The diamond pyramid structure in electroless copper deposit, its atomic model and molecular dynamics simulation

In this seminar, I will talk about the discovery of the diamond pyramid structures in the electroless copper deposits on both epoxy and stainless steel substrates. The surface morphology of the structure was characterized with scanning electron microscopy (SEM). According to the morphological feature of the structure, an atom model was brought forward in order to describe the possible mechanism of forming such structure. Molecular dynamics simulations were then carried out to investigate the growing process of the diamond pyramid structure. The final structures of the simulation were compared with the SEM images and the atomic model. The radial distribution function of the final structures of the simulation was compared with that calculated from the X-ray diffraction pattern of the electroless copper deposit sample.

A Novel Packet Marking Function for Real-Time Interactive MPEG-4 Video Applications in a Differentiated Services Network

The future convergence of voice, video and data applications on the Internet requires that next generation technology provides bandwidth and delay guarantees. Current technology trends are moving towards scalable aggregate-based systems where applications are grouped together and guarantees are provided at the aggregate level only. This solution alone is not enough for interactive video applications with sub-second delay bounds. This paper introduces a novel packet marking scheme that controls the end-to-end delay of an individual flow as it traverses a network enabled to supply aggregate- granularity Quality of Service (QoS). IPv6 Hop-by-Hop extension header fields are used to track the packet delay encountered at each network node and autonomous decisions are made on the best queuing strategy to employ. The results of network simulations are presented and it is shown that when the proposed mechanism is employed the requested delay bound is met with a 20% reduction in resource reservation and no packet loss in the network.

Network biology: a direct approach to study biological function

In this paper we discuss the dualism of gene networks and their role in systems biology. We argue that gene networks ( 1) can serve as a conceptual framework, forming a fundamental level of a phenomenological description, and ( 2) are a means to represent and analyze data. The latter point does not only allow a systems analysis but is even amenable for a direct approach to study biological function. Here we focus on the clarity of our main arguments and conceptual meaning of gene networks, rather than the causal inference of gene networks from data. (C) 2010 John Wiley & Sons, Inc. WIREs Syst Biol Med 2011 3 379-391 DOI: 10.1002/wsbm.134

Neurobiological model of visuo-spatial cognition in young Williams Syndrome children: measures of dorsal-stream and frontal function

We examine hypotheses for the neural basis of the profile of visual cognition in young children with Williams syndrome (WS). These are: (a) that it is a consequence of anomalies in sensory visual processing; (b) that it is a deficit of the dorsal relative to the ventral cortical stream; (c) that it reflects deficit of frontal function, in particular of fronto-parietal interaction; (d) that it is related to impaired function in the right hemisphere relative to the left. The tests reported here are particularly relevant to (b) and (c). They form part of a more extensive programme of investigating visual, visuospatial, and cognitive function in large group of children with WS children, aged 8 months to 15 years. To compare performance across tests, avoiding floor and ceiling effects, we have measured performance in children with WS in terms of the ‘age equivalence’ for typically developing children. In this paper the relation between dorsal and ventral function was tested by motion and form coherence thresholds respectively. We confirm the presence of a subgroup of children with WS who perform particularly poorly on the motion (dorsal) task. However, such performance is also characteristic of normally developingchildren up to 5 years: thus the WS performance may reflect an overall persisting immaturity of visuospatial processing which is particularly evident in the dorsal stream. Looking at the performance on the global coherence tasks of the entire WS group, we find that there is also a subgroup who have both high form and motion coherence thresholds, relative to the performance of children of the same chronological age and verbal age on the BPVS, suggesting a more general global processing deficit. Frontal function was tested by a counterpointing task, ability to retrieve a ball from a ‘detour box’, and the Stroop-like ‘day-night’ task, all of which require inhibition of a familiar response. When considered in relation to overall development as indexed by vocabulary, the day-night task shows little specific impairment, the detour box shows a significant delay relative to controls, and the counterpointing task shows a marked and persistent deficit in many children. We conclude that frontal control processes show most impairment in WS when they are associated with spatially directed responses, reflecting a deficit of fronto-parietal processing. However, children with WS may successfully reduce the effect of this impairment by verbally mediated strategies. On all these tasks we find a range of difficulties across individual children and a small subset of WS who show very good performance, equivalent to chronological age norms of typically developing children. Neurobiological models of visuo-spatial cognition in children with WS p.4 Overall, we conclude that children with WS have specific processing difficulties with tasks involving frontoparietal circuits within the spatial domain. However, some children with WS can achieve similar performance to typically developing children on some tasks involving the dorsal stream, although the strategies and processing may be different in the two groups.

Performance analysis of an improved power-saving medium access protocol for IEEE 802.11 point coordination function WLAN

Wireless enabled portable devices must operate with the highest possible energy efficiency while still maintaining a minimum level and quality of service to meet the user's expectations. The authors analyse the performance of a new pointer-based medium access control protocol that was designed to significantly improve the energy efficiency of user terminals in wireless local area networks. The new protocol, pointer controlled slot allocation and resynchronisation protocol (PCSAR), is based on the existing IEEE 802.11 point coordination function (PCF) standard. PCSAR reduces energy consumption by removing the need for power saving stations to remain awake and listen to the channel. Using OPNET, simulations were performed under symmetric channel loading conditions to compare the performance of PCSAR with the infrastructure power saving mode of IEEE 802.11, PCF-PS. The simulation results demonstrate a significant improvement in energy efficiency without significant reduction in performance when using PCSAR. For a wireless network consisting of an access point and 8 stations in power saving mode, the energy saving was up to 31% while using PCSAR instead of PCF-PS, depending upon frame error rate and load. The results also show that PCSAR offers significantly reduced uplink access delay over PCF-PS while modestly improving uplink throughput.

Optimal basis set for electronic structure calculations in periodic systems

An efficient method for calculating the electronic structure of systems that need a very fine sampling of the Brillouin zone is presented. The method is based on the variational optimization of a single (i.e., common to all points in the Brillouin zone) basis set for the expansion of the electronic orbitals. Considerations from k.p-approximation theory help to understand the efficiency of the method. The accuracy and the convergence properties of the method as a function of the optimal basis set size are analyzed for a test calculation on a 16-atom Na supercell.

UKCP: A Collaborative network of cerebral palsy registers in the United Kingdom

Cerebral palsy (CP) is a relatively rare condition with enormous social and financial impact. Information about CP is not routinely collected in the United Kingdom. We have pooled non-identifiable data from the five currently active UK CP registers to form the UKCP database: birth years 1960–1997. This article describes the rationale behind this collaboration and the creation of the database. Data about 6910 children with CP are currently held. The mean annual prevalence rate was 2.0 per 1000 live births for birth years 1986–1996. Where type is known, 91 per cent have spastic CP. Where data are available, nearly one-third of children have severely impaired lower limb function, and nearly a quarter have severely impaired upper limb function. As well as describing the range and complexity of motor and associated impairments, the pooled data from the UKCP database provide a platform for studies of aetiology, long-term outcomes, participation and service needs. The UKCP database is an important national resource for the surveillance of CP and the study of its epidemiology in the United Kingdom.

Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling

Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules, which are defined as groups of reactions with correlated fluxes, there is a need for experimental verification. We show here that multivariate statistical analysis of the NMR-derived intra- and extracellular metabolite profiles of single-gene deletion mutants in specific metabolic pathways in the yeast Saccharomyces cerevisiae identified outliers whose profiles were markedly different from those of the other mutants in their respective pathways. Application of flux coupling analysis to a metabolic model of this yeast showed that the deleted gene in an outlying mutant encoded an enzyme that was not part of the same functional network module as the other enzymes in the pathway. We suggest that metabolomic methods such as this, which do not require any knowledge of how a gene deletion might perturb the metabolic network, provide an empirical method for validating and ultimately refining the predicted network structure.

Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains.

Macro domains constitute a protein module family found associated with specific histones and proteins involved in chromatin metabolism. In addition, a small number of animal RNA viruses, such as corona- and toroviruses, alphaviruses, and hepatitis E virus, encode macro domains for which, however, structural and functional information is extremely limited. Here, we characterized the macro domains from hepatitis E virus, Semliki Forest virus, and severe acute respiratory syndrome coronavirus (SARS-CoV). The crystal structure of the SARS-CoV macro domain was determined at 1.8-Å resolution in complex with ADP-ribose. Information derived from structural, mutational, and sequence analyses suggests a close phylogenetic and, most probably, functional relationship between viral and cellular macro domain homologs. The data revealed that viral macro domains have relatively poor ADP-ribose 1"-phosphohydrolase activities (which were previously proposed to be their biologically relevant function) but bind efficiently free and poly(ADP-ribose) polymerase 1-bound poly(ADP-ribose) in vitro. Collectively, these results suggest to further evaluate the role of viral macro domains in host response to viral infection.

The dermis contains langerin+ dendritic cells that develop and function independently of epidermal Langerhans cells.

Langerhans cells (LCs) constitute a subset of dendritic cells (DCs) that express the lectin langerin and that reside in their immature state in epidermis. Paradoxically, in mice permitting diphtheria toxin (DT)-mediated ablation of LCs, epidermal LCs reappeared with kinetics that lagged behind that of their putative progeny found in lymph nodes (LNs). Using bone marrow (BM) chimeras, we showed that a major fraction of the langerin(+), skin-derived DCs found in LNs originates from a developmental pathway that is independent from that of epidermal LCs. This pathway, the existence of which was unexpected, originates in the dermis and gives rise to langerin(+) dermal DCs (DDCs) that should not be confused with epidermal LCs en route to LNs. It explains that after DT treatment, some langerin(+), skin-derived DCs reappear in LNs long before LC-derived DCs. Using CD45 expression and BrdU-labeling kinetics, both LCs and langerin(+) DDCs were found to coexist in wild-type mice. Moreover, DT-mediated ablation of epidermal LCs opened otherwise filled niches and permitted repopulation of adult noninflammatory epidermis with BM-derived LCs. Our results stress that the langerin(+) DC network is more complex than originally thought and have implications for the development of transcutaneous vaccines and the improvement of humanized mouse models.

Genetic algorithms for local controller network construction

Local Controller Networks (LCNs) provide nonlinear control by interpolating between a set of locally valid, subcontrollers covering the operating range of the plant. Constructing such networks typically requires knowledge of valid local models. This paper describes a new genetic learning approach to the construction of LCNs directly from the dynamic equations of the plant, or from modelling data. The advantage is that a priori knowledge about valid local models is not needed. In addition to allowing simultaneous optimisation of both the controller and validation function parameters, the approach aids transparency by ensuring that each local controller acts independently of the rest at its operating point. It thus is valuable for simultaneous design of the LCNs and identification of the operating regimes of an unknown plant. Application results from a highly nonlinear pH neutralisation process and its associated neural network representation are utilised to illustrate these issues.

Abnormal Functional Connectivity of Hippocampus During Episodic Memory Retrieval Processing Network in Amnestic Mild Cognitive Impairment.

BACKGROUND: Functional connectivity magnetic resonance imaging technique has revealed the importance of distributed network structures in higher cognitive processes in the human brain. The hippocampus has a key role in a distributed network supporting memory encoding and retrieval. Hippocampal dysfunction is a recurrent finding in memory disorders of aging such as amnestic mild cognitive impairment (aMCI) in which learning- and memory-related cognitive abilities are the predominant impairment. The functional connectivity method provides a novel approach in our attempts to better understand the changes occurring in this structure in aMCI patients. METHODS: Functional connectivity analysis was used to examine episodic memory retrieval networks in vivo in twenty 28 aMCI patients and 23 well-matched control subjects, specifically between the hippocampal structures and other brain regions. RESULTS: Compared with control subjects, aMCI patients showed significantly lower hippocampus functional connectivity in a network involving prefrontal lobe, temporal lobe, parietal lobe, and cerebellum, and higher functional connectivity to more diffuse areas of the brain than normal aging control subjects. In addition, those regions associated with increased functional connectivity with the hippocampus demonstrated a significantly negative correlation to episodic memory performance. CONCLUSIONS: aMCI patients displayed altered patterns of functional connectivity during memory retrieval. The degree of this disturbance appears to be related to level of impairment of processes involved in memory function. Because aMCI is a putative prodromal syndrome to Alzheimer's disease (AD), these early changes in functional connectivity involving the hippocampus may yield important new data to predict whether a patient will eventually develop AD.

Structural basis of substrate selectivity in the glycerol-3-phosphate: phosphate antiporter GlpT.

Major facilitators represent the largest superfamily of secondary active transporter proteins and catalyze the transport of an enormous variety of small solute molecules across biological membranes. However, individual superfamily members, although they may be architecturally similar, exhibit strict specificity toward the substrates they transport. The structural basis of this specificity is poorly understood. A member of the major facilitator superfamily is the glycerol-3-phosphate (G3P) transporter (GlpT) from the Escherichia coli inner membrane. GlpT is an antiporter that transports G3P into the cell in exchange for inorganic phosphate (Pi). By combining large-scale molecular-dynamics simulations, mutagenesis, substrate-binding affinity, and transport activity assays on GlpT, we were able to identify key amino acid residues that confer substrate specificity upon this protein. Our studies suggest that only a few amino acid residues that line the transporter lumen act as specificity determinants. Whereas R45, K80, H165, and, to a lesser extent Y38, Y42, and Y76 contribute to recognition of both free Pi and the phosphate moiety of G3P, the residues N162, Y266, and Y393 function in recognition of only the glycerol moiety of G3P. It is the latter interactions that give the transporter a higher affinity to G3P over Pi.

Strategy in a religious network: A bourdieuian critique of the sociology of spirituality

Within the sociology of religion there has emerged a discourse on spirituality that views contemporary developments as involving the assertion of individuals’ self-authority. This perspective’s theoretical roots have been persistently criticised for their conceptualisation of agency; in contrast, this paper draws upon Bourdieu’s concept of strategy to examine action in an English religious network of the sort often classified ‘New Age’. In particular, one informant is discussed in order to provide focus for an understanding of what Lahire calls sociology at the level of the individual. Her actions, better explained as strategic improvisations than as choices made on the basis of self-authority, help to illuminate the peculiarities of this religious setting, which is characterised in terms of ‘nonformativeness’. By emphasising social contextualisation, this approach addresses people’s meaningful actions in a way that may be applied not only more widely within the religious field but also in other fields of action.