The binding site distance test score: a robust method for the assessment of predicted protein binding sites

We propose a novel method for scoring the accuracy of protein binding site predictions – the Binding-site Distance Test (BDT) score. Recently, the Matthews Correlation Coefficient (MCC) has been used to evaluate binding site predictions, both by developers of new methods and by the assessors for the community wide prediction experiment – CASP8. Whilst being a rigorous scoring method, the MCC does not take into account the actual 3D location of the predicted residues from the observed binding site. Thus, an incorrectly predicted site that is nevertheless close to the observed binding site will obtain an identical score to the same number of nonbinding residues predicted at random. The MCC is somewhat affected by the subjectivity of determining observed binding residues and the ambiguity of choosing distance cutoffs. By contrast the BDT method produces continuous scores ranging between 0 and 1, relating to the distance between the predicted and observed residues. Residues predicted close to the binding site will score higher than those more distant, providing a better reflection of the true accuracy of predictions. The CASP8 function predictions were evaluated using both the MCC and BDT methods and the scores were compared. The BDT was found to strongly correlate with the MCC scores whilst also being less susceptible to the subjectivity of defining binding residues. We therefore suggest that this new simple score is a potentially more robust method for future evaluations of protein-ligand binding site predictions.

Impact of transmission errors in enhanced relay-enabled distributed coordination function

This paper analyzes the performance of Enhanced relay-enabled Distributed Coordination Function (ErDCF) for wireless ad hoc networks under transmission errors. The idea of ErDCF is to use high data rate nodes to work as relays for the low data rate nodes. ErDCF achieves higher throughput and reduces energy consumption compared to IEEE 802.11 Distributed Coordination Function (DCF) in an ideal channel environment. However, there is a possibility that this expected gain may decrease in the presence of transmission errors. In this work, we modify the saturation throughput model of ErDCF to accurately reflect the impact of transmission errors under different rate combinations. It turns out that the throughput gain of ErDCF can still be maintained under reasonable link quality and distance.

Analysis of enhanced relay-enabled distributed coordination function under transmission errors

This paper analyzes the performance of enhanced relay-enabled distributed coordination function (ErDCF) for wireless ad hoc networks under transmission errors. The idea of ErDCF is to use high data rate nodes to work as relays for the low data rate nodes. ErDCF achieves higher throughput and reduces energy consumption compared to IEEE 802.11 distributed coordination function (DCF) in an ideal channel environment. However, there is a possibility that this expected gain may decrease in the presence of transmission errors. In this work, we modify the saturation throughput model of ErDCF to accurately reflect the impact of transmission errors under different rate combinations. It turns out that the throughput gain of ErDCF can still be maintained under reasonable link quality and distance.

Dual-orthogonal radial basis function networks for nonlinear time series prediction

A new structure of Radial Basis Function (RBF) neural network called the Dual-orthogonal RBF Network (DRBF) is introduced for nonlinear time series prediction. The hidden nodes of a conventional RBF network compare the Euclidean distance between the network input vector and the centres, and the node responses are radially symmetrical. But in time series prediction where the system input vectors are lagged system outputs, which are usually highly correlated, the Euclidean distance measure may not be appropriate. The DRBF network modifies the distance metric by introducing a classification function which is based on the estimation data set. Training the DRBF networks consists of two stages. Learning the classification related basis functions and the important input nodes, followed by selecting the regressors and learning the weights of the hidden nodes. In both cases, a forward Orthogonal Least Squares (OLS) selection procedure is applied, initially to select the important input nodes and then to select the important centres. Simulation results of single-step and multi-step ahead predictions over a test data set are included to demonstrate the effectiveness of the new approach.

The variability of tropical ice cloud properties as a function of the large-scale context from ground-based radar-lidar observations over Darwin, Australia

