Logarithmic spin, logarithmic rate and material frame-indifferent generalized plasticity

In this work we present a new rate type formulation of large deformation generalized plasticity which is based on the consistent use of the logarithmic rate concept. For this purpose, the basic constitutive equations are initially established in a local rotationally neutralized configuration which is defined by the logarithmic spin. These are then rephrased in their spatial form, by employing some standard concepts from the tensor analysis on manifolds. Such an approach, besides being compatible with the notion of (hyper)elasticity, offers three basic advantages, namely:(i) The principle of material frame-indifference is trivially satisfied ; (ii) The structure of the infinitesimal theory remains essentially unaltered ; (iii) The formulation does not preclude anisotropic response. A general integration scheme for the computational implementation of generalized plasticity models which are based on the logarithmic rate is also discussed. The performance of the scheme is tested by two representative numerical examples

On the constitution of polar fiber-reinforced materials

This article presents important constitutive refinements and simplifications in the theory of polar elasticity of materials reinforced by a single family of fibres resistant in bending. One of these simplifications is achieved by paying attention to forms of the strain energy which are symmetric with respect to the symmetric and the antisymmetric parts of the fibre gradient tensor. This leads to the identification of a restricted version of the theory that is predominantly influenced by the fibre-splay mode of deformation. The lack of ellipticity of the governing equations of polar elasticity and the anticipation of existence of weak discontinuity surfaces even in the small deformation regime are also investigated. The manner in which potential activation of such surfaces is related with the action of either the fibre-bending or the fibre-splay deformation mode, as well as with their conjoined combination and coupling with their fibre-twist counterpart, is examined. The proposed constitutive equations can be simplified via the use of a new set of fourteen independent spectral invariants of the deformation. This set serves as an irreducible functional basis of relevant invariants or as an irreducible integrity basis of polynomial invariants. For instance, its use here enables identification of fourteen classical invariants that emerge as mutually independent from the known set of thirty-three in total classical invariants. In the special case of polynomial invariants, this result paves the way for identification of a corresponding minimal integrity basis

Martini: using literature keywords to compare gene sets

Life scientists are often interested to compare two gene sets to gain insight into differences between two distinct, but related, phenotypes or conditions. Several tools have been developed for comparing gene sets, most of which find Gene Ontology (GO) terms that are significantly over-represented in one gene set. However, such tools often return GO terms that are too generic or too few to be informative. Here, we present Martini, an easy-to-use tool for comparing gene sets. Martini is based, not on GO, but on keywords extracted from Medline abstracts; Martini also supports a much wider range of species than comparable tools. To evaluate Martini we created a benchmark based on the human cell cycle, and we tested several comparable tools (CoPub, FatiGO, Marmite and ProfCom). Martini had the best benchmark performance, delivering a more detailed and accurate description of function. Martini also gave best or equal performance with three other datasets (related to Arabidopsis, melanoma and ovarian cancer), suggesting that Martini represents an advance in the automated comparison of gene sets. In agreement with previous studies, our results further suggest that literature-derived keywords are a richer source of gene-function information than GO annotations. Martini is freely available at http://martini.embl.de

Insomnia and its correlates in a representative sample of the Greek population

<p>Abstract</p> <p>Background</p> <p>Insomnia is a major public health concern affecting about 10% of the general population in its chronic form. Furthermore, epidemiological surveys demonstrate that poor sleep and sleep dissatisfaction are even more frequent problems (10-48%) in the community. This is the first report on the prevalence of insomnia in Greece, a southeastern European country which differs in several socio-cultural and climatic aspects from the rest of European Community members. Data obtained from a national household survey (n = 1005) were used to assess the relationship between insomnia symptoms and a variety of sociodemographic variables, life habits, and health-related factors.</p> <p>Methods</p> <p>A self-administered questionnaire with questions pertaining to general health and related issues was given to the participants. The Short Form-36 (Mental Health subscale), the Athens Insomnia Scale (AIS) as a measure of insomnia-related symptoms, and the International Physical Activity Questionnaire (IPAQ) were also used for the assessment.</p> <p>Results</p> <p>The prevalence of insomnia in the total sample was 25.3% (n = 254); insomnia was more frequent in women than men (30.7% vs. 19.5%) and increased with age. Multiple regression analysis revealed a significant association of insomnia with low socio-economical status and educational level, physical inactivity, existence of a chronic physical or mental disease and increased number of hospitalizations in the previous year.</p> <p>Conclusions</p> <p>The present study confirms most findings reported from other developed countries around the world regarding the high prevalence of insomnia problems in the general population and their association with several sociodemographic and health-related predisposing factors. These results further indicate the need for more active interventions on the part of physicians who should suspect and specifically ask about such symptoms.</p

