NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation ill each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA ar rd RNA duplex structures.

Next generation sequencing identifies novel CACNA1A gene mutations in Episodic Ataxia type 2

Episodic Ataxia type 2 (EA2) is a rare autosomal dominantly inherited neurological disorder characterized by recurrent disabling imbalance, vertigo and episodes of ataxia lasting minutes to hours. EA2 is caused most often by loss of function mutations of the calcium channel gene CACNA1A. In addition to EA2, mutations in CACNA1A are responsible for two other allelic disorders: familial hemiplegic migraine type1 (FHM1) and spinocerebellar ataxia type 6 (SCA6). Herein, we have utilised Next Generation Sequencing (NGS) to screen the coding sequence, exon-intron boundaries and UTRs of five genes where mutation is known to produce symptoms related to EA2, including CACNA1A. We performed this screening in a group of 31 unrelated patients with EA2 symptoms. Both novel and known mutations were detected through NGS technology, and confirmed through Sanger sequencing. Genetic testing showed in total 15 mutation bearing patients (48%), of which 9 were novel mutations (6 missense and 3 small frameshift deletion mutations) and six known mutations (4 missense and 2 nonsense).These results demonstrate the efficiency of our NGS-panel for detecting known and novel mutations for EA2 in the CACNA1A gene, also identifying a novel missense mutation in ATP1A2 which is not a normal target for EA2 screening.

Microbial aspects of acid generation and bioremediation with relevance to indian mining

The role of Acidithiobacillus group of bacteria in acid generation and heavy metal dissolution was studied with relevance to some Indian mines. Microorganisms implicated in acid generation such as Acidithiobacillus Acidithicibacillus thiooxidans and Leptospirillum ferrooxidans were isolated from abandoned mines, waste rocks and tailing dumps. Arsenite oxidizing Thiomonas and Bacillus group of bacteria were isolated and their ability to oxidize As (111) to As (V) established. Mine isolated Sulfate reducing bacteria were used to remove dissolved copper, zinc, iron and arsenic from solutions.

Ce0.67Cr0.33O2.11: A New Low-Temperature O-2 Evolution Material and H-2 Generation Catalyst by Thermochemical Splitting of Water

Ce0.67Cr0.33O2.11 was synthesized by hydrothermal method using diethylenetriamine as complexing agent (Chem. Mater. 2008, 20, 7268). Ce0.67Cr0.33O2.11 being the only compound likes UO2+delta to have excess oxygen, it releases a large proportion of its lattice oxygen (0.167 M [O]/mole of compound) at relatively low temperature (465 degrees C) directly and it has been utilized for generation of H-2 by thermo-splitting of water. An almost stoichiometric amount of H-2 (0.152 M/Mole of compound) is generated at much lower temperature (65 degrees C). There is an almost comparable amount of oxygen release and hydrogen generation over this material at very low temperature comparedto other CeO2-MOx (Mn, Fe, Cu, and Ni) mixed-oxide solid solutions (O-2 evolution >= 1300 degrees C and H-2 generation at 1000 degrees C). The reversible nature of oxygen release and intake of this material is attributed to its fluorite Structure and coupling between the Ce4+/Ce3+ and Cr4+/6+/Cr3+ redox couples. Compound shows reversible oxygen release and intake by H2O absorption and subsequent hydrogen release to gain parent structure and hence this material can be utilized for generation of H-2 at very low temperature by thermo-chemical splitting of water.

A discrete wavelet transform approach to multiresolution complex SAR image generation

We present a signal processing approach using discrete wavelet transform (DWT) for the generation of complex synthetic aperture radar (SAR) images at an arbitrary number of dyadic scales of resolution. The method is computationally efficient and is free from significant system-imposed limitations present in traditional subaperture-based multiresolution image formation. Problems due to aliasing associated with biorthogonal decomposition of the complex signals are addressed. The lifting scheme of DWT is adapted to handle complex signal approximations and employed to further enhance the computational efficiency. Multiresolution SAR images formed by the proposed method are presented.

