Cysteine tagging for MS-based proteomics

Amino acid-tagging strategies are widespread in proteomics. Because of the central role of mass spectrometry (MS) as a detection technique in protein sciences, the term "mass tagging" was coined to describe the attachment of a label, which serves MS analysis and/or adds analytical value to the measurements. These so-called mass tags can be used for separation, enrichment, detection, and quantitation of peptides and proteins. In this context, cysteine is a frequent target for modifications because the thiol function can react specifically by nucleophilic substitution or addition. Furthermore, cysteines present natural modifications of biological importance and a low occurrence in the proteome that justify the development of strategies to specifically target them in peptides or proteins. In the present review, the mass-tagging methods directed to cysteine residues are comprehensively discussed, and the advantages and drawbacks of these strategies are addressed. Some concrete applications are given to underline the relevance of cysteine-tagging techniques for MS-based proteomics.     

Efficient surrogate construction by combining response surface methodology and reduced order modeling

Response surface methodology is an efficient method for approximating the output of complex, computationally expensive codes. Challenges remain however in decreasing their construction cost as well as in approximating high dimensional output instead of scalar values. We propose a novel approach addressing both these challenges simultaneously for cases where the expensive code solves partial differential equations involving the resolution of a large system of equations, such as by finite element. Our method is based on the combination of response surface methodology and reduced order modeling by projection, also known as reduced basis modeling. The novel idea is to carry out the full resolution of the system only at a small, appropriately chosen, number of points. At the other points only the inexpensive reduced basis solution is computed while controlling the quality of the approximation being sought. A first application of the proposed surrogate modeling approach is presented for the problem of identification of orthotropic elastic constants from full field displacement measurements based on a tensile test on a plate with a hole. A surrogate of the entire displacement field was constructed using the proposed method. A second application involves the construction of a surrogate for the temperature field in a rocket engine combustion chamber wall. Compared to traditional response surface methodology a reduction by about an order of magnitude in the total system resolution time was achieved using the proposed sequential surrogate construction strategy.     

Productivity and mobility in academic research: evidence from mathematicians

Using an exhaustive database on academic publications in mathematics all over the world, we study the patterns of productivity by mathematicians over the period 1984–2006. We uncover some surprising facts, such as the weakness of age related decline in productivity and the relative symmetry of international movements, rejecting the presumption of a massive “brain drain” towards the US. We also analyze the determinants of success by top US departments. In conformity with recent studies in other fields, we find that selection effects are much stronger than local interaction effects: the best departments are most successful in hiring the most promising mathematicians, but not necessarily at stimulating positive externalities among them. Finally we analyze the impact of career choices by mathematicians: mobility almost always pays, but early specialization does not.     

A four-scale bidirectional reflectance model based on canopyarchitecture

Open boreal forests present a challenge in understanding remote sensing signals acquired with various solar and view geometries. Much research is needed to improve our ability to model the bidirectional reflectance distribution (BRD) for retrieving the surface information using measurements at a few angles. The geometric-optical bidirectional reflectance model presented in this paper considers four scales of canopy architecture: tree groups, tree crowns, branches and shoots. It differs from the Li-Strahler's model in the following respects: 1) the assumption of random spatial distribution of trees is replated by the Neyman distribution which is able to model the patchiness or clumpiness of a forest stand; 2) the multiple mutual shadowing effect between tree crowns is considered using a negative binomial and the Neyman distribution theory; 3) the effect of the sunlit background is modeled using a canopy gap size distribution function that affects the magnitude and width of the hotspot; 4) the branch architecture affecting the directional reflectance is simulated using a simple angular radiation penetration function; and 5) the tree crown surface is treated as a complex surface with microscale structures which themselves generate mutual shadows and a hotspot. All these scales of canopy architecture are shown to have effects on the directional distribution of the reflected radiance from conifer forests. The model results compare well with a data set from a boreal spruce forest     

General Adaptive Neighborhood Image Processing

The so-called General Adaptive Neighborhood Image Processing (GANIP) approach is presented in a two parts paper dealing respectively with its theoretical and practical aspects. The General Adaptive Neighborhood (GAN) paradigm, theoretically introduced in Part I [20], allows the building of new image processing transformations using context-dependent analysis. With the help of a specified analyzing criterion, such transformations perform a more significant spatial analysis, taking intrinsically into account the local radiometric, morphological or geometrical characteristics of the image. Moreover they are consistent with the physical and/or physiological settings of the image to be processed, using general linear image processing frameworks. In this paper, the GANIP approach is more particularly studied in the context of Mathematical Morphology (MM). The structuring elements, required for MM, are substituted by GAN-based structuring elements, fitting to the local contextual details of the studied image. The resulting morphological operators perform a really spatially-adaptive image processing and notably, in several important and practical cases, are connected, which is a great advantage compared to the usual ones that fail to this property.     

Reflections on 19 cases of asbestosis discovered by chance in the population of an industrial region in the Basse-Sambre]

The authors describe 19 cases of definite or highly probable asbestosis which were observed among unselected out-patients at a hospital in the industrial area of the "Basse-Sambre". These cases were of various types and were, almost exclusively, of occupational origin. The variety and severity of the asbestosis in many of the cases justify a more thorough survey in this area. Those people who have handled and inhaled asbestos fibres at work will be examined in the first place. A radiological pulmonary survey will also be organized among the people living in the neighbourhood of factories using asbestos. Precise information about the origin, quality and characteristics of the inhaled dust as well as the intensity and duration of exposure will be obtained. Cases discovered in the survey will be investigated systematically by means of an extensive range of techniques: frontal and oblique X-rays with an appropriate kilovoltage for the detection of pleural calcifications and of the reticular thickening of the parenchyma; spirometry and measurement of the transfer factor for CO; arterial blood gases at rest and during exercise; search for ferruginous bodies in sputum; pathological studies of pulmonary and pleural tissues and of the ultrastructure of pleural tumours.     

Development of novel 1,2,3,4-tetrahydroisoquinoline derivatives and closely related compounds as potent and selective dopamine D3 receptor ligands

Based on N-alkylated 1,2,3,4-tetrahydroisoquinoline derivatives, which are structurally related to the partial agonist BP 897, a series of novel, selective dopamine D3 receptor antagonists has been synthesised. Derivatisation included changes in the arylamide moiety and the tetrahydroisoquinoline substructure leading to compounds with markedly improved selectivities and affinities in the low nanomolar concentration range. From the 55 structures presented here, (E)-3-(4-iodophenyl)-N-(4-(1,2,3,4-tetrahydroisoquinolin-2-yl)butyl)acrylamide (51) has high affinity (Ki(hD3)=12 nM) and a 123-fold preference for the D3 receptor relative to the D2 receptor subtype. Its pharmacological profile offers the prospect of a novel radioligand as a tool for various dopamine D3-receptor-related in vitro and in vivo investigations.     

High Definition Digital Fabrication of Active Organic Devices by Molecular Jet Printing

We introduce a high resolution molecular jet (MoJet) printing technique for vacuum deposition of evaporated thin films and apply it to fabrication of 30 μm pixelated (800 ppi) molecular organic light emitting devices (OLEDs) based on aluminum tris(8‐hydroxyquinoline) (Alq₃) and fabrication of narrow channel (15 μm) organic field effect transistors (OFETs) with pentacene channel and silver contacts. Patterned printing of both organic and metal films is demonstrated, with the operating properties of MoJet‐printed OLEDs and OFETs shown to be comparable to the performance of devices fabricated by conventional evaporative deposition through a metal stencil. We show that the MoJet printing technique is reconfigurable for digital fabrication of arbitrary patterns with multiple material sets and high print accuracy (of better than 5 μm), and scalable to fabrication on large area substrates. Analogous to the concept of “drop‐on‐demand” in Inkjet printing technology, MoJet printing is a “flux‐on‐demand” process and we show it capable of fabricating multi‐layer stacked film structures, as needed for engineered organic devices.