LabelFusion: A Pipeline for Generating Ground Truth Labels for Real RGBD Data of Cluttered Scenes

Deep neural network (DNN) architectures have been shown to outperform traditional pipelines for object segmentation and pose estimation using RGBD data, but the performance of these DNN pipelines is directly tied to how representative the training data is of the true data. Hence a key requirement for employing these methods in practice is to have a large set of labeled data for your specific robotic manipulation task, a requirement that is not generally satisfied by existing datasets. In this paper we develop a pipeline to rapidly generate high quality RGBD data with pixelwise labels and object poses. We use an RGBD camera to collect video of a scene from multiple viewpoints and leverage existing reconstruction techniques to produce a 3D dense reconstruction. We label the 3D reconstruction using a human assisted ICP-fitting of object meshes. By reprojecting the results of labeling the 3D scene we can produce labels for each RGBD image of the scene. This pipeline enabled us to collect over 1,000,000 labeled object instances in just a few days. We use this dataset to answer questions related to how much training data is required, and of what quality the data must be, to achieve high performance from a DNN architecture

Breast pumps as an incentive for breastfeeding: a mixed methods study of acceptability

Increasing breastfeeding rates would improve maternal and child health, but multiple barriers to breastfeeding persist. Breast pump provision has been used as an incentive for breastfeeding, although effectiveness is unclear. Women's use of breast pumps is increasing and a high proportion of mothers express breastmilk. No research has yet reported women's and health professionals' perspectives on breast pumps as an incentive for breastfeeding. In the Benefits of Incentives for Breastfeeding and Smoking cessation in pregnancy (BIBS) study, mixed methods research explored women's and professionals' views of breast pumps as an incentive for breastfeeding. A survey of health professionals across Scotland and North West England measured agreement with ‘a breast pump costing around£40 provided for free on the NHS’ as an incentive strategy. Qualitative interviews and focus groups were conducted in two UK regions with a total of 68 participants (pregnant women, new mothers, and their significant others and health professionals) and thematic analysis undertaken. The survey of 497 health professionals found net agreement of 67.8% (337/497) with the breast pump incentive strategy, with no predictors of agreement shown by a multiple ordered logistic regression model. Qualitative research found interrelated themes of the ‘appeal and value of breast pumps’, ‘sharing the load’, ‘perceived benefits’, ‘perceived risks’ and issues related to ‘timing’. Qualitative participants expressed mixed views on the acceptability of breast pumps as an incentive for breastfeeding. Understanding the mechanisms of action for pump type, timing and additional support required for effectiveness is required to underpin trials of breast pump provision as an incentive for improving breastfeeding outcomes

A long and abundant non-coding RNA in Lactobacillus salivarius

Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq) transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L. salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon

Continuous Humanoid Locomotion over Uneven Terrain using Stereo Fusion

Abstract — For humanoid robots to fulfill their mobility po-tential they must demonstrate reliable and efficient locomotion over rugged and irregular terrain. In this paper we present the perception and planning algorithms which have allowed a humanoid robot to use only passive stereo imagery (as opposed to actuating a laser range sensor) to safely plan footsteps to continuously walk over rough and uneven surfaces without stopping. The perception system continuously integrates stereo imagery to build a consistent 3D model of the terrain which is then used by our footstep planner which reasons about obstacle avoidance, kinematic reachability and foot rotation through mixed-integer quadratic optimization to plan the required step positions. We illustrate that our stereo imagery fusion approach can measure the walking terrain with sufficient accuracy that it matches the quality of terrain estimates from LIDAR. To our knowledge this is the first such demonstration of the use of computer vision to carry out general purpose terrain estimation on a locomoting robot — and additionally to do so in continuous motion. A particular integration challenge was ensuring that these two computationally intensive systems oper-ate with minimal latency (below 1 second) to allow re-planning while walking. The results of extensive experimentation and quantitative analysis are also presented. Our results indicate that a laser range sensor is not necessary to achieve locomotion in these challenging situations. I

Optimization-based locomotion planning, estimation, and control design for the atlas humanoid robot

