A pattern recognition-based approach for phylogenetic network construction with constrained recombination

The tree representation of evolutionary relationship oversimplifies the view of the process of evolution as it cannot take into account the events such as horizontal gene transfer, hybridization, homoplasy and genetic recombination. Several algorithms exist for constructing phylogenetic networks which result from events such as horizontal gene transfer, hybridization and homoplasy. Very little work has been published on the algorithmic detail of phylogenetic networks with constrained recombination. The problem of minimizing the number of recombinations in a phylogenetic network, constructed using binary DNA sequences, is NP-hard. In this paper, we propose a pattern recognition-based O(n²) time approach for constructing the phylogenetic network, where n is the number of nodes or sequences in the input data. The network is constructed with the restriction that no two cycles in the network share a common node.     

Improvement of the wavelength switching behavior of semiconductor tunable lasers through optical feedback from a periodic reference filter based on a novel prism-based implementation of a Fox-Smith resonator

We show that the wavelength switching behavior of semiconductor tunable lasers can be improved through optical feedback from a stable reference filter. The filter is based on a novel prism-based implementation of a Fox-Smith resonator and has a response consisting of periodically spaced peaks, both in reflection and transmission. The improvement of the wavelength switching behavior stems from the suppression of the thermally induced wavelength drift associated with the switching of the tuning currents.     

Octave-tunable miniature RF resonators

The development and testing of a miniaturized, high-Q, broadly tunable resonator is described. An exemplary device, with a center frequency that is continuously tunable from 1.2 to 2.6GHz, was tested in detail. Experimental results demonstrated a resonator Q of up to 380, and typical insertion loss of -1.9dB for a 25MHz 3-dB bandwidth. These resonators have been used to stabilize a broadly-tunable oscillator with phase noise of -132dBc/Hz at 100-kHz offset, with a center frequency tunable from 1.2-2.6GHz, and a tuning speed of 1GHz/ms.     

Screen‐printed biosensor for allergens

Allergen levels in indoor environments, leading to many diseases, eg asthma, rhinitis and conjunctivitis, affect a large and increasing fraction of the population. A quite effective and inexpensive method of a rough but very rapid overall assessment of total allergen level in the environment has been developed. The method involved estimation of protein in allergen extracts by screen‐printed electrodes using two different techniques. The biosensor comprised a rhodinised carbon working electrode, a silver/silver chloride reference electrode and a carbon counter electrode. In the first method the enzyme protease reacted with allergen protein to release amino acid, which produced hydrogen peroxide in the presence of amino acid oxidase. This was detected amperometrically. The second method used potassium bromide as electrolyte and the electrode was subjected to dual potential. Bromine, released due to electrolysis at higher potential, was consumed by the allergen protein at lower potential. In the first method, a unique technique was used to microencapsulate the enzyme protease and immobilise it on the surface of the electrode by in‐situ polymerisation to avoid contact with the amino acid oxidase. A total of seven allergens were tested and the results gave a good correlation with the standard protein measurement method. Environmental specimens from indoors, schools and workplaces can be evaluated for the aeroallergens produced by dust mites, animal hairs, cockroach debris, pollens, etc as a means of determining the exposure risk. Copyright © 2005 Society of Chemical Industry     

Nitrification parameter measurement for plant design: experience and experimental issues with new methods.

Nitrification kinetics are important for process design, optimization, and capacity rating of activated sludge wastewater treatment plants. A Water Environment Research Foundation (WERF) project on Methods for Wastewater Characterization in Activated Sludge Modeling (WERF, 2003) focused significantly on the development of procedures for measuring the nitrifier maximum specific growth rate, micro(AUT). In addition, the importance of (and lack of data for) the nitrifier decay rate, b(AUT), was identified. This paper describes three bench-scale methods for measuring micro(AUT): the Low F/M SBR, Washout and High F/M methods. During the WERF project, the importance of pH and temperature control was investigated briefly; this paper summarizes further experimental work performed to address these issues. A summary of micro(AUT) measurements in a number of locations and using the different measurement techniques is provided.     

Removal of E. coli and helminth eggs in UASB: Polishing pond systems in Brazil.

Ponds following anaerobic reactors, such as Upflow Anaerobic Sludge Blanket (UASB) reactors, have been termed polishing ponds in the literature. The present paper analyses the removal of E. coli and helminth eggs in five UASB-polishing pond systems in Brazil. Since there were ponds in series, the total number of ponds was 10. The ponds had average retention times varying from 2 to 21 days, and depths ranging from 0.40 to 2.00 m. The shallow ponds in series, even with low retention times, were able to produce effluents complying with the coliform WHO guidelines for unrestricted irrigation (< or = 1000 MPN/100 ml). An equation for the coliform decay coefficient was proposed: Kb (dispersed flow) = 0.710H(-0955) (20 degrees C). The equation highlights the inverse relationship between the pond depth and the decay coefficient. All polishing pond systems were able to produce effluents with helminth eggs concentrations predominantly equal to zero, and satisfying the WHO guidelines for unrestricted and restricted irrigation (< or = 1 egg/L, arithmetic mean). The approximate range of helminth eggs removal efficiency was predicted satisfactorily.     

A time-based energy-efficient analog-to-digital converter

Dual-slope converters use time to perform analog-to-digital conversion but require 2/sup N+1/ clock cycles to achieve N bits of precision. We describe a novel current-mode algorithm that also uses time to perform analog-to-digital conversion but requires 5N clock cycles to achieve N bits of precision via a successive subranging technique. The algorithm requires one asynchronous comparator, two capacitors, one current source, and a state machine. Amplification of two is achieved without the use of an explicit amplifier by simply doing things twice in time. The use of alternating voltage-to-time and time-to-voltage conversions provides natural error cancellation of comparator offset and delay, 1/f noise, and switching charge-injection. The use of few components and an efficient mechanism for amplification and error cancellation allow for energy-efficient operation: in a 0.35-/spl mu/m implementation, we were able to achieve 12 bit of DNL limited precision or 11 bit of thermal noise-limited precision at a sampling frequency of 31.25 kHz with 75 /spl mu/W of total analog and digital power consumption. These numbers yield a thermal noise-limited energy efficiency of 1.17 pJ per quantization level, making it one of the most energy-efficient converters to date in the 10-12 bit precision range.     

A 4-MB on-chip L2 cache for a 90-nm 1.6-GHz 64-bit microprocessor

A 4-MB L2 data cache was implemented for a 64-bit 1.6-GHz SPARC(r) RISC microprocessor. Static sense amplifiers were used in the SRAM arrays and for global data repeaters, resulting in robust and flexible timing operation. Elimination of the global clock grid over the SRAM array saves power, enabled by combining the clock information with array select signals. Redundancy was implemented flexibly, with shift circuits outside the main data array for area efficiency. The chip integrates 315 million transistors and uses an 8-metal-layer 90-nm CMOS process.     

Reactive Power Compensation Technologies: State-of-the-Art Review

This paper presents an overview of the state of the art in reactive power compensation technologies. The principles of operation, design characteristics and application examples of Var compensators implemented with thyristors and self-commutated converters are presented. Static Var generators are used to improve voltage regulation, stability, and power factor in ac transmission and distribution systems. Examples obtained from relevant applications describing the use of reactive power compensators implemented with new static Var technologies are also described.     

Parallel transport: a new transport layer paradigm for enabling Internet quality of service

The transport layer in the network protocol stack serves as a liaison between the application and the underlying network. Any quality of service provided by the network thus has to be effectively translated by the transport layer protocol in order to be enjoyed by the applications. In this article, we argue for a fundamental rethinking of the transport layer design to facilitate such QoS delivery. We identify the key requirement for a QoS enabling transport layer protocol as the ability to effectively handle multiplicity in terms of user differentiation levels, network resources, and service models. However, TCP, the transport layer protocol predominantly used in the Internet, is unable to support such multiplicity due to its single-state design. We extend TCP to a parallel transport layer protocol called parallel TCP (pTCP) that can tackle the different dimensions of multiplicity, and hence enable varying classes of QoS to applications. We discuss the applicability of pTCP in three specific domains with different levels of network support for QoS, and present simulation results substantiating our arguments.