C2x: a tool for visualisation and input preparation for Castep and other electronic structure codes

The c2x code fills two distinct roles. Its first role is in acting as a converter between the binary format .check files from the widely-used Castep electronic structure code and various visualisation programs. Its second role is to manipulate and analyse the input and output files from a variety of electronic structure codes, including Castep, Onetep and Vasp, as well as the widely-used ‘Gaussian cube’ file format. Analysis includes symmetry analysis, and manipulation arbitrary cell transformations. It continues to be under development, with growing functionality, and is written in a form which would make it easy to extend it to working directly with files from other electronic structure codes. Data which c2x is capable of extracting from Castep’s binary checkpoint files include charge densities, spin densities, wavefunctions, relaxed atomic positions, forces, the Fermi level, the total energy, and symmetry operations. It can recreate .cell input files from checkpoint files. Volumetric data can be output in formats usable by many common visualisation programs, and c2x will itself calculate integrals, expand data into supercells, and interpolate data via combinations of Fourier and trilinear interpolation. It can extract data along arbitrary lines (such as lines between atoms) as 1D output. C2x is able to convert between several common formats for describing molecules and crystals, including the .cell format of Castep. It can construct supercells, reduce cells to their primitive form, and add specified k-point meshes. It uses the spglib library to report symmetry information, which it can add to .cell files. C2x is a command-line utility, so is readily included in scripts. It is avail- able under the GPL and can be obtained from http://www.c2x.org.uk. It is believed to be the only open-source code which can read Castep’s .check files, so it will have utility in other projects.This work was supported by EPSRC grant numbers EP/J017639/1, EP/P003532/1 and EP/M011925/1

Molecules with dipoles in periodic boundary conditions in a tetragonal cell.

When a system which contains a dipole, and whose dimensionality is less than three, is studied in a code which imposes periodic boundary conditions in all three dimensions, an artificial electric field arises which keeps the potential periodic. This has an impact on the total energy of the system, and on any other attribute which would respond to an electric field. Simple corrections are known for 0D systems embedded in a cubic geometry, and 2D slab systems. This paper shows how the 0D result can be extended to tetragonal geometries, and that for a particular c/a ratio the correction is zero. It also considers an exponential error term absent from the usual consideration of 2D slab geometries, and discusses an empirical form for this

The counter and consultation room work explored in the Netherlands

Objective To determine the frequency and nature of conversations at the counter and of private consultations at three Dutch community pharmacies. Methods In a purposive and convenience sample of three Dutch community pharmacies two work categories were investigated: counter work and consultation room work with self-reporting tally. The study took 6 weeks: 2 weeks at each pharmacy. Main outcome measure The number of care related conversations and consultations emerging in the counter work and consultation room work. Results About 43% of all counter conversations consisted of the provision of pharmaceutical information and 72% of the consultations in the separate consultation room dealt with care related activities. However, only 18 consultations were held in this latter room: 0.4% of all reported conversations. Conclusion The proportion of care related work at the counter and in the consultation room did have significant substance. There are however serious possibilities to change pharmaceutical care for the better. It is suggested that standard procedures at the counter may help increasing care related work. The presence of a separate consultation room may increase the number of consultations held in private, when combined with raising patient awareness of its existence

Fluoxetine: a case history of its discovery and preclinical development

Introduction: Depression is a multifactorial mood disorder with a high prevalence worldwide. Until now, treatments for depression have focused on the inhibition of monoaminergic reuptake sites, which augment the bioavailability of monoamines in the CNS. Advances in drug discovery have widened the therapeutic options with the synthesis of so-called selective serotonin reuptake inhibitors (SSRIs), such as fluoxetine. Areas covered: The aim of this case history is to describe and discuss the pharmacokinetic and pharmacodynamic profiles of fluoxetine, including its acute effects and the adaptive changes induced after long-term treatment. Furthermore, the authors review the effect of fluoxetine on neuroplasticity and adult neurogenesis. In addition, the article summarises the preclinical behavioural data available on fluoxetine’s effects on depressive-like behaviour, anxiety and cognition as well as its effects on other diseases. Finally, the article describes the seminal studies validating the antidepressant effects of fluoxetine. Expert opinion: Fluoxetine is the first selective SSRI that has a recognised clinical efficacy and safety profile. Since its discovery, other molecules that mimic its mechanism of action have been developed, commencing a new age in the treatment of depression. Fluoxetine has also demonstrated utility in the treatment of other disorders for which its prescription has now been approved

Autoreactive T cell profiles are altered following allogeneic islet transplantation with alemtuzumab induction and re‐emerging phenotype is associated with graft function

