Language learning in infancy

Although immensely complex, speech is also a very efficient means of communication between humans. Understanding how we acquire the skills necessary for perceiving and producing speech remains an intriguing goal for research. However, while learning is likely to begin as soon as we start hearing speech, the tools for studying the language acquisition strategies in the earliest stages of development remain scarce. One prospective strategy is statistical learning. In order to investigate its role in language development, we designed a new research method. The method was tested in adults using magnetoencephalography (MEG) as a measure of cortical activity. Neonatal brain activity was measured with electroencephalography (EEG). Additionally, we developed a method for assessing the integration of seen and heard syllables in the developing brain as well as a method for assessing the role of visual speech when learning phoneme categories. The MEG study showed that adults learn statistical properties of speech during passive listening of syllables. The amplitude of the N400m component of the event-related magnetic fields (ERFs) reflected the location of syllables within pseudowords. The amplitude was also enhanced for syllables in a statistically unexpected position. The results suggest a role for the N400m component in statistical learning studies in adults. Using the same research design with sleeping newborn infants, the auditory event-related potentials (ERPs) measured with EEG reflected the location of syllables within pseudowords. The results were successfully replicated in another group of infants. The results show that even newborn infants have a powerful mechanism for automatic extraction of statistical characteristics from speech. We also found that 5-month-old infants integrate some auditory and visual syllables into a fused percept, whereas other syllable combinations are not fully integrated. Auditory syllables were paired with visual syllables possessing a different phonetic identity, and the ERPs for these artificial syllable combinations were compared with the ERPs for normal syllables. For congruent auditory-visual syllable combinations, the ERPs did not differ from those for normal syllables. However, for incongruent auditory-visual syllable combinations, we observed a mismatch response in the ERPs. The results show an early ability to perceive speech cross-modally. Finally, we exposed two groups of 6-month-old infants to artificially created auditory syllables located between two stereotypical English syllables in the formant space. The auditory syllables followed, equally for both groups, a unimodal statistical distribution, suggestive of a single phoneme category. The visual syllables combined with the auditory syllables, however, were different for the two groups, one group receiving visual stimuli suggestive of two separate phoneme categories, the other receiving visual stimuli suggestive of only one phoneme category. After a short exposure, we observed different learning outcomes for the two groups of infants. The results thus show that visual speech can influence learning of phoneme categories. Altogether, the results demonstrate that complex language learning skills exist from birth. They also suggest a role for the visual component of speech in the learning of phoneme categories.

Perpetuation of immunological memory through common MHC-I binding modes of peptidomimic and antigenic peptides

Understanding the molecular mechanisms of immunological memory assumes importance in vaccine design. We had earlier hypothesized a mechanism for the maintenance of immunological memory through the operation of a network of idiotypic and anti-idiotypic antibodies (Ab2). Peptides derived from an internal image carrying anti-idiotypic antibody are hypothesized to facilitate the perpetuation of antigen specific T cell memory through similarity in peptide-MHC binding as that of the antigenic peptide. In the present work, the existence of such peptidomimics of the antigen in the Ab2 variable region and their similarity of MHC-I binding was examined by bioinformatics approaches. The analysis employing three known viral antigens and one tumor-associated antigen shows that peptidomimics from Ab2 variable regions have structurally similar MHC-I binding patterns as compared to antigenic peptides, indicating a structural basis for memory perpetuation. (C)) 2007 Elsevier Inc. All rights reserved.

Selective dissemination of XML documents based on genetically learned user model and Support Vector Machines

Extensible Markup Language ( XML) has emerged as a medium for interoperability over the Internet. As the number of documents published in the form of XML is increasing, there is a need for selective dissemination of XML documents based on user interests. In the proposed technique, a combination of Adaptive Genetic Algorithms and multi class Support Vector Machine ( SVM) is used to learn a user model. Based on the feedback from the users, the system automatically adapts to the user's preference and interests. The user model and a similarity metric are used for selective dissemination of a continuous stream of XML documents. Experimental evaluations performed over a wide range of XML documents, indicate that the proposed approach significantly improves the performance of the selective dissemination task, with respect to accuracy and efficiency.

Three-dimensional structure of heat shock protein 90 from Plasmodium falciparum: molecular modelling approach to rational drug design against malaria

We have recently implicated heat shock protein 90 from Plasmodium falciparum (PfHsp90) as a potential drug target against malaria. Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory effects on development of malarial parasite in human erythrocytes. To gain better understanding of the vital role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length structure of yeast Hsp90. Sequence similarity found between PfHsp90 and yeast Hsp90 allowed us to model the core structure with high confidence. The superimposition of the predicted structure with that of the template yeast Hsp90 structure reveals an RMSD of 3.31 angstrom. The N-terminal and middle domains showed the least RMSD (1.76 angstrom) while the more divergent C-terminus showed a greater RMSD (2.84 angstrom) with respect to the template. The structure shows overall conservation of domains involved in nucleotide binding, ATPase activity, co-chaperone binding as well as inter-subunit interactions. Important co-chaperones known to modulate Hsp90 function in other eukaryotes are conserved in malarial parasite as well. An acidic stretch of amino acids found in the linker region, which is uniquely extended in PfHsp90 could not be modeled in this structure suggesting a flexible conformation. Our results provide a basis to compare the overall structure and functional pathways dependent on PfHsp90 in malarial parasite. Further analysis of differences found between human and parasite Hsp90 may make it possible to design inhibitors targeted specifically against malaria.

Eddy diffusivity: A single dispersion analysis of high resolution drifters in a tidal shallow estuary

In an estuary, mixing and dispersion resulting from turbulence and small scale fluctuation has strong spatio-temporal variability which cannot be resolved in conventional hydrodynamic models while some models employs parameterizations large water bodies. This paper presents small scale diffusivity estimates from high resolution drifters sampled at 10 Hz for periods of about 4 hours to resolve turbulence and shear diffusivity within a tidal shallow estuary (depth < 3 m). Taylor's diffusion theorem forms the basis of a first order estimate for the diffusivity scale. Diffusivity varied between 0.001 – 0.02 m2/s during the flood tide experiment. The diffusivity showed strong dependence (R2 > 0.9) on the horizontal mean velocity within the channel. Enhanced diffusivity caused by shear dispersion resulting from the interaction of large scale flow with the boundary geometries was observed. Turbulence within the shallow channel showed some similarities with the boundary layer flow which include consistency with slope of 5/3 predicted by Kolmogorov's similarity hypothesis within the inertial subrange. The diffusivities scale locally by 4/3 power law following Okubo's scaling and the length scale scales as 3/2 power law of the time scale. The diffusivity scaling herein suggests that the modelling of small scale mixing within tidal shallow estuaries can be approached from classical turbulence scaling upon identifying pertinent parameters.

Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules,naiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. (C) 2009 Elsevier Ltd. All rights reserved.

Unraveling the packing pattern leading to gelation using SS NMR and X-ray diffraction: direct observation of the evolution of self-assembled fibers

A detailed understanding of the mode of packing patterns that leads to the gelation of low molecular mass gelators derived from bile acid esters was carried out using solid state NMR along with complementary techniques such as powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and polarizing optical microscopy (POM). Solid state C-13{H-1} cross polarization (CP) magic angle spinning (MAS) NMR of the low molecularmass gel in its native state was recorded for the first time. A close resemblance in the packing patterns of the gel, xerogel and bulk solid states was revealed upon comparing their C-13{H-1} CPMAS NMR spectral pattern. A doublet resonance pattern of C-13 signals in C-13{H-1}CPMAS NMR spectra were observed for the gelator molecules, whereas the non-gelators showed simple singlet resonance or resulted inthe formation of inclusion complexes/solvates. PXRD patterns revealed a close isomorphous nature of the gelators indicating the similarity in the mode of the packing pattern in their solid state. Direct imaging of the evolution of nanofibers (sol-gel transition) was carried out using POM, which proved the presence of self-assembled fibrillar networks (SAFINs) in the gel. Finally powder X-ray structure determination revealed the presence of two non-equivalent molecules in an asymmetric unit which is responsible for the doublet resonance pattern in the solid state NMR spectra.

