Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org

Toward a first-principles integrated simulation of tokamak edge plasmas

Performance of the ITER is anticipated to be highly sensitive to the edge plasma condition. The edge pedestal in ITER needs to be predicted from an integrated simulation of the necessary first-principles, multi-scale physics codes. The mission of the SciDAC Fusion Simulation Project (FSP) Prototype Center for Plasma Edge Simulation (CPES) is to deliver such a code integration framework by (1) building new kinetic codes XGC0 and XGC1, which can simulate the edge pedestal buildup; (2) using and improving the existing MHD codes ELITE, M3D-OMP, M3D-MPP and NIMROD, for study of large-scale edge instabilities called Edge Localized Modes (ELMs); and (3) integrating the codes into a framework using cutting-edge computer science technology. Collaborative effort among physics, computer science, and applied mathematics within CPES has created the first working version of the End-to-end Framework for Fusion Integrated Simulation (EFFIS), which can be used to study the pedestal-ELM cycles

Algebraic damping in the one-dimensional Vlasov equation

We investigate the asymptotic behavior of a perturbation around a spatially non homogeneous stable stationary state of a one-dimensional Vlasov equation. Under general hypotheses, after transient exponential Landau damping, a perturbation evolving according to the linearized Vlasov equation decays algebraically with the exponent -2 and a well defined frequency. The theoretical results are successfully tested against numerical $N$-body simulations, corresponding to the full Vlasov dynamics in the large $N$ limit, in the case of the Hamiltonian mean-field model. For this purpose, we use a weighted particles code, which allows us to reduce finite size fluctuations and to observe the asymptotic decay in the $N$-body simulations.Comment: 26 pages, 8 figures; text slightly modified, references added, typos correcte

Patient-reported outcome measures for cancer caregivers: a systematic review

Purpose Informal caregivers provide invaluable help and support to people with cancer. As treatments extend survival and the potential burdens on carers increase, there is a need to assess the impact of the role. This systematic review identified instruments that measure the impact of caregiving, evaluated their psychometric performance specifically in cancer and appraised the content. Methods A 2-stage search strategy was employed to: 1. identify instruments that measure the impact of caregiving, 2. run individual searches on each measure to identify publications evaluating psychometric performance in the target population. Searches were conducted in Medline, Embase, CINAHL and Psychinfo and restricted to English for instrument used and article language. Psychometric performance was evaluated for content and construct validity, internal consistency, test-retest reliability, precision, responsiveness and acceptability. Individual scale items were extracted and systematically categorised into conceptual domains. Results 10 papers were included reporting on the psychometric properties of 8 measures. Although construct validity and internal consistency were most frequently evaluated, no study comprehensively evaluated all relevant properties. Few studies met our inclusion criteria so it was not possible to consider the psychometric performance of the measures across a group of studies. Content analysis resulted in 16 domains with 5 overarching themes: lifestyle disruption; wellbeing; health of the caregiver; managing the situation and relationships. Conclusions Few measures of caregiver impact have been subject to psychometric evaluation in cancer caregivers. Those that have do not capture well changes in roles and responsibilities within the family and career, indicating the need for a new instrument

Psi-Series Solution of Fractional Ginzburg-Landau Equation

One-dimensional Ginzburg-Landau equations with derivatives of noninteger order are considered. Using psi-series with fractional powers, the solution of the fractional Ginzburg-Landau (FGL) equation is derived. The leading-order behaviours of solutions about an arbitrary singularity, as well as their resonance structures, have been obtained. It was proved that fractional equations of order $alpha$ with polynomial nonlinearity of order $s$ have the noninteger power-like behavior of order $\alpha/(1-s)$ near the singularity.Comment: LaTeX, 19 pages, 2 figure

Fractional Variations for Dynamical Systems: Hamilton and Lagrange Approaches

Fractional generalization of an exterior derivative for calculus of variations is defined. The Hamilton and Lagrange approaches are considered. Fractional Hamilton and Euler-Lagrange equations are derived. Fractional equations of motion are obtained by fractional variation of Lagrangian and Hamiltonian that have only integer derivatives.Comment: 21 pages, LaTe

Life Satisfaction and Sense of Coherence of Breast Cancer Survivors Compared to Women with Mental Depression, Arterial Hypertension and Healthy Controls

The purpose of the study was to compare the life satisfaction (LS) and sense of coherence (SOC) of women recovering from breast cancer (BC) to LS and SOC of women with depression or hypertension and of healthy controls. Finnish Health and Social Support (HeSSup) follow-up survey data in 2003 was linked with national health registries. BC patients were followed up for mortality until the end of 2012. The statistical computations were carried out with SAS (R). There were no significant differences in LS and SOC between the groups with BC, arterial hypertension or healthy controls. Women recovering from BC are as satisfied with their life as healthy controls, and their perceived LS is better and SOC is stronger compared to women with depression. SOC correlated positively (r(2) = 0.36, p <0.001) with LS. However, more studies on determinants of the LS are needed for designing and organizing health care services for BC survivors.Peer reviewe

Convergent Validity of a Single Question with Multiple Classification Options for Depression Screening in Medical Settings

The purpose of this study was to assess the convergent validity of a single depression question with multiple classification options for depression screening. Participants were 40 medical inpatients. The age range of our sample was 18 to 85 years (M = 56.15, SD = 17.66). A clinical interview and the BDI-II were administered. The correlation between patients’ self-rating classification of depression and their BDI-II classification was significant, rs(38) = .90, p < .01. Follow-up repeated-measures chi-square revealed a statistically significant association between BDI-II classification and patients’ self-rating classification, χ2(9, N = 40) = 47.79, p < .005. Significant positive standardized residuals revealed a clear linear relationship between BDI-II and patient self-rating classifications. Our data support the use of a single depression question with multiple classification options as a useful and valid means of quickly screening for the presence of depression by frontline health care professionals

A Racial/Ethnic Performance Disparity on the Facial Recognition Test

The Facial Recognition Test is a widely used psychometric instrument for assessing visuoperceptual functioning. Only two prior studies have examined the effects of race/ethnicity on this test. Given that the United States has become more culturally diverse since the creation of the test, it is important to re-visit the effects of this demographic variable on performance. Participants were 75 males and 75 females between the ages of 18 and 43 years (M = 21.91, SD = 5.33). Racial/ethnic categories utilized by the U.S. Census Bureau were equally represented. No gender differences were observed. The race/ethnicity main effect was significant. The gender x race/ethnicity interaction was not significant. The data revealed a clear racial/ethnic performance disparity on the Facial Recognition Test