Islet transplantation is an effective therapy for life‐threatening hypoglycemia, but graft function gradually declines over time in many recipients. We characterized islet‐specific T cells in recipients within an islet transplant program favoring alemtuzumab (ATZ) lymphodepleting induction and examined associations with graft function. Fifty‐eight recipients were studied: 23 pretransplant and 40 posttransplant (including 5 with pretransplant phenotyping). The proportion with islet‐specific T cell responses was not significantly different over time (pre‐Tx: 59%; 1–6 m posttransplant: 38%; 7–12 m: 44%; 13–24 m: 47%; and >24 m: 45%). However, phenotype shifted significantly, with IFN‐γ–dominated response in the pretransplant group replaced by IL‐10–dominated response in the 1–6 m posttransplant group, reverting to predominantly IFN‐γ–oriented response in the >24 m group. Clustering analysis of posttransplant responses revealed two main agglomerations, characterized by IFN‐γ and IL‐10 phenotypes, respectively. IL‐10–oriented posttransplant response was associated with relatively low graft function. Recipients within the IL‐10+ cluster had a significant decline in C‐peptide levels in the period preceding the IL‐10 response, but stable graft function following the response. In contrast, an IFN‐γ response was associated with subsequently decreased C‐peptide. Islet transplantation favoring ATZ induction is associated with an initial altered islet‐specific T cell phenotype but reversion toward pretransplant profiles over time. Posttransplant autoreactive T cell phenotype may be a predictor of subsequent graft function

Observation of Electron-Hole Puddles in Graphene Using a Scanning Single Electron Transistor

The electronic density of states of graphene is equivalent to that of relativistic electrons. In the absence of disorder or external doping the Fermi energy lies at the Dirac point where the density of states vanishes. Although transport measurements at high carrier densities indicate rather high mobilities, many questions pertaining to disorder remain unanswered. In particular, it has been argued theoretically, that when the average carrier density is zero, the inescapable presence of disorder will lead to electron and hole puddles with equal probability. In this work, we use a scanning single electron transistor to image the carrier density landscape of graphene in the vicinity of the neutrality point. Our results clearly show the electron-hole puddles expected theoretically. In addition, our measurement technique enables to determine locally the density of states in graphene. In contrast to previously studied massive two dimensional electron systems, the kinetic contribution to the density of states accounts quantitatively for the measured signal. Our results suggests that exchange and correlation effects are either weak or have canceling contributions.Comment: 13 pages, 5 figure

Spatial contrast sensitivity in adolescents with autism spectrum disorders

Adolescents with autism spectrum disorders (ASD) and typically developing (TD) controls underwent a rigorous psychophysical assessment that measured contrast sensitivity to seven spatial frequencies (0.5-20 cycles/degree). A contrast sensitivity function (CSF) was then fitted for each participant, from which four measures were obtained: visual acuity, peak spatial frequency, peak contrast sensitivity, and contrast sensitivity at a low spatial frequency. There were no group differences on any of the four CSF measures, indicating no differential spatial frequency processing in ASD. Although it has been suggested that detail-oriented visual perception in individuals with ASD may be a result of differential sensitivities to low versus high spatial frequencies, the current study finds no evidence to support this hypothesis

Externalizing behaviors in preadolescents: familial risk to externalizing behaviors and perceived parenting styles

The aim was to investigate the contribution of familial risk to externalizing behaviors (FR-EXT), perceived parenting styles, and their interactions to the prediction of externalizing behaviors in preadolescents. Participants were preadolescents aged 10–12 years who participated in TRAILS, a large prospective population-based cohort study in the Netherlands (N = 2,230). Regression analyses were used to determine the relative contribution of FR-EXT and perceived parenting styles to parent and teacher ratings of externalizing behaviors. FR-EXT was based on lifetime parental externalizing psychopathology and the different parenting styles (emotional warmth, rejection, and overprotection) were based on the child’s perspective. We also investigated whether different dimensions of perceived parenting styles had different effects on subdomains of externalizing behavior. We found main effects for FR-EXT (vs. no FR-EXT), emotional warmth, rejection, and overprotection that were fairly consistent across rater and outcome measures. More specific, emotional warmth was the most consistent predictor of all outcome measures, and rejection was a stronger predictor of aggression and delinquency than of inattention. Interaction effects were found for FR-EXT and perceived parental rejection and overprotection; other interactions between FR-EXT and parenting styles were not significant. Correlations between FR-EXT and perceived parenting styles were absent or very low and were without clinical significance. Predominantly main effects of FR-EXT and perceived parenting styles independently contribute to externalizing behaviors in preadolescents, suggesting FR-EXT and parenting styles to be two separate areas of causality. The relative lack of gene–environment interactions may be due to the epidemiological nature of the study, the preadolescent age of the subjects, the measurement level of parenting and the measurement level of FR-EXT, which might be a consequence of both genetic and environmental factors

Family-Centered Preventive Intervention for Military Families: Implications for Implementation Science

In this paper, we report on the development and dissemination of a preventive intervention, Families OverComing Under Stress (FOCUS), an eight-session family-centered intervention for families facing the impact of wartime deployments. Specific attention is given to the challenges of rapidly deploying a prevention program across diverse sites, as well as to key elements of implementation success. FOCUS, developed by a UCLA-Harvard team, was disseminated through a large-scale demonstration project funded by the United States Bureau of Navy Medicine and Surgery (BUMED) beginning in 2008 at 7 installations and expanding to 14 installations by 2010. Data are presented to describe the range of services offered, as well as initial intervention outcomes. It proved possible to develop the intervention rapidly and to deploy it consistently and effectively