Linear Bellman combination for control of character animation

Controllers are necessary for physically-based synthesis of character animation. However, creating controllers requires either manual tuning or expensive computer optimization. We introduce linear Bellman combination as a method for reusing existing controllers. Given a set of controllers for related tasks, this combination creates a controller that performs a new task. It naturally weights the contribution of each component controller by its relevance to the current state and goal of the system. We demonstrate that linear Bellman combination outperforms naive combination often succeeding where naive combination fails. Furthermore, this combination is provably optimal for a new task if the component controllers are also optimal for related tasks. We demonstrate the applicability of linear Bellman combination to interactive character control of stepping motions and acrobatic maneuvers.Singapore-MIT GAMBIT Game LabNational Science Foundation (U.S.) (Grant 2007043041)National Science Foundation (U.S.) (Grant CCF-0810888)Adobe SystemsPixar (Firm

Real Time Animation of Virtual Humans: A Trade-off Between Naturalness and Control

Virtual humans are employed in many interactive applications using 3D virtual environments, including (serious) games. The motion of such virtual humans should look realistic (or ‘natural’) and allow interaction with the surroundings and other (virtual) humans. Current animation techniques differ in the trade-off they offer between motion naturalness and the control that can be exerted over the motion. We show mechanisms to parametrize, combine (on different body parts) and concatenate motions generated by different animation techniques. We discuss several aspects of motion naturalness and show how it can be evaluated. We conclude by showing the promise of combinations of different animation paradigms to enhance both naturalness and control

Ten Simple Rules for Taking Advantage of Git and GitHub.

Bioinformatics is a broad discipline in which one common denominator is the need to produce and/or use software that can be applied to biological data in different contexts. To enable and ensure the replicability and traceability of scientific claims, it is essential that the scientific publication, the corresponding datasets, and the data analysis are made publicly available [1,2]. All software used for the analysis should be either carefully documented (e.g., for commercial software) or, better yet, openly shared and directly accessible to others [3,4]. The rise of openly available software and source code alongside concomitant collaborative development is facilitated by the existence of several code repository services such as SourceForge, Bitbucket, GitLab, and GitHub, among others. These resources are also essential for collaborative software projects because they enable the organization and sharing of programming tasks between different remote contributors. Here, we introduce the main features of GitHub, a popular web-based platform that offers a free and integrated environment for hosting the source code, documentation, and project-related web content for open-source projects. GitHub also offers paid plans for private repositories (see Box 1) for individuals and businesses as well as free plans including private repositories for research and educational use.Biotechnology and Biological Sciences Research CouncilThis is the final version of the article. It first appeared from Public Library of Science via https://doi.org/10.1371/journal.pcbi.1004947

How accurately is ncRNA aligned within whole-genome multiple alignments?

<p>Abstract</p> <p>Background</p> <p>Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated.</p> <p>Results</p> <p>We evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. In particular, we find 638 instances of chimeric and partial alignments to human noncoding RNA elements, of which at least 225 can be improved by straightforward means. As a byproduct of our procedure, we predict many novel instances of known ncRNA families that are suggested by the alignment.</p> <p>Conclusion</p> <p>MULTIZ does a fairly accurate job of aligning these genomes in these difficult regions. However, our experiments indicate that better alignments exist in some regions.</p

Strain-dependent host transcriptional responses to toxoplasma infection are largely conserved in mammalian and avian hosts