The high complexity of cloud parameterizations now held in models puts more pressure on observational studies to provide useful means to evaluate them. One approach to the problem put forth in the modelling community is to evaluate under what atmospheric conditions the parameterizations fail to simulate the cloud properties and under what conditions they do a good job. It is the ambition of this paper to characterize the variability of the statistical properties of tropical ice clouds in different tropical "regimes" recently identified in the literature to aid the development of better process-oriented parameterizations in models. For this purpose, the statistical properties of non-precipitating tropical ice clouds over Darwin, Australia are characterized using ground-based radar-lidar observations from the Atmospheric Radiation Measurement (ARM) Program. The ice cloud properties analysed are the frequency of ice cloud occurrence, the morphological properties (cloud top height and thickness), and the microphysical and radiative properties (ice water content, visible extinction, effective radius, and total concentration). The variability of these tropical ice cloud properties is then studied as a function of the large-scale cloud regimes derived from the International Satellite Cloud Climatology Project (ISCCP), the amplitude and phase of the Madden-Julian Oscillation (MJO), and the large-scale atmospheric regime as derived from a long-term record of radiosonde observations over Darwin. The vertical variability of ice cloud occurrence and microphysical properties is largest in all regimes (1.5 order of magnitude for ice water content and extinction, a factor 3 in effective radius, and three orders of magnitude in concentration, typically). 98 % of ice clouds in our dataset are characterized by either a small cloud fraction (smaller than 0.3) or a very large cloud fraction (larger than 0.9). In the ice part of the troposphere three distinct layers characterized by different statistically-dominant microphysical processes are identified. The variability of the ice cloud properties as a function of the large-scale atmospheric regime, cloud regime, and MJO phase is large, producing mean differences of up to a factor 8 in the frequency of ice cloud occurrence between large-scale atmospheric regimes and mean differences of a factor 2 typically in all microphysical properties. Finally, the diurnal cycle of the frequency of occurrence of ice clouds is also very different between regimes and MJO phases, with diurnal amplitudes of the vertically-integrated frequency of ice cloud occurrence ranging from as low as 0.2 (weak diurnal amplitude) to values in excess of 2.0 (very large diurnal amplitude). Modellers should now use these results to check if their model cloud parameterizations are capable of translating a given atmospheric forcing into the correct statistical ice cloud properties.

Conformational analysis of oriented non-crystalline polymers using wide angle X-ray scattering

A procedure is presented for obtaining conformational parameters from oriented but non-crystalline polymers. This is achieved by comparison of the experimental wide angle X-ray scattering with that calculated from models but in such a way that foreknowledge of the orientation distribution function is not required. X-ray scattering intensity values for glassy isotactic poly(methylmethacrylate) are analysed by these techniques. The method could be usefully applied to other oriented molecular systems such as liquid crystalline materials.

Long-distance dispersal and its influence on adaptation to host resistance in a heterogeneous landscape

Small propagules like pollen or fungal spores may be dispersed by the wind over distances of hundreds or thousands of kilometres,even though the median dispersal may be only a few metres. Such long-distance dispersal is a stochastic event which may be exceptionally important in shaping a population. It has been found repeatedly in field studies that subpopulations of wind-dispersed fungal pathogens virulent on cultivars with newly introduced, effective resistance genes are dominated by one or very few genotypes. The role of propagule dispersal distributions with distinct behaviour at long distances in generating this characteristic population structure was studied by computer simulation of dispersal of clonal organisms in a heterogeneous environment with fields of unselective and selective hosts. Power-law distributions generated founder events in which new, virulent genotypes rapidly colonized fields of resistant crop varieties and subsequently dominated the pathogen population on both selective and unselective varieties, in agreement with data on rust and powdery mildew fungi. An exponential dispersal function, with extremely rare dispersal over long distances, resulted in slower colonization of resistant varieties by virulent pathogens or even no colonization if the distance between susceptible source and resistant target fields was sufficiently large. The founder events resulting from long-distance dispersal were highly stochastic and exact quantitative prediction of genotype frequencies will therefore always be difficult.

Televised Whorf: cognitive restructuring in advanced foreign language learners as a function of audio-visual media exposure

The encoding of goal-oriented motion events varies across different languages. Speakers of languages without grammatical aspect (e.g., Swedish) tend to mention motion endpoints when describing events, e.g., “two nuns walk to a house,”, and attach importance to event endpoints when matching scenes from memory. Speakers of aspect languages (e.g., English), on the other hand, are more prone to direct attention to the ongoingness of motion events, which is reflected both in their event descriptions, e.g., “two nuns are walking.”, and in their non-verbal similarity judgements. This study examines to what extent native speakers of Swedish (n = 82) with English as a foreign language (FL) restructure their categorisation of goal-oriented motion as a function of their English proficiency and experience with the English language (e.g., exposure, learning). Seventeen monolingual native English speakers from the United Kingdom (UK) were engaged for comparison purposes. Data on motion event cognition were collected through a memory-based triads matching task, in which a target scene with an intermediate degree of endpoint orientation was matched with two alternative scenes with low and high degrees of endpoint orientation, respectively. Results showed that the preference among the Swedish speakers of L2 English to base their similarity judgements on ongoingness rather than event endpoints was correlated with their use of English in their everyday lives, such that those who often watched television in English approximated the ongoingness preference of the English native speakers. These findings suggest that event cognition patterns may be restructured through the exposure to FL audio-visual media. The results thus add to the emerging picture that learning a new language entails learning new ways of observing and reasoning about reality.

