Morphing of Triangular Meshes in Shape Space

We present a novel approach to morph between two isometric poses of the same non-rigid object given as triangular meshes. We model the morphs as linear interpolations in a suitable shape space $\mathcal{S}$. For triangulated 3D polygons, we prove that interpolating linearly in this shape space corresponds to the most isometric morph in $\mathbb{R}^3$. We then extend this shape space to arbitrary triangulations in 3D using a heuristic approach and show the practical use of the approach using experiments. Furthermore, we discuss a modified shape space that is useful for isometric skeleton morphing. All of the newly presented approaches solve the morphing problem without the need to solve a minimization problem.Comment: Improved experimental result

The Complexity of Order Type Isomorphism

The order type of a point set in $R^d$ maps each $(d{+}1)$-tuple of points to its orientation (e.g., clockwise or counterclockwise in $R^2$). Two point sets $X$ and $Y$ have the same order type if there exists a mapping $f$ from $X$ to $Y$ for which every $(d{+}1)$-tuple $(a_1,a_2,\ldots,a_{d+1})$ of $X$ and the corresponding tuple $(f(a_1),f(a_2),\ldots,f(a_{d+1}))$ in $Y$ have the same orientation. In this paper we investigate the complexity of determining whether two point sets have the same order type. We provide an $O(n^d)$ algorithm for this task, thereby improving upon the $O(n^{\lfloor{3d/2}\rfloor})$ algorithm of Goodman and Pollack (1983). The algorithm uses only order type queries and also works for abstract order types (or acyclic oriented matroids). Our algorithm is optimal, both in the abstract setting and for realizable points sets if the algorithm only uses order type queries.Comment: Preliminary version of paper to appear at ACM-SIAM Symposium on Discrete Algorithms (SODA14

Fully Automatic Expression-Invariant Face Correspondence

We consider the problem of computing accurate point-to-point correspondences among a set of human face scans with varying expressions. Our fully automatic approach does not require any manually placed markers on the scan. Instead, the approach learns the locations of a set of landmarks present in a database and uses this knowledge to automatically predict the locations of these landmarks on a newly available scan. The predicted landmarks are then used to compute point-to-point correspondences between a template model and the newly available scan. To accurately fit the expression of the template to the expression of the scan, we use as template a blendshape model. Our algorithm was tested on a database of human faces of different ethnic groups with strongly varying expressions. Experimental results show that the obtained point-to-point correspondence is both highly accurate and consistent for most of the tested 3D face models

Gaming with eutrophication: Contribution to integrating water quantity and quality management at catchment level

The Metropolitan Region of Sao Paulo (MRSP) hosts 18 million inhabitants. A complex system of 23 interconnected reservoirs was built to ensure its water supply. Half of the potable water produced for MRSP's population (35 m3/s) is imported from a neighbour catchment, the other half is produced within the Alto Tietê catchment, where 99% of the population lives. Perimeters of land use restriction were defined to contain uncontrolled urbanization, as domestic effluents were causing increasing eutrophication of some of these reservoirs. In the 90's catchment committees and sub committees were created to promote discussion between stakeholders and develop catchment plans. The committees are very well structured "on paper". However, they are not very well organised and face a lack of experience. The objective of this work was to design tools that would strengthen their discussion capacities. The specific objective of the AguAloca process was to integrate the quality issue and its relation to catchment management as a whole in these discussions. The work was developed in the Alto Tietê Cabeceiras sub-catchment, one of the 5 sub catchments of the Alto-Tietê. It contains 5 interconnected dams, and presents competitive uses such as water supply, industry, effluent dilution and irrigated agriculture. A RPG was designed following a companion modelling approach (Etienne et al., 2003). It contains a friendly game-board, a set of individual and collective rules and a computerized biophysical model. The biophysical model is used to simulate water allocation and quality processes at catchment level. It articulates 3 modules. A simplified nutrient discharge model permits the estimation of land use nutrient exportation. An arc-node model simulates water flows and associated nutrient charges from one point of the hydrographical network to another. The Vollenweider model is used for simulating specific reservoir dynamics. The RPG allows players to make individual and collective decisions related to water allocation and the management of its quality. Impacts of these decisions are then simulated using the biophysical model. Specific indicators of the game are then updated and may influence player's behaviour (actions) in following rounds. To introduce discussions on the management of water quality at a catchment level, an issue that is rarely explicitly dealt with, four game sessions were implemented involving representatives of basin committees and water and sanitation engineers. During the game session, the participants took advantage of the water quality output of the biophysical model to test management alternatives such as rural sewage collection or effluent dilution. The biophysical model accelerated calculations of flows and eutrophication rates that were then returned to the game board with explicit indicators of quantity and quality. Players could easily test decisions impacting on qualitative water processes and visualize the simulation results directly on the game board that was representing a friendly, virtual and simplified catchment. The Agualoca game proved its ability to turn complex water processes understandable for a non totally initiated public. This experience contributed to a better understanding of multiple-use water management and also of joint management of water quality and quantity. (Résumé d'auteur