Toxoplasma gondii has a remarkable ability to infect an enormous variety of mammalian and avian species. Given this, it is surprising that three strains (Types I/II/III) account for the majority of isolates from Europe/North America. The selective pressures that have driven the emergence of these particular strains, however, remain enigmatic. We hypothesized that strain selection might be partially driven by adaptation of strains for mammalian versus avian hosts. To test this, we examine in vitro, strain-dependent host responses in fibroblasts of a representative avian host, the chicken (Gallus gallus). Using gene expression profiling of infected chicken embryonic fibroblasts and pathway analysis to assess host response, we show here that chicken cells respond with distinct transcriptional profiles upon infection with Type II versus III strains that are reminiscent of profiles observed in mammalian cells. To identify the parasite drivers of these differences, chicken fibroblasts were infected with individual F1 progeny of a Type II x III cross and host gene expression was assessed for each by microarray. QTL mapping of transcriptional differences suggested, and deletion strains confirmed, that, as in mammalian cells, the polymorphic rhoptry kinase ROP16 is the major driver of strain-specific responses. We originally hypothesized that comparing avian versus mammalian host response might reveal an inversion in parasite strain-dependent phenotypes; specifically, for polymorphic effectors like ROP16, we hypothesized that the allele with most activity in mammalian cells might be less active in avian cells. Instead, we found that activity of ROP16 alleles appears to be conserved across host species; moreover, additional parasite loci that were previously mapped for strain-specific effects on mammalian response showed similar strain-specific effects in chicken cells. These results indicate that if different hosts select for different parasite genotypes, the selection operates downstream of the signaling occurring during the beginning of the host's immune response. © 2011 Ong et al

A descriptive study of a manual therapy intervention within a randomised controlled trial for hamstring and lower limb injury prevention

The journal has been informed by its publisher BioMed Central that contrary to the statement in this article [Wayne Hoskins, Henry Pollard, Chiropractic & Osteopathy 2010, 18:23], they have been advised by the authors' institution Macquarie University, that its Human Research Ethics Committee did not approve this study. Because the study was conducted without institutional ethics committee approval it has been retracted

The connecting health and technology study: A 6-month randomized controlled trial to improve nutrition behaviours using a mobile food record and text messaging support in young adults

© 2016 Kerr et al. Background: Early adulthood represents the transition to independent living which is a period when changes in diet and body weight are likely to occur. This presents an ideal time for health interventions to reduce the effect of health problems and risk factors for chronic disease in later life. As young adults are high users of mobile devices, interventions that use this technology may improve engagement. The Connecting Health and Technology study aimed to evaluate the effectiveness of tailored dietary feedback and weekly text messaging to improve dietary intake of fruit, vegetables and junk food over 6 months among a population-based sample of men and women (aged 18-30 years). Methods: A three-arm, parallel, randomized control trial was conducted. After baseline assessments, participants were randomized to one of three groups: A) dietary feedback and weekly text messages, B) dietary feedback only or C) control group. Dietary intake was assessed using a mobile food record App (mFR) where participants captured images of foods and beverages consumed over 4-days at baseline and post-intervention. The primary outcomes were changes in serves of fruits, vegetables, energy-dense nutrient-poor (EDNP) foods and sugar-sweetened beverages (SSB). The intervention effects were assessed using linear mixed effect models for change in food group serves. Results: Young adults (n = 247) were randomized to group A (n = 82), group B (n = 83), or group C (n = 82). Overall, no changes in food group serves for either intervention groups were observed. An unanticipated outcome was a mean weight reduction of 1.7 kg (P = .02) among the dietary feedback only. Men who received dietary feedback only, significantly reduced their serves of EDNP foods by a mean of 1.4 serves/day (P = .02). Women who received dietary feedback only significantly reduced their intake of SSB (P = .04) by an average of 0.2 serves/day compared with controls. Conclusions: Tailored dietary feedback only resulted in a decrease in EDNP foods in men and SSB in women, together with a reduction in body weight. Using a mobile food record for dietary assessment and tailored feedback has great potential for future health promotion interventions targeting diet and weight in young adults. Trial Registration: Australian Clinical Trials Registry Registration number: ACTRN12612000250831

The 12-item World Health Organization Disability Assessment Schedule II (WHO-DAS II): a nonparametric item response analysis

<p>Abstract</p> <p>Background</p> <p>Previous studies have analyzed the psychometric properties of the World Health Organization Disability Assessment Schedule II (WHO-DAS II) using classical omnibus measures of scale quality. These analyses are sample dependent and do not model item responses as a function of the underlying trait level. The main objective of this study was to examine the effectiveness of the WHO-DAS II items and their options in discriminating between changes in the underlying disability level by means of item response analyses. We also explored differential item functioning (DIF) in men and women.</p> <p>Methods</p> <p>The participants were 3615 adult general practice patients from 17 regions of Spain, with a first diagnosed major depressive episode. The 12-item WHO-DAS II was administered by the general practitioners during the consultation. We used a non-parametric item response method (Kernel-Smoothing) implemented with the TestGraf software to examine the effectiveness of each item (item characteristic curves) and their options (option characteristic curves) in discriminating between changes in the underliying disability level. We examined composite DIF to know whether women had a higher probability than men of endorsing each item.</p> <p>Results</p> <p>Item response analyses indicated that the twelve items forming the WHO-DAS II perform very well. All items were determined to provide good discrimination across varying standardized levels of the trait. The items also had option characteristic curves that showed good discrimination, given that each increasing option became more likely than the previous as a function of increasing trait level. No gender-related DIF was found on any of the items.</p> <p>Conclusions</p> <p>All WHO-DAS II items were very good at assessing overall disability. Our results supported the appropriateness of the weights assigned to response option categories and showed an absence of gender differences in item functioning.</p

Interpretation of DAS28 and its components in the assessment of inflammatory and non-inflammatory aspects of rheumatoid arthritis

Background: DAS28 is interpreted as the inflammatory disease activity of RA. Non-inflammatory pain mechanisms can confound assessment. We aimed to examine the use of DAS28 components or DAS28-derived measures that have been published as indices of non-inflammatory pain mechanisms, to inform interpretation of disease activity. Methods: Data were used from multiple observational epidemiology studies of people with RA. Statistical characteristics of DAS28 components and derived indices were assessed using baseline and follow up data from British Society for Rheumatology Biologics Registry participants [1] commencing anti-TNF therapy (n = 10813), or [2] changing between non-biologic DMARDs (n=2992), [3] Early Rheumatoid Arthritis Network participants (n=813), and [4] participants in a cross-sectional study exploring fibromyalgia and pain thresholds (n=45). Repeatability was tested in 34 patients with active RA. Derived indices were the proportion of DAS28 attributable to patient-reported components (DAS28-P), tender-swollen difference and tender:swollen ratio. Pressure pain detection threshold (PPT) was used as an index of pain sensitisation. Results: DAS28, tender joint count, visual analogue scale, DAS28-P, tender-swollen difference and tender:swollen ratio were more strongly associated with pain, PPT and fibromyalgia status than were swollen joint count or erythrocyte sedimentation rate. DAS28-P, tender-swollen difference and tender:swollen ratio better predicted pain over 1 year than did DAS28 or its individual components. Conclusions: DAS28 is strongly associated both with inflammation and with patient-reported outcomes. DAS28-derived indices such as tender-swollen difference are associated with non-inflammatory pain mechanisms, can predict future pain and should inform how DAS28 is interpreted as an index of inflammatory disease activity in RA

Characterization of Engineered Actin Binding Proteins That Control Filament Assembly and Structure

Eukaryotic cells strictly regulate the structure and assembly of their actin filament networks in response to various stimuli. The actin binding proteins that control filament assembly are therefore attractive targets for those who wish to reorganize actin filaments and reengineer the cytoskeleton. Unfortunately, the naturally occurring actin binding proteins include only a limited set of pointed-end cappers, or proteins that will block polymerization from the slow-growing end of actin filaments. Of the few that are known, most are part of large multimeric complexes that are challenging to manipulate.We describe here the use of phage display mutagenesis to generate of a new class of binding protein that can be targeted to the pointed-end of actin. These proteins, called synthetic antigen binders (sABs), are based on an antibody-like scaffold where sequence diversity is introduced into the binding loops using a novel "reduced genetic code" phage display library. We describe effective strategies to select and screen for sABs that ensure the generated sABs bind to the pointed-end surface of actin exclusively.From our set of pointed-end binders, we identify three sABs with particularly useful properties to systematically probe actin dynamics: one protein that caps the pointed end, a second that crosslinks actin filaments, and a third that severs actin filaments and promotes disassembly