A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity

Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat, Multiz, and OMA. In head-to-head comparisons, these methods are shown to significantly outperform one another 12-30% of the time. This high complementarity motivates the presentation of the first tool for integrating methodologically diverse OD methods. We term this program MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization. Relative to component and competing methods, we demonstrate that MOSAIC more than quintuples the number of alignments for which all species are present, while simultaneously maintaining or improving functional-, phylogenetic-, and sequence identity-based measures of ortholog quality. Further, we demonstrate that this improvement in alignment quality yields 40-280% more confidently aligned sites. Combined, these factors translate to higher estimated levels of overall conservation, while at the same time allowing for the detection of up to 180% more positively selected sites. MOSAIC is available as python package. MOSAIC alignments, source code, and full documentation are available at http://pythonhosted.org/bio-MOSAIC

Representation results for defeasible logic

The importance of transformations and normal forms in logic programming, and generally in computer science, is well documented. This paper investigates transformations and normal forms in the context of Defeasible Logic, a simple but efficient formalism for nonmonotonic reasoning based on rules and priorities. The transformations described in this paper have two main benefits: on one hand they can be used as a theoretical tool that leads to a deeper understanding of the formalism, and on the other hand they have been used in the development of an efficient implementation of defeasible logic.Comment: 30 pages, 1 figur

Continuous repetition rate tuning with timing window independent self-seeding of a gain-switched Fabry-PÉrot Laser

In this work, we propose a novel self-seeding technique that yields timing window independent operation allowing continuous repetition rate tuning of the self-seeded gain-switched (SSGS) laser. This is achieved by employing a highly linearly chirped fiber Bragg grating (LC FBG) as a wavelength selective element. The reflected gain-switched pulses are dispersed to such an extent, that temporal overlap occurs between them. This overlap creates a pseudo continues wave like signal that is re-injected into the gain-switched laser

Mobile learning in pre-service teacher education: Examining the use of professional learning networks

© 2019. Interest in how to use mobile devices to support teaching and learning has increased as technologies have become more sophisticated and ubiquitous. A recent focus in teacher education is the use of mobile devices to support teachers' professional learning networks (PLNs). This study investigates how pre-service teachers (PSTs) use mobile technologies to support different aspects of their PLN activities. The study uses a qualitative methodology, where data from focus group discussions, artefact collection, and participant journals kept by 11 final year PSTs provided nuanced insights into their mobile learning practices. A validated mobile pedagogical framework (Kearney, Schuck, Burden, & Aubusson, 2012) is used to analyse the data. Findings uncover a deeper understanding of exemplary mobile learning approaches in initial teacher education and have implications for effective preparation of PSTs for career-long professional learning

Wavelength tunable lasers in future optical communication systems

Monolithic tunable lasers (TL) have been an important component in dense wavelength division multiplexed (DWDM) systems mainly because of their ability to reduce inventory costs associated with different part numbers for fixed wavelength distributed feedback (DFB) lasers. Moreover, the use of wavelength agile laser diodes in DWDM networks has gained a lot of interest in recent years, due to emerging new applications such as optical switching and routing, which require fast switching lasers in the nanosecond regime (Coldren et al., 2000). Employment of such lasers as tunable transmitters in wavelength packet switched (WPS) networks is one of the possible applications of these devices. In such systems, the information to be transmitted could be encoded onto a destination dependent wavelength and the routing of traffic could be performed on a packet-by-packet basis. The utilization of TLs in an optical switching and routing environment would put stringent requirements on its performance. This would include increased tuning range, high side mode suppression ratio (SMSR), reduced switching time and excellent wavelength stability. The sampled-grating distributed Bragg reflector (SG DBR) TL proves to be an ideal candidate, due to its large tuning range (40 nm), high output power (10 dBm), high side mode suppression ratio (SMSR > 30 dB) and simplicity of integration

Frequency drift characterisation of directly modulated SGDBR tunable lasers

Tunable Lasers (TL) are rapidly becoming key components in Dense Wavelength Division Multiplexed (DWDM) systems, packet switched schemes and access networks. They are being introduced as alternatives to fixed wavelength sources to provide a greater degree of flexibility and to reduce large inventory [1]. The SGDBR laser is an ideal candidate due to its large tuning range (40 nm), high output power (10 dBm), large Side Mode Suppression Ratio (>30 dB) and its ability to be monolithically integrated with other semiconductor devices. Such integration could comprise of a Semiconductor Optical Amplifier (SOA), allowing for extended reach tunable operation, in a very compact and low cost footprint [2]. Thus far, external modulation has been the most popular modulation technique used with TLs. However, the addition of the modulator introduces loss to the transmitted signal due to high insertion and coupling losses. Addressing these short comings would result in increased cost and complexity of the transmitter. Alternatively, direct modulation is one of the simplest and cost efficient ways to modulate the lightwave signal. Hence, it is rational to investigate the performance of a directly modulated SGDBR laser in order to verify its usefulness in a WDM based access network scenario. Previous work in this area has mainly focused on bandwidth characterisation and transmission experiments [3, 4]. In this paper, we characterise the frequency drift associated with a directly modulated SGDBR laser incorporating a wavelength locker. Focus is placed on investigating the magnitude and settling time of this drift. In addition, we also demonstrate how the frequency drift has a detrimental effect on DWDM system performance when the modulated channel is passed through a narrow Optical Band-Pass Filter (OBPF) centred at the target emission frequency

Method Effects and the Need for Cognition Scale

Individual differences in the need for cognition are typically assessed using the 18-item Need for cognition scale (NCS) developed by Cacioppo and Petty (1982). However, in contrast to the unidimensional model proposed by the scale developers, recent factor analyses have introduced two -and three- dimensional models of the scale. Confirmatory factor analyses were used in this study to evaluate different measurement models based on data provided by 590 (236 males, 354 females) young adult members of the general public. Although some alternative models showed promise, a single factor model with method effects associated with positively and negatively worded items provided best fit. Implications for the asses sment of need for cognition are considered

Effect of Fines Content on the Cyclic Undrained Behavior of Sand

The influence of fines on the liquefaction potential of sandy soils has been studied by conducting isotropically consolidated stress controlled triaxial tests. Experimental results are compared with predictions using the theory developed by Nasser and Shokooh which is based on energy considerations. The theory determines the excess pore water pressure in terms of the number of cycles N, the dimensionless shear stress amplitude, and the initial and minimum values of the void ratio. The comparisons show good agreement between experimental data and model predictions for the pore water generation under cyclic loading for both loose and medium sands and medium silty soils

Characterization of wavelength tunable lasers for future optical communication systems

The use of tunable lasers (TL) in dense wavelength division multiplexed (DWDM) networks for optical switching, routing and networking has gained a lot of interest in recent years. Employment of such TLs as tunable transmitters in wavelength packet switched (WPS) networks is one of the possible applications of these devices. In such systems, the information to be transmitted could be encoded onto a destination dependent wavelength and the routing of traffic could be performed on a packet-by-packet basis. The authors investigate the possibility of using TLs in DWDM WPS networks by focusing on the characterisation of the instantaneous frequency drift of a TL due to wavelength tuning and direct modulation. Characterization of the linewidth of the TLs is also presented to verify the feasibility of using TLs in systems employing advanced modulation formats