Selective dissemination of XML documents based on genetically learned user model and Support Vector Machines

Extensible Markup Language ( XML) has emerged as a medium for interoperability over the Internet. As the number of documents published in the form of XML is increasing, there is a need for selective dissemination of XML documents based on user interests. In the proposed technique, a combination of Adaptive Genetic Algorithms and multi class Support Vector Machine ( SVM) is used to learn a user model. Based on the feedback from the users, the system automatically adapts to the user's preference and interests. The user model and a similarity metric are used for selective dissemination of a continuous stream of XML documents. Experimental evaluations performed over a wide range of XML documents, indicate that the proposed approach significantly improves the performance of the selective dissemination task, with respect to accuracy and efficiency.

Unusual RNA plant virus integration in the soybean genome leads to the production of small RNAs

Horizontal gene transfer (HGT) is known to be a major force in genome evolution. The acquisition of genes from viruses by eukaryotic genomes is a well-studied example of HGT, including rare cases of non-retroviral RNA virus integration. The present study describes the integration of cucumber mosaic virus RNA-1 into soybean genome. After an initial metatranscriptomic analysis of small RNAs derived from soybean, the de novo assembly resulted a 3029-nt contig homologous to RNA-1. The integration of this sequence in the soybean genome was confirmed by DNA deep sequencing. The locus where the integration occurred harbors the full RNA-1 sequence followed by the partial sequence of an endogenous mRNA and another sequence of RNA-1 as an inverted repeat and allowing the formation of a hairpin structure. This region recombined into a retrotransposon located inside an exon of a soybean gene. The nucleotide similarity of the integrated sequence compared to other Cucumber mosaic virus sequences indicates that the integration event occurred recently. We described a rare event of non-retroviral RNA virus integration in soybean that leads to the production of a double-stranded RNA in a similar fashion to virus resistance RNAi plants.

Characterization of the interaction of lipid A and lipopolysaccharide with human serum albumin: implications for an endotoxin carrier function for albumin

The interactions of lipid A and lipopolysaccharide (LPS) with human serum albumin (HSA) were examined using fluorescence methods. Lipid A binds HSA with a stoichiometry of 2:1 with dissociation constants of 1.0 µM and 6.0 µM for the high- and low-affinity interactions, respectively. Lipid A displaces HSA-bound dansylsarcosine competitively, but not HSA-bound warfarin, suggesting that domain III-A, and not domain 11-A, is a lipid A binding site. Domain I does not contribute a site for lipid A. Based on these data, and the structural similarity between subdomains III-A and III-B, it is proposed that these two regions of HSA represent the high- and low-affinity sites of interaction of lipid A. Whole LPS also binds HSA, displacing dansylsarcosine, and its lipid A moiety appears to be the interaction site. However, there are differences between LPS and free lipid A. Polymyxin B forms ternary complexes with LPS bound to HSA, suggesting that the regions on LPS recognized by HSA and polymyxin B are different. The observed affinity of lipid A for HSA and mass action effects due to its abundance in the circulation would imply a major LPS carrier function for HSA.

Exploring the interaction energies for the binding of hydroxydiphenyl ethers to enoyl-acyl carrier protein reductases

It is now well established that the potent anti-microbial compound, triclosan, interrupts the type II fatty acid synthesis by inhibiting the enzyme enoyl-ACP reductase in a number of organisms. Existence of a high degree of similarity between the recently discovered enoyl-ACP reductase from R falciparum and B. napus enzyme permitted building of a satisfactory model for the former enzyme that explained some of the key aspects of the enzyme such as its specificity for binding to the cofactor and the inhibitor. We now report the interaction energies between triclosan and other hydroxydiphenyl ethers with the enzymes from B. napus, E. coli and R falciparum. Examination of the triclosan-enzyme interactions revealed that subtle differences exist in the ligand binding sites of the enzymes from different sources i.e., B. napus, E. coli and P falciparum. A comparison of their binding propensities thus determined should aid in the design of effective inhibitors for the respective enzymes.

Selective dissemination of XML documents using GAs and SVM

XML has emerged as a medium for interoperability over the Internet. As the number of documents published in the form of XML is increasing there is a need for selective dissemination of XML documents based on user interests. In the proposed technique, a combination of Self Adaptive Migration Model Genetic Algorithm (SAMCA)[5] and multi class Support Vector Machine (SVM) are used to learn a user model. Based on the feedback from the users the system automatically adapts to the user's preference and interests. The user model and a similarity metric are used for selective dissemination of a continuous stream of XML documents. Experimental evaluations performed over a wide range of XML documents indicate that the proposed approach significantly improves the performance of the selective dissemination task, with respect to accuracy and efficiency.

