Geophysical signatures associated with fluid flow and gas hydrate occurrence in a tectonically quiescent sequence, Qiongdongnan Basin, South China Sea

Interpretation of high-resolution two-dimensional (2D) and three-dimensional (3D) seismic data collected in the Qiongdongnan Basin, South China Sea reveals the presence of polygonal faults, pockmarks, gas chimneys and slope failure in strata of Pliocene and younger age. The gas chimneys are characterized by low-amplitude reflections, acoustic turbidity and low P-wave velocity indicating fluid expulsion pathways. Coherence time slices show that the polygonal faults are restricted to sediments with moderate-amplitude, continuous reflections. Gas hydrates are identified in seismic data by the presence of bottom simulating reflectors (BSRs), which have high amplitude, reverse polarity and are subparallel to seafloor. Mud diapirism and mounded structures have variable geometry and a great diversity regarding the origin of the fluid and the parent beds. The gas chimneys, mud diapirism, polygonal faults and a seismic facies-change facilitate the upward migration of thermogenic fluids from underlying sediments. Fluids can be temporarily trapped below the gas hydrate stability zone, but fluid advection may cause gas hydrate dissociation and affect the thickness of gas hydrate zone. The fluid accumulation leads to the generation of excess pore fluids that release along faults, forming pockmarks and mud volcanoes on the seafloor. These features are indicators of fluid flow in a tectonically-quiescent sequence, Qiongdongnan Basin. Geofluids (2010) 10, 351-368.

Effective ac response in weakly nonlinear composites

The perturbation method is developed to deal with the problem of determining the effective nonlinear conductivity of Kerr-like nonlinear media under an external ac electric field. As an example, we have considered the cylindrical inclusion embedded in a host under the sinusoidal external field E-1 sin(omegat) + E-3 sin(3omegat) with frequencies omega and 3omega. The potentials of composites at higher harmonics are derived in both local inclusion particle and host regions. The effective responses of bulk nonlinear composites at basic frequency and harmonics are given for cylindrical composites in the dilute limit. Moreover, the relationships between the nonlinear effective responses at the basic frequency and the third harmonics are derived.

A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta

Background: There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum. Results: The mitochondrial genome of P. esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups. Conclusion: This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

Mitochondrial cytochrome b sequence variation and phylogenetics of the highly specialized schizothoracine fishes (Teleostei : Cyprinidae) in the Qinghai-Tibet Plateau

The complete 1140 bp mitochondial cytochrome b sequences were obtained from 39 individuals representing five species of all four genera of highly specialized schizothoracine fishes distributed in the Qinghai-Tibet plateau. Sequence variation of the cytochrome b gene was surveyed among the 39 individuals as well as three primitive schizothoracines and one outgroup. Phylogenetic analysis suggested that the group assignment based on 1140 bp of the cytochrome b sequence is obviously; different from previous assignments, and the highly specialized schizothoracine fishes (Schizopygopsis pylzovi, Gymnocypris przewalskii, G. eckloni, Chuanchia lablosa, and Platypharodon extremus) form a monophyletic group that is sister to the clade formed by the primitive schizothoracine fishes (Schizothorax prenanti, S. pseudaksaiensis, and S. argentatus). The haplotypes of Schizopygopsis pylzovi and G. przewalskii were paraphyletic based on cytochrome b data, which most likely reflected incomplete sorting of mitochondrial DNA lineages. The diploid chromosome numbers of Schizofhoracinae were considered in phylogenetic analysis and provided a clear pattern of relationships. Molecular dating estimated for highly specialized schizothoracine fishes suggested that the highly specialized schizothoracine fishes diverged in the late Miocene Pliocene to Pleistocene (4.5x10(4)-4.05x10(6) Years BP). The relationship between the cladogenesis of highly specialized schizothoracine fishes and geographical events of the Qinghai-Tibet plateau is discussed.

Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation

The vegetation of the northeast Qinghai-Tibetan Plateau is dominated by alpine meadow and desert-steppe with sparse forests scattered within it. To obtain a better understanding of the phylogeography of one constituent species of the forests in this region, we examined chloroplast trnT-trnF and trnS-trnG sequence variation within Juniperus przewalskii, a key endemic tree species. Sequence data were obtained from 392 trees in 20 populations covering the entire distribution range of the species. Six cpDNA haplotypes were identified. Significant population subdivision was detected (G(ST) = 0.772, N-ST = 0.834), suggesting low levels of recurrent gene flow among populations and significant phylogeographic structure (N-ST > G(ST), P < 0.05). Eight of the nine disjunct populations surveyed on the high-elevation northeast plateau were fixed for a single haplotype (A), while the remaining, more westerly population, contained the same haplotype at high frequency together with two low frequency haplotypes (C and F). In contrast, most populations that occurred at lower altitudes at the plateau edge were fixed or nearly fixed for one of two haplotypes, A or E. However, two plateau edge populations had haplotype compositions different from the rest. In one, four haplotypes (A, B, D and E) were present at approximately equivalent frequencies, which might reflect a larger refugium in the area of this population during the last glacial period. Phylogenetic analysis indicated that the most widely distributed haplotype A is not ancestral to other haplotypes. The contrasting phylogeographic structures of the haplotype-rich plateau edge area and the almost haplotype-uniform plateau platform region indicate that the plateau platform was recolonized by J. przewalskii during the most recent postglacial period. This is supported by the findings of a nested clade analysis, which inferred that postglacial range expansion from the plateau edge followed by recent fragmentation is largely responsible for the present-day spatial distribution of cpDNA haplotypes within the species.

A new species of Saussurea (Asteraceae) from Tibet and its systematic position based on ITS sequence analysis

A new species of Saussurea, S. erecta S. W Liu, J. T Pan A J. Q. Liu sp. nov., is described from Tibet. It resembles S. kingii but may be distinguished by having distinct stems and glabrous achenes. Saussurea kingii was placed in sect. Pseudoeriocoryne of subgen. Eriocoryne; this section was circumscribed by acaulescence and an inflorescence with congested capitula surrounded by a rosette of leaves. The discovery of S. erecta with distinct stems, cauline leaves and corymbose capitula blurred the delimitation of sect. Pseudoeriocoryne and suggested that the section may be polyphyletic. Both the close relationship and the significant difference between S. erecta and S. kingii were confirmed by analyses of nrDNA ITS sequences. The resulting phylogenies based on ITS data further suggest that Saussurea sect. Pseudoeriocoryne, as traditionally defined, does not constitute a monophyletic group. The rapid radiation and speciation of Saussurea in the Qinghai-Tibetan Plateau, as inferred from ITS phylogeny, are discussed. (c) 2005 The Linnean Society of London.

Comonomer sequence distribution in metallocene-based ethylene/1-butene (S-34) and ethylene/1-hexene (S-43) copolymers

Metallocene based polyethylenes were prepared by SMOPEC's "metallocene adduct" technology in a gas phase fluidized bed model reactor. The C-13-NMR spectra of ethylene/1-butene (S-34) and ethylene/1-hexene(S-43) copolymers were studied in a manner analogous to that established by Hsieh and Cheng. The comonomer sequence distributions of copolymer samples were obtained. The results show that these metallocene based copolymers contain a small amount of butene and hexene, and the EE and EEE sequences are dominant.

Sequence-Seeking and Counter Streams: A Model for Information Processing in the Cortex

This paper presents a model for the general flow in the neocortex. The basic process, called "sequence-seeking," is a search for a sequence of mappings or transformations, linking source and target representations. The search is bi-directional, "bottom-up" as well as "top-down," and it explores in parallel a large numbe rof alternative sequences. This operation is implemented in a structure termed "counter streams," in which multiple sequences are explored along two separate, complementary pathways which seeking to meet. The first part of the paper discusses the general sequence-seeking scheme and a number of related processes, such as the learning of successful sequences, context effects, and the use of "express lines" and partial matches. The second part discusses biological implications of the model in terms of connections within and between cortical areas. The model is compared with existing data, and a number of new predictions are proposed.

Homology Induction: the use of machine learning to improve sequence similarity searches

Karwath, A. King, R. Homology induction: the use of machine learning to improve sequence similarity searches. BMC Bioinformatics. 23rd April 2002. 3:11 Additional File Describes the title organims species declaration in one string [http://www.biomedcentral.com/content/supplementary/1471- 2105-3-11-S1.doc] Sponsorship: Andreas Karwath and Ross D. King were supported by the EPSRC grant GR/L62849.

Learning styles and performance in the introductory programming sequence

Thomas, L., Ratcliffe, M., Woodbury, J., and Jarman, E. 2002. Learning styles and performance in the introductory programming sequence. SIGCSE Bull. 34, 1 (Mar. 2002), 33-37.

Analysis of Sequence Periodicity in E. coli Proteins: Empirical Investigation of the ?Duplication and Divergence? Theory of Protein Evolution

Gatherer, D., and McEwan, N.R. (2003). Analysis of sequence periodicity in E. coli proteins: empirical investigation of the 'duplication and divergence' theory of protein evolution. Journal of Molecular Evolution 57, 149-158. RAE2008

A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data

Mark Pagel, Andrew Meade (2004). A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Systematic Biology, 53(4), 571-581. RAE2008

From Parallel Sequence Representations to Calligraphic Control: A Conspiracy of Neural Circuits

Calligraphic writing presents a rich set of challenges to the human movement control system. These challenges include: initial learning, and recall from memory, of prescribed stroke sequences; critical timing of stroke onsets and durations; fine control of grip and contact forces; and letter-form invariance under voluntary size scaling, which entails fine control of stroke direction and amplitude during recruitment and derecruitment of musculoskeletal degrees of freedom. Experimental and computational studies in behavioral neuroscience have made rapid progress toward explaining the learning, planning and contTOl exercised in tasks that share features with calligraphic writing and drawing. This article summarizes computational neuroscience models and related neurobiological data that reveal critical operations spanning from parallel sequence representations to fine force control. Part one addresses stroke sequencing. It treats competitive queuing (CQ) models of sequence representation, performance, learning, and recall. Part two addresses letter size scaling and motor equivalence. It treats cursive handwriting models together with models in which sensory-motor tmnsformations are performed by circuits that learn inverse differential kinematic mappings. Part three addresses fine-grained control of timing and transient forces, by treating circuit models that learn to solve inverse dynamics problems.

SOVEREIGN: An Autonomous Neural System for Incrementally Learning Planned Action Sequence to Navigate Towards a Rewarded Goal

How do reactive and planned behaviors interact in real time? How are sequences of such behaviors released at appropriate times during autonomous navigation to realize valued goals? Controllers for both animals and mobile robots, or animats, need reactive mechanisms for exploration, and learned plans to reach goal objects once an environment becomes familiar. The SOVEREIGN (Self-Organizing, Vision, Expectation, Recognition, Emotion, Intelligent, Goaloriented Navigation) animat model embodies these capabilities, and is tested in a 3D virtual reality environment. SOVEREIGN includes several interacting subsystems which model complementary properties of cortical What and Where processing streams and which clarify similarities between mechanisms for navigation and arm movement control. As the animat explores an environment, visual inputs are processed by networks that are sensitive to visual form and motion in the What and Where streams, respectively. Position-invariant and sizeinvariant recognition categories are learned by real-time incremental learning in the What stream. Estimates of target position relative to the animat are computed in the Where stream, and can activate approach movements toward the target. Motion cues from animat locomotion can elicit head-orienting movements to bring a new target into view. Approach and orienting movements are alternately performed during animat navigation. Cumulative estimates of each movement are derived from interacting proprioceptive and visual cues. Movement sequences are stored within a motor working memory. Sequences of visual categories are stored in a sensory working memory. These working memories trigger learning of sensory and motor sequence categories, or plans, which together control planned movements. Predictively effective chunk combinations are selectively enhanced via reinforcement learning when the animat is rewarded. Selected planning chunks effect a gradual transition from variable reactive exploratory movements to efficient goal-oriented planned movement sequences. Volitional signals gate interactions between model subsystems and the release of overt behaviors. The model can control different motor sequences under different motivational states and learns more efficient sequences to rewarded goals as exploration proceeds.