macroscopic material properties. Transmission coefficients, angular spread of transmitted particles, and discharge characteristics of the target are investigated. Partial agreement with experiment is found

Penetration Depth Scaling for Impact Into Wet Granular Packings

We present experimental measurements of penetration depths for the impact of spheres into wetted granular media. We observe that the penetration depth in the liquid saturated case scales with projectile density, size, and drop height in a fashion consistent with the scaling observed in the dry case, but with smaller penetrations. Neither viscous drag nor density effects can explain the enhancement to the stopping force. The penetration depth exhibits a complicated dependence on liquid fraction, accompanied by a change in the drop-height dependence, that must be the consequence of accompanying changes in the conformation of the liquid phase in the interstices

Monte Carlo Methods for Rough Free Energy Landscapes: Population Annealing and Parallel Tempering

Parallel tempering and population annealing are both effective methods for simulating equilibrium systems with rough free energy landscapes. Parallel tempering, also known as replica exchange Monte Carlo, is a Markov chain Monte Carlo method while population annealing is a sequential Monte Carlo method. Both methods overcome the exponential slowing associated with high free energy barriers. The convergence properties and efficiency of the two methods are compared. For large systems, population annealing initially converges to equilibrium more rapidly than parallel tempering for the same amount of computational work. However, parallel tempering converges exponentially and population annealing inversely in the computational work so that ultimately parallel tempering approaches equilibrium more rapidly than population annealing.Comment: 10 pages, 3 figure

Modeling and Analyzing Biomolecular Networks

The authors argue for the need to model and analyze biological networks at molecular and cellular levels. They propose a computational toolbox for biologists. Central to their approach is the paradigm of hybrid models in which discrete events are combined with continuous differential equations to capture switching behavior

FRET Dyes Significantly Affect SAXS Intensities of Proteins

Structural analyses in biophysics aim at revealing a relationship between a molecule's dynamic structure and its physiological function. Förster resonance energy transfer (FRET) and small‐angle X‐ray scattering (SAXS) are complementary experimental approaches to this. Their concomitant application in combined studies has recently opened a lively debate on how to interpret FRET measurements in the light of SAXS data with the popular example of the radius of gyration, commonly derived from both FRET and SAXS. There still is a lack of understanding in how to mutually relate and interpret quantities equally obtained from FRET or SAXS, and to what extent FRET dyes affect SAXS intensities in combined applications. In the present work, we examine the interplay of FRET and SAXS from a computational simulation perspective. Molecular simulations are a valuable complement to experimental approaches and supply instructive information on dynamics. As FRET depends not only on the mutual separation but also on the relative orientations, the dynamics, and therefore also the shapes of the dyes, we utilize a novel method for simulating FRET‐dye‐labeled proteins to investigate these aspects in atomic detail. We perform structure‐based simulations of four different proteins with and without dyes in both folded and unfolded conformations. In‐silico derived radii of gyration are different with and without dyes and depend on the chosen dye pair. The dyes apparently influence the dynamics of unfolded systems. We find that FRET dyes attached to a protein have a significant impact on theoretical SAXS intensities calculated from simulated structures, especially for small proteins. Radii of gyration from FRET and SAXS deviate systematically, which points to further underlying mechanisms beyond prevalent explanation approaches

Stability and reachability analysis of a hybrid model of luminescence in the marine bacterium \u3ci\u3eVibrio fischeri\u3c/i\u3e

This paper addresses the mathematical modeling and analysis of the quorum sensing system found in unicellular bacteria that exhibit bioluminescence. The luminescence is governed by the expression of genes in the cell, which in turn is controlled by the density of cells in a population. The paper illustrates the application of standard tools in control theory and some recent tools in hybrid systems to the quorum sensing system, and demonstrates that bioluminescence can be modeled and understood as the output of a switched dynamical system