Basement depths in the Parecis Basin (Amazon) with receiver functions from small local earthquakes in the Porto dos Gauchos seismic zone

Receiver functions from small local earthquakes were used to determine sediment thicknesses in Porto dos Gauchos seismic zone (PGSZ), Parecis basin, Amazonian craton, Brazil. The high velocity contrast between basement and sediments (P-wave velocities of 6.1 and 3.0 km/s, respectively) favors the generation of clear P-to-S converted phases (Ps) seen in the radial component, and also S-to-P conversions (Sp) seen in the vertical component. A reference 10 velocity model determined with shallow refraction experiment in PGSZ helped to convert Ps P time differences to basement depths at 15 stations deployed for aftershocks studies. The results of receiver function integrated with the shallow refraction reveal that the basement depths in the PGSZ increases from the basin border in the north up to about 600 m depth in the south. The basement topography, however, does not vary smoothly and a basement high with a steep topography was detected near the epicentral area. A 400 m elevation difference within 1.7 km distance suggests a possible border fault of a buried graben. This feature seems to be oriented roughly WSW-ENE and could indicate basement structures related to the seismicity of the Porto dos Gauchos Seismic Zone. (C) 2011 Elsevier Ltd. All rights reserved.

Percolation in a network with long-range connections: Implications for cytoskeletal structure and function

Cell shape, signaling, and integrity depend on cytoskeletal organization. In this study we describe the cytoskeleton as a simple network of filamentary proteins (links) anchored by complex protein structures (nodes). The structure of this network is regulated by a distance-dependent probability of link formation as P = p/d(s), where p regulates the network density and s controls how fast the probability for link formation decays with node distance (d). It was previously shown that the regulation of the link lengths is crucial for the mechanical behavior of the cells. Here we examined the ability of the two-dimensional network to percolate (i.e. to have end-to-end connectivity), and found that the percolation threshold depends strongly on s. The system undergoes a transition around s = 2. The percolation threshold of networks with s < 2 decreases with increasing system size L, while the percolation threshold for networks with s > 2 converges to a finite value. We speculate that s < 2 may represent a condition in which cells can accommodate deformation while still preserving their mechanical integrity. Additionally, we measured the length distribution of F-actin filaments from publicly available images of a variety of cell types. In agreement with model predictions, cells originating from more deformable tissues show longer F-actin cytoskeletal filaments. (C) 2008 Elsevier B.V. All rights reserved.

Discourse strategies and power roles in student-led distance learning

The assertion of identity and power via computer-mediated communication in the context of distance or web-based learning presents challenges to both teachers and students. When regular, face-to-face classroom interaction is replaced by online chat or group discussion forums, participants must avail themselves of new techniques and tactics for contributing to and furthering interaction, discussion, and learning. During student-only chat sessions, the absence of teacher-led, face-to-face classroom activities requires the students to assume leadership roles and responsibilities normally associated with the teacher. This situation raises the questions of who teaches and who learns; how students discursively negotiate power roles; and whether power emerges as a function of displayed expertise and knowledge or rather the use of authoritative language. This descriptive study represents an examination of a corpus of task-based discussion logs among Vietnamese students of distance learning courses in English linguistics. The data reveal recurring discourse strategies for 1) negotiating the progression of the discussion sessions, 2) asserting and questioning knowledge, and 3) assuming or delegating responsibility. Power is defined ad hoc as the ability to successfully perform these strategies. The data analysis contributes to a better understanding of how working methods and materials can be tailored to students in distance learning courses, and how such students can be empowered by being afforded opportunities and effectively encouraged to assert their knowledge and authority.

Distance teacher education – some experiences from Dalarna University, SwedenPaper presented at the 33rd Annual ATEE Conference Brussels, Belgium, 23rd – 27th August 2008

