Adaptive Path Planning for Depth Constrained Bathymetric Mapping with an Autonomous Surface Vessel

This paper describes the design, implementation and testing of a suite of algorithms to enable depth constrained autonomous bathymetric (underwater topography) mapping by an Autonomous Surface Vessel (ASV). Given a target depth and a bounding polygon, the ASV will find and follow the intersection of the bounding polygon and the depth contour as modeled online with a Gaussian Process (GP). This intersection, once mapped, will then be used as a boundary within which a path will be planned for coverage to build a map of the Bathymetry. Methods for sequential updates to GP's are described allowing online fitting, prediction and hyper-parameter optimisation on a small embedded PC. New algorithms are introduced for the partitioning of convex polygons to allow efficient path planning for coverage. These algorithms are tested both in simulation and in the field with a small twin hull differential thrust vessel built for the task.Comment: 21 pages, 9 Figures, 1 Table. Submitted to The Journal of Field Robotic

Seeds and the Art of Genome Maintenance

Successful germination represents a crucial developmental transition in the plant lifecycle and is important both for crop yields and plant survival in natural ecosystems. However, germination potential decreases during storage and seed longevity is a key determinant of crop production. Decline in germination vigor is initially manifest as an increasing delay to radicle emergence and the completion of germination and eventually culminating in loss of seed viability. The molecular mechanisms that determine seed germination vigor and viability remain obscure, although deterioration in seed quality is associated with the accumulation of damage to cellular structures and macromolecules including lipids, protein, and nucleic acids. In desiccation tolerant seeds, desiccation/rehydration cycles and prolonged periods in the dry quiescent state are associated with remarkable levels of stress to the embryo genome which can result in mutagenesis of the genetic material, inhibition of transcription and replication and delayed growth and development. An increasing number of studies are revealing DNA damage accumulated in the embryo genome, and the repair capacity of the seed to reverse this damage, as major factors that determine seed vigor and viability. Recent findings are now establishing important roles for the DNA damage response in regulating germination, imposing a delay to germination in aged seed to minimize the deleterious consequences of DNA damage accumulated in the dry quiescent state. Understanding the mechanistic basis of seed longevity will underpin the directed improvement of crop varieties and support preservation of plant genetic resources in seed banks

Assessing spatial and temporal variability of acid-extractable organics in oil sands process-affected waters

The acid-extractable organic compounds (AEOs), including naphthenic acids (NAs), present within oil sands process-affected water (OSPW) receive great attention due to their known toxicity. While recent progress in advanced separation and analytical methodologies for AEOs has improved our understanding of the composition of these mixtures, little is known regarding any variability (i.e., spatial, temporal) inherent within, or between, tailings ponds. In this study, 5 samples were collected from the same location of one tailings pond over a 2-week period. In addition, 5 samples were collected simultaneously from different locations within a tailings pond from a different mine site, as well as its associated recycling pond. In both cases, the AEOs were analyzed using SFS, ESI-MS, HRMS, GC×GC-ToF/MS, and GC- & LC-QToF/MS (GC analyses following conversion to methyl esters). Principal component analysis of HRMS data was able to distinguish the ponds from each other, while data from GC×GC-ToF/MS, and LC- and GC-QToF/MS were used to differentiate samples from within the temporal and spatial sample sets, with the greater variability associated with the latter. Spatial differences could be attributed to pond dynamics, including differences in inputs of tailings and surface run-off. Application of novel chemometric data analyses of unknown compounds detected by LC- and GC-QToF/MS allowed further differentiation of samples both within and between data sets, providing an innovative approach for future fingerprinting studies

Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond

Precise genome editing with CRISPR/Cas paves the way for many biochemical, biotechnological, and medical applications, and consequently, it may enable treatment of already known and still-to-be-found genetic diseases. Meanwhile, another rapidly emerging field—structural DNA nanotechnology—provides a customizable and modular platform for accurate positioning of nanoscopic materials, for e.g., biomedical uses. This addressability has just recently been applied in conjunction with the newly developed gene engineering tools to enable impactful, programmable nanotechnological applications. As of yet, self-assembled DNA nanostructures have been mainly employed to enhance and direct the delivery of CRISPR/Cas, but lately the groundwork has also been laid out for other intriguing and complex functions. These recent advances will be described in this perspective

An ontology-based modelling system (OBMS) for representing behaviour change theories applied to 76 theories [version 1; peer review: awaiting peer review]

BACKGROUND: To efficiently search, compare, test and integrate behaviour change theories, they need to be specified in a way that is clear, consistent and computable. An ontology-based modelling system (OBMS) has previously been shown to be able to represent five commonly used theories in this way. We aimed to assess whether the OBMS could be applied more widely and to create a database of behaviour change theories, their constructs and propositions. METHODS: We labelled the constructs within 71 theories and used the OBMS to represent the relationships between the constructs. Diagrams of each theory were sent to authors or experts for feedback and amendment. The 71 finalised diagrams plus the five previously generated diagrams were used to create a searchable database of 76 theories in the form of construct-relationship-construct triples. We conducted a set of illustrative analyses to characterise theories in the database. RESULTS: All 71 theories could be satisfactorily represented using this system. In total, 35 (49%) were finalised with no or very minor amendment. The remaining 36 (51%) were finalised after changes to the constructs (seven theories), relationships between constructs (15 theories) or both (14 theories) following author/expert feedback. The mean number of constructs per theory was 20 (min. = 6, max. = 72), with the mean number of triples per theory 31 (min. = 7, max. = 89). Fourteen distinct relationship types were used, of which the most commonly used was ‘influences’, followed by ‘part of’. CONCLUSIONS: The OBMS can represent a wide array of behavioural theories in a precise, computable format. This system should provide a basis for better integration and synthesis of theories than has hitherto been possible

