Molecular Shape Analysis based uponthe Morse-Smale Complexand the Connolly Function

Docking is the process by which two or several molecules form a complex. Docking involves the geometry of the molecular surfaces, as well as chemical and energetical considerations. In the mid-eighties, Connolly proposed a docking algorithm matching surface {\em knobs} with surface {\em depressions}. Knobs and depressions refer to the extrema of the {\em Connolly} function, which is defined as follows. Given a surface \calM bounding a three-dimensional domain $X$, and a sphere $S$ centered at a point $p$ of \calM, the Connolly function is equal to the solid angle of the portion of $S$ containing within $X$. We recast the notions of knob and depression of the Connolly function in the framework of Morse theory for functions defined over two-dimensional manifolds. First, we study the critical points of the Connolly function for smooth surfaces. Second, we provide an efficient algorithm for computing the Connolly function over a triangulated surface. Third, we introduce a Morse-Smale decomposition based on Forman's discrete Morse theory, and provide an $O(n\log n)$ algorithm to construct it. This decomposition induces a partition of the surface into regions of homogeneous flow, and provides an elegant way to relate local quantities to global ones ---from critical points to Euler's characteristic of the surface. Fourth, we apply this Morse-Smale decomposition to the discrete gradient vector field induced by Connolly's function, and present experimental results for several mesh models

Learning Graph-Convolutional Representations for Point Cloud Denoising

Point clouds are an increasingly relevant data type but they are often corrupted by noise. We propose a deep neural network based on graph-convolutional layers that can elegantly deal with the permutation-invariance problem encountered by learning-based point cloud processing methods. The network is fully-convolutional and can build complex hierarchies of features by dynamically constructing neighborhood graphs from similarity among the high-dimensional feature representations of the points. When coupled with a loss promoting proximity to the ideal surface, the proposed approach significantly outperforms state-of-the-art methods on a variety of metrics. In particular, it is able to improve in terms of Chamfer measure and of quality of the surface normals that can be estimated from the denoised data. We also show that it is especially robust both at high noise levels and in presence of structured noise such as the one encountered in real LiDAR scans.Comment: European Conference on Computer Vision (ECCV) 202

Uniform convergence of discrete curvatures from nets of curvature lines

We study discrete curvatures computed from nets of curvature lines on a given smooth surface, and prove their uniform convergence to smooth principal curvatures. We provide explicit error bounds, with constants depending only on properties of the smooth limit surface and the shape regularity of the discrete net.Comment: 21 pages, 8 figure

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewedThe authors would like to acknowledge support from the Spanish Ministry of Economy and Competitiveness through grants BIO2013-44647-R and BIO2016-76400-R (AEI/ FEDER, UE), Comunidad Autonoma de Madrid through grant S2017/BMD-3817, Instituto de Salud Carlos III through grants PT13 /0001/0009 and PT17/0009/0010,the European Union (EU) and Horizon 2020 through West-Life (EINFRA- 2015-1, Proposal 675858), CORBEL (INFRADEV-1-2014-1, Proposal 654248), ELIXIR–EXCELERATE (INFRADEV-3- 2015, Proposal 676559), iNEXT (INFRAIA-1-2014-2015, Proposal 653706), EOSCpilot (INFRADEV-04-2016, Proposal 739563) and the National Institutes of Health (P41 GM 103712) (IB

The screen test 1915–1930:how stars were born

This article examines the emergence of the screen test as a cultural phenomenon during the silent era in the US and Europe and its role in the development of the star system. The lore that grew up around the screen test almost from its inception held out the possibility for members of the public to cross a threshold into the rarefied world of celebrity. The screen test itself is situated in the liminal space not only between audience and actor, but also between fiction and non-fiction, Europe and Hollywood, the silent era and the talkies, and the public and private spheres. In order to trace the ways in which the screen test as such was narrativized and conceptualized in its foundational stages, this article will analyse accounts from Hollywood and European fan magazines of the silent era, including articles, short fiction, and early cinema apocrypha. The article culminates in a discussion of the film Prix de Beauté / Beauty Prize (Augusto Genina, 1930), which starred Louise Brooks, herself a transnational film icon whose film career spanned the divide between Hollywood and Europe. The film’s final scene, in which a beauty queen is shot dead by her jealous husband as she watches a screen test of herself, has been invoked by a number of film scholars as an allegory of the work performed by cinema, which preserves and disseminates the image of the star far beyond the actor’s physical presence. Speaking to historical conditions of star-making while also capturing its resonance in cultural mythology, the conclusion of Prix de Beauté allows us to consider the origins and functions of screen test discourse itself

A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

<p>Abstract</p> <p>Background</p> <p>In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user.</p> <p>Results</p> <p>We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects.</p> <p>Conclusion</p> <p>Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies) of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.</p