This paper describes a collection of optimization algorithms for achieving dynamic planning, control, and state estimation for a bipedal robot designed to operate reliably in complex environments. To make challenging locomotion tasks tractable, we describe several novel applications of convex, mixed-integer, and sparse nonlinear optimization to problems ranging from footstep placement to whole-body planning and control. We also present a state estimator formulation that, when combined with our walking controller, permits highly precise execution of extended walking plans over non-flat terrain. We describe our complete system integration and experiments carried out on Atlas, a full-size hydraulic humanoid robot built by Boston Dynamics, Inc.United States. Air Force Office of Scientific Research (FA8750-12-1-0321)United States. Office of Naval Research (N00014-12-1-0071)United States. Office of Naval Research (N00014-10-1-0951)National Science Foundation (U.S.) (IIS-0746194)National Science Foundation (U.S.) (IIS-1161909

Program evaluation with high-dimensional data

Background It has become increasingly apparent that establishing and maintaining a complex and diverse gut microbiome is fundamental to human health. There are growing efforts to identify methods that can modulate and influence the microbiome, especially in individuals who due to disease or circumstance have experienced a disruption in their native microbiome. Faecal microbial transplantation (FMT) is one method that restores diversity to the microbiome of an individual by introducing microbes from a healthy donor. FMT introduces a complete microbiome into the recipient, including the bacteriome, archaeome, mycome and virome. In this study we investigated whether transplanting an autochthonous faecal virome consisting primarily of bacteriophages could impact a bacteriome disrupted by antibiotic treatment (Faecal Virome Transplantation; FVT).Results Following disruption of the bacteriome by penicillin and streptomycin, test mice (n=8) received a bacteria free, faecal transplant, while Control mice (n=8) received a heated and nuclease treated control. The bacteriomes (as determined via 16S rRNA sequencing) of mice that received an FVT, in which bacteriophages predominate, separated from those of the Control mice as determined by principle co-ordinate analysis (PCoA), and contained differentially abundant taxa that reshaped the bacteriome profile such that it more closely resembled that of the pre-treatment mice. Similarly, metagenomic sequencing of the virome confirmed that the bacteriophages present in the gut of treatment and Control mice differed over time in both abundance and diversity, with transplanted phages seen to colonise the FVT mice.Conclusions An autochthonous virome transplant impacts on the bacteriome and virome of mice following antibiotic treatment. The virome, consisting mainly of bacteriophages, reshapes the bacteriome such that it more closely resembles the pre-antibiotic state. To date, faecal transplants have largely focussed on transferring living microbes, but given that bacteriophage are inert biological entities incapable of colonising in the absence of a sensitive host they could form a viable alternative that may have fewer safety implications and that could be delivered as a robust formulation

Benefits of Incentives for Breastfeeding and Smoking cessation in pregnancy (BIBS): a mixed-methods study to inform trial design

