PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

Physical Activity, Gender, Weight Status, and Wellbeing in 9- to 11-Year-Old Children: A Cross-Sectional Survey

Background: The aim of this study was to examine the relationship between physical activity and wellbeing in children, and to further explore the extent to which this may vary by gender and weight status. Method: A representative sample of 1424 9- to 11-year-olds completed a self-report measure of physical activity, the Child Health and Illness Profile, KIDSCREEN, and a self-esteem scale. Body Mass Index (BMI) measurements were also obtained. Results: 24% of children achieved the recommended level of 60 minutes of moderate-tovigorous intensity physical activity (MVPA) per day, with more boys than girls achieving this level. Children achieving the recommended level of MVPA scored significantly higher on measures of the Child Health and Illness Profile (F(5, 1354) = 5.03; P < .001), KIDSCREEN (F(3, 1298) = 4.68; P = .003), and self-esteem (F(1,1271) = 18.73; P = .003) than less active children although the effect sizes were small (ηp2 ≈ .01). Substantial gender differences in wellbeing were found reflecting gender specific behaviors and socialization. Weight status had negligible influence on wellbeing. Conclusions: Children who meet the recommended guidelines of MVPA were more likely to have better wellbeing. When attempting to raise children’s physical activity levels consideration should be given to the specific relationships between wellbeing and physical activity.

Streets for people, or why we should reuse buildings in the city centre

Cities are constantly changing, and city centres are the pinnacle of that change. In the last hundred years these changes have been dramatic, transforming city centres from a complex combination of uses into exclusively retail and leisure areas. Meanwhile, most residents of city centres fled to the suburbs, removing much of the livelihood of central areas. These transformations has been stronger in Northern Europe and especially in English speaking countries, where zoning policies were instrumental in urban development since the 1960s. This process along with the rise of shopping malls left many city centre streets lifeless, which in turn caused the dereliction and demolition of significant heritage areas and buildings. Belfast is no exception, where the broad process of suburbanization and zoning since the 1970s produced a city centre for either retail or dereliction, where much built heritage has been lost or is at risk of being lost.

Old truths and new politics:Does truth commission 'publicness' impact democratization?

This article analyzes the relationship between truth and politics by asking whether the 'publicness' of a truth commission - defined by whether it has public hearings, releases a public report, and names perpetrators - contributes to democratization. The article reviews scholarship relevant to the potential democratizing effects of truth commissions and derives mechanisms that help explain this relationship. Work from the transitional justice field as well as democratization and political transition more generally is considered. Using a newly-constructed Truth Commission Publicness Dataset (TCPD), the analysis finds that even after statistically controlling for initial levels of democracy, democratic trends in the years prior to a commission, level of wealth, amnesties and/or trials, the influence of the South African Truth and Reconciliation Commission, and different cutoff points for measuring democratization across a number of models, more publicness predicts higher levels of democracy years after the commission has finished its work. The more public a truth commission is, the more it will contribute to democratization. The finding that more public truth commissions are associated with higher levels of democratization indicates particular strategies that policymakers, donors, and civil society activists may take to improve prospects for democracy in a country planning a truth commission in the wake of violence and/or government abuse. © The Author(s) 2012.

Periodontal Manifestations of Chronic Atypical Neutrophilic Dermatosis With Lipodystrophy and Elevated Temperature (CANDLE) Syndrome in an 11 Year Old Patient

Introduction: Chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE) is an auto inflammatory syndrome caused by an autosomal recessive gene mutation. This very rare syndrome has been reported in only 14 patients worldwide. A number of clinical signs have been reported including joint contractures, muscle atrophy, microcytic anaemia, and panniculitis-induced childhood lipodystrophy. Further symptoms include recurrent fevers, purpuric skin lesions, periorbital erythema and failure to thrive. This is the first reported case of periodontal manifestations associated with CANDLE syndrome. 
Case Presentation: An 11 year old boy was referred to Cork University Dental School and Hospital with evidence of severe periodontal destruction. The patient’s medical condition was managed in Great Ormond Street Children’s Hospital, London. The patient’s dental management included initial treatment to remove teeth of hopeless prognosis followed by prosthodontic rehabilitation using removable partial dentures. This was followed by further non-surgical periodontal treatment and maintenance. In the long term, the potential definitive restorative options, including dental implants, will be evaluated in discussion with the patient’s medical team.
Conclusion: Periodontitis as a manifestation of systemic disease is one of seven categories of periodontitis as defined by the American Academy of Periodontology 1999 classification system. A number of systemic diseases have been associated with advanced periodontal destruction including Diabetes Mellitus, Leukaemia and Papillon-Lefevre Syndrome. In the case described, treatment necessitated a multidisciplinary approach with input from medical and dental specialities for a young patient with severe periodontal destruction associated with CANDLE syndrome.

Cytokine and C-reactive protein profiles induced by porcine circovirus type 2 experimental infection in 3-week-old piglets

The purpose of this study was to determine serum profiles of cytokines at a protein level and Creactive protein (CRP) during the development of postweaning multisystemic wasting syndrome (PMWS) in experimentally inoculated pigs. Levels of serum IFN-alpha, IL-6, IL-10, and CRP were examined for a 35-day period in 10 piglets experimentally infected with PCV2 at 3 weeks of age. Four of the infected piglets developed severe PMWS at 14 to 21 days post-infection (d.p.i.) and died prior to termination of the experiment. The remaining six PCV2-infected piglets experienced transient fever, but did not display overt clinical signs of PMWS and were considered as subclinically infected. A bioassay was used to detect IL-6 and ELISAs were used to detect IFN-alpha, IL-10, and CRP. There were no significant differences in cytokine or CRP expression from 0 to 7 d.p.i. between the PMWS-affected and the subclinically infected piglets. Levels of IL-10 and CRP were elevated from 10 and 14 d.p.i. respectively in the PMWS-affected piglets compared to the subclinically infected piglets. There were no significant differences in IFN-alpha and IL-6 expression between the PMWS-affected piglets and the subclinically infected piglets. The present study shows that elevated levels of serum CRP and IL-10 were associated with PCV2-infected piglets that subsequently developed severe PMWS. This may help to provide further insight into the immunoaetiogenesis of this syndrome.

Young, Old, and Weathered Carbon—Part 1: Using Radiocarbon and Stable Isotopes to Identify Carbon Sources in an Alkaline, Humic Lake

This article presents a case study of Lower Lough Erne, a humic, alkaline lake in northwest Ireland, and uses the radiocarbon method to determine the source and age of carbon to establish whether terrestrial carbon is utilized by heterotrophic organisms or buried in sediment. Stepped combustion was used to estimate the degree of the burial of terrestrial carbon in surface sediment. ∆14C, δ13C, and δ15N values were measured for phytoplankton, dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), and particulate organic carbon (POC). ∆14C values were used to indicate the presence of different sources of carbon, including bedrock-derived inorganic carbon, “modern,” “recent,” “subsurface,” and “subfossil” terrestrial carbon in the lake. The use of 14C in conjunction with novel methods (e.g. stepped combustion) allows the determination of the pathway of terrestrial carbon in the system, which has implications for regional and global carbon cycling.