“Savages Who Speak French”: Folklore, Primitivism and Morals in Robert Hertz

Hertz's analysis of the Alpine cult of Saint Besse apparently marks a break from his studies of death, sin and the left to folkloric studies. This analysis helps one to understand the personality of Robert Hertz. His sociological curiosity about folklore reveals his ambiguous position in social sciences at the beginning of the twentieth century. His text appears to be a variation from the Durkheimian norm, but another reading could suggest that Hertz continued and went beyond Durkheimian thought to something between sociology of the modern world and engaged socialism. Through this study, Hertz linked his political ideals, his work in ethnology and his desire for social involvement. The cult of Saint Besse perpetuated as much religious tradition as local identity. The Alpine people were presented in the text as wilful perpetuators of an ideal social order, whose loss for his contemporary city dwellers Hertz feared. The alpine Other, marked by a material and moral backwardness, represented for activist and socialist Hertz one of the paths of balanced social organization that stabilized the identity of a group across time if it fit rather well into the folkloric stereotypes of the beginning of the twentieth century. Finally, by linking events in Herz's life (e.g., the accidental Alpine death of his father), this article suggests that the legend of Saint Besse embodied several recurring motifs in Hertz' career: the accidental deaths of saint and father by falls, the military role of the saint and of Hertz himself

Primary mediastinal large B-cell lymphoma (PMLBCL): long-term results from a retrospective multicentre Italian experience in 138 patients treated with CHOP or MACOP-B/VACOP-B

The optimal treatment of primary mediastinal large B-cell lymphoma (PMLBCL) is still undefined. In the absence of randomised studies, we retrospectively analysed: (a) the effectiveness of two chemotherapy regimens (CHOP vs MACOP-B/VACOP-B) in complete remission (CR) achievement and event-free survival (EFS) and (b) the role of mediastinal involved-field radiotherapy (IF-RT) as consolidation. From 1982 to 1999, 138 consecutive patients affected by PMLBCL were treated in 13 Italian institutions with CHOP (43) or MACOP-B/VACOP-B (95). The two groups of patients were similar as regard to age, gender, presence of bulky mediastinal mass, pleural effusion, stage and international prognostic indexes category of risk. Overall, 75.5% of patients in CR received IF-RT as consolidation. Complete remission was 51.1% in the CHOP group and 80% in MACOP-B/VACOP-B (P<0.001). Relapse occurred in 22.7% of CHOP- and in 9.2% of MACOP-B/VACOP-B-treated patients (n.s.). Event-free patients were 39.5% in CHOP and 75.7% in the MACOP-B/VACOP-B group (P<0.001). The addition of IF-RT as consolidation improved the outcome, irrespectively of the type of chemotherapy (P=0.04). At a multivariate analysis, achievement of CR (P<0.0001) and type of CT (MACOP-B/VACOP-B) retained the significance for OS (P=0.008) and EFS (P=0.03). In our experience, MACOP-B/VACOP-B appears to positively influence OS and EFS in patients affected by PMLBCL, as compared to CHOP. Consolidation IF-RT on mediastinum further improves the outcome of CR patients

Beta-Strand Interfaces of Non-Dimeric Protein Oligomers Are Characterized by Scattered Charged Residue Patterns

Protein oligomers are formed either permanently, transiently or even by default. The protein chains are associated through intermolecular interactions constituting the protein interface. The protein interfaces of 40 soluble protein oligomers of stœchiometries above two are investigated using a quantitative and qualitative methodology, which analyzes the x-ray structures of the protein oligomers and considers their interfaces as interaction networks. The protein oligomers of the dataset share the same geometry of interface, made by the association of two individual β-strands (β-interfaces), but are otherwise unrelated. The results show that the β-interfaces are made of two interdigitated interaction networks. One of them involves interactions between main chain atoms (backbone network) while the other involves interactions between side chain and backbone atoms or between only side chain atoms (side chain network). Each one has its own characteristics which can be associated to a distinct role. The secondary structure of the β-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular β-sheets (MCWIV). The intermolecular specificity is provided by the side chain networks via positioning different types of charged residues at the extremities (arginine) and in the middle (glutamic acid and histidine) of the interface. Such charge distribution helps discriminating between sequences of intermolecular β-strands, of intramolecular β-strands and of β-strands forming β-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the β-strands of the cholera toxin B subunit interface, when produced individually as synthetic peptides, are capable of inhibiting the assembly of the toxin into pentamers. Thus, their sequences contain the features necessary for a β-interface formation. Such β-strands could be considered as ‘assemblons’, independent associating units, by homology to the foldons (independent folding unit). Such property would be extremely valuable in term of assembly inhibitory drug development