Tetrisation of triangular meshes and its application in shape blending

The As-Rigid-As-Possible (ARAP) shape deformation framework is a versatile technique for morphing, surface modelling, and mesh editing. We discuss an improvement of the ARAP framework in a few aspects: 1. Given a triangular mesh in 3D space, we introduce a method to associate a tetrahedral structure, which encodes the geometry of the original mesh. 2. We use a Lie algebra based method to interpolate local transformation, which provides better handling of rotation with large angle. 3. We propose a new error function to compile local transformations into a global piecewise linear map, which is rotation invariant and easy to minimise. We implemented a shape blender based on our algorithm and its MIT licensed source code is available online

Lead, cadmium and aluminum in Canadian infant formulae, oral electrolytes and glucose solutions

Lead (Pb), cadmium (Cd) and aluminum (Al) were determined in 437 individual samples of infant formulae, oral electrolytes and 5% glucose solutions available in Canada. In the electrolytes, Cd and Pb concentrations were all below 0.01 and 0.041 ng g−1, respectively. In the 5% glucose solutions, Pb and Cd levels averaged 0.01 and 0.09 ng g−1, respectively. Reported on an as-consumed basis, Pb levels in milk- and soya-based formulae averaged 0.90 and 1.45 ng g−1, respectively, while Cd levels averaged 0.23 and 1.18 ng g−1, respectively Average Al levels on an as-consumed basis were 440 ng g−1 (range 10–3400 ng g−1) in milk-based formulae and 730 ng g−1 (range 230–1100 ng g−1) in soy-based formulae. Al concentrations increased in the following order: plain formula < low-iron formula < iron-supplemented formula < casein hydrolysate formula ≈ premature formula ≤ soy formula. For example, in the powdered formulae, average Al concentrations were 18 ng g−1 for plain milk-based, 37 ng g−1 for low-iron, 128 ng g−1 for iron supplemented, 462 ng g−1 for lactose-free, 518 ng g−1 for hypoallergenic and 619 ng g−1 for soy-based formula. Al concentrations, as-consumed, increased with decreasing levels of concentration: powder < concentrated liquid < ready-to-use. Formulae stored in glass bottles contained between 100 and 300 ng g−1 more Al than the same formulae stored in cans. The source of the increased Al did not appear to be the glass itself, because most electrolytes and glucose solutions, also stored in glass, contained less than 8 ng g−1 Al. Corresponding differences in Pb and Cd levels were not observed. Al concentrations varied substantially among manufacturers; however, all manufacturers were able to produce plain milk-based formulae containing less than 50 ng g−1 Al, i.e. within the range of Al concentrations found in human milk. Next to soya-based and hypoallergenic formulae, premature formulae contained among the highest concentrations of Al, ranging 851–909 ng g−1 from one manufacturer and 365–461 ng g−1 from another

Bulk Segregant Analysis Using Single Nucleotide Polymorphism Microarrays

Bulk segregant analysis (BSA) using microarrays, and extreme array mapping (XAM) have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however, require the identification of single feature polymorphisms (SFP) between the cross parents for each new combination of genotypes, which raises the cost of experiments. The availability of the genomic polymorphism data in Arabidopsis thaliana, coupled with the efficient designs of Single Nucleotide Polymorphism (SNP) genotyping arrays removes the requirement for SFP detection and lowers the per array cost, thereby lowering the overall cost per experiment. To demonstrate that these approaches would be functional on SNP arrays and determine confidence intervals, we analyzed hybridizations of natural accessions to the Arabidopsis ATSNPTILE array and simulated BSA or XAM given a variety of gene models, populations, and bulk selection parameters. Our results show a striking degree of correlation between the genotyping output of both methods, which suggests that the benefit of SFP genotyping in context of BSA can be had with the cheaper, more efficient SNP arrays. As a final proof of concept, we hybridized the DNA from bulks of an F2 mapping population of a Sulfur and Selenium ionomics mutant to both the Arabidopsis ATTILE1R and ATSNPTILE arrays, which produced almost identical results. We have produced R scripts that prompt the user for the required parameters and perform the BSA analysis using the ATSNPTILE1 array and have provided them as supplemental data files

Biodiversity of Mineral Nutrient and Trace Element Accumulation in Arabidopsis thaliana

In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17–19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene×environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org

Strategies to overcome physician shortages in northern Ontario: A study of policy implementation over 35 years

<p>Abstract</p> <p>Background</p> <p>Shortages and maldistibution of physicians in northern Ontario, Canada, have been a long-standing issue. This study seeks to document, in a chronological manner, the introduction of programmes intended to help solve the problem by the provincial government over a 35-year period and to examine several aspects of policy implementation, using these programmes as a case study.</p> <p>Methods</p> <p>A programme analysis approach was adopted to examine each of a broad range of programmes to determine its year of introduction, strategic category, complexity, time frame, and expected outcome. A chronology of programme initiation was constructed, on the basis of which an analysis was done to examine changes in strategies used by the provincial government from 1969 to 2004.</p> <p>Results</p> <p>Many programmes were introduced during the study period, which could be grouped into nine strategic categories. The range of policy instruments used became broader in later years. But conspicuous by their absence were programmes of a directive nature. Programmes introduced in more recent years tended to be more complex and were more likely to have a longer time perspective and pay more attention to physician retention. The study also discusses the choice of policy instruments and use of multiple strategies.</p> <p>Conclusion</p> <p>The findings suggest that an examination of a policy is incomplete if implementation has not been taken into consideration. The study has revealed a process of trial-and-error experimentation and an accumulation of past experience. The study sheds light on the intricate relationships between policy, policy implementation and use of policy instruments and programmes.</p

