Extending semantic long-term knowledge on the basis of episodic short-term knowledge

Voss I, Wachsmuth I. Extending semantic long-term knowledge on the basis of episodic short-term knowledge. In: Schmalhofer F, Young RM, Katz G, eds. Proceedings of the EuroCogSci03. Mahwah, NJ, USA: Lawrence Erlbaum Associates; 2003: 445-445

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

Bell Inequality Experiment for a High Brightness Time-Energy Entangled Source

A periodically poled MgO - doped LiNbO3 (MgO:LN) non-degenerate photon pair source is utilized for spontaneous parametric down-conversion of 532-nanometer photons into time-energy entangled pairs of 800- and 1600-nanometer photons. The entangled photons are separated using previously detailed sorting optics, such that each wavelength is independently directed through one of two modified Mach-Zehnder interferometers - also known as a Franson interferometer - after which they are fiber-optically guided to high-efficiency photon detectors. Output from the detectors is sent to a high resolution time tagger, where coincidences between the entangled photons are recorded. By varying the length of the long path in one Mach-Zehnder interferometer, it is possible to observe high visibility sinusoidal fringes in the measured coincidence rates (while no variation is seen in single photon detection rates). These fringes - due to interference between the photon probability amplitudes - are indicative of a violation of the Bell inequality, and confirm inconsistencies with local hidden variable theory for the correlations of the time-energy entangled photon pairs

Position statement of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) on APC I1307K and cancer risk

While constitutional pathogenic variants in the APC gene cause familial adenomatous polyposis, APC c.3920T>A; p.Ile1307Lys (I1307K) has been associated with a moderate increased risk of colorectal cancer (CRC), particularly in individuals of Ashkenazi Jewish descent. However, published data include relatively small sample sizes, generating inconclusive results regarding cancer risk, particularly in non-Ashkenazi populations. This has led to different country/continental-specific guidelines regarding genetic testing, clinical management and surveillance recommendations for I1307K. A multidisciplinary international expert group endorsed by the International Society for Gastrointestinal Hereditary Tumours (InSiGHT), has generated a position statement on the APC I1307K allele and its association with cancer predisposition. Based on a systematic review and meta-analysis of the evidence published, the aim of this document is to summarise the prevalence of the APC I1307K allele and analysed the evidence of the associated cancer risk in different populations. Here we provide recommendations on the laboratory classification of the variant, define the role of predictive testing for I1307K, suggest recommendations for cancer screening in I1307K heterozygous and homozygous individuals and identify knowledge gaps to be addressed in future research studies. Briefly, I1307K, classified as pathogenic, low penetrance, is a risk factor for CRC in individuals of Ashkenazi Jewish origin and should be tested in this population, offering carriers specific clinical surveillance. There is not enough evidence to support an increased risk of cancer in other populations/subpopulations. Therefore, until/unless future evidence indicates otherwise, individuals of non-Ashkenazi Jewish descent harbouring I1307K should be enrolled in national CRC screening programmes for average-risk individuals

Developing an award program for children's settings to support healthy eating and physical activity and reduce the risk of overweight and obesity

<p>Abstract</p> <p>Background</p> <p>This paper aimed to identify the best way to engage, motivate and support early childhood services (ECS) and primary schools (PS) to create policy and practise changes to promote healthy eating and physical activity. This information would be used to develop a suitable program to implement within these children's settings to reduce the risk of childhood overweight and obesity.</p> <p>Methods</p> <p>The Medical Research Council's (UK) framework for the design and evaluation of complex interventions was used to guide the development of the healthy eating and physical activity program suitable for ECS and PS. Within this framework a range of evaluation methods, including stakeholder planning, in-depth interviews with ECS and PS staff and acceptability and feasibility trials in one local government area, were used to ascertain the best way to engage and support positive changes in these children's settings.</p> <p>Results</p> <p>Both ECS and PS identified that they had a role to play to improve children's healthy eating and physical activity. ECS identified their role in promoting healthy eating and physical activity as important for children's health, and instilling healthy habits for life. PS felt that these were health issues, rather than educational issues; however, schools saw the link between healthy eating and physical activity and student learning outcomes. These settings identified that a program that provides a simple guide that recognises good practise in these settings, such as an award scheme using a health promoting schools approach, as a feasible and acceptable way for them to support children's healthy eating and physical activity.</p> <p>Conclusion</p> <p>Through the process of design and evaluation a program - <it>Kids - 'Go for your life'</it>, was developed to promote and support children's healthy eating and physical activity and reduce the risk of childhood overweight and obesity. <it>Kids - 'Go for your life' </it>used an award program, based on a health promoting schools approach, which was demonstrated to be a suitable model to engage ECS and PS and was acceptable and feasible to create policy and practise changes to support healthy eating and physical activity for children.</p

Evaluating the Impact of Intravitreal Aflibercept on Diabetic Retinopathy Progression in the VIVID-DME and VISTA-DME Studies