Acute phase inflammation is characterized by rapid changes in plasma/peritoneal fluid N-glycosylation in mice.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.Murine zymosan-induced peritonitis is a widely used model for studying the molecular and cellular events responsible for the initiation, persistence and/or resolution of inflammation. Among these events, it is becoming increasingly evident that changes in glycosylation of proteins, especially in the plasma and at the site of inflammation, play an important role in the inflammatory response. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based glycosylation profiling, we investigated the qualitative and quantitative effect of zymosan-induced peritonitis on N-glycosylation in mouse plasma and peritoneal fluid. Our results show that both N-glycomes exhibit highly similar glycosylation patterns, consisting mainly of diantennary and triantennary complex type N-glycans with high levels (>95 %) of galactosylation and sialylation (mostly NeuGc) and a medium degree of core fucosylation (30 %). Moreover, MS/MS structural analysis, assisted by linkage-specific derivatization of sialic acids, revealed the presence of O-acetylated sialic acids as well as disialylated antennae ("branching sialylation") characterized by the presence of α2-6-linked NeuGc on the GlcNAc of the NeuGcα2-3-Galβ1-3-GlcNAc terminal motif. A significant decrease of (core) fucosylation together with an increase of both α2-3-linked NeuGc and "branching sialylation" were observed in N-glycomes of mice challenged with zymosan, but not in control mice injected with PBS. Importantly, substantial changes in glycosylation were already observed 12 h after induction of peritonitis, thereby demonstrating an unexpected velocity of the biological mechanisms involved.Dutch Arthritis Association (Reumafonds) LLP-24 Innovative Medicines Initiative Joint Undertaking (IMI JU)/ 115142-2 Netherlands Genomic Initiative/93511033 info:eu-repo/grantAgreement/EC/FP7/278535info:eu-repo/grantAgreement/EC/FP7/27853

IgA N- and O-glycosylation profiling reveals no association with the pregnancy-related improvement in rheumatoid arthritis

Background: The Fc glycosylation of immunoglobulin G (IgG) is well known to associate with rheumatoid arthritis (RA) disease activity. The same may be true for other classes of Igs. In the present study, we sought to determine whether the glycosylation of IgA was different between healthy subjects and patients with RA, as well as whether it was associated with RA disease activity, in particular with the pregnancy-associated improvement thereof or the flare after delivery. Methods: A recently developed high-throughput method for glycoprofiling of IgA1 was applied to affinity-captured IgA from sera of patients with RA (n = 252) and healthy control subjects (n = 32) collected before, during and after pregnancy. Results: IgA1 O-glycans bore more sialic acids in patients with RA than in control subjects. In addition, levels of bisecting N-acetylglucosamine of the N-glycans at asparagine 144 were higher in the patients with RA. The levels of several N-glycosylation traits were shown to change with pregnancy, similar to what has been shown before for IgG. However, the changes in IgA glycosylation were not associated with improvement or a flare of disease activity. Conclusions: The glycosylation of IgA differs between patients with RA and healthy control subjects. However, our data suggest only a minor, if any, association of IgA glycosylation with RA disease activity