Regeneration ecology and woody species diversity in the remnant natural forest at Wondo Genet, Ethiopia – Potential for landscape restoration

Regeneration ecology, diversity of native woody species and its potential for landscape restoration was studied in the remnant natural forest at the College of Forestry and Natural Resources at Wondo Genet, Ethiopia. The type of forest is Afromontane rainforest , with many valuable tree species like Aningeria adolfi-friederici, and it is an important provider of ecological, social and economical services for the population that lives in this area. The study contains two parts, natural regeneration studies (at the natural forest) and interviews with farmers in the nearby village of the remnant patch. The objective of the first part was to investigate the floristic composition, densitiy and regeneration profiles of native woody species in the forest, paying special attention to woody species that are considered the most relevant (socio-economic). The second part provided information on woody species preferred by the farmers and on multiple uses of the adjacent natural forest, it also provided information and analysed perceptions on forest degradation. Systematic plot sampling was used in the forest inventory. Twenty square plots of 20 x 20 m were assessed, with 38 identified woody species (the total number of species was 45), representing 26 families. Of these species 61% were trees, 13% shrubs, 11% lianas and 16% species that could have both life forms. An analysis of natural regeneration of five important tree species in the natural forest showed that Aningeria adolfi-friederici had the best regeneration results. An analysis of population structure (as determined by height classes) of two commercially important woody species in the forest, Aningeria adolfi-friederici and Podocarpus falcatus, showed a marked difference: Aningeria had a typical “reversed J” frequency distribution, while Podocarpus showed very low values in all height classes. Multi dimensional scaling (MDS) was used to map the sample plots according to their similarity in species composition, using the Sørensen quantitative index, coupled with indicator species analysis .Three groups were identified with respective indicator species: Group 1 – Adhatoda schimperiana, Group 2 – Olea hochstetteri , Group 3 – Acacia senegal and Aningeria adolfi-friederici. Thirty questionnaire interviews were conducted with farmers in the village of Gotu Onoma that use the nearby remant forest patch. Their tree preferences were exotic species such as Eucalyptus globulus for construction and fuelwood and Grevillea robusta for shade and fertility. Considering forest land degradation farmers were aware of the problem and suggested that the governmental institutions address the problem by planting more Eucalyptus globulus. The natural forest seemed to have moderate levels of disturbance and it was still floristically diverse. However, the low rate of natural regeneration of Podocarpus falcatus suggested that this species is threatened and must be a priority in conservation actions. Plantations and agroforestry seem to be possible solutions for rehabilitation of the surrounding degraded lands, thereby decreasing the existent pressure in the remnant natural forest.

Propagation of a spherical shock in an inhomogeneous self-gravitating or nongravitating system

The propagation of a shock wave of finite strength due to an explosion into inhomogeneous nongravitating and self-gravitating systems has been considered, using similarity principles, supposing that the density varies as an inverse power of distance from the centre of explosion. A large number of systems, characterised by different density exponents and different adiabatic coefficients of the gas have been considered for different shock strengths. The numerical integration from the shock inward has been continued to the surface of singularity where density tends to infinity and which acts like a piston in the self-gravitating case and to the surface where the velocity gradient tends to infinity in the nongravitating case. The effect of variation of shock strength, density exponent and adiabatic coefficient on the location of these singularities and on the distribution of flow parameters behind the shock has been studied. The initial energy of the system and the manner of release of the explosion energy influence strongly the flow behind the shock. The results have been graphically depicted.

The buoyant plume above a heat source

The boundary-layer type conservation equations of mass, momentum and energy for the steady free turbulent flow in gravitational convection over heat sources are set up for both two-dimensional and axisymmetric cases. These are reduced to ordinary differential equations in a similarity parameter by suitable transformations. The three classical hypotheses of turbulent diffusion-the Constant Exchange Coefficient hypothesis, Prandtl's Momentum Transfer theory and Taylor's Vorticity Transfer theory-are then incorporated into these equations in succession. The resulting equations are solved numerically and the results compared with some experimental results on gravitational convection over heat sources reported by Rouse et al.