The timing of Neotropical speciation dynamics: A reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data

Neotropical forests have brought forth a large proportion of the world`s terrestrial biodiversity, but the underlying evolutionary mechanisms and their timing require further elucidation. Despite insights gained from phylogenetic studies, uncertainties about molecular clock rates have hindered efforts to determine the timing of diversification processes. Moreover, most molecular research has been detached from the extensive body of data on Neotropical geology and paleogeography. We here examine phylogenetic relationships and the timing of speciation events in a Neotropical flycatcher genus (Myiopagis) by using calibrations from modern geologic data in conjunction with a number of recently developed DNA sequence dating algorithms and by comparing these estimates with those based on a range of previously proposed molecular clock rates. We present a well-supported hypothesis of systematic relationships within the genus. Our age estimates of Myiopagis speciation events based on paleogeographic data are in close agreement with nodal ages derived from a ""traditional"" avian mitochondrial 2%/My clock, while contradicting other clock rates. Our comparative approach corroborates the consistency of the traditional avian mitochondrial clock rate of 2%/My for tyrant-flycatchers. Nevertheless, our results argue against the indiscriminate use of molecular clock rates in evolutionary research and advocate the verification of the appropriateness of the traditional clock rate by means of independent calibrations in individual studies. (C) 2009 Elsevier Inc. All rights reserved.

Three-dimensional Reconstruction of Ovaries of Leaf-cutting Ant (Atta sexdens rubropilosa) Queens (Hymenoptera: Formicidae)

In this study, the ovary morphology of newly emerged ant queens of Atta sexdens rubropilosa was studied in whole mount preparations by confocal microscopy. The ovaries are composed of approximately 40 ovarioles, showing non-synchronic oocyte maturation. The terminal filament with clusters of undifferentiated cells was found at the distal end of the ovarioles. Next to this region is the germarium, composed of several elongated cystocytes interconnected by cytoplasmic bridges. The nurse cells (23-28 cells) result from asymmetric mitosis. Cytoskeleton analysis showed F-actin concentrated at the muscle cells of the external tunica and in fusomes inside the ovarioles. Microtubules were concentrated around the nuclei of the nurse and follicular cells. In contrast, the oocytes and the external tunica showed faint staining for tubulin.

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Components Separation Technique With Limited Subcutaneous Undermining A Cadaver Study

The purpose of this study is to evaluate the influence of the undermining of the subcutaneous tissue on the tension of the abdominal wall, after the components separation of the abdominal muscles. Twenty adult cadavers were studied. The resistance of the medial advancement of both anterior and posterior recti sheaths was represented by the traction index and measured in 2 levels-3 cm above and 2 cm below the umbilicus. Traction indices were compared in the following 3 consecutive dissection situations: (1) after the subcutaneous tissue undermining laterally to the semilunaris line; (2) after the dissection of the rectus muscle from its posterior sheath associated with the release of the external oblique muscle; (3) after the subcutaneous tissue undermining laterally to the anterior axillary line. Friedman and Spearman tests were used to compare the results. There was no statistical significant difference between the subcutaneous tissue undermining laterally to the semilunaris line and that laterally to the anterior axillary line, when associated with the musculoaponeurotic dissections. In conclusion, limited subcutaneous undermining does not influence the tension of closure of the musculoaponeurotic layer after the components separation technique in cadavers.

The role of carbon impurities on the Si(001)-c(4 x 4) surface reconstruction: Theoretical calculations

In this work we employ the state-of-the-art pseudopotential method, within a generalized gradient approximation to the density functional theory, combined with a recently developed method for the calculation of HREELS spectra to study a series of different proposed models for carbon incorporation on the silicon (001) surface. A fully discussion on the geometry, energetics and specially the comparison between experimental and theoretical STM images and electron energy loss spectra indicate that the Si(100)-c(4 x 4) is probably induced by Si-C surface dinners, in agreement with recent experimental findings. (C) 2009 Elsevier B.V. All rights reserved.

Performance Improvement of Tomographic Image Reconstruction Based on DSP Processors

This paper presents the use of a multiprocessor architecture for the performance improvement of tomographic image reconstruction. Image reconstruction in computed tomography (CT) is an intensive task for single-processor systems. We investigate the filtered image reconstruction suitability based on DSPs organized for parallel processing and its comparison with the Message Passing Interface (MPI) library. The experimental results show that the speedups observed for both platforms were increased in the same direction of the image resolution. In addition, the execution time to communication time ratios (Rt/Rc) as a function of the sample size have shown a narrow variation for the DSP platform in comparison with the MPI platform, which indicates its better performance for parallel image reconstruction.