Distance teaching is now-a-days used in different shapes. However, it is something different from traditional campus organised education as it systematically uses Information Communication Technology (ICT) as a key element. When the distance teacher education started in Sweden many teacher educators doubted the wisdom of this. They expressed that the educational process to become a teacher would be deteriorated. For instance, they feared for high drop out rates and difficulties to examine in a proper way. The Swedish National Agency for Higher Education has recently edited a report that showed that this form of teacher education was well adapted to the labour market, but the possibilities for the teacher students to shape their education were relatively limited. However, we still know quite little about the effects of this way to educate teacher students. This paper explores the possibility of using distance teacher education.In a case study 20 students, who were the first to finish a complete a distance teacher education at Högskolan Dalarna, were asked in a questionnaire how they had apprehended their education. We also interviewed four of these students, as well as five teacher educators.One of our findings were that the distance teacher education reached new target groups, who not had been able to participate in university studies if it not had been offered in this form. Especially, this was valid for the middle-aged women, living a long distance away from a university, with social responsibilities for children or old parents. Other findings were that these students in general were target oriented and ambitious, wrote more than the campus students and developed that kind of skill better. Marratech, an ICT system for small groups, e-mail and chat were used for the communication. Marratech was considered to permit free and spontaneous communication, both of the teacher educators and the students. Initially the teacher educators were sceptical to distance teacher education, but afterwards they were surprised of how well it had worked. They declared that they had better and nearer contact with their students and more control over the students´ performance, but some parts of the teacher education were better suitable for campus education, for example, power of creating characters. Distance teacher education was considered time consuming and demanded much activity from the teacher educators as the students wanted rapid responses. This study indicates that distance teacher education works well for mature individuals with high motivation. However, it demands more time from the teacher educators, but it gives in general good results. Still, there are pedagogical challenges to overcome. Maybe we should reflect on a mix of distance teacher education and campus based teacher education, instead of separated ways of accomplishing teacher education?

On the production of randomly-oriented recrystallization nuclei for selective growth experiments

The ideal starting condition for selective growth experiments is one having a layer of randomly-oriented nuclei adjacent to a matrix with negligible orientational variation but sufficient stored energy to promote growth. In practice, cutting or deformation processes are used in an attempt to approximate these ideal conditions, but the degree to which this is achieved has not been rigorously quantified. In this work, Fe-3wt%Si single crystals were cut or deformed using six different processes. The variation in texture with distance from the cut or deformed surface was measured using electron backscatter diffraction (EBSD) in a field emission gun scanning electron microscope (FEG-SEM) in order to assess the ability of each process to create conditions suitable for selective growth experiments. While grooving with a machine tool produced the best spread of orientations at the cut surface, the suitability of this process is diminished by the presence of a differently-textured deformed layer between the cut surface and the single crystal matrix. Grinding produced a less ideal distribution of orientations at the cut surface, but the presence of these orientations in a very thin layer adjacent to the matrix makes this process preferable for preparing crystals for selective growth experiments, provided the results are corrected for the deviation in the distribution of nuclei orientations from a random distribution.

The use of home experimentation kits for distance students in first-year undergraduate electronics

Laboratory and practical classes are an important part of the education of students in electronics and electrical engineering. "Hands-on" experience is critical for any engineer working in these fields in particular. For many years, delivering engineering practicals to distance-education students has been a tremendous challenge for universities. For a number of years now, students enrolled in the common first-year electronics course by distance mode at Deakin University have received a home experimentation kit. Using the kit and a laboratory manual, students are required to complete a number of experiments based on components included in the kit. The kit supports a full range of practical activities for digital electronics, and a more limited range of activities for analog electronics. With the kit, off campus students are supplied software for simulating AC electronic circuits, such as amplifiers and rectifiers. In this report we examine the past use of this kit and software,
review anecdotal student experiences with the package, and propose changes to it and to other curriculum resources, aiming to enhance the use of the kit by distance students. Key curriculum resources planned are a web-based 'companion' for the components in and the use of the kit, and two additions to the kit itself: a battery powered function generator, and a PC-based oscilloscope.

Forces due to structure in a thin liquid crystal film

Measurements of the force as a function of distance between two solids separated by a liquid crystal film give information on the structure of the film. We report such measurements for two molecularly smooth surfaces of mica separated by the nematic liquid crystal 4'-n-pentyl 4-cyanobiphenyl (5CB) in both the planar and homeotropic orientations at room temperature. The force is determined by measuring the deflection of a spring supporting one of the mica pieces, while an optical technique is used to measure the film thickness to an accuracy of ± (0.1-0.2) nm. The technique also allows the refractive indices of the nematic to be measured, and hence a determination of the average density and order parameter of the liquid crystal film as a function of its thickness. Three distinct forces were measured, each reflecting a type of ordering of the liquid crystal near the mica surfaces. The first one results from elastic déformation in the liquid crystal ; it was only observed in a twisted planar sample where the 5CB molecules are oriented in different directions at the two mica surfaces. The second, measured in both the planar and homeotropic orientations, is attributed to an enhanced order parameter near the surfaces. Both of these are monotonic repulsive forces measurable below 80 nm. Finally, there is a short-range force which oscillates as a function of thickness, up to about six molecular layers, between attraction and repulsion. This results from ordering of the molecules in layers adjacent to the smooth solid surface. It is observed in both the planar and homeotropic orientations, and also in isotropic liquids.