Background: Smoking in pregnancy and/or not breastfeeding have considerable negative health outcomes for mother and baby. Aim: To understand incentive mechanisms of action for smoking cessation in pregnancy and breastfeeding, develop a taxonomy and identify promising, acceptable and feasible interventions to inform trial design. Design: Evidence syntheses, primary qualitative survey, and discrete choice experiment (DCE) research using multidisciplinary, mixed methods. Two mother-and-baby groups in disadvantaged areas collaborated throughout. Setting: UK. Participants: The qualitative study included 88 pregnant women/recent mothers/partners, 53 service providers, 24 experts/decision-makers and 63 conference attendees. The surveys included 1144 members of the general public and 497 health professionals. The DCE study included 320 women with a history of smoking. Methods: (1) Evidence syntheses: incentive effectiveness (including meta-analysis and effect size estimates), delivery processes, barriers to and facilitators of smoking cessation in pregnancy and/or breastfeeding, scoping review of incentives for lifestyle behaviours; (2) qualitative research: grounded theory to understand incentive mechanisms of action and a framework approach for trial design; (3) survey: multivariable ordered logit models; (4) DCE: conditional logit regression and the log-likelihood ratio test. Results: Out of 1469 smoking cessation and 5408 breastfeeding multicomponent studies identified, 23 smoking cessation and 19 breastfeeding studies were included in the review. Vouchers contingent on biochemically proven smoking cessation in pregnancy were effective, with a relative risk of 2.58 (95% confidence interval 1.63 to 4.07) compared with non-contingent incentives for participation (four studies, 344 participants). Effects continued until 3 months post partum. Inconclusive effects were found for breastfeeding incentives compared with no/smaller incentives (13 studies) but provider commitment contracts for breastfeeding show promise. Intervention intensity is a possible confounder. The acceptability of seven promising incentives was mixed. Women (for vouchers) and those with a lower level of education (except for breastfeeding incentives) were more likely to disagree. Those aged ≤ 44 years and ethnic minority groups were more likely to agree. Agreement was greatest for a free breast pump and least for vouchers for breastfeeding. Universal incentives were preferred to those targeting low-income women. Initial daily text/telephone support, a quitting pal, vouchers for > £20.00 per month and values up to £80.00 increase the likelihood of smoking cessation. Doctors disagreed with provider incentives. A ‘ladder’ logic model emerged through data synthesis and had face validity with service users. It combined an incentive typology and behaviour change taxonomy. Autonomy and well-being matter. Personal difficulties, emotions, socialising and attitudes of others are challenges to climbing a metaphorical ‘ladder’ towards smoking cessation and breastfeeding. Incentive interventions provide opportunity ‘rungs’ to help, including regular skilled flexible support, a pal, setting goals, monitoring and outcome verification. Individually tailored and non-judgemental continuity of care can bolster women’s capabilities to succeed. Rigid, prescriptive interventions placing the onus on women to behave ‘healthily’ risk them feeling pressurised and failing. To avoid ‘losing face’, women may disengage. Limitations: Included studies were heterogeneous and of variable quality, limiting the assessment of incentive effectiveness. No cost-effectiveness data were reported. In surveys, selection bias and confounding are possible. The validity and utility of the ladder logic model requires evaluation with more diverse samples of the target population. Conclusions: Incentives provided with other tailored components show promise but reach is a concern. Formal evaluation is recommended. Collaborative service-user involvement is importan

Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation

Background: It has become increasingly accepted that establishing and maintaining a complex and diverse gut microbiota is fundamental to human health. There are growing efforts to identify means of modulating and influencing the microbiota, especially in individuals who have experienced a disruption in their native microbiota. Faecal microbiota transplantation (FMT) is one method that restores diversity to the microbiota of an individual by introducing microbes from a healthy donor. FMT introduces the total microbial load into the recipient, including the bacteria, archaea, yeasts, protists and viruses. In this study, we investigated whether an autochthonous faecal viral transfer (FVT), in the form of a sterile faecal filtrate, could impact the recovery of a bacteriome disrupted by antibiotic treatment. Results: Following antibiotic disruption of the bacteriome, test mice received an FVT harvested prior to antibiotic treatment, while control mice received a heat- and nuclease-treated FVT. In both groups of mice, the perturbed microbiome reverted over time to one more similar to the pre-treatment one. However, the bacteriomes of mice that received an FVT, in which bacteriophages predominate, separated from those of the control mice as determined by principal co-ordinate analysis (PCoA). Moreover, analysis of the differentially abundant taxa indicated a closer resemblance to the pre-treatment bacteriome in the test mice that had received an FVT. Similarly, metagenomic sequencing of the virome confirmed that faecal bacteriophages of FVT and control mice differed over time in both abundance and diversity, with the phages constituting the FVT persisting in mice that received them. Conclusions: An autochthonous virome transfer reshaped the bacteriomes of mice post-antibiotic treatment such that they more closely resembled the pre-antibiotic microbiota profile compared to mice that received non-viable phages. Thus, FVT may have a role in addressing antibiotic-associated microbiota alterations and potentially prevent the establishment of post-antibiotic infection. Given that bacteriophages are biologically inert in the absence of their host bacteria, they could form a safe and effective alternative to whole microbiota transplants that could be delivered during/following perturbation of the gut flora

An Architecture for Online Affordance-based Perception and Whole-body Planning

The DARPA Robotics Challenge Trials held in December 2013 provided a landmark demonstration of dexterous mobile robots executing a variety of tasks aided by a remote human operator using only data from the robot's sensor suite transmitted over a constrained, field-realistic communications link. We describe the design considerations, architecture, implementation and performance of the software that Team MIT developed to command and control an Atlas humanoid robot. Our design emphasized human interaction with an efficient motion planner, where operators expressed desired robot actions in terms of affordances fit using perception and manipulated in a custom user interface. We highlight several important lessons we learned while developing our system on a highly compressed schedule

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy