A comparative social network analysis of wasp colonies and classrooms: Linking network structure to functioning

A major question in current network science is how to understand the relationship between structure and functioning of real networks. Here we present a comparative network analysis of 48 wasp and 36 human social networks. We have compared the centralisation and small world character of these interaction networks and have studied how these properties change over time. We compared the interaction networks of (1) two congeneric wasp species (Ropalidia marginata and Ropalidia cyathiformis), (2) the queen-right (with the queen) and queen-less (without the queen) networks of wasps, (3) the four network types obtained by combining (1) and (2) above, and (4) wasp networks with the social networks of children in 36 classrooms. We have found perfect (100%) centralisation in a queen-less wasp colony and nearly perfect centralisation in several other queen-less wasp colonies. Note that the perfectly centralised interaction network is quite unique in the literature of real-world networks. Differences between the interaction networks of the two wasp species are smaller than differences between the networks describing their different colony conditions. Also, the differences between different colony conditions are larger than the differences between wasp and children networks. For example, the structure of queen-right R. marginata colonies is more similar to children social networks than to that of their queen-less colonies. We conclude that network architecture depends more on the functioning of the particular community than on taxonomic differences (either between two wasp species or between wasps and humans).

A comparative study of speaker adaptation methods

For the problem of speaker adaptation in speech recognition, the performance depends on the availability of adaptation data. In this paper, we have compared several existing speaker adaptation methods, viz. maximum likelihood linear regression (MLLR), eigenvoice (EV), eigenspace-based MLLR (EMLLR), segmental eigenvoice (SEV) and hierarchical eigenvoice (HEV) based methods. We also develop a new method by modifying the existing HEV method for achieving further performance improvement in a limited available data scenario. In the sense of availability of adaptation data, the new modified HEV (MHEV) method is shown to perform better than all the existing methods throughout the range of operation except the case of MLLR at the availability of more adaptation data.

p53 and little brother p53/47: linking IRES activities with protein functions

The tumor suppressor p53 represents a paradigm for gene regulation. Its rapid induction in response to DNA damage conditions has been attributed to both increased half-life of p53 protein and also increased translation of p53 mRNA. Recent advances in our understanding of the post-transcriptional regulation of p53 include the discovery of internal ribosome entry sites (IRESs) within the p53 mRNA. These IRES elements regulate the translation of the full length as well as the N-terminally truncated isoform, p53/47. The p53/47 isoform is generated by alternative initiation at an internal AUG codon present within the p53 ORF. The aim of this review is to summarize the role of translational control mechanisms in regulating p53 functions. We discuss here in detail how diverse cellular stress pathways trigger alterations in the cap-dependent and cap-independent translation of p53 mRNA and how changes in the relative expression levels of p53 isoforms result in more differentiated p53 activity.

Design of speaker identification schemes for large number of speakers (A)

Design of speaker identification schemes for a small number of speakers (around 10) with a high degree of accuracy in controlled environment is a practical proposition today. When the number of speakers is large (say 50–100), many of these schemes cannot be directly extended, as both recognition error and computation time increase monotonically with population size. The feature selection problem is also complex for such schemes. Though there were earlier attempts to rank order features based on statistical distance measures, it has been observed only recently that the best two independent measurements are not the same as the combination in two's for pattern classification. We propose here a systematic approach to the problem using the decision tree or hierarchical classifier with the following objectives: (1) Design of optimal policy at each node of the tree given the tree structure i.e., the tree skeleton and the features to be used at each node. (2) Determination of the optimal feature measurement and decision policy given only the tree skeleton. Applicability of optimization procedures such as dynamic programming in the design of such trees is studied. The experimental results deal with the design of a 50 speaker identification scheme based on this approach.

Architecture of Physalis Mottle Tymovirus as Probed by Monoclonal Antibodies and Cross-Linking Studies

Physalis mottle tymovirus (previously named belladonna mottle virus, Iowa strain) RNA was cross-linked to its coat protein by exposure of the intact virus to ultraviolet light. The site of cross-linking of the coat protein with the RNA was identified as Lys-10 by sequencing the oligonucleotide-linked tryptic peptide obtained upon HPLC separation subsequent to enzymetic digestion of the cross-linked and dissociated virus. Three monoclonal antibodies PA3B2, PB5G9, and PF12C9, obtained using denatured coat protein as antigen, cross-reacted effectively with the intact virus indicating that the epitopes recognized by these monoclonals are on the surface of the virus. Using the peptides generated by digestion with CNBr, clostripain, V-8 protease, or trypsin and a recombinant protein lacking the N-terminal 21 residues expressed from a cDNA clone, it was shown that PA3B2 recognizes the sequence 22-36 on the coat protein while PB5G9 and PF12C9 recognize region 75-110. These results suggest that Lys-10 is one of the specific sites through which the RNA interacts in the intact virus. The polypeptide segment (region 22-36) following this buried portion as well as the epitope within the region 75-110 are exposed in the intact virus. These observations are consistent with the canonical β-barrel structure observed in certain other plant viruses.

Characterization of the DNA-binding domain of beta protein, a component of phage lambda Red-pathway by UV catalyzed cross-linking

beta protein, a key component of Red-pathway of phage lambda is necessary for its growth and general genetic recombination in recombination-deficient mutants of Escherichia coli. To facilitate studies on structure-function relationships, we overexpressed beta protein and purified it to homogeneity. A chemical cross-linking reagent, glutaraldehyde, was used to stabilize the physical association of beta protein in solution. A 67-kDa band, corresponding to homodimer, was identified after separation by SDS-polyacrylamide gel electrophoresis. Stoichiometric measurements indicated a site-size of 1 monomer of beta protein/5 nucleotide residues. Electrophoretic gel mobility shift assays suggested that beta protein formed stable nucleoprotein complexes with 36-mer, but not with 27- or 17-mer DNA. Interestingly, the interaction of beta protein with DNA and the stability of nucleoprotein complexes was dependent on the presence of MgCl2, and the binding was abolished by 250 mM NaCl. The K-d of beta protein binding to 36-mer DNA was on the order of 1.8 x 10(-6) M. Photochemical cross-linking of native beta protein or its fragments, generated by chymotrypsin, to 36-mer DNA was performed to identify its DNA-binding domain. Characterization of the cross-linked peptide disclosed that amino acids required for DNA-binding specificity resided within a 20-kDa peptide at the N-terminal end. These findings provide a basis for further understanding oi the structure and function of beta protein.

Azide and Alkyne Terminated Polybutadiene Binders: Synthesis, Cross-linking, and Propellant Studies

In composite solid propellants, the fuel and oxidizer are held together by a polymer binder. Among the different types of polymeric binders used in solid propellants, hydroxyl terminated polybutadiene (HTPB) is considered as the most versatile. HTPB is conventionally cured using isocyanates to form polyurethanes. However, the incompatibility of isocyanates with energetic oxidizers such as ammonium dinitramide and hydrazinium nitroformate, the short pot life of the propellant slurry, and undesirable side reactions with moisture are limiting factors which adversely affect the mechanical properties of HTPB based propellant. With an aim of resolving these problems, HTPB was chemically transformed to azidoethoxy carbonyl amine terminated polybutadiene and propargyloxy carbonyl amine terminated polybutadiene by adopting appropriate synthesis strategies and characterizing them by spectroscopic and chromatographic techniques. This is the first report on 1,3-dipolar addition reaction involving azide and alkyne end groups for cross-linking HTPB. The blend of these two polymers underwent curing under mild temperature (60 degrees C) conditions through 1,3-dipolar cycloaddition reaction resulting in triazoletriazoline networks. The curing parameters were studied using differential scanning calorimetry. The kinetic parameter, viz., activation energy, was computed to be 107.6 kJ/mol, the preexponential factor was 2.79 x 10(12) s-(1), and the rate constant at 60 degrees C was computed to be 3.64 x 10-(5) s-(1). The cure profile at a given temperature was predicted using the kinetic parameters. Rheological studies revealed that the gel time for curing through the 1,3-dipolar addition is 280 min compared to 120 min for curing through the urethane route. The mechanical properties of the resultant cured polybutadiene network were superior to those of polyurethanes. The cured triazolinetriazole polymer network exhibited biphasic morphology with two glass transitions (T-g) at -56 and 42 degrees C in contrast to the polyurethane which exhibited a single transition at -60 degrees C. This was corroborated by associated morphological changes observed by scanning probe microscopy. The propellant processed using this binder has the advantages of improved pot life as indicated by the end of the mix viscosity which is 165 Pas as compared with 352 Pas for the polyurethane system along with a slow build- up rate. The mechanical properties of the propellant are superior to polyurethane with an improvement of 14% in tensile strength, 22% enhancement in elongation at break, and 12% in modulus.

