Detecting Object Affordances with Convolutional Neural Networks

We present a novel and real-time method to detect object affordances from RGB-D images. Our method trains a deep Convolutional Neural Network (CNN) to learn deep features from the input data in an end-to-end manner. The CNN has an encoder-decoder architecture in order to obtain smooth label predictions. The input data are represented as multiple modalities to let the network learn the features more effectively. Our method sets a new benchmark on detecting object affordances, improving the accuracy by 20% in comparison with the state-of-the-art methods that use hand-designed geometric features. Furthermore, we apply our detection method on a full-size humanoid robot (WALK-MAN) to demonstrate that the robot is able to perform grasps after efficiently detecting the object affordances

Comparison of Two Tricalcium Phosphate Varnishes and a Comparator Fluoride Varnish on Tubular Occlusion

Objectives The aim of the present study involved comparing the tubular occluding properties of three varnishes, two Clinpro™ varnishes and a Colgate® Duraphat® Varnish. Method Nine caries-free premolar dentine discs were prepared and treated with the three varnishes and subsequently observed under SEM at 0o and 90o angle to assess their ability to cover the dentine surface. The tubule occluding properties were measured using a modified Pashley cell hydraulic conductance model. A further 9 caries-free extracted molars were sectioned into 500μ thick dentine discs. The fluid flow rate was assessed after a) immersing the discs in 6% citric acid for 2 minutes, b) treating the dentine disc with the experimental varnishes and c) subjecting the treated discs to an acid challenge (6% citric acid for 2 minutes). Results SEM investigation showed uniform occlusion of the dentinal tubules, with varying depths of penetration. Hydraulic conductance tests showed no statistically significant differences in the fluid flow rate (expressed as percentages) when all the three varnishes were compared at different stages of treatment (p = 0.33). However, after subjecting the discs to an acid challenge, there was a statistically significant increase in the fluid flow rate with the Colgate® Duraphat® Varnish treated discs, whereas the ClinproTM White Varnish and Clinpro™ XT Varnish discs showed no statistically significant differences (p = 0.99 and p= 0.83 respectively). Conclusions All the tested varnishes (Colgate® Duraphat® Varnish, ClinproTM White Varnish and ClinproTM XT varnish) were effective in blocking the dentinal tubules as demonstrated in this in vitro study. However, the tricalcium phosphate varnishes (ClinproTM) were more resistant to an in vitro acid challenge compared to the sodium fluoride varnish (Colgate® Duraphat®)

Complete quantum teleportation using nuclear magnetic resonance

Quantum mechanics provides spectacular new information processing abilities (Bennett 1995, Preskill 1998). One of the most unexpected is a procedure called quantum teleportation (Bennett et al 1993) that allows the quantum state of a system to be transported from one location to another, without moving through the intervening space. Partial implementations of teleportation (Bouwmeester et al 1997, Boschi et al 1998) over macroscopic distances have been achieved using optical systems, but omit the final stage of the teleportation procedure. Here we report an experimental implementation of the full quantum teleportation operation over inter-atomic distances using liquid state nuclear magnetic resonance (NMR). The inclusion of the final stage enables for the first time a teleportation implementation which may be used as a subroutine in larger quantum computations, or for quantum communication. Our experiment also demonstrates the use of quantum process tomography, a procedure to completely characterize the dynamics of a quantum system. Finally, we demonstrate a controlled exploitation of decoherence as a tool to assist in the performance of an experiment.Comment: 15 pages, 2 figures. Minor differences between this and the published versio

Specific Internalisation of Gold Nanoparticles into Engineered Porous Protein Cages via Affinity Binding

Porous protein cages are supramolecular protein self-assemblies presenting pores that allow the access of surrounding molecules and ions into their core in order to store and transport them in biological environments. Protein cages’ pores are attractive channels for the internalisation of inorganic nanoparticles and an alternative for the preparation of hybrid bioinspired nanoparticles. However, strategies based on nanoparticle transport through the pores are largely unexplored, due to the difficulty of tailoring nanoparticles that have diameters commensurate with the pores size and simultaneously displaying specific affinity to the cages’ core and low non-specific binding to the cages’ outer surface. We evaluated the specific internalisation of single small gold nanoparticles, 3.9 nm in diameter, into porous protein cages via affinity binding. The E2 protein cage derived from the Geobacillus stearothermophilus presents 12 pores, 6 nm in diameter, and an empty core of 13 nm in diameter. We engineered the E2 protein by site-directed mutagenesis with oligohistidine sequences exposing them into the cage’s core. Dynamic light scattering and electron microscopy analysis show that the structures of E2 protein cages mutated with bis- or penta-histidine sequences are well conserved. The surface of the gold nanoparticles was passivated with a self-assembled monolayer made of a mixture of short peptidols and thiolated alkane ethylene glycol ligands. Such monolayers are found to provide thin coatings preventing non-specific binding to proteins. Further functionalisation of the peptide coated gold nanoparticles with Ni2+ nitrilotriacetic moieties enabled the specific binding to oligohistidine tagged cages. The internalisation via affinity binding was evaluated by electron microscopy analysis. From the various mutations tested, only the penta-histidine mutated E2 protein cage showed repeatable and stable internalisation. The present work overcomes the limitations of currently available approaches and provides a new route to design tailored and well-controlled hybrid nanoparticles