Development, validation and clinical utility of a risk prediction model for adverse pregnancy outcomes in women with gestational diabetes:The PeRSonal GDM model

BACKGROUND: The ability to calculate the absolute risk of adverse pregnancy outcomes for an individual woman with gestational diabetes mellitus (GDM) would allow preventative and therapeutic interventions to be delivered to women at high-risk, sparing women at low-risk from unnecessary care. We aimed to develop, validate and evaluate the clinical utility of a prediction model for adverse pregnancy outcomes in women with GDM. METHODS: A prediction model development and validation study was conducted on data from a observational cohort. Participants included all women with GDM from three metropolitan tertiary teaching hospitals in Melbourne, Australia. The development cohort comprised those who delivered between 1 July 2017 to 30 June 2018 and the validation cohort those who delivered between 1 July 2018 to 31 December 2018. The main outcome was a composite of critically important maternal and perinatal complications (hypertensive disorders of pregnancy, large-for-gestational age neonate, neonatal hypoglycaemia requiring intravenous therapy, shoulder dystocia, perinatal death, neonatal bone fracture and nerve palsy). Model performance was measured in terms of discrimination and calibration and clinical utility evaluated using decision curve analysis. FINDINGS: The final PeRSonal (Prediction for Risk Stratified care for women with GDM) model included body mass index, maternal age, fasting and 1-hour glucose values (75-g oral glucose tolerance test), gestational age at GDM diagnosis, Southern and Central Asian ethnicity, East Asian ethnicity, nulliparity, past delivery of an large-for-gestational age neonate, past pre-eclampsia, GWG until GDM diagnosis, and family history of diabetes. The composite adverse pregnancy outcome occurred in 27% (476/1747) of women in the development (1747 women) and in 26% (244/955) in the validation (955 women) cohorts. The model showed excellent calibration with slope of 0.99 (95% CI 0.75 to 1.23) and acceptable discrimination (c-statistic 0.68; 95% CI 0.64 to 0.72) when temporally validated. Decision curve analysis demonstrated that the model was useful across a range of predicted probability thresholds between 0.15 and 0.85 for adverse pregnancy outcomes compared to the alternatives of managing all women with GDM as if they will or will not have an adverse pregnancy outcome. INTERPRETATION: The PeRSonal GDM model comprising of routinely available clinical data shows compelling performance, is transportable across time, and has clinical utility across a range of predicted probabilities. Further external validation of the model to a more disparate population is now needed to assess the generalisability to different centres, community based care and low resource settings, other healthcare systems and to different GDM diagnostic criteria. FUNDING: This work is supported by the Mothers and Gestational Diabetes in Australia 2 NHMRC funded project #1170847

Caipirini: using gene sets to rank literature

<p>Abstract</p> <p>Background</p> <p>Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that the user judges to be 'interesting'. Some methods go further by allowing the user to provide a second input set of 'uninteresting' abstracts; these two input sets are then used to search and rank literature by relevance. In this work we present the service 'Caipirini' (<url>http://caipirini.org</url>) that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes.</p> <p>Results</p> <p>To evaluate the usefulness of Caipirini, we used two test cases, one related to the human cell cycle, and a second related to disease defense mechanisms in <it>Arabidopsis thaliana</it>. In both cases, the new method achieved high precision in finding literature related to the biological mechanisms underlying the input data sets.</p> <p>Conclusions</p> <p>To our knowledge Caipirini is the first service enabling literature search directly based on biological relevance to gene sets; thus, Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via high-throughput experiments.</p

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Since 2012, the United States of America has experienced a biennial spike in pediatric acute flaccid myelitis (AFM)1-6. Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF)2. CSF from children with AFM (n = 42) and other pediatric neurologic disease controls (n = 58) were investigated for intrathecal antiviral antibodies, using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). Metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n = 20 cases) was also performed, both unbiased sequencing and with targeted enrichment for EVs. Using VirScan, the viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n = 29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n = 22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology frequently identified high levels of CSF EV-specific antibodies in AFM compared with controls, providing further evidence for a causal role of non-polio EVs in AFM

Demonstration of Zero-touch Device and L3-VPN Service Management using the TeraFlow Cloud-native SDN Controller

We demonstrate zero-touch device bootstrapping, monitoring, and L3-VPN service management using the novel TeraFlow OS SDN controller prototype. TeraFlow aims at producing a cloud-native carrier-grade SDN controller offering scalability, extensibility, high-performance, and high-availability features