Gamma oscillations in the midbrain spatial attention network: linking circuits to function

Gamma-band (25-140 Hz) oscillations are ubiquitous in mammalian forebrain structures involved in sensory processing, attention, learning and memory. The optic tectum (01) is the central structure in a midbrain network that participates critically in controlling spatial attention. In this review, we summarize recent advances in characterizing a neural circuit in this midbrain network that generates large amplitude, space-specific, gamma oscillations in the avian OT, both in vivo and in vitro. We describe key physiological and pharmacological mechanisms that produce and regulate the structure of these oscillations. The extensive similarities between midbrain gamma oscillations in birds and those in the neocortex and hippocampus of mammals, offer important insights into the functional significance of a midbrain gamma oscillatory code.

Voice source characterization using pitch synchronous discrete cosine transform for speaker identification

A characterization of the voice source (VS) signal by the pitch synchronous (PS) discrete cosine transform (DCT) is proposed. With the integrated linear prediction residual (ILPR) as the VS estimate, the PS DCT of the ILPR is evaluated as a feature vector for speaker identification (SID). On TIMIT and YOHO databases, using a Gaussian mixture model (GMM)-based classifier, it performs on par with existing VS-based features. On the NIST 2003 database, fusion with a GMM-based classifier using MFCC features improves the identification accuracy by 12% in absolute terms, proving that the proposed characterization has good promise as a feature for SID studies. (C) 2015 Acoustical Society of America

Linking carbon metabolism to carotenoid production in mycobacteria using Raman spectroscopy

Bacteria can utilize multiple sources of carbon for growth, and for pathogenic bacteria like Mycobacterium tuberculosis, this ability is crucial for survival within the host. In addition, phenotypic changes are seen in mycobacteria grown under different carbon sources. In this study, we use Raman spectroscopy to analyze the biochemical components present in M. smegmatis cells when grown in three differently metabolized carbon sources. Our results show that carotenoid biosynthesis is enhanced when M. smegmatis is grown in glucose compared to glycerol and acetate. We demonstrate that this difference is most likely due to transcriptional upregulation of the carotenoid biosynthesis operon (crt) mediated by higher levels of the stress-responsive sigma factor SigF. Moreover, we find that increased SigF and carotenoid levels correlate with greater resistance of glucose-grown cells to oxidative stress. Thus, we demonstrate the use of Raman spectroscopy in unraveling unknown aspects of mycobacterial physiology and describe a novel effect of carbon source variation on mycobacteria.

Linking monazite geochronology with fluid infiltration and metamorphic histories: Nature and experiment

Migmatised metapelites from the Kodaikanal region, central Madurai Block, southern India have undergone ultrahigh-temperature metamorphism (950-1000 degrees C; 7-8 kbar). In-situ electron microprobe Th-U-Pb isochron (CHIME) dating of monazites in a leucosome and surrounding silica-saturated and silica-poor restites from the same outcrop indicates three principal ages that can be linked to the evolutionary history of these rocks. Monazite grains from the silica-saturated restite have well-defined, inherited cores with thick rims that yield an age of ca. 1684 Ma. This either dates the metamorphism of the original metapelite or is a detrital age of inherited monazite. Monazite grains from the silica-poor restite, thick rims from the silica-saturated restite, and monazite cores from the leucosome have ages ranging from 520 to 540 Ma suggesting a mean age of 530 Ma within the error bars. In the leucosome the altered rim of the monazite gives an age of ca. 502 Ma. Alteration takes the form of Th-depleted lobes of monazite with sharp curvilinear boundaries extending from the monazite grain rim into the core. We have replicated experimentally these altered rims in a monazite-leucosome experiment at 800 degrees C and 2 kbar. This experiment, coupled with earlier published monazite-fluid experiments involving high pH alkali-bearing fluids at high P-T, helps to confirm the idea that alkali-bearing fluids, in the melt and along grain boundaries during crystallization, were responsible for the formation of the altered monazite grain rims via the process of coupled dissolution-reprecipitation. (C) 2015 Elsevier B.V. All rights reserved.