Recording from Two Neurons: Second-Order Stimulus Reconstruction from Spike Trains and Population Coding

We study the reconstruction of visual stimuli from spike trains, representing the reconstructed stimulus by a Volterra series up to second order. We illustrate this procedure in a prominent example of spiking neurons, recording simultaneously from the two H1 neurons located in the lobula plate of the fly Chrysomya megacephala. The fly views two types of stimuli, corresponding to rotational and translational displacements. Second-order reconstructions require the manipulation of potentially very large matrices, which obstructs the use of this approach when there are many neurons. We avoid the computation and inversion of these matrices using a convenient set of basis functions to expand our variables in. This requires approximating the spike train four-point functions by combinations of two-point functions similar to relations, which would be true for gaussian stochastic processes. In our test case, this approximation does not reduce the quality of the reconstruction. The overall contribution to stimulus reconstruction of the second-order kernels, measured by the mean squared error, is only about 5% of the first-order contribution. Yet at specific stimulus-dependent instants, the addition of second-order kernels represents up to 100% improvement, but only for rotational stimuli. We present a perturbative scheme to facilitate the application of our method to weakly correlated neurons.

Accurate velocity reconstruction for Discontinuous Galerkin approximations of two-phase porous media flows

We consider Discontinuous Galerkin approximations of two-phase, immiscible porous media flows in the global pressure/fractional flow formulation with capillary pressure. A sequential approach is used with a backward Euler step for the saturation equation, equal-order interpolation for the pressure and the saturation, and without any limiters. An accurate total velocity field is recovered from the global pressure equation to be used in the saturation equation. Numerical experiments show the advantages of the proposed reconstruction. To cite this article: A. Ern et al., C R. Acad. Sci. Paris, Ser. 1347 (2009). (C) 2009 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Ontology of building in war and reconstruction

Post-war cities epitomise both a disjuncture and resonance between the end of the nation-state, on the one hand, and a preoccupation with reinventing the city through building, on the other. Programs of 'reconstruction' and 'remaking a city' are preceded by destruction: a destructive force has altered the face of the city, buildings have been destroyed and damaged, their ordered and ordering materiality is eroded, and the city is no longer an image of an idealized symbol of unity and identity. Belying the mythical power of architecture as a material and symbolic force, is also its fragility. Architecture can be monumentally erected and can have a presence and persistence that inspires awe and wonder, but it can also, just as easily be de-erected, demolished, destroyed. It can be de-constructed in a way that the literal sense of the term signals its symbolic frailty. Perceiving the symbolic as intrinsically tied to the physical articulation and presence of the architectural edifice, both reveals and conceals that the symbolic is also tied to fantasy, memory and fiction. Drawings that precede construction are projections of an idealized image of something that does not yet exist, and photographs that remain after a building is demolished are representations of a past realist that is now fictional.

Recovery from gynaecological day surgery : are we underestimating the process

This paper reports a study investigating the post operative experiences of 80 women following gynaecological day surgery. Women kept a diary for the first 4 days following surgery. The diary included a recovery rating scale and a symptom management index focusing particularly on symptoms. A telephone interview conducted on post-operative day 10 further explored experiences. Results at day 4 indicated women experienced significant problems with pain, moving around and tiredness. By day 10, women were still experiencing tiredness, pain and other lingering problems. The study indicates that patients experience more problems than discharge education assumes.

"I could see, and yet, mon, I could na` see" : William Macewen, the agnosias, and brain surgery

Two little noticed cases in which William Macewen used symptoms of visual agnosia to plan brain surgery on the angular gyrus are reviewed and evaluated. Following a head injury, Macewen’s first patient had an immediate and severe visual object agnosia that lasted for about 2 weeks. After that he gradually became homicidal and depressed and it was for those symptoms that Macewen first saw him, some 11 months after the accident. From his examination, Macewen concluded that the agnosia clearly indicated a lesion in “the posterior portion of the operculum or in the angular gyrus.” When he removed parts of the internal table that had penetrated those structures the homicidal impulses disappeared. Macewen’s second patient was seen for a chronic middle ear infection and, although neither aphasic nor deaf, was ‘word deaf.’ Slightly later he became ‘psychically blind’ as well. Macewen suspected a cerebral abscess pressing on both the angular gyrus and the first temporal convolution. A large subdural abscess was found there and the symptoms disappeared after it was treated. The patients are discussed and Macewen’s positive results analysed in the historical context of the dispute over the proposed role of the angular gyrus as the visual centre.

Localisation and William Macewen`s early brain surgery part I: the controversy

Neurosurgery for the removal of brain tumours based on localising signs is usually dated from the 1884 operation by Bennett and Godlee. However, within weeks of that operation claims were made on behalf of William Macewen, the Glasgow surgeon, to have been the real pioneer of such surgery. According to Macewen's protagonists, he had conducted seven similar operations earlier than Bennett and Godlee and, in a notable 1888 address, Macewen described these seven pre-1884 cases and a number of others operated on after 1884. This paper, which is in two parts, contains an evaluation of the claims made for the priority of Macewen's pre-1884 operations. Part I deals mainly with Macewen's work in fields other than brain surgery that are relevant to it and sets out the facts of the controversy. It begins with a brief biography of Macewen, describes his pioneering work in antiseptic and aseptic surgery, his work on osteotomy and bone regeneration, and his use in brain surgery of the knowledge so gained. Part I concludes with an examination of the battle waged in the newspapers between Macewen's and Bennett's and Godlee's supporters, and of previously unpublished correspondence between Macewen himself, David Ferrier and Hughes Bennett. The primary records of the patients on whom Macewen operated, together with other materials relevant to the controversy, are examined in Part II.