The Resolution in X-ray Crystallography and Single-Particle Cryogenic Electron Microscopy

X-ray crystallography and single-particle analysis cryogenic electron microscopy are essential techniques for uncovering the three-dimensional structures of biological macromolecules. Both techniques rely on the Fourier transform to calculate experimental maps. However, one of the crucial parameters, resolution, is rather broadly defined. Here, the methods to determine the resolution in X-ray crystallography and single-particle analysis are summarized. In X-ray crystallography, it is becoming increasingly more common to include reflections discarded previously by traditionally used standards, allowing for the inclusion of incomplete and anisotropic reflections into the refinement process. In general, the resolution is the smallest lattice spacing given by Bragg’s law for a particular set of X-ray diffraction intensities; however, typically the resolution is truncated by the user during the data processing based on certain parameters and later it is used during refinement. However, at which resolution to perform such a truncation is not always clear and this makes it very confusing for the novices entering the structural biology field. Furthermore, it is argued that the effective resolution should be also reported as it is a more descriptive measure accounting for anisotropy and incompleteness of the data. In single particle cryo-EM, the situation is not much better, as multiple ways exist to determine the resolution, such as Fourier shell correlation, spectral signal-to-noise ratio and the Fourier neighbor correlation. The most widely accepted is the Fourier shell correlation using a threshold of 0.143 to define the resolution (so-called “gold-standard”), although it is still debated whether this is the correct threshold. Besides, the resolution obtained from the Fourier shell correlation is an estimate of varying resolution across the density map. In reality, the interpretability of the map is more important than the numerical value of the resolution

The Value of Information in Container Transport: Leveraging the Triple Bottom Line

Planning the transport of maritime containers from the sea port to final destinations while using multiple transport modes is challenged by uncertainties regarding the time the container is released for further transport or the transit time from the port to its final destination. This paper assesses the value of information in container transport in terms of multiple performance dimensions, i.e. logistics costs, reliability, security, and emissions. The analysis is done using a single period model where a decision maker allocates arriving containers to two transport modes (slow, low price, no flexible departure times, versus fast, high price, flexible departure times). We construct a frontier of Pareto optimal decisions under each of the information scenarios and show that these frontiers move in a favorable direction when the level of information progresses. Each of the Pareto frontiers help strike the balance between the aforementioned performance dimensions. The mathematical results are illustrated using two numerical examples involving barge transport and train transport

A generalization of heterochromatic graphs

In 2006, Suzuki, and Akbari & Alipour independently presented a necessary and sufficient condition for edge-colored graphs to have a heterochromatic spanning tree, where a heterochromatic spanning tree is a spanning tree whose edges have distinct colors. In this paper, we propose $f$-chromatic graphs as a generalization of heterochromatic graphs. An edge-colored graph is $f$-chromatic if each color $c$ appears on at most $f(c)$ edges. We also present a necessary and sufficient condition for edge-colored graphs to have an $f$-chromatic spanning forest with exactly $m$ components. Moreover, using this criterion, we show that a $g$-chromatic graph $G$ of order $n$ with $|E(G)|>\binom{n-m}{2}$ has an $f$-chromatic spanning forest with exactly $m$ ($1 \le m \le n-1$) components if $g(c) \le \frac{|E(G)|}{n-m}f(c)$ for any color $c$.Comment: 14 pages, 4 figure

Network analysis in the Caribbean

The Caribbean region is a cross road of international and regional container traffic. Most of the islands in the region have also adopted ambitious strategies to become prime locations for container transshipment. This paper introduces a tool that can be used to visualise and analyse the Caribbean container flows. The tool is constructed on the basis of a multi-layered graph structure and is highly parameterized to allow for flexible selection of flows and ports. The tool supports the assessment of the potential for the development of logistics and transport hub through the calculation of relevant indicators using available information on container flows in the region. Much of the empirical work centers on the estimation of the origin-destination matrix of container flows in the region. The paper presents a case study for the island of Curacao

Class of correlated random networks with hidden variables

We study a class models of correlated random networks in which vertices are characterized by \textit{hidden variables} controlling the establishment of edges between pairs of vertices. We find analytical expressions for the main topological properties of these models as a function of the distribution of hidden variables and the probability of connecting vertices. The expressions obtained are checked by means of numerical simulations in a particular example. The general model is extended to describe a practical algorithm to generate random networks with an \textit{a priori} specified correlation structure. We also present an extension of the class, to map non-equilibrium growing networks to networks with hidden variables that represent the time at which each vertex was introduced in the system

Development of a quantitative real-time detection assay for hepatitis B virus DNA and comparison with two commercial assays

A highly reproducible and sensitive real-time detection assay based on TaqMan technology was developed for the detection of hepatitis B viru

Identification of a new variant in the YMDD motif of the hepatitis B virus polymerase gene selected during lamivudine therapy

A new hepatitis B virus variant selected during lamivudine treatment was detected, in which the methionine (rtM204) in the so-called YMDD motif in the C

Mean-field analysis of the q-voter model on networks

We present a detailed investigation of the behavior of the nonlinear q-voter model for opinion dynamics. At the mean-field level we derive analytically, for any value of the number q of agents involved in the elementary update, the phase diagram, the exit probability and the consensus time at the transition point. The mean-field formalism is extended to the case that the interaction pattern is given by generic heterogeneous networks. We finally discuss the case of random regular networks and compare analytical results with simulations.Comment: 20 pages, 10 figure