The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 {\AA} for RHF and MP2, respectively.Comment: Revised manuscrip

On Counting Triangles through Edge Sampling in Large Dynamic Graphs

Traditional frameworks for dynamic graphs have relied on processing only the stream of edges added into or deleted from an evolving graph, but not any additional related information such as the degrees or neighbor lists of nodes incident to the edges. In this paper, we propose a new edge sampling framework for big-graph analytics in dynamic graphs which enhances the traditional model by enabling the use of additional related information. To demonstrate the advantages of this framework, we present a new sampling algorithm, called Edge Sample and Discard (ESD). It generates an unbiased estimate of the total number of triangles, which can be continuously updated in response to both edge additions and deletions. We provide a comparative analysis of the performance of ESD against two current state-of-the-art algorithms in terms of accuracy and complexity. The results of the experiments performed on real graphs show that, with the help of the neighborhood information of the sampled edges, the accuracy achieved by our algorithm is substantially better. We also characterize the impact of properties of the graph on the performance of our algorithm by testing on several Barabasi-Albert graphs.Comment: A short version of this article appeared in Proceedings of the 2017 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2017

Interpreting ambiguous ‘trace’ results in Schistosoma mansoni CCA Tests: Estimating sensitivity and specificity of ambiguous results with no gold standard

Background The development of new diagnostics is an important tool in the fight against disease. Latent Class Analysis (LCA) is used to estimate the sensitivity and specificity of tests in the absence of a gold standard. The main field diagnostic for Schistosoma mansoni infection, Kato-Katz (KK), is not very sensitive at low infection intensities. A point-of-care circulating cathodic antigen (CCA) test has been shown to be more sensitive than KK. However, CCA can return an ambiguous ‘trace’ result between ‘positive’ and ‘negative’, and much debate has focused on interpretation of traces results. Methodology/Principle findings We show how LCA can be extended to include ambiguous trace results and analyse S. mansoni studies from both Côte d’Ivoire (CdI) and Uganda. We compare the diagnostic performance of KK and CCA and the observed results by each test to the estimated infection prevalence in the population. Prevalence by KK was higher in CdI (13.4%) than in Uganda (6.1%), but prevalence by CCA was similar between countries, both when trace was assumed to be negative (CCAtn: 11.7% in CdI and 9.7% in Uganda) and positive (CCAtp: 20.1% in CdI and 22.5% in Uganda). The estimated sensitivity of CCA was more consistent between countries than the estimated sensitivity of KK, and estimated infection prevalence did not significantly differ between CdI (20.5%) and Uganda (19.1%). The prevalence by CCA with trace as positive did not differ significantly from estimates of infection prevalence in either country, whereas both KK and CCA with trace as negative significantly underestimated infection prevalence in both countries. Conclusions Incorporation of ambiguous results into an LCA enables the effect of different treatment thresholds to be directly assessed and is applicable in many fields. Our results showed that CCA with trace as positive most accurately estimated infection prevalence

A robotic microsurgical forceps for transoral laser microsurgery

Purpose: In transoral laser microsurgery (TLM), the close curved cylindrical structure of the laryngeal region offers functional challenges to surgeons who operate on its malignancies with rigid, single degree-of-freedom (DOF) forceps. These challenges include surgeon hand tremors, poor reachability, poor tissue surface perception, and reduced ergonomy in design. The integrated robotic microsurgical forceps presented here is capable of addressing the above challenges through tele-operated tissue manipulation in TLM. Methods: The proposed device is designed in compliance with the spatial constraints in TLM. It incorporates a novel 2-DOF motorized microsurgical forceps end-effector, which is integrated with a commercial 6-DOF serial robotic manipulator. The integrated device is tele-operated through the haptic master interface, Omega.7. The device is augmented with a force sensor to measure tissue gripping force. The device is called RMF-2F, i.e. robotic microsurgical forceps with 2-DOF end-effector and force sensing. RMF-2F is evaluated through validation trials and pick-n-place experiments with subjects. Furthermore, the device is trialled with expert surgeons through preliminary tasks in a simulated surgical scenario. Results: RMF-2F shows a motion tracking error of less than 400 μm. User trials demonstrate the device’s accuracy in task completion and ease of manoeuvrability using the Omega.7 through improved trajectory following and execution times. The tissue gripping force shows better regulation with haptic feedback (1.624 N) than without haptic feedback (2.116 N). Surgeons positively evaluated the device with appreciation for improved access in the larynx and gripping force feedback. Conclusions: RMF-2F offers an ergonomic and intuitive interface for intraoperative tissue manipulation in TLM. The device performance, usability, and haptic feedback capability were positively evaluated by users as well as expert surgeons. RMF-2F introduces the benefits of robotic teleoperation including, (i) overcoming hand tremors and wrist excursions, (ii) improved reachability and accuracy, and (iii) tissue gripping feedback for safe tissue manipulation

Retrospective harm benefit analysis of pre-clinical animal research for six treatment interventions

The harm benefit analysis (HBA) is the cornerstone of animal research regulation and is considered to be a key ethical safeguard for animals. The HBA involves weighing the anticipated benefits of animal research against its predicted harms to animals but there are doubts about how objective and accountable this process is.i. To explore the harms to animals involved in pre-clinical animal studies and to assess these against the benefits for humans accruing from these studies; ii. To test the feasibility of conducting this type of retrospective HBA.Data on harms were systematically extracted from a sample of pre-clinical animal studies whose clinical relevance had already been investigated by comparing systematic reviews of the animal studies with systematic reviews of human studies for the same interventions (antifibrinolytics for haemorrhage, bisphosphonates for osteoporosis, corticosteroids for brain injury, Tirilazad for stroke, antenatal corticosteroids for neonatal respiratory distress and thrombolytics for stroke). Clinical relevance was also explored in terms of current clinical practice. Harms were categorised for severity using an expert panel. The quality of the research and its impact were considered. Bateson's Cube was used to conduct the HBA.The most common assessment of animal harms by the expert panel was 'severe'. Reported use of analgesia was rare and some animals (including most neonates) endured significant procedures with no, or only light, anaesthesia reported. Some animals suffered iatrogenic harms. Many were kept alive for long periods post-experimentally but only 1% of studies reported post-operative care. A third of studies reported that some animals died prior to endpoints. All the studies were of poor quality. Having weighed the actual harms to animals against the actual clinical benefits accruing from these studies, and taking into account the quality of the research and its impact, less than 7% of the studies were permissible according to Bateson's Cube: only the moderate bisphosphonate studies appeared to minimise harms to animals whilst being associated with benefit for humans.This is the first time the accountability of the HBA has been systematically explored across a range of pre-clinical animal studies. The regulatory systems in place when these studies were conducted failed to safeguard animals from severe suffering or to ensure that only beneficial, scientifically rigorous research was conducted. Our findings indicate a pressing need to: i. review regulations, particularly those that permit animals to suffer severe harms; ii. reform the processes of prospectively assessing pre-clinical animal studies to make them fit for purpose; and iii. systematically evaluate the benefits of pre-clinical animal research to permit a more realistic assessment of its likely future benefits

The UN in the lab

We consider two alternatives to inaction for governments combating terrorism, which we term Defense and Prevention. Defense consists of investing in resources that reduce the impact of an attack, and generates a negative externality to other governments, making their countries a more attractive objective for terrorists. In contrast, Prevention, which consists of investing in resources that reduce the ability of the terrorist organization to mount an attack, creates a positive externality by reducing the overall threat of terrorism for all. This interaction is captured using a simple 3×3 “Nested Prisoner’s Dilemma” game, with a single Nash equilibrium where both countries choose Defense. Due to the structure of this interaction, countries can benefit from coordination of policy choices, and international institutions (such as the UN) can be utilized to facilitate coordination by implementing agreements to share the burden of Prevention. We introduce an institution that implements a burden-sharing policy for Prevention, and investigate experimentally whether subjects coordinate on a cooperative strategy more frequently under different levels of cost sharing. In all treatments, burden sharing leaves the Prisoner’s Dilemma structure and Nash equilibrium of the game unchanged. We compare three levels of burden sharing to a baseline in a between-subjects design, and find that burden sharing generates a non-linear effect on the choice of the efficient Prevention strategy and overall performance. Only an institution supporting a high level of mandatory burden sharing generates a significant improvement in the use of the Prevention strategy