Release of oxidizing fluids in subduction zones recorded by iron isotope zonation in garnet

Subduction zones are key regions of chemical and mass transfer between the Earth’s surface and mantle. During subduction, oxidized material is carried into the mantle and large amounts of water are released due to the breakdown of hydrous minerals such as lawsonite. Dehydration accompanied by the release of oxidizing species may play a key role in controlling redox changes in the subducting slab and overlying mantle wedge. Here we present measurements of oxygen fugacity, using garnet–epidote oxybarometry, together with analyses of the stable iron isotope composition of zoned garnets from Sifnos, Greece. We find that the garnet interiors grew under relatively oxidized conditions whereas garnet rims record more reduced conditions. Garnet δ56Fe increases from core to rim as the system becomes more reduced. Thermodynamic analysis shows that this change from relatively oxidized to more reduced conditions occurred during lawsonite dehydration. We conclude that the garnets maintain a record of progressive dehydration and that the residual mineral assemblages within the slab became more reduced during progressive subduction-zone dehydration. This is consistent with the hypothesis that lawsonite dehydration accompanied by the release of oxidizing species, such as sulfate, plays an important and measurable role in the global redox budget and contributes to sub-arc mantle oxidation in subduction zones

Considering methodological options for reviews of theory: illustrated by a review of theories linking income and health

Background: Review of theory is an area of growing methodological advancement. Theoretical reviews are particularly useful where the literature is complex, multi-discipline, or contested. It has been suggested that adopting methods from systematic reviews may help address these challenges. However, the methodological approaches to reviews of theory, including the degree to which systematic review methods can be incorporated, have received little discussion in the literature. We recently employed systematic review methods in a review of theories about the causal relationship between income and health. Methods: This article discusses some of the methodological issues we considered in developing the review and offers lessons learnt from our experiences. It examines the stages of a systematic review in relation to how they could be adapted for a review of theory. The issues arising and the approaches taken in the review of theories in income and health are considered, drawing on the approaches of other reviews of theory. Results: Different approaches to searching were required, including electronic and manual searches, and electronic citation tracking to follow the development of theories. Determining inclusion criteria was an iterative process to ensure that inclusion criteria were specific enough to make the review practical and focused, but not so narrow that key literature was excluded. Involving subject specialists was valuable in the literature searches to ensure principal papers were identified and during the inductive approaches used in synthesis of theories to provide detailed understanding of how theories related to another. Reviews of theory are likely to involve iterations and inductive processes throughout, and some of the concepts and techniques that have been developed for qualitative evidence synthesis can be usefully translated to theoretical reviews of this kind. Conclusions: It may be useful at the outset of a review of theory to consider whether the key aim of the review is to scope out theories relating to a particular issue; to conduct in-depth analysis of key theoretical works with the aim of developing new, overarching theories and interpretations; or to combine both these processes in the review. This can help decide the most appropriate methodological approach to take at particular stages of the review

Root Suberin Forms an Extracellular Barrier That Affects Water Relations and Mineral Nutrition in Arabidopsis

Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots. Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root and both water movement through the plant and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates and increased water-use efficiency during their vegetative growth period. Furthermore, these changes in suberin and water transport were associated with decreases in the accumulation of Ca, Mn, and Zn and increases in the accumulation of Na, S, K, As, Se, and Mo in the shoot. Here, we present direct genetic evidence establishing that suberin in the roots plays a critical role in controlling both water and mineral ion uptake and transport to the leaves. The changes observed in the elemental accumulation in leaves are also interpreted as evidence that a significant component of the radial root transport of Ca, Mn, and Zn occurs in the apoplast

Dynamical Mean-Field Theory

The dynamical mean-field theory (DMFT) is a widely applicable approximation scheme for the investigation of correlated quantum many-particle systems on a lattice, e.g., electrons in solids and cold atoms in optical lattices. In particular, the combination of the DMFT with conventional methods for the calculation of electronic band structures has led to a powerful numerical approach which allows one to explore the properties of correlated materials. In this introductory article we discuss the foundations of the DMFT, derive the underlying self-consistency equations, and present several applications which have provided important insights into the properties of correlated matter.Comment: Chapter in "Theoretical Methods for Strongly Correlated Systems", edited by A. Avella and F. Mancini, Springer (2011), 31 pages, 5 figure

Variation in Molybdenum Content Across Broadly Distributed Populations of Arabidopsis thaliana Is Controlled by a Mitochondrial Molybdenum Transporter (MOT1)

Molybdenum (Mo) is an essential micronutrient for plants, serving as a cofactor for enzymes involved in nitrate assimilation, sulfite detoxification, abscisic acid biosynthesis, and purine degradation. Here we show that natural variation in shoot Mo content across 92 Arabidopsis thaliana accessions is controlled by variation in a mitochondrially localized transporter (Molybdenum Transporter 1 - MOT1) that belongs to the sulfate transporter superfamily. A deletion in the MOT1 promoter is strongly associated with low shoot Mo, occurring in seven of the accessions with the lowest shoot content of Mo. Consistent with the low Mo phenotype, MOT1 expression in low Mo accessions is reduced. Reciprocal grafting experiments demonstrate that the roots of Ler-0 are responsible for the low Mo accumulation in shoot, and GUS localization demonstrates that MOT1 is expressed strongly in the roots. MOT1 contains an N-terminal mitochondrial targeting sequence and expression of MOT1 tagged with GFP in protoplasts and transgenic plants, establishing the mitochondrial localization of this protein. Furthermore, expression of MOT1 specifically enhances Mo accumulation in yeast by 5-fold, consistent with MOT1 functioning as a molybdate transporter. This work provides the first molecular insight into the processes that regulate Mo accumulation in plants and shows that novel loci can be detected by association mapping