Internet privatization, WikiLeaks, and free expression

In late 2010, the online nonprofit media organization WikiLeaks published classified documents detailing correspondence between the U.S. State Department and its diplomatic missions around the world, numbering around 250,000 cables. These diplomatic cables contained classified information with comments on world leaders, foreign states, and various international and domestic issues. Negative reactions to the publication of these cables came from both the U.S. political class (which was generally condemnatory of WikiLeaks, invoking national security concerns and the jeopardizing of U.S. interests abroad) and the corporate world, with various companies ceasing to continue to provide services to WikiLeaks despite no legal measure (e.g., a court injunction) forcing them to do so. This article focuses on the legal remedies available to WikiLeaks against this corporate suppression of its speech in the U.S. and Europe since these are the two principle arenas in which the actors concerned are operating. The transatlantic legal protection of free expression will be considered, yet, as will be explained in greater detail, the legal conception of this constitutional and fundamental right comes from a time when the state posed the greater threat to freedom. As a result, it is not generally enforceable against private, non-state entities interfering with speech and expression which is the case here. Other areas of law, namely antitrust/competition, contract and tort will then be examined to determine whether WikiLeaks and its partners can attempt to enforce their right indirectly through these other means. Finally, there will be some concluding thoughts about the implications of the corporate response to the WikiLeaks embassy cables leak for freedom of expression online.

Modeling and analysis of a tunable piezoelectric structure for transverse shear wave generation

An analytical investigation of the transverse shear wave mode tuning with a resonator mass (packing mass) on a Lead Zirconium Titanate (PZT) crystal bonded together with a host plate and its equivalent electric circuit parameters are presented. The energy transfer into the structure for this type of wave modes are much higher in this new design. The novelty of the approach here is the tuning of a single wave mode in the thickness direction using a resonator mass. First, a one-dimensional constitutive model assuming the strain induced only in the thickness direction is considered. As the input voltage is applied to the PZT crystal in the thickness direction, the transverse normal stress distribution induced into the plate is assumed to have parabolic distribution, which is presumed as a function of the geometries of the PZT crystal, packing mass, substrate and the wave penetration depth of the generated wave. For the PZT crystal, the harmonic wave guide solution is assumed for the mechanical displacement and electric fields, while for the packing mass, the former is solved using the boundary conditions. The electromechanical characteristics in terms of the stress transfer, mechanical impedance, electrical displacement, velocity and electric field are analyzed. The analytical solutions for the aforementioned entities are presented on the basis of varying the thickness of the PZT crystal and the packing mass. The results show that for a 25% increase in the thickness of the PZT crystal, there is ~38% decrease in the first resonant frequency, while for the same change in the thickness of the packing mass, the decrease in the resonant frequency is observed as ~35%. Most importantly the tuning of the generated wave can be accomplished with the packing mass at lower frequencies easily. To the end, an equivalent electric circuit, for tuning the transverse shear wave mode is analyzed.

Analytical models for capacity estimation of IEEE 802.11 WLANs using DCF for internet applications

We provide analytical models for capacity evaluation of an infrastructure IEEE 802.11 based network carrying TCP controlled file downloads or full-duplex packet telephone calls. In each case the analytical models utilize the attempt probabilities from a well known fixed-point based saturation analysis. For TCP controlled file downloads, following Bruno et al. (In Networking '04, LNCS 2042, pp. 626-637), we model the number of wireless stations (STAs) with ACKs as a Markov renewal process embedded at packet success instants. In our work, analysis of the evolution between the embedded instants is done by using saturation analysis to provide state dependent attempt probabilities. We show that in spite of its simplicity, our model works well, by comparing various simulated quantities, such as collision probability, with values predicted from our model. Next we consider N constant bit rate VoIP calls terminating at N STAs. We model the number of STAs that have an up-link voice packet as a Markov renewal process embedded at so called channel slot boundaries. Analysis of the evolution over a channel slot is done using saturation analysis as before. We find that again the AP is the bottleneck, and the system can support (in the sense of a bound on the probability of delay exceeding a given value) a number of calls less than that at which the arrival rate into the AP exceeds the average service rate applied to the AP. Finally, we extend the analytical model for VoIP calls to determine the call capacity of an 802.11b WLAN in a situation where VoIP calls originate from two different types of coders. We consider N-1 calls originating from Type 1 codecs and N-2 calls originating from Type 2 codecs. For G711 and G729 voice coders, we show that the analytical model again provides accurate results in comparison with simulations.

OFDM-MAC algorithms and their impact on TCP performance in next generation mobile networks

Next generation wireless systems employ Orthogonal frequency division multiplexing (OFDM) physical layer owing to the high data rate transmissions that are possible without increase in bandwidth. While TCP performance has been extensively studied for interaction with link layer ARQ, little attention has been given to the interaction of TCP with MAC layer. In this work, we explore cross-layer interactions in an OFDM based wireless system, specifically focusing on channel-aware resource allocation strategies at the MAC layer and its impact on TCP congestion control. Both efficiency and fairness oriented MAC resource allocation strategies were designed for evaluating the performance of TCP. The former schemes try to exploit the channel diversity to maximize the system throughput, while the latter schemes try to provide a fair resource allocation over sufficiently long time duration. From a TCP goodput standpoint, we show that the class of MAC algorithms that incorporate a fairness metric and consider the backlog outperform the channel diversity exploiting schemes.

Multiple excitation nano-spot generation and confocal detection for far-field microscopy

An imaging technique is developed for the controlled generation of multiple excitation nano-spots for far-field microscopy. The system point spread function (PSF) is obtained by interfering two counter-propagating extended depth-of-focus PSF (DoF-PSF), resulting in highly localized multiple excitation spots along the optical axis. The technique permits (1) simultaneous excitation of multiple planes in the specimen; (2) control of the number of spots by confocal detection; and (3) overcoming the point-by-point based excitation. Fluorescence detection from the excitation spots can be efficiently achieved by Z-scanning the detector/pinhole assembly. The technique complements most of the bioimaging techniques and may find potential application in high resolution fluorescence microscopy and nanoscale imaging.

Place making for knowledge generation and innovation: Planning and branding Brisbane’s knowledge community precincts

Knowledge generation and innovation have been a priority for global city administrators particularly during the last couple of decades. This is mainly due to the growing consensus in identifying knowledge-based urban development as a panacea to the burgeoning economic problems. Place making has become a critical element for success in knowledge-based urban development as planning and branding places is claimed to be an effective marketing tool for attracting investment and talent. This paper aims to investigate the role of planning and branding in place making by assessing the effectiveness of planning and branding strategies in the development of knowledge and innovation milieus. The methodology of the study comprises reviewing the literature thoroughly, developing an analysis framework, and utilizing this framework in analyzing Brisbane’s knowledge community precincts—namely Boggo Road Knowledge Precinct, Kelvin Grove Urban Knowledge Village, and Sippy Downs Knowledge Town. The analysis findings generate invaluable insights in Brisbane’s journey in place making for knowledge and innovation milieus and communities. The results suggest as much as good planning, branding strategies and practice, the requirements of external and internal conditions also need to be met for successful place making in knowledge community precincts.

The internet of playful things

This one-day workshop brings together researchers and practitioners to share knowledge and practices on how people can connect and interact with the Internet of Things in a playful way. Open to participants with a diverse range of interests and expertise, and by exploring novel ways to playfully connect people through their everyday objects and activities, the workshop will facilitate discussion across a range of HCI discipline areas. The outcomes from the workshop will include an archive of participants' initial position papers along with the materials created during the workshop. The result will be a road map to support the development of a Model of Playful Connectedness, focusing on how best to design and make playful networks of things, identifying the challenges that need to be addressed in order to do so.

Multilevel Dodecagonal Space Vector Generation for Open-end Winding Induction Motor Drive Using Conventional Three Level Inverters

A novel dodecagonal space vector structure for induction motor drive is presented in this paper. It consists of two dodecagons, with the radius of the outer one twice the inner one. Compared to existing dodecagonal space vector structures, to achieve the same PWM output voltage quality, the proposed topology lowers the switching frequency of the inverters and reduces the device ratings to half. At the same time, other benefits obtained from existing dodecagonal space vector structure are retained here. This includes the extension of the linear modulation range and elimination of all 6+/-1 harmonics (n=odd) from the phase voltage. The proposed structure is realized by feeding an open-end winding induction motor with two conventional three level inverters. A detailed calculation of the PWM timings for switching the space vector points is also presented. Simulation and experimental results indicate the possible application of the proposed idea for high power drives.