Purpose To evaluate the impact of intravitreal aflibercept (EYLEA, Regeneron Pharmaceuticals, Tarrytown, NY) versus laser on progression of diabetic retinopathy (DR) severity in Intravitreal Aflibercept Injection in Vision Impairment due to DME (VIVID-DME) and Study of Intravitreal Aflibercept Injection in Patients with Diabetic Macular Edema (VISTA-DME). Design Secondary and exploratory analyses of 2 phase 3, randomized, controlled studies. Participants All patients with a baseline Diabetic Retinopathy Severity Scale (DRSS) score based on fundus photograph (full analysis), patients who progressed to proliferative DR (PDR) (safety analysis) in VIVID-DME (n = 403) and VISTA-DME (n = 459), or both. Methods We randomized patients with diabetic macular edema (DME) to intravitreal aflibercept 2 mg every 4 weeks (2q4), intravitreal aflibercept 2 mg every 8 weeks after 5 initial monthly doses (2q8), or macular laser photocoagulation at baseline and sham injections at every visit. Main Outcome Measures Proportions of patients with 2-step or more and 3-step or more improvements from baseline in DRSS score, who progressed to PDR, and who underwent panretinal photocoagulation (PRP). Results Among patients with an assessable baseline DRSS score, most showed moderately severe or severe nonproliferative DR. The proportions of patients treated with 2q4, 2q8, and laser with a 2-step or more improvement in DRSS score at week 100 were 29.3%, 32.6%, and 8.2%, respectively, in VIVID-DME and 37.0%, 37.1%, and 15.6%, respectively, in VISTA-DME; the proportions with a 3-step or more improvement in DRSS score were 7.3%, 2.3%, and 0%, respectively, and 22.7%, 19.9%, and 5.2%, respectively. Fewer patients in the 2q4 and 2q8 groups versus the laser group progressed to PDR at week 100 in VISTA-DME (1.5% and 2.2% vs. 5.3%) and VIVID-DME (3.2% and 2.0% vs. 12.3%). The proportions of patients who underwent PRP were 2.9%, 0.7%, and 4.5%, respectively, in VIVID-DME and 1.9%, 0.7%, and 5.2%, respectively, in VISTA-DME. The most frequent serious ocular adverse event at week 100 was cataract (pooled intravitreal aflibercept, 1.7% of patients; laser, 3.5% of patients). Conclusions These analyses demonstrate the benefit of intravitreal aflibercept over laser with respect to DR progression, suggesting a benefit on DME, and on underlying DR

nIFTy galaxy cluster simulations – II. Radiative models

We have simulated the formation of a massive galaxy cluster (M$_{200}^{\rm crit}$ = 1.1$\times$10$^{15}h^{-1}M_{\odot}$) in a $\Lambda$CDM universe using 10 different codes (RAMSES, 2 incarnations of AREPO and 7 of GADGET), modeling hydrodynamics with full radiative subgrid physics. These codes include Smoothed-Particle Hydrodynamics (SPH), spanning traditional and advanced SPH schemes, adaptive mesh and moving mesh codes. Our goal is to study the consistency between simulated clusters modeled with different radiative physical implementations - such as cooling, star formation and AGN feedback. We compare images of the cluster at $z=0$, global properties such as mass, and radial profiles of various dynamical and thermodynamical quantities. We find that, with respect to non-radiative simulations, dark matter is more centrally concentrated, the extent not simply depending on the presence/absence of AGN feedback. The scatter in global quantities is substantially higher than for non-radiative runs. Intriguingly, adding radiative physics seems to have washed away the marked code-based differences present in the entropy profile seen for non-radiative simulations in Sembolini et al. (2015): radiative physics + classic SPH can produce entropy cores. Furthermore, the inclusion/absence of AGN feedback is not the dividing line -as in the case of describing the stellar content- for whether a code produces an unrealistic temperature inversion and a falling central entropy profile. However, AGN feedback does strongly affect the overall stellar distribution, limiting the effect of overcooling and reducing sensibly the stellar fraction.Comment: 20 pages, 13 figures, submitted to MNRA

A Research and Development (R&D) roadmap for influenza vaccines: Looking toward the future

Improved influenza vaccines are urgently needed to reduce the burden of seasonal influenza and to ensure a rapid and effective public-health response to future influenza pandemics. The Influenza Vaccines Research and Development (R&D) Roadmap (IVR) was created, through an extensive international stakeholder engagement process, to promote influenza vaccine R&D. The roadmap covers a 10-year timeframe and is organized into six sections: virology; immunology; vaccinology for seasonal influenza vaccines; vaccinology for universal influenza vaccines; animal and human influenza virus infection models; and policy, finance, and regulation. Each section identifies barriers, gaps, strategic goals, milestones, and additional R&D priorities germane to that area. The roadmap includes 113 specific R&D milestones, 37 of which have been designated high priority by the IVR expert taskforce. This report summarizes the major issues and priority areas of research outlined in the IVR. By identifying the key issues and steps to address them, the roadmap not only encourages research aimed at new solutions, but also provides guidance on the use of innovative tools to drive breakthroughs in influenza vaccine R&D.publishedVersio