Linear chemically sensitive electron tomography using DualEELS and compressed sensing

No abstract available

Linear chemically sensitive electron tomography using DualEELS and dictionary-based compressed sensing

We have investigated the use of DualEELS in elementally sensitive tilt series tomography in the scanning transmission electron microscope. A procedure is implemented using deconvolution to remove the effects of multiple scattering, followed by normalisation by the zero loss peak intensity. This is performed to produce a signal that is linearly dependent on the projected density of the element in each pixel. This method is compared with one that does not include deconvolution (although normalisation by the zero loss peak intensity is still performed). Additionaly, we compare the 3D reconstruction using a new compressed sensing algorithm, DLET, with the well-established SIRT algorithm. VC precipitates, which are extracted from a steel on a carbon replica, are used in this study. It is found that the use of this linear signal results in a very even density throughout the precipitates. However, when deconvolution is omitted, a slight density reduction is observed in the cores of the precipitates (a so-called cupping artefact). Additionally, it is clearly demonstrated that the 3D morphology is much better reproduced using the DLET algorithm, with very little elongation in the missing wedge direction. It is therefore concluded that reliable elementally sensitive tilt tomography using EELS requires the appropriate use of DualEELS together with a suitable reconstruction algorithm, such as the compressed sensing based reconstruction algorithm used here, to make the best use of the limited data volume and signal to noise inherent in core-loss EELS

C2 Odontoid Fracture Associated with C1-C2 Rotatory Dislocation: A Retrospective Analysis of 2 Surgical Techniques.

Odontoid fractures in association with a C1-C2 rotatory luxation reports are seldom found in the literature. The fusion between the lateral mass of C1 and C2 could be of interest to ensure adequate treatment in these particular cases. We report 23 cases where there was coexistence of an odontoid fracture and rotatory subluxation, which were treated surgically using cages between C1 and C2 or just traditional Goel-Harms technique. We evaluated the radiologic fusion rate, reoperation rate, and complications. This was a single-center, retrospective, cohort study of patients with C2 fractures (mixed type and C1-C2 rotatory luxation according to the Fielding classification) who were treated surgically. Radiologic computed tomography scans were used to assess fusion (presence of bridging trabecular bone end plate or pseudoarthrosis) between 6 months and 1.5 years after the surgery. Twenty-three patients were diagnosed with C2 fractures and C1-C2 rotatory luxation that were treated surgically and were suitable for the analysis; 11 patients underwent C1-C2 fusion with intra-articular cages, and 12 underwent a classical Goel-Harms technique. The fusion rate at the C1-C2 joint was higher in the cages group. Only 12 patients exhibited fusion at the level of the odontoid fracture. C2 fractures associated with C1-C2 rotatory dislocation are rare. The fusion rate at the level of the odontoid in these patients appears to be lower than that reported in patients without rotatory dislocation. It may be of special interest to obtain a clear fusion at the C1-C2 joint, where this type of implant seems to offer an advantage

Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome

Changes in the physical interaction between cis-regulatory DNA sequences and proteins drive the evolution of gene expression. However, it has proven difficult to accurately quantify evolutionary rates of such binding change or to estimate the relative effects of selection and drift in shaping the binding evolution. Here we examine the genome-wide binding of CTCF in four species of Drosophila separated by between ~2.5 and 25 million years. CTCF is a highly conserved protein known to be associated with insulator sequences in the genomes of human and Drosophila. Although the binding preference for CTCF is highly conserved, we find that CTCF binding itself is highly evolutionarily dynamic and has adaptively evolved. Between species, binding divergence increased linearly with evolutionary distance, and CTCF binding profiles are diverging rapidly at the rate of 2.22% per million years (Myr). At least 89 new CTCF binding sites have originated in the Drosophila melanogaster genome since the most recent common ancestor with Drosophila simulans. Comparing these data to genome sequence data from 37 different strains of Drosophila melanogaster, we detected signatures of selection in both newly gained and evolutionarily conserved binding sites. Newly evolved CTCF binding sites show a significantly stronger signature for positive selection than older sites. Comparative gene expression profiling revealed that expression divergence of genes adjacent to CTCF binding site is significantly associated with the gain and loss of CTCF binding. Further, the birth of new genes is associated with the birth of new CTCF binding sites. Our data indicate that binding of Drosophila CTCF protein has evolved under natural selection, and CTCF binding evolution has shaped both the evolution of gene expression and genome evolution during the birth of new genes

Initiator Elements Function to Determine the Activity State of BX-C Enhancers

A >300 kb cis-regulatory region is required for the proper expression of the three bithorax complex (BX-C) homeotic genes. Based on genetic and transgenic analysis, a model has been proposed in which the numerous BX-C cis-regulatory elements are spatially restricted through the activation or repression of parasegment-specific chromatin domains. Particular early embryonic enhancers, called initiators, have been proposed to control this complex process. Here, in order to better understand the process of domain activation, we have undertaken a systematic in situ dissection of the iab-6 cis-regulatory domain using a new method, called InSIRT. Using this method, we create and genetically characterize mutations affecting iab-6 function, including mutations specifically modifying the iab-6 initiator. Through our mutagenesis of the iab-6 initiator, we provide strong evidence that initiators function not to directly control homeotic gene expression but rather as domain control centers to determine the activity state of the enhancers and silencers within a cis-regulatory domain

Chromosomal organization at the level of gene complexes

Metazoan genomes primarily consist of non-coding DNA in comparison to coding regions. Non-coding fraction of the genome contains cis-regulatory elements, which ensure that the genetic code is read properly at the right time and space during development. Regulatory elements and their target genes define functional landscapes within the genome, and some developmentally important genes evolve by keeping the genes involved in specification of common organs/tissues in clusters and are termed gene complex. The clustering of genes involved in a common function may help in robust spatio-temporal gene expression. Gene complexes are often found to be evolutionarily conserved, and the classic example is the hox complex. The evolutionary constraints seen among gene complexes provide an ideal model system to understand cis and trans-regulation of gene function. This review will discuss the various characteristics of gene regulatory modules found within gene complexes and how they can be characterized

A nanometre-sized porous phase in iron-carbon-boron system

A porous phase is detected in a Fe-0.28 wt.%C-0.1 wt.%B alloy. The porous phase is mainly located at the grain boundary region and the pore size ranges from about 10 nm to 500 nm. The chemical composition of the porous phase is very close to Fe 3(B 0.7C 0.3) with an orthorhombic lattice. The result shows an opportunity to produce bulk steel matrix composites with a porous second phase. © 2010 Elsevier B.V. All rights reserved.link_to_subscribed_fulltex

TEM study of NbC heterogeneous precipitation in ferrite

International audienceThe heterogeneous precipitation of NbC in ferrite has been quantitatively characterised by Transmission Electron Microscopy in a Fe-C-Nb model alloy for different isothermal heat treatments. Elongation and size distribution of precipitates have been derived from Dark Field imaging. For each precipitation states, the precipitation of NbC is occurring on dislocations due to the as-quenched state. This precipitation mechanism leads to characteristic arrays of precipitates in which precipitates grow in a self-similar manner. A detailed study of these arrays has shown that most dislocations decorated by these arrays are edge dislocations with type line vectors. There is only one variant on a given dislocation. This selection can be interpreted by the interaction between dislocation and precipitate strain fields

Linear chemically sensitive electron tomography using DualEELS and compressed sensing

No abstract available

Characterization of a cDNA encoding an alpha-tyroid hormone receptor in muscovy duckling

International audienc