Visual interfaces: The human perceiver

How knowledge of visual perception can be applied to achieve teleoperation and virtual worlds is discussed

Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers

Nucleic acid aptamers can potentially be developed as broad-spectrum antiviral agents. Single-stranded DNA (ssDNA) aptamer RT1t49 inhibits reverse transcriptases (RT) from HIV-1 and diverse lentiviral subtypes with low nanomolar values of Kd and IC50. To dissect the structural requirements for inhibition, RT-catalyzed DNA polymerization was measured in the presence of RT1t49 variants. Three structural domains were found to be essential for RT inhibition by RT1t49: a 5′ stem (stem I), a connector and a 3′ stem (stem II) capable of forming multiple secondary structures. Stem I tolerates considerable sequence plasticity, suggesting that it is recognized by RT more by structure than by sequence-specific contacts. Truncating five nucleotides from the 3′ end prevents formation of the most stable stem II structure, yet has little effect on IC50 across diverse HIV-1, HIV-2 and SIVCPZ RT. When bound to wild-type RT or an RNase H active site mutant, site-specifically generated hydroxyl radicals cleave after nucleotide A32. Cleavage is eliminated by either of two polymerase (pol)-active site mutants, strongly suggesting that A32 lies within the RT pol-active site. These data suggest a model of ssDNA aptamer–RT interactions and provide an improved molecular understanding of a potent, broad-spectrum ssDNA aptamer

Quantitative measurement of tool embodiment for virtual reality input alternatives

Funding: Ontario Ministry of Research and Innovation and Science and the Natural Sciences and Engineering Research Council of Canada for funding.Virtual reality (VR) strives to replicate the sensation of the physical environment by mimicking people’s perceptions and experience of being elsewhere. These experiences are often mediated by the objects and tools we interact with in the virtual world (e.g., a controller). Evidence from psychology posits that when using the tool proficiently, it becomes embodied (i.e., an extension of one’s body). There is little work, however, on how to measure this phenomenon in VR, and on how different types of tools and controllers can affect the experience of interaction. In this work, we leverage cognitive psychology and philosophy literature to construct the Locus-of-Attention Index (LAI), a measure of tool embodiment. We designed and conducted a study that measures readiness-to-hand and unreadiness-to-hand for three VR interaction techniques: hands, a physical tool, and a VR controller. The study shows that LAI can measure differences in embodiment with working and broken tools and that using the hand directly results in more embodiment than using controllers.Postprin

Efficient real-time monitoring of an emerging influenza pandemic: How feasible?

A prompt public health response to a new epidemic relies on the ability to monitor and predict its evolution in real time as data accumulate. The 2009 A/H1N1 outbreak in the UK revealed pandemic data as noisy, contaminated, potentially biased and originating from multiple sources. This seriously challenges the capacity for real-time monitoring. Here, we assess the feasibility of real-time inference based on such data by constructing an analytic tool combining an age-stratified SEIR transmission model with various observation models describing the data generation mechanisms. As batches of data become available, a sequential Monte Carlo (SMC) algorithm is developed to synthesise multiple imperfect data streams, iterate epidemic inferences and assess model adequacy amidst a rapidly evolving epidemic environment, substantially reducing computation time in comparison to standard MCMC, to ensure timely delivery of real-time epidemic assessments. In application to simulated data designed to mimic the 2009 A/H1N1 epidemic, SMC is shown to have additional benefits in terms of assessing predictive performance and coping with parameter nonidentifiability

Doping-dependent study of the periodic Anderson model in three dimensions

We study a simple model for $f$-electron systems, the three-dimensional periodic Anderson model, in which localized $f$ states hybridize with neighboring $d$ states. The $f$ states have a strong on-site repulsion which suppresses the double occupancy and can lead to the formation of a Mott-Hubbard insulator. When the hybridization between the $f$ and $d$ states increases, the effects of these strong electron correlations gradually diminish, giving rise to interesting phenomena on the way. We use the exact quantum Monte-Carlo, approximate diagrammatic fluctuation-exchange approximation, and mean-field Hartree-Fock methods to calculate the local moment, entropy, antiferromagnetic structure factor, singlet-correlator, and internal energy as a function of the $f-d$ hybridization for various dopings. Finally, we discuss the relevance of this work to the volume-collapse phenomenon experimentally observed in f-electron systems.Comment: 12 pages, 8 figure

(Vi)-rushed Into Online Group Schema Therapy Based Day-Treatment for Older Adults by the COVID-19 Outbreak in the Netherlands