Pregnancy-associated serum N-glycome changes studied by high-throughput MALDI-TOF-MS

Pregnancy requires partial suppression of the immune system to ensure maternal-foetal tolerance. Protein glycosylation, and especially terminal sialic acid linkages, are of prime importance in regulating the pro- and anti-inflammatory immune responses. However, little is known about pregnancy-associated changes of the serum N-glycome and sialic acid linkages. Using a combination of recently developed methods, i.e. derivatisation that allows the distinction between α2,3- and α2,6-linked sialic acids by high-throughput MALDI-TOF-MS and software-assisted data processing, we analysed the serum N-glycome of a cohort of 29 healthy women at 6 time points during and after pregnancy. A total of 77 N-glycans were followed over time, confirming in part previous findings while also revealing novel associations (e.g. an increase of FA2BG1S1(6), FA2G1S1(6) and A2BG2S2(6) with delivery). From the individual glycans we calculated 42 derived traits. With these, an increase during pregnancy and decrease after delivery was observed for both α2,3- and α2,6-linked sialylation. Additionally, a difference in the recovery speed after delivery was observed for α2,3- and α2,6-linked sialylation of triantennary glycans. In conclusion, our new high-throughput workflow allowed the identification of novel plasma glycosylation changes with pregnancy

IgG1 Fc N-glycan galactosylation as a biomarker for immune activation.

Immunoglobulin G (IgG) Fc N-glycosylation affects antibody-mediated effector functions and varies with inflammation rooted in both communicable and non-communicable diseases. Worldwide, communicable and non-communicable diseases tend to segregate geographically. Therefore, we studied whether IgG Fc N-glycosylation varies in populations with different environmental exposures in different parts of the world. IgG Fc N-glycosylation was analysed in serum/plasma of 700 school-age children from different communities of Gabon, Ghana, Ecuador, the Netherlands and Germany. IgG1 galactosylation levels were generally higher in more affluent countries and in more urban communities. High IgG1 galactosylation levels correlated with low total IgE levels, low C-reactive protein levels and low prevalence of parasitic infections. Linear mixed modelling showed that only positivity for parasitic infections was a significant predictor of reduced IgG1 galactosylation levels. That IgG1 galactosylation is a predictor of immune activation is supported by the observation that asthmatic children seemed to have reduced IgG1 galactosylation levels as well. This indicates that IgG1 galactosylation levels could be used as a biomarker for immune activation of populations, providing a valuable tool for studies examining the epidemiological transition from communicable to non-communicable diseases

Software-Assisted Data Processing Workflow for Intact Glycoprotein Mass Spectrometry

Intact protein analysis by mass spectrometry is important for several applications such as assessing post-translational modifications and biotransformation. In particular, intact protein analysis allows the detection of proteoforms that are commonly missed by other approaches such as proteolytic digestion followed by bottom-up analysis. Two quantification methods are mainly used for intact protein data quantification, namely the extracted ion and deconvolution approaches. However, a consensus with regard to a single best practice for intact protein data processing is lacking. Furthermore, many data processing tools are not fit-for-purpose and, as a result, the analysis of intact proteins is laborious and lacks the throughput required to be implemented for the analysis of clinical cohorts. Therefore, in this study, we investigated the application of a software-assisted data analysis and processing workflow in order to streamline intact protein integration, annotation, and quantification via deconvolution. In addition, the assessment of orthogonal data sets generated via middle-up and bottom-up analysis enabled the cross-validation of cleavage proteoform assignments present in seminal prostate-specific antigen (PSA). Furthermore, deconvolution quantification of PSA from patients' urine revealed results that were comparable with manually performed quantification based on extracted ion electropherograms. Overall, the presented workflow allows fast and efficient processing of intact protein data. The raw data is available on MassIVE using the identifier MSV000086699.</p

Serum sialylation changes in cancer

Proteomic