Supporting the planning of a community fisheries monitoring and evaluation database: a collaborative project undertaken by CFDO, FLD, STREAM, VSO and AYAD

Cambodia is one of the poorest countries in the world; much of its population live in rural areas and many live below the local poverty line. The management of common property aquatic resources is of over-riding importance to food security and sustainable rural development in Cambodia. Aquatic resources are utilized principally by subsistence fishers and the landless, for whom aquatic resource use is an important livelihood activity. Subsistence fishers access mainly the rivers, lakes and inundated forests in Tonle Sap provinces, the lower Mekong and Bassac regions and the upper part of the Mekong. Freshwater capture fisheries probably contribute more to national food security and the national economy in Cambodia than in any other country in the world. (PDF contains 52 pages

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the corresponding map obtained using phases from the final refined model. Here, ten different measures of experimental map quality were examined using a set of 1359 maps calculated by re-analysis of 246 solved MAD, SAD and MIR data sets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. It was found that a Bayesian estimator based on the skewness of the density values in an electron-density map is the most accurate of the ten individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skewness of electron density with the local correlation of r.m.s. density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. The PHENIX AutoSol wizard carries out automated structure solution based on any combination of SAD, MAD, SIR or MIR data sets. The wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest quality solutions after experimental phasing

Exotic states in a simple network of nanoelectromechanical oscillators.

Synchronization of oscillators, a phenomenon found in a wide variety of natural and engineered systems, is typically understood through a reduction to a first-order phase model with simplified dynamics. Here, by exploiting the precision and flexibility of nanoelectromechanical systems, we examined the dynamics of a ring of quasi-sinusoidal oscillators at and beyond first order. Beyond first order, we found exotic states of synchronization with highly complex dynamics, including weak chimeras, decoupled states, traveling waves, and inhomogeneous synchronized states. Through theory and experiment, we show that these exotic states rely on complex interactions emerging out of networks with simple linear nearest-neighbor coupling. This work provides insight into the dynamical richness of complex systems with weak nonlinearities and local interactions

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks

Outside the gate: sub-urban legal practices in early medieval England

Many aspects of English early medieval (Anglo-Saxon) legal landscapes can be discerned in archaeological and toponymic evidence, ranging from the locations of legislative councils and judicial assemblies to sites of capital punishment. Among the corpus of such sites a striking group can be detected at the periphery of urban spaces. Gates into a number of towns appear to have functioned as legislative meeting-places, and even gave their names to some legally constituted communities, while suburban locations also feature prominently as sites of gallows and public punishment. In this paper historical, archaeological and toponymic evidence is used to examine this phenomenon of suburban legal practices and to pose questions about the wider dimensions of the early medieval legal landscape

PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms

Recruiting Care Homes to a Randomised Controlled Trial

Background There are over a quarter of a million individuals aged ≥65 years resident in care homes in England and Wales. Care home residents have high levels of cognitive impairment, physical disability, multimorbidity and polypharmacy. Research is needed to ensure there are robust, evidence-based interventions to improve the quality of life of this frail group. However, there is a paucity of research studies in this area. Recruiting care homes and their residents to research is challenging. A feasibility, cluster randomised controlled trial was undertaken as part of a research programme to identify ways to develop and test methods to enhance the physical activity of care home residents. This paper describes two methods of recruiting care homes to the trial and draws out learning to inform future studies. Methods Eligible care homes: were within a defined geographical area in the north of England; provided residential care for adults ≥65 years of age; had not previously been involved in the research programme; were not taking part in a conflicting study; were not recorded on the Care Quality Commission website as ‘inadequate’ or ‘requiring improvements’ in any area; had ≥10 beds. Care homes were identified by: a ‘systematic approach’ using the Care Quality Commission website database of care homes; a ‘targeted approach’ via a network of research-ready care homes. A standardised method was used to recruit care homes including: eligibility screening; invitation letters; telephone contact; visits; formal letter of agreement. Results In the systematic approach, 377 care homes were screened, 230 (61%) were initially eligible and invited to participate, 11 were recruited (recruitment rate (RR) 4.8%). In the targeted approach, 15 care homes were invited to participate, two were recruited (RR 13.3%). Overall, 245 care homes were approached and 13 recruited (RR 5.3%). A variety of care homes were recruited to the trial in terms of size, location, ownership and care provision. Conclusions Systematic recruitment of care homes to the study was time-consuming and resource-heavy but led to a variety of care homes being recruited. The targeted approach led to a higher recruitment rate. Trial registration ISRCTN registry, ISRCTN16076575. Registered 25 June 2015, http://www.isrctn.com/ISRCTN1607657

Flodoard of Rheims and the Historiography of the Tenth-Century West

Flodoard of Rheims is one of the most important authors of tenth-century Europe, and the only contemporary historian to document the momentous struggles between kings and nobles in Francia in the wake of the demise of the Carolingian Empire. Flodoard’s era stands at the center of major historiographical debates concerning the nature of political and social change and the origins of European institutions. Yet, despite his singularity, his substantial histories have received little attention from scholars examining the profound transformations of the period. Exploring this discrepancy, this article offers an overview of Flodoard’s career and reviews how his histories have been invoked in some of the great scholarly debates about tenth-century Europe. It further proposes to recontextualize Flodoard and to reread his histories from the bottom up in order to gain a subtler understanding of how one contemporary perceived and represented the dramatic events and changes taking place around him

The CCP4 suite : integrative software for macromolecular crystallography

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world