Automating embedded analysis capabilities and managing software complexity in multiphysics simulation part II: application to partial differential equations

A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application

Spatial structure normalises working memory performance in Parkinson\u27s disease

Cognitive deficits are a frequent symptom of Parkinson\u27s disease (PD), particularly in the domain of spatial working memory (WM). Despite numerous demonstrations of aberrant WM in patients, there is a lack of understanding about how, if at all, their WM is fundamentally altered. Most notably, it is unclear whether span – the yardstick upon which most WM models are built – is compromised by the disease. Moreover, it is also unknown whether WM deficits occur in all patients or only exist in a sub-group who are executively impaired. We assessed the factors that influenced spatial span in medicated patients by varying the complexity of to-be-remembered items. Principally, we manipulated the ease with which items could enter – or be blocked from – WM by varying the level of structure in memoranda. Despite having similar levels of executive performance to controls, PD patients were only impaired when remembering information that lacked spatial, easy-to-chunk, structure. Patients\u27 executive function, however, did not influence this effect. The ease with which patients could control WM was further examined by presenting irrelevant information during encoding, varying the level of structure in irrelevant information and manipulating the amount of switching between relevant and irrelevant information. Disease did not significantly alter the effect of these manipulations. Rather, patients\u27 executive performance constrained the detrimental effect of irrelevant information on WM. Thus, PD patients\u27 spatial span is predominantly determined by level of structure in to-be-remembered information, whereas their level of executive function may mitigate against the detrimental effect of irrelevant information

Uncertainty estimates and L_2 bounds for the Kuramoto-Sivashinsky equation

We consider the Kuramoto-Sivashinsky (KS) equation in one spatial dimension with periodic boundary conditions. We apply a Lyapunov function argument similar to the one first introduced by Nicolaenko, Scheurer, and Temam, and later improved by Collet, Eckmann, Epstein and Stubbe, and Goodman, to prove that ||u||_2 < C L^1.5. This result is slightly weaker than that recently announced by Giacomelli and Otto, but applies in the presence of an additional linear destabilizing term. We further show that for a large class of Lyapunov functions \phi the exponent 1.5 is the best possible from this line of argument. Further, this result together with a result of Molinet gives an improved estimate for L_2 boundedness of the Kuramoto-Sivashinsky equation in thin rectangular domains in two spatial dimensions.Comment: 17 pages, 1 figure; typos corrected, references added; figure modifie

The postcranial skeleton of monolophosaurus jiangi (dinosauria: Theropoda) from the Middle Jurassic of Xinjiang, China, and a review of Middle Jurassic Chinese theropods

The Middle Jurassic was a critical time in the evolution of theropod dinosaurs, highlighted by the origination and radiation of the large-bodied and morphologically diverse Tetanurae. Middle Jurassic tetanurans are rare but have been described from Europe, South America and China. In particular, China has yielded a number of potential basal tetanurans, but these have received little detailed treatment in the literature. Here we redescribe the postcranial skeleton of one of the most complete Chinese Middle Jurassic theropods, Monolophosaurus. Several features confirmthe tetanuran affinities of Monolophosaurus, but the possession of ‘primitive’ traits such as a double-faceted pubic peduncle of the ilium and a hood-like supracetabular crest suggest a basal position within Tetanurae. This conflicts with most published cladistic analyses that place Monolophosaurus in a more derived position within Allosauroidea.We review the Middle Jurassic record of Chinese theropods and compare Monolophosaurus to other Middle Jurassic theropods globally. These comparisons suggest that Monolophosaurus and Chuandongocoelurus formed an endemic theropod clade limited to the Middle Jurassic of Asia. Other Middle Jurassic Chinese theropods deserve further study

What makes you not a Sikh? : a preliminary mapping of values

This study sets out to establish which Sikh values contrasted with or were shared by non-Sikh adolescents. A survey of attitude toward a variety of Sikh values was fielded in a sample of 364 non-Sikh schoolchildren aged between 13 and 15 in London. Values where attitudes were least positive concerned Sikh duties/code of conduct, festivals, rituals, prayer Gurdwara attendance, listening to scripture recitation, the amrit initiation. Sikh values empathized with by non-Sikhs concerned family pride, charity, easy access to ordination and Gurdwaras, maintaining the five Ks, seeing God in all things, abstaining from meat and alcohol and belief in the stories of Guru Nanak. Further significant differences of attitude toward Sikhism were found in comparisons by sex, age and religious affiliation. Findings are applied to teaching Sikhism to pupils of no faith adherence. The study recommends the extension of values mapping to specifically Sikh populations

Multicentre, randomised clinical trial of paediatric concussion assessment of rest and exertion (PedCARE): a study to determine when to resume physical activities following concussion in children.

