The resolution of complex spectral patterns by cochlear implant and normal-hearing listeners

The differences in spectral shape resolution abilities among cochlear implant ~CI! listeners, and between CI and normal-hearing ~NH! listeners, when listening with the same number of channels ~12!, was investigated. In addition, the effect of the number of channels on spectral shape resolution was examined. The stimuli were rippled noise signals with various ripple frequency-spacings. An adaptive 4IFC procedure was used to determine the threshold for resolvable ripple spacing, which was the spacing at which an interchange in peak and valley positions could be discriminated. The results showed poorer spectral shape resolution in CI compared to NH listeners ~average thresholds of approximately 3000 and 400 Hz, respectively!, and wide variability among CI listeners ~range of approximately 800 to 8000 Hz!. There was a significant relationship between spectral shape resolution and vowel recognition. The spectral shape resolution thresholds of NH listeners increased as the number of channels increased from 1 to 16, while the CI listeners showed a performance plateau at 4–6 channels, which is consistent with previous results using speech recognition measures. These results indicate that this test may provide a measure of CI performance which is time efficient and non-linguistic, and therefore, if verified, may provide a useful contribution to the prediction of speech perception in adults and children who use CIs.

XSophe-Sophe-XeprView (R). A computer simulation software suite (v. 1.1.3) for the analysis of continuous wave EPR spectra

The XSophe-Sophe-XeprView((R)) computer simulation software suite enables scientists to easily determine spin Hamiltonian parameters from isotropic, randomly oriented and single crystal continuous wave electron paramagnetic resonance (CW EPR) spectra from radicals and isolated paramagnetic metal ion centers or clusters found in metalloproteins, chemical systems and materials science. XSophe provides an X-windows graphical user interface to the Sophe programme and allows: creation of multiple input files, local and remote execution of Sophe, the display of sophelog (output from Sophe) and input parameters/files. Sophe is a sophisticated computer simulation software programme employing a number of innovative technologies including; the Sydney OPera HousE (SOPHE) partition and interpolation schemes, a field segmentation algorithm, the mosaic misorientation linewidth model, parallelization and spectral optimisation. In conjunction with the SOPHE partition scheme and the field segmentation algorithm, the SOPHE interpolation scheme and the mosaic misorientation linewidth model greatly increase the speed of simulations for most spin systems. Employing brute force matrix diagonalization in the simulation of an EPR spectrum from a high spin Cr(III) complex with the spin Hamiltonian parameters g(e) = 2.00, D = 0.10 cm(-1), E/D = 0.25, A(x) = 120.0, A(y) = 120.0, A(z) = 240.0 x 10(-4) cm(-1) requires a SOPHE grid size of N = 400 (to produce a good signal to noise ratio) and takes 229.47 s. In contrast the use of either the SOPHE interpolation scheme or the mosaic misorientation linewidth model requires a SOPHE grid size of only N = 18 and takes 44.08 and 0.79 s, respectively. Results from Sophe are transferred via the Common Object Request Broker Architecture (CORBA) to XSophe and subsequently to XeprView((R)) where the simulated CW EPR spectra (1D and 2D) can be compared to the experimental spectra. Energy level diagrams, transition roadmaps and transition surfaces aid the interpretation of complicated randomly oriented CW EPR spectra and can be viewed with a web browser and an OpenInventor scene graph viewer.

Clustering Process Analysis in a Large-Size Dropshaft and in a Hydraulic Jump

Recent efforts in the characterization of air-water flows properties have included some clustering process analysis. A cluster of bubbles is defined as a group of two or more bubbles, with a distinct separation from other bubbles before and after the cluster. The present paper compares the results of clustering processes two hydraulic structures. That is, a large-size dropshaft and a hydraulic jump in a rectangular horizontal channel. The comparison highlighted some significant differences in clustering production and structures. Both dropshaft and hydraulic jump flows are complex turbulent shear flows, and some clustering index may provide some measure of the bubble-turbulence interactions and associated energy dissipation.

Biomolecular interaction analysis of IFN gamma-induced signaling events in whole-cell lysates: Prevalence of latent STAT1 in high-molecular weight complexes

The basic framework for the JAK/STAT pathway is well documented. Recruitment of latent cytoplasmic STAT transcription factors to tyrosine phosphorylated docking sites on cytokine receptors and their JAK-mediated phosphorylation instigates their translocation to the nucleus and their ability to bind DNA, The biochemical processes underlying recruitment and activation of this pathway have commonly been studied in reconstituted in vitro systems using previously defined recombinant signaling components. We have dissected the Interferon gamma (IFN gamma) signal transduction pathway in crude extracts from wild-type and STAT1-negative mutant cell Lines by real-time BIAcore analysis, size-exclusion (SE) chromatography and immune-detection. The data indicate that in detergent-free cell extracts: (1) the phospho-tyrosine (Y440P)-containing peptide motif of the IFN gamma-receptor ct-chain interacts directly with STAT1, or STAT1 complexes, and no other protein; (2) nonactivated STAT 1 is present in a higher molecular weight complex(es) and, at least for IFN gamma-primed cells, is available for recruitment to the activated IFN gamma-receptor from only a subset of such complexes; (3) activated STAT1 is released from the receptor as a monomer.

Th structure of the P-II-ATP complex

P-II is a signal transduction protein that is part of the cellular machinery used by many bacteria to regulate the activity of glutamine synthetase and the transcription of its gene. The structure of P-II was solved using a hexagonal crystal form (form I). The more physiologically relevant form of P-II is a complex with small molecule effecters. We describe the structure of P-II with ATP obtained by analysis of two different crystal forms (forms II and III) that were obtained by co-crystallization of P-II with ATP. Both structures have a disordered recognition (T) loop and show differences at their C termini. Comparison of these structures with the form I protein reveals changes that occur on binding ATP. Surprisingly, the structure of the P-II/ATP complex differs with that of GlnK, a functional homologue. The two proteins bind the base and sugar of ATP in a similar manner but show differences in the way that they interact with the phosphates. The differences in structure could account for the differences in their activities, and these have been attributed to a difference in sequence at position 82. It has been demonstrated recently that P-II and GlnK form functional heterotrimers in vivo. We construct models of the heterotrimers and examine the junction between the subunits.

A computational analysis of substrate binding strength by phosphorylase kinase and protein kinase A

Protein kinases exhibit various degrees of substrate specificity. The large number of different protein kinases in the eukaryotic proteomes makes it impractical to determine the specificity of each enzyme experimentally. To test if it were possible to discriminate potential substrates from non-substrates by simple computational techniques, we analysed the binding enthalpies of modelled enzyme-substrate complexes and attempted to correlate it with experimental enzyme kinetics measurements. The crystal structures of phosphorylase kinase and cAMP-dependent protein kinase were used to generate models of the enzyme with a series of known peptide substrates and non-substrates, and the approximate enthalpy of binding assessed following energy minimization. We show that the computed enthalpies do not correlate closely with kinetic measurements, but the method can distinguish good substrates from weak substrates and non-substrates. Copyright (C) 2002 John Wiley Sons, Ltd.

3D reconstruction and quantification of macropores using X-ray computed tomography and image analysis

Axial X-ray Computed tomography (CT) scanning provides a convenient means of recording the three-dimensional form of soil structure. The technique has been used for nearly two decades, but initial development has concentrated on qualitative description of images. More recently, increasing effort has been put into quantifying the geometry and topology of macropores likely to contribute to preferential now in soils. Here we describe a novel technique for tracing connected macropores in the CT scans. After object extraction, three-dimensional mathematical morphological filters are applied to quantify the reconstructed structure. These filters consist of sequences of so-called erosions and/or dilations of a 32-face structuring element to describe object distances and volumes of influence. The tracing and quantification methodologies were tested on a set of undisturbed soil cores collected in a Swiss pre-alpine meadow, where a new earthworm species (Aporrectodea nocturna) was accidentally introduced. Given the reduced number of samples analysed in this study, the results presented only illustrate the potential of the method to reconstruct and quantify macropores. Our results suggest that the introduction of the new species induced very limited chance to the soil structured for example, no difference in total macropore length or mean diameter was observed. However. in the zone colonised by, the new species. individual macropores tended to have a longer average length. be more vertical and be further apart at some depth. Overall, the approach proved well suited to the analysis of the three-dimensional architecture of macropores. It provides a framework for the analysis of complex structures, which are less satisfactorily observed and described using 2D imaging. (C) 2002 Elsevier Science B.V. All rights reserved.

The sit-up: complex kinematics and muscle activity in voluntary axial movement

This paper describes the kinematics and muscle activity associated with the standard sit-up, as a first step in the investigation of complex motor coordination. Eight normal human subjects lay on a force table and performed at least 15 sit-ups, with the arms across the chest and the legs straight and unconstrained. Several subjects also performed sit-ups with an additional weight added to the head. Support surface forces were recorded to calculate the location of the center of pressure and center of gravity; conventional motion analysis was used to measure segmental positions; and surface EMG was recorded from eight muscles. While the sit-up consists of two serial components, 'trunk curling' and 'footward pelvic rotation', it can be further subdivided into five phases, based on the kinematics. Phases I and II comprise trunk curling. Phase I consists of neck and upper trunk flexion, and phase II consists of lumbar trunk lifting. Phase II corresponds to the point of peak muscle contraction and maximum postural instability, the 'critical point' of the sit-up. Phases III-V comprise footward pelvic rotation. Phase III begins with pelvic rotation towards the feet. phase W with leg lowering, and phase V with contact between the legs and the support surface. The overall pattern of muscle activity was complex with times of EMG onset, peak activity, offset, and duration differing for different muscles. This complex pattern changed qualitatively from one phase to the next, suggesting that the roles of different muscles and, as a consequence, the overall form of coordination, change during the sit-up. (C) 2003 Elsevier Science Ltd. All rights reserved.

Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA - Crystal structure of an oligomeric complex of yeast SmF

Sm and Sm-like proteins are key components of small ribonucleoproteins involved in many RNA and DNA processing pathways. In eukaryotes, these complexes contain seven unique Sm or Sm-like (Lsm) proteins assembled as hetero-heptameric rings, whereas in Archaea and bacteria six or seven-membered rings are made from only a single polypeptide chain. Here we show that single Sm and Lsm proteins from yeast also have the capacity to assemble into homo-oligomeric rings. Formation of homo-oligomers by the spliceosomal small nuclear ribonucleoprotein components SmE and SmF preclude hetero-interactions vital to formation of functional small nuclear RNP complexes in vivo. To better understand these unusual complexes, we have determined the crystal structure of the homomeric assembly of the spliceosomal protein SmF. Like its archaeal/bacterial homologs, the SmF complex forms a homomeric ring but in an entirely novel arrangement whereby two heptameric rings form a co-axially stacked dimer via interactions mediated by the variable loops of the individual SmF protein chains. Furthermore, we demonstrate that the homomeric assemblies of yeast Sm and Lsm proteins are capable of binding not only to oligo(U) RNA but, in the case of SmF, also to oligo(dT) single-stranded DNA.

The amygdaloid complex: Anatomy and physiology

A converging body of literature over the last 50 years has implicated the amygdala in assigning emotional significance or value to sensory information. In particular, the amygdala has been shown to be an essential component of the circuitry underlying fear-related responses. Disorders in the processing of fear-related information are likely to be the underlying cause of some anxiety disorders in humans such as posttraumatic stress. The amygdaloid complex is a group of more than 10 nuclei that are located in the midtemporal lobe. These nuclei can be distinguished both on cytoarchitectonic and connectional grounds. Anatomical tract tracing studies have shown that these nuclei have extensive intranuclear and internuclear connections. The afferent and efferent connections of the amygdala have also been mapped in detail, showing that the amygdaloid complex has extensive connections with cortical and subcortical regions. Analysis of fear conditioning in rats has suggested that long-term synaptic plasticity of inputs to the amygdala underlies the acquisition and perhaps storage of the fear memory. In agreement with this proposal, synaptic plasticity has been demonstrated at synapses in the amygdala in both in vitro and in vivo studies. In this review, we examine the anatomical and physiological substrates proposed to underlie amygdala function.

Taxonomic re-examination of the hermit crab species Pagurus forceps and Pagurus comptus (Decapoda: Paguridae) by molecular analysis

The current taxonomy of two poorly known hermit crab species Pagurus forceps H. Milne Edwards, 1836 and Pagurus comptus White, 1847 from temperate Pacific and Atlantic coastlines of South America is based only on adult morphology. Past studies have questioned the separation of these two very similar species, which occur sympatrically. We included specimens morphologically assignable to P. forceps and P. comptus in a phylogenetic analysis, along with other selected anomuran decapods, based on 16S ribosomal gene sequences. Differences between samples putatively assigned to either P. forceps and P. comptus were moderate, with sequence similarity ranging from 98.2 to 99.4% for the fragments analyzed. Our comparison of mitochondrial DNA sequences (16S rRNA) revealed diagnostic differences between the two putative species, suggesting that P. forceps and P. comptus are indeed phylogenetically close but different species, with no genetic justification to support their synonymization. The polyphyly of Pagurus is not corroborated here among the represented Atlantic species, despite obviously complex relationships among the members of the genus.

Does Petrolisthes armatus (Anomura, Porcellanidae) form a Species Complex or Are We Dealing with Just One Widely Distributed Species?

Fernando L. Mantelatto, Leonardo G. Pileggi, Ivana Miranda, and Ingo S. Wehrtmann (2011) Does Petrolisthes armatus (Anomura, Porcellanidae) form a species complex or are we dealing with just one widely distributed species? Zoological Studies 50(3): 372-384. Petrolisthes armatus has the widest distribution known among members of the family Porcellanidae and is one of the most ubiquitous and locally abundant intertidal decapods along the Atlantic coast of the Americas. Considering its geographical distribution and morphological plasticity, several authors postulated the existence of a P. armatus species complex. In the present study we used genetic data from the mitochondrial 16S ribosomal gene to determine the genetic variability of P. armatus from selected locations within its eastern tropical Pacific and western Atlantic distributions. Our phylogenic analysis included 49 specimens represented by 26 species of the genus Petrolisthes and 16 specimens from 10 species and 4 related genera. Genetic distances estimated among the analyzed Petrolisthes species ranged from 2.6%-22.0%; varied between 0%-5.7% for 16S. Additionally, the revision of P. armatus specimens from Pacific Costa Rica and Brazilian Waters showed no geographically significant morphological variations among the analyzed specimens. Therefore, our morphological and genetic data do not support the hypothesis of a P. armatus complex within the specimens studied herein from the Americas, but convincingly confirm the monophyly and non-separateness of the members assigned as P. armatus. http://zoolstud.sinica.edu.tw/Journals/50.3/372.pdf

Synthesis and Study of the Photophysical Properties of a New Eu(3+) Complex with 3-Hydroxypicolinamide

This work reports on the synthesis and characterization of a new complex of Eu(3+) with the 3-hydroxypicolinamide ligand (Hhpa). Here we present an approach for obtaining bis[2-carbamoyl(kappa O)pyridin-3-olato(kappa O`)] lanthanide complexes, which were characterized through elemental analysis, thermal analysis, infrared and photoluminescence spectroscopies (emission, excitation, luminescence lifetimes, quantum efficiencies, Judd-Ofelt parameters and quantum yields). Although hpa can act as a bidentate ligand in different conformations, the results attest for the occurrence of a unique coordination site of low symmetry for the Eu(3+) ions, in which two anionic hpa ligands coordinate the cations through an O/O chelating system. The phosphorescence of the synthesized gadolinium complex provides the energy of the triplet state, which is determined to be at 20,830 cm(-1) over the ground state. This makes the Hhpa ligand very adequate for sensitizing the Eu(3+) luminescence, which leads to a very efficient antenna effect and opens a wide range of applications for the complex in light emitting organic-inorganic devices.

Electrical burns: A retrospective analysis across a 5-year period

This study aims to review the experience, at an institution, with patients who suffered electrical burns and study the peculiar characteristics of this type of burn as well as its complications and epidemiological aspects. The study includes medical records of patients with electrical burns who were admitted to the Burn Unit of Hospital das Clinicas in Sao Paulo, Brazil, from November 2001 to October 2006. They were classified into four categories: high voltage (>= 1000 V), low voltage (<1000 V), `flash burn` (in which there is no electrical current flow through the body of the patient) and burns caused by lightning. The complications were more severe and common in the high-voltage group, while longer hospital stays and more complex surgical procedures due to the greater depth of burns were also observed in this group. High-voltage burns are mainly labour-/occupation-related. The majority of the patients were young men at the beginning of their professional lives. This factor generates an important socio-economic impact due to the high incidence of sequelae, resulting in amputations, rendering them unable to maintain their occupations. (C) 2009 Elsevier Ltd and ISBI. All rights reserved.

Mutational analysis of the necdin gene in patients with congenital isolated hypogonadotropic hypogonadism

Context: Necdin activates GNRH gene expression and is fundamental for the development, migration, and axonal extension of murine GNRH neurons. In humans, necdin plays a potential role in the hypogonadotropic hypogonadism phenotype in patients with Prader-Willi syndrome. Aim: To investigate necdin gene (NDN) variants in patients with isolated hypogonadotropic hypogonadism (IHH). Patients and methods: We studied 160 Brazilian patients with IHH, which includes 92 with Kallmann syndrome and 68 with normosmic IHH. Genomic DNA was extracted and the single NDN exon was amplified and sequenced. To measure GNRH transcriptional activity, luciferase reporter plasmids containing GNRH regulatory regions were transiently transfected into GT1-7 cells in the presence and absence of overexpressed wild-type or mutant necdin. Results: A heterozygous variant of necdin, p.V318A, was identified in a 23-year-old male with Kallmann syndrome. The p.V318A was also present in affected aunt and his father and was absent in 100 Brazilian control subjects. Previous FGFR1 gene analysis revealed a missense mutation (p.P366L) in this family. Functional studies revealed a minor difference in the activation of GNRH transcription by mutant protein compared with wild type in that a significant impairment of the necdin protein activity threshold was observed. Conclusion: A rare variant of necdin (p.V318A) was described in a family with Kallmann syndrome associated with a FGFR1 mutation. Familial segregation and in vitro analysis suggested that this non-synonymous variant did not have a direct causative role in the hypogonadism phenotype. NDN mutations are not a frequent cause of congenital IHH.