BACKGROUND: Societal measures in context of the COVID-19 outbreak forced us to transform our schema therapy based day-treatment for older adults with chronic affective disorders and personality problems into an online program. The objective of this paper is to present first impressions of this transformation. METHODS: Using over-the-phone instructions initially, all patients were able to participate with the online therapy program. To reduce screen-time for patients, the nonverbal therapies were shortened. Four patients, aged 64-70 years, started our online program. RESULTS: Therapists were positive about the online capabilities and resilience of patients to adapt to the new situation. Prejudices on limited effectiveness of online psychotherapy were counteracted. Sending homework by email and mail seems to facilitate therapy adherence. Nonverbal therapy could be important to stimulate the online group process. CONCLUSION: We were positively surprised by the online capabilities of our geriatric mental healthcare patients and encourage further formal effectiveness studies

Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype

Economic crisis and the construction of a neo-liberal regulatory regime in Korea

A consistent theme of the literature on the ontology of the 1997 South Korean crisis is the key role played by regulatory failures and the growing weakness of the state. This paper seeks to briefly highlight both the insights and the limitations of this approach to understanding the crisis. Having done so, we shall set out the argument that the crisis created an opportunity for reformist Korean élites to advance their longstanding, but previously frustrated, project to create a comprehensive unambiguously neo-liberal regulatory regime. This paper will also seek to highlight the implications of our reading of the development of the Korean political economy for broader debates on economic liberalisation, crisis and the future of the developmental state

A justification of whistleblowing

Penultimate version accepted for publicationWhistleblowing is the act of disclosing information from a public or private organization in order to reveal cases of corruption that are of immediate or potential danger to the public. Blowing the whistle involves personal risk, especially when legal protection is absent, and charges of betrayal, which often come in the form of legal prosecution under treason laws. In this article we argue that whistleblowing is justified when disclosures are made with the proper intent and fulfill specific communicative constraints in addressing issues of public interest. Three communicative constraints of informativeness, truthfulness and evidence are discussed in this regard. We develop a ‘harm test’ to assess the intent for disclosures, concluding that it is not sufficient for justification. Along with the proper intent, a successful act of whistleblowing should provide information that serves the public interest. Taking cognizance of the varied conceptions of public interest, we present an account of public interest that fits the framework of whistleblowing disclosures. In particular, we argue that whistleblowing is justified inter alia when the information it conveys is of a presumptive interest for a public insofar as it reveals an instance of injustice or violation of a civil or political right done against and unbeknown to some members of a polity.Project: ‘Change of Direction. Fostering Whistleblowing in the Fight against Corruption’ co-funded by the Internal Security Fund of the European Union (Grant Agreement Number: HOME/2014/ISFP/AG/EFCE/7233); SFRH/BPD/108669/2015info:eu-repo/semantics/publishedVersio

Aggregate structure of hydroxyproline-rich glycoprotein (HRGP) and HRGP assisted dispersion of carbon nanotubes

Hydroxyproline-rich glycoproteins (HRGP) comprise a super-family of extracellular structural glycoproteins whose precise roles in plant cell wall assembly and functioning remain to be elucidated. However, their extended structure and repetitive block co-polymer character of HRGPs may mediate their self-assembly as wall scaffolds by like-with-like alignment of their hydrophobic peptide and hydrophilic glycopeptide modules. Intermolecular crosslinking further stabilizes the scaffold. Thus the design of HRGP-based scaffolds may have practical applications in bionanotechnology and medicine. As a first step, we have used single-molecule or single-aggregate atomic force microscopy (AFM) to visualize the structure of YK20, an amphiphilic HRGP comprised entirely of 20 tandem repeats of: Ser-Hyp4-Ser-Hyp-Ser-Hyp4-Tyr-Tyr-Tyr-Lys. YK20 formed tightly aggregated coils at low ionic strength, but networks of entangled chains with a porosity of ~0.5–3 μm at higher ionic strength. As a second step we have begun to design HRGP-carbon nanotube composites. Single-walled carbon nanotubes (SWNTs) can be considered as seamless cylinders rolled up from graphene sheets. These unique all-carbon structures have extraordinary aromatic and hydrophobic properties and form aggregated bundles due to strong inter-tube van der Waals interactions. Sonicating aggregated SWNT bundles with aqueous YK20 solubilized them presumably by interaction with the repetitive, hydrophobic, Tyr-rich peptide modules of YK20 with retention of the extended polyproline-II character. This may allow YK20 to form extended structures that could potentially be used as scaffolds for site-directed assembly of nanomaterials