INTRODUCTION: Rest until symptom-free, followed by a progressive stepwise return to activities, is often prescribed in the management of paediatric concussions. Recent evidence suggests prolonged rest may hinder recovery, and early resumption of physical activity may be associated with more rapid recovery postconcussion. The primary objective is to determine whether the early reintroduction of non-contact physical activity beginning 72 hours postinjury reduces postconcussive symptoms at 2 weeks in children following an acute concussion as compared with a rest until asymptomatic protocol. METHODS AND ANALYSIS: This study is a randomised clinical trial across three Canadian academic paediatric emergency departments. A total of 350 participants, aged 10-17.99 years, who present within 48 hours of an acute concussion, will be recruited and randomly assigned to either the study intervention protocol (resumption of physical activity 72 hours postconcussion even if experiencing symptoms) or physical rest until fully asymptomatic. Participants will document their daily physical and cognitive activities. Follow-up questionnaires will be completed at 1, 2 and 4 weeks postinjury. Compliance with the intervention will be measured using an accelerometer (24 hours/day for 14 days). Symptoms will be measured using the validated Health and Behaviour Inventory. A linear multivariable model, adjusting for site and prognostically important covariates, will be tested to determine differences between groups. The proposed protocol adheres to the RCT-CONSORT guidelines. DISCUSSION: This trial will determine if early resumption of non-contact physical activity following concussion reduces the burden of concussion and will provide healthcare professionals with the evidence by which to recommend the best timing of reintroducing physical activities

Baseline and longitudinal grey matter changes in newly diagnosed Parkinson\u27s disease: ICICLE-PD study

Mild cognitive impairment in Parkinson\u27s disease is associated with progression to dementia (Parkinson\u27s disease dementia) in a majority of patients. Determining structural imaging biomarkers associated with prodromal Parkinson\u27s disease dementia may allow for the earlier identification of those at risk, and allow for targeted disease modifying therapies. One hundred and five non-demented subjects with newly diagnosed idiopathic Parkinson\u27s disease and 37 healthy matched controls had serial 3 T structural magnetic resonance imaging scans with clinical and neuropsychological assessments at baseline, which were repeated after 18 months. The Movement Disorder Society Task Force criteria were used to classify the Parkinson\u27s disease subjects into Parkinson\u27s disease with mild cognitive impairment (n = 39) and Parkinson\u27s disease with no cognitive impairment (n = 66). Freesurfer image processing software was used to measure cortical thickness and subcortical volumes at baseline and follow-up. We compared regional percentage change of cortical thinning and subcortical atrophy over 18 months. At baseline, cases with Parkinson\u27s disease with mild cognitive impairment demonstrated widespread cortical thinning relative to controls and atrophy of the nucleus accumbens compared to both controls and subjects with Parkinson\u27s disease with no cognitive impairment. Regional cortical thickness at baseline was correlated with global cognition in the combined Parkinson\u27s disease cohort. Over 18 months, patients with Parkinson\u27s disease with mild cognitive impairment demonstrated more severe cortical thinning in frontal and temporo-parietal cortices, including hippocampal atrophy, relative to those with Parkinson\u27s disease and no cognitive impairment and healthy controls, whereas subjects with Parkinson\u27s disease and no cognitive impairment showed more severe frontal cortical thinning compared to healthy controls. At baseline, Parkinson\u27s disease with no cognitive impairment converters showed bilateral temporal cortex thinning relative to the Parkinson\u27s disease with no cognitive impairment stable subjects. Although loss of both cortical and subcortical volume occurs in non-demented Parkinson\u27s disease, our longitudinal analyses revealed that Parkinson\u27s disease with mild cognitive impairment shows more extensive atrophy and greater percentage of cortical thinning compared to Parkinson\u27s disease with no cognitive impairment. In particular, an extension of cortical thinning in the temporo-parietal regions in addition to frontal atrophy could be a biomarker in therapeutic studies of mild cognitive impairment in Parkinson\u27s disease for progression towards dementia

The Vehicle, 1967, Vol. 10 no. 1

Vol. 10, No. 1 Table of Contents Christy Bowercover Photographpage 4 The CityCatherine Waitepage 4 A New DealAnonymouspage 5 The Penny Ride of Carnation PinkAstaire Pappaspage 8 RapeSharon Nelsonpage 10 Born AgainCharles J. Mertzpage 10 DrawingRourkepage 11 UntitledRourkepage 11 DialogueMolly Evanspage 12 SeldomJamse Jonsepage 12 The DifferenceDennis Muchmorepage 13 First LoveBruce Czeluscinskipage 15 Photographpage 15 Immorality of Troilus and Criseyde Milo S. Metcalfpage 16 Answer UnknownDave Owenpage 20 I Am LostJean Lacypage 21 Photographpage 22 On the Eve of No TomorrowsJane Careypage 23 Unrelated TwinsByron Nelsonpage 24 if i sitRoger Zulaufpage 25 if i sitDennis Muchmorepage 26 Drawingpage 27 Bibliographypage 28https://thekeep.eiu.edu/vehicle/1015/thumbnail.jp

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

BACKGROUND: Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications. RESULTS: Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5). CONCLUSION: Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms