The relation between speech recognition in noise and the speech-evoked brainstem response in normal-hearing and hearing-impaired individuals

Little is known about the way speech in noise is processed along the auditory pathway. The purpose of this study was to evaluate the relation between listening in noise using the R-Space system and the neurophysiologic response of the speech-evoked auditory brainstem when recorded in quiet and noise in adult participants with mild to moderate hearing loss and normal hearing.

Speech recognition in reverberation in biomodal cochlear implant users

The purpose of the present study was to evaluate the effects of bimodal (implant plus hearing aid) listening on speech recognition in four different environment conditions. Results indicate that there was little difference in the cochlear implant only and bimodal conditions.

PHYLOGENETIC AFFINITIES OF "CHANTRANSIA" STAGES IN MEMBERS OF THE BATRACHOSPERMALES AND THOREALES (RHODOPHYTA)

This study evaluated the phylogenetic relationship among samples of ""Chantransia"" stage of the Batrachospermales and Thoreales from several regions of the world based on sequences of two genes-the plastid-encoded RUBISCO LSU gene (rbcL) and the nuclear SSU ribosomal DNA gene (SSU rDNA). All sequences of ""Chantransia macrospora"" were shown to belong to Batrachospermum macrosporum based on both molecular markers, confirming evidence from previous studies. In contrast, nine species are now associated with ""Chantransia pygmaea,"" including seven species of the Batrachospermales and two of the Thoreales. Therefore, the presence of ""C. macrospora"" in a stream can be considered reliable evidence that it belongs to B. macrosporum, whereas the occurrence of ""C. pygmaea"" does not allow the recognition of any particular species, since it is associated with at least nine species. Affinities of ""Chantransia"" stages to particular taxa were congruent for 70.5% of the samples comparing the rbcL and SSU analyses, which were associated with the same or closely related species for both markers. Sequence divergences have been reported in the ""Chantransia"" stage in comparison to the respective gametophyte, and this matter deserves further attention.

Molecular phylogeny of tribe Rhipsalideae (Cactaceae) and taxonomic implications for Schlumbergera and Hatiora

Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding the classification of Rhipsalideae, no studies have ever attempted to reconstruct phylogenetic relationships among its members or to test the monophyly of its genera using DNA sequence data; all classifications formerly proposed for this tribe have only employed morphological data. In this study, we reconstruct the phylogeny of Rhipsalideae using plastid (trnQ-rps16, rpl32-trnL, psbA-trnH) and nuclear (ITS) markers to evaluate the classifications previously proposed for the group. We also examine morphological features traditionally used to delimit genera within Rhipsalideae in light of the resulting phylogenetic trees. In total new sequences for 35 species of Rhipsalideae were produced (out of 55: 63%). The molecular phylogeny obtained comprises four main clades supporting the recognition of genera Lepismium, Rhipsalis, Hatiora and Schlumbergera. The evidence gathered indicate that a broader genus Schlumbergera, including Hatiora subg. Rhipsalidopsis, should be recognized. Consistent morphological characters rather than homoplastic features are used in order to establish a more coherent and practical classification for the group. Nomenclatural changes and a key for the identification of the genera currently included in Rhipsalideae are provided. (C) 2011 Elsevier Inc. All rights reserved.

Generic relationships and dating of lineages in Winteraceae based on nuclear (ITS) and plastid (rpS16 and psbA-trnH) sequence data

Phylogenetic analyses of representative species from the five genera of Winteraceae (Drimys, Pseudowintera, Takhtajania, Tasmannia, and Zygogynum s.l.) were performed using ITS nuclear sequences and a combined data-set of ITS + psbA-trnH + rpS16 sequences (sampling of 30 and 15 species, respectively). Indel informativity using simple gap coding or gaps as a fifth character was examined in both data-sets. Parsimony and Bayesian analyses support the monophyly of Drimys, Tasmannia, and Zygogynum s.l., but do not support the monophyly of Belliolum, Zygogynum s.s., and Bubbia. Within Drimys, the combined data-set recovers two subclades. Divergence time estimates suggest that the splitting between Drimys and its sister clade (Pseudowintera + Zygogynum s.l.) occurred around the end of the Cretaceous; in contrast, the divergence between the two subclades within Drimys is more recent (15.5-18.5 MY) and coincides in time with the Andean uplift. Estimates suggest that the earliest divergences within Winteraceae could have predated the first events of Gondwana fragmentation. (C) 2009 Elsevier Inc. All rights reserved.

Characterizations of juvenile stages of some semaeostome Scyphozoa (Cnidaria), with recognition of a new family (Phacellophoridae)

Phacellophora camtschatica has long been assigned to the semaeostome scyphozoan family Ulmaridae. Early stages (scyphistomae, strobilae, ephyrae, postephyrae, and young medusae) of the species were compared with those of several other semaeostomes currently assigned to Ulmaridae, Pelagiidae, and Cyaneidae. Juveniles of P. camtschatica did not strictly conform with characters of those of any of these families, and appeared intermediate between Cyaneidae and Ulmaridae. A new family, Phacellophoridae, is proposed to accommodate P. camtschatica.

Mycoplasmal lipid-associated membrane proteins and Mycoplasma arthritidis mitogen recognition by serum antibodies from patients with rheumatoid arthritis

Mycoplasmal lipid-associated membrane proteins (LAMPs) and Mycoplasma arthritidis mitogen (MAM superantigen) are potent stimulators of the immune system. The objective of this work was to detect antibodies to MAM and LAMPs of Mycoplasma hominis and M. fermentans in the sera of patients affected by rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) to identify mycoplasmal products that can be involved in the etiopathogenesis of these autoimmune diseases. Serum samples from female RA and SLE patients and controls, recombinant MAM, and LAMPs of M. hominis PG21 and M. fermentans PG18 were used in Western blot assays. A similar frequency of sera from patients and controls reactive to MAM was detected. A larger number of M. hominis and M. fermentans LAMPs were recognized by sera from RA patients than controls, but no differences were detected between sera from SLE patients and controls. Among the LAMPs recognized by IgG antibodies from RA patients, proteins of molecular masses in a range of < 49 and a parts per thousand yen20 KDa (M. hominis) and < 102 and a parts per thousand yen58 KDa (M. fermentans) were the most reactive. These preliminary results demonstrate the strong reactivity of antibodies of RA patients with some M. hominis and M. fermentans LAMPs. These LAMPs could be investigated as mycoplasmal antigens that can take part in the induction or amplification of human autoimmune responses.

Sequence diversity and evolutionary dynamics of the dimorphic antigen merozoite surface protein-6 and other Msp genes of Plasmodium falciparum

Immune evasion by Plasmodium falciparum is favored by extensive allelic diversity of surface antigens. Some of them, most notably the vaccine-candidate merozoite surface protein (MSP)-1, exhibit a poorly understood pattern of allelic dimorphism, in which all observed alleles group into two highly diverged allelic families with few or no inter-family recombinants. Here we describe contrasting levels and patterns of sequence diversity in genes encoding three MSP-1-associated surface antigens of P. falciparum, ranging from an ancient allelic dimorphism in the Msp-6 gene to a near lack of allelic divergence in Msp-9 to a more classical multi-allele polymorphism in Msp-7 Other members of the Msp-7 gene family exhibit very little polymorphism in non-repetitive regions. A comparison of P. falciparum Msp-6 sequences to an orthologous sequence from P. reichenowi provided evidence for distinct evolutionary histories of the 5` and 3` segments of the dimorphic region in PfMsp-6, consistent with one dimorphic lineage having arisen from recombination between now-extinct ancestral alleles. In addition. we uncovered two surprising patterns of evolution in repetitive sequence. Firsts in Msp-6, large deletions are associated with (nearly) identical sequence motifs at their borders. Second, a comparison of PfMsp-9 with the P. reichenowi ortholog indicated retention of a significant inter-unit diversity within an 18-base pair repeat within the coding region of P. falciparum, but homogenization in P. reichenowi. (C) 2009 Elsevier B.V. All rights reserved.

Circadian phase and intertrial interval interfere with social recognition memory

A modified version of the social habituation/dis-habituation paradigm was employed to examine social recognition memory in Wistar rats during two opposing (active and inactive) circadian phases, using different intertrial intervals (30 and 60 min). Wheel-running activity was monitored continuously to identify circadian phase. To avoid possible masking effects of the light-dark cycle, the rats were synchronized to a skeleton photoperiod, which allowed testing during different circadian phases under identical lighting conditions. In each trial, an infantile intruder was introduced into an adult`s home-cage for a 5-minute interaction session, and social behaviors were registered. Rats were exposed to 5 trials per day for 4 consecutive days: oil days I and 2, each resident was exposed to the same intruder; on days 3 and 4, each resident was exposed to a different intruder in each trial. I he resident`s social investigatory behavior was more intense when different intruders were presented compared to repeated presentation of the same intruder, suggesting social recognition memory. This effect was stronger when the rats were tested during the inactive phase and when the intertrial interval was 60 min, These findings Suggest that social recognition memory, as evaluated in this modified habituation/dis-habituation paradigm, is influenced by the circadian rhythm phase during which testing is performed, and by intertrial interval. (C) 2008 Elsevier Inc. All rights reserved.

A pattern recognition approach to complex networks

Complex networks exist in many areas of science such as biology, neuroscience, engineering, and sociology. The growing development of this area has led to the introduction of several topological and dynamical measurements, which describe and quantify the structure of networks. Such characterization is essential not only for the modeling of real systems but also for the study of dynamic processes that may take place in them. However, it is not easy to use several measurements for the analysis of complex networks, due to the correlation between them and the difficulty of their visualization. To overcome these limitations, we propose an effective and comprehensive approach for the analysis of complex networks, which allows the visualization of several measurements in a few projections that contain the largest data variance and the classification of networks into three levels of detail, vertices, communities, and the global topology. We also demonstrate the efficiency and the universality of the proposed methods in a series of real-world networks in the three levels.

Crystal Engineering of an Anti-HIV Drug Based on the Recognition of Assembling Molecular Frameworks

A rational strategy was employed for design of an orthorhombic structure of lamivudine with maleic acid. On the basis of the lamivudine saccharinate structure reported in the literature, maleic acid was chosen to synthesize a salt with the anti-HIV drug because of the structural similarities between the salt formers. Maleic acid has an acid-ionization constant of the anti first proton and an arrangement of their hydrogen bonding functionalities similar to those of saccharin. Likewise, there is a saccharin-like conformational rigidity in maleic acid because of the hydrogen-bonded ring formation and the Z-configuration around the C=C double bond. As was conceivably predicted, lamivudine maleate assembles into a structure whose intermolecular architecture is related to that of saccharinate salt of the drug. Therefore, a molecular framework responsible for crystal assembly into a lamivudine saccharinate-like structure could be recognized in the salt formers. Furthermore, structural correlations and structure-solubility relationships were established for lamivudine maleate and saccharinate. Although there is a same molecular framework in maleic acid and saccharin, these salt formers are Structurally different in some aspects. When compared to saccharin, neither out-of-plane SO(2) oxygens nor a benzene group occur in maleic acid. Both features could be related to higher solubility of lamivudine maleate. Here, we also anticipate that multicomponent molecular crystals of lamivudine with other salt formers possessing the molecular framework responsible for crystal assembly can be engineered successfully.

Ionic Recognition by 7-Nitro-1,3,5-triaza Adamantane: First Thermodynamic Study

A thermodynamic study involving 7-nitro-1,3,5-triaza adamantane, 1, and its interaction with metal cations in nonaqueous media is first reported. Solubility data of 1 in various solvents were used to derive the standard Gibbs energies of solution, Delta G(s)degrees in these solvents. The effect of solvation in the different media was assessed from the Gibbs energy of transfer taking acetonitrile as a reference solvent. (1)H NMR studies of the interaction of 1 and metal cations were carried out in CD(3)CN and CD(3)OD and the data are reported. Conductance measurements revealed that this ligand forms lead(II) or zinc complexes of 1: 1 stoichiometry in acetonitrile. It also revealed a stoichiometry of two molecules of 1 per mercury(II) and two cadmiu (II) ions per molecule of 1. The addition of silver salt to 1 led to the precipitation of the silver-1 complex which was isolated and characterized by X-ray crystallography. At variance with conductance measurements in solution, in the solid state the X-ray structure show`s a 1:1 stoichiometry in the Hg(II) complex. The themiodynamics of complexation of 1 and these cations provide a quantitative assessment of the selective behavior of this ligand for ions of environmental relevance.

Novel Zn(2+)-binding Sites in Human Transthyretin IMPLICATIONS FOR AMYLOIDOGENESIS AND RETINOL-BINDING PROTEIN RECOGNITION

Human transthyretin (TTR) is a homotetrameric protein involved in several amyloidoses. Zn(2+) enhances TTR aggregation in vitro, and is a component of ex vivo TTR amyloid fibrils. We report the first crystal structure of human TTR in complex with Zn(2+) at pH 4.6-7.5. All four structures reveal three tetra-coordinated Zn(2+)-binding sites (ZBS 1-3) per monomer, plus a fourth site (ZBS 4) involving amino acid residues from a symmetry-related tetramer that is not visible in solution by NMR.Zn(2+) binding perturbs loop E-alpha-helix-loop F, the region involved in holo-retinol-binding protein (holo-RBP) recognition, mainly at acidic pH; TTR affinity for holo-RBP decreases similar to 5-fold in the presence of Zn(2+). Interestingly, this same region is disrupted in the crystal structure of the amyloidogenic intermediate of TTR formed at acidic pH in the absence of Zn(2+). HNCO and HNCA experiments performed in solution at pH 7.5 revealed that upon Zn(2+) binding, although the alpha-helix persists, there are perturbations in the resonances of the residues that flank this region, suggesting an increase in structural flexibility. While stability of the monomer of TTR decreases in the presence of Zn(2+), which is consistent with the tertiary structural perturbation provoked by Zn(2+) binding, tetramer stability is only marginally affected by Zn(2+). These data highlight structural and functional roles of Zn(2+) in TTR-related amyloidoses, as well as in holo-RBP recognition and vitamin A homeostasis.

Recognition by the Thyroid Hormone Receptor of Canonical DNA Response Elements

To shed more light on the molecular requirements for recognition of thyroid response elements (TRES) by thyroid receptors (TRs), we compared the specific aspects of DNA TRE recognition by different TR constructs. Using fluorescence anisotropy, we performed a detailed and hierarchical study of TR-TRE binding. This wits done by comparing the binding affinities of three different TR constructs for four different TRE DNA elements, including palindromic sequences and direct repeats (F2, PAL, DR-1, and DR-4) as well as their interactions with nonspecific DNA sequences. The effect of MgCl(2) on suppressing of nonselective DNA binding to TR was also investigated. Furthermore, we determined the dissociation constants of the hTR beta DBD (DNA binding domain) and hTR beta DBD-LBD (DNA binding and ligand binding domains) for specific TRES. We found that a minimum DNA recognition peptide derived from DBD (H1TR) is sufficient for recognition and interaction with TREs, whereas scrambled DNA sequences were unrecognized. Additionally, we determined that the TR DBD binds to F2, PAL, and DR-4 with high affinity and similar K(d) values. The TR DBD-LBD recognizes all the tested TRES but binds preferentially to F2, with even higher affinity. Finally, our results demonstrate the important role played by LBDs in modulating TR-DNA binding.

Probing conformational changes in orphan nuclear receptor: The NGFI-B intermediate is a partially unfolded dimer

Human nerve growth factor-induced B (NGFI-B) is a member of the NR4A subfamily of orphan nuclear receptors (NRs). Lacking identified ligands, orphan NRs show particular co-regulator proteins binding properties, different from other NRs, and they might have a non-classical quaternary organization. A body of evidence suggests that NRs recognition of and binding to ligands, DNA, homo- and heterodimerization partners and co-regulator proteins involve significant conformational changes of the NR ligand-binding domains (LBDs). To shed light on largely unknown biophysical properties of NGFI-B, here we studied structural organization and unfolding properties of NGFI-B ligand (like)-binding domain induced by chemical perturbation. Our results show that NGFI-B LBD undergoes a two-state guanidine hydrochloride (GndHCl) induced denaturation, as judged by changes in the a-helical content of the protein monitored by circular dichroism spectroscopy (CD). In contrast, changes in the tertiary structure of NGFI-B LBD, reported by intrinsic fluorescence, reveal a clear intermediate state. Additionally, SAXS results demonstrate that the intermediate observed by intrinsic fluorescence is a partially folded homodimeric structure, which further unfolds without dissociation at higher GndHCl concentrations. This partially unfolded dimeric assembly of NGFI-B LBD might resemble an intermediate that this domain access momentarily in the native state upon interactions with functional partners. (C) 2008 Elsevier B.V. All rights reserved.