A new version of the HBSC Family Affluence Scale - FAS III: Scottish qualitative findings from the International FAS Development Study

A critical review of the Family Affluence Scale (FAS) concluded that FAS II was no longer discriminatory within very rich or very poor countries, where a very high or a very low proportion of children were categorised as high FAS or low FAS respectively (Currie et al. 2008). The review concluded that a new version of FAS - FAS III - should be developed to take into account current trends in family consumption patterns across the European region, the US and Canada. In 2012, the FAS Development and Validation Study was conducted in eight countries - Denmark, Greenland, Italy, Norway, Poland, Romania, Slovakia and Scotland. This paper describes the Scottish qualitative findings from this study. The Scottish qualitative fieldwork comprising cognitive interviews and focus groups sampled from 11, 13 and 15 year-old participants from 18 of the most- and least- economically deprived schools. These qualitative results were used to inform the final FAS III recommendations.Publisher PDFPeer reviewe

The increase of the functional entropy of the human brain with age

We use entropy to characterize intrinsic ageing properties of the human brain. Analysis of fMRI data from a large dataset of individuals, using resting state BOLD signals, demonstrated that a functional entropy associated with brain activity increases with age. During an average lifespan, the entropy, which was calculated from a population of individuals, increased by approximately 0.1 bits, due to correlations in BOLD activity becoming more widely distributed. We attribute this to the number of excitatory neurons and the excitatory conductance decreasing with age. Incorporating these properties into a computational model leads to quantitatively similar results to the fMRI data. Our dataset involved males and females and we found significant differences between them. The entropy of males at birth was lower than that of females. However, the entropies of the two sexes increase at different rates, and intersect at approximately 50 years; after this age, males have a larger entropy

Use of the distributions of adamantane acids to profile short-term temporal and pond-scale spatial variations in the composition of oil sands process-affected waters

© The Royal Society of Chemistry. Oil industry produced waters, such as the oils sands process-affected waters (OSPW) of Alberta, Canada, represent a challenge in terms of risk assessment and reclamation due to their extreme complexity, particularly of the organic chemical constituents, including the naphthenic acids (NA). The identification of numerous NA in single samples has raised promise for the use of NA distributions for profiling OSPW. However, monitoring of the success of containment is still difficult, due to the lack of knowledge of the homogeneity (or otherwise) of OSPW composition within, and between, different industry containments. Here we used GC×GC-MS to compare the NA of five OSPW samples from each of two different industries. Short-term temporal and pond-scale spatial variations in the distributions of known adamantane acids and diacids and other unknown tricyclic acids were examined and a statistical appraisal of the replicate data made. The presence/absence of individual acids easily distinguished the OSPW NA of one industry from those of the other. The proportions of tricyclic acids with different carbon numbers also varied significantly between the OSPW of the two industries. The pond-scale spatial variation in NA in OSPW samples was higher than the short-term (2 weeks) temporal variations. An OSPW sample from an aged pond was exceptionally high in the proportion of C<inf>15,16,17</inf> compounds, possibly due to increased biotransformation. Such techniques could possibly also help to distinguish different sources of NA in the environment

A synbiotic-containing amino acid-based formula improves gut microbiota in non-IgE-mediated allergic infants

BACKGROUND: Prebiotics and probiotics (synbiotics) can modify gut microbiota and have potential in allergy management when combined with amino acid-based formula (AAF) for infants with cow's milk allergy (CMA). METHODS: This multicenter, double-blind, randomized controlled trial investigated the effects of an AAF including synbiotic blend on percentages of bifidobacteria and Eubacterium rectale/Clostridium coccoides group (ER/CC) in feces from infants with suspected non-IgE-mediated CMA. Feces from age matched healthy breastfed infants were used as reference (HBR) for primary outcomes. CMA subjects were randomized and received test or control formula for 8 weeks. Test formula was a hypoallergenic, nutritionally complete AAF including a prebiotic blend of fructo-oligosaccharides and the probiotic strain Bifidobacterium breve M-16V. Control formula was AAF without synbiotics. RESULTS: Thirty-five (test) and 36 (control) subjects were randomized; HBR included 51 infants. At week 8, median percentage of bifidobacteria was higher in test group vs control group (35.4 vs. 9.7%, respectively P<0.001), whereas ER/CC was lower (9.5 vs. 24.2%, respectively; P<0.001). HBR levels of bifidobacteria and ER/CC were 55 and 6.5%, respectively. CONCLUSION: AAF including specific synbiotics, which results in levels of bifidobacteria and ER/CC approximating levels in HBR group, improves the fecal microbiota of infants with suspected non-IgE-mediated CMA