Revealing differences in gene network inference algorithms on the network level by ensemble methods

Motivation: The inference of regulatory networks from large-scale expression data holds great promise because of the potentially causal interpretation of these networks. However, due to the difficulty to establish reliable methods based on observational data there is so far only incomplete knowledge about possibilities and limitations of such inference methods in this context.

Results: In this article, we conduct a statistical analysis investigating differences and similarities of four network inference algorithms, ARACNE, CLR, MRNET and RN, with respect to local network-based measures. We employ ensemble methods allowing to assess the inferability down to the level of individual edges. Our analysis reveals the bias of these inference methods with respect to the inference of various network components and, hence, provides guidance in the interpretation of inferred regulatory networks from expression data. Further, as application we predict the total number of regulatory interactions in human B cells and hypothesize about the role of Myc and its targets regarding molecular information processing.

The level sets of the resolvent norm and convexity properties of Banach spaces

We construct a bounded linear operator on a separable, reflexive and strictly convex Banach space whose resolvent norm is constant in a neighbourhood of zero.

A hybrid metaheuristic approach to the university course timetabling problem

This paper describes the development of a novel metaheuristic that combines an electromagnetic-like mechanism (EM) and the great deluge algorithm (GD) for the University course timetabling problem. This well-known timetabling problem assigns lectures to specific numbers of timeslots and rooms maximizing the overall quality of the timetable while taking various constraints into account. EM is a population-based stochastic global optimization algorithm that is based on the theory of physics, simulating attraction and repulsion of sample points in moving toward optimality. GD is a local search procedure that allows worse solutions to be accepted based on some given upper boundary or ‘level’. In this paper, the dynamic force calculated from the attraction-repulsion mechanism is used as a decreasing rate to update the ‘level’ within the search process. The proposed method has been applied to a range of benchmark university course timetabling test problems from the literature. Moreover, the viability of the method has been tested by comparing its results with other reported results from the literature, demonstrating that the method is able to produce improved solutions to those currently published. We believe this is due to the combination of both approaches and the ability of the resultant algorithm to converge all solutions at every search process.

The role of proximity in university-business cooperation for innovation

The potential for universities to contribute positively to business innovation has received much attention in recent years. While the determinants of university-business cooperation have been examined extensively, less attention has been given to the mediating influence of proximity in this relationship. The analysis in this paper builds on theUKbusiness innovation survey (2002–2005) by incorporating measures of the university research environment for each of the 16,500 businesses surveyed. These measures allow us to look beyond business-level characteristics as determinants of the geography of university cooperation and account for the character of the local university environment. Measures include the distance from each business to its nearest university, the quality of local university research and the density of the university research environment. The findings suggest that significant differences exist between those businesses that cooperate with local universities and those that cooperate with non-local universities. These differences relate to business size, sales profile, location, absorptive capacity and innovation activity. In addition, we also find that if a business is located close to a research excellent university, cooperation tends to remain local, however, the distance between businesses and the nearest university is not a significant determinant of university-business cooperation and further, the higher the concentration of universities in the business locale, the more likely businesses are to cooperate with non-local universities.

Rapid changes in the level of Kluane Lake in Yukon Territory over the last millennium

The level of Kluane Lake, the largest lake in Yukon Territory, was lower than at present during most of the Holocene. The lake rose rapidly in the late seventeenth century to a level 12 m above present, drowning forest and stranding driftwood on a conspicuous high-stand beach, remnants of which are preserved at the south end of the lake. Kluane Lake fell back to near its present level by the end of the eighteenth century and has fluctuated within a range of about 3 m over the last 50 yr. The primary control on historic fluctuations in lake level is the discharge of Slims River, the largest source of water to the lake. We use tree ring and radiocarbon ages, stratigraphy and sub-bottom acoustic data to evaluate two explanations for the dramatic changes in the level of Kluane Lake. Our data support the hypothesis of Hugh Bostock, who suggested in 1969 that the maximum Little Ice Age advance of Kaskawulsh Glacier deposited large amounts of sediment in the Slims River valley and established the present course of Slims River into Kluane Lake. Bostock argued that these events caused the lake to rise and eventually overflow to the north. The overflowing waters incised the Duke River fan at the north end of Kluane Lake and lowered the lake to its present level. This study highlights the potentially dramatic impacts of climate change on regional hydrology during the Little Ice Age in glacierised mountains. © 2006 University of Washington.

“I miss being spoon-fed”. A comparison of transition from school to university education from the perspective of undergraduate pharmacy students

Background: The transition from school to university can be challenging and there is increasing concern among academics that students are inadequately prepared for entry to university courses.Aims: To investigate students’ views on transition from school to university education.Method: A focus group was conducted with first-year students and analysed using thematic analysis. Students were invited to participate in an electronic questionnaire; responses were analysed via SPSS for Windows. The Mann– Whitney U test was utilised with p<0.05 set as significant.Results: A response rate of 60% (88/147) was obtained for the questionnaire. Differences included staff-student interactions, learning methods, examination preparation and feedback provision. Many (85%) agreed that the main emphasis in school was on examination preparation; 29.6% considered this to be the case at university (z=-8.315; p<0.05). Most students (95.4%) considered the feedback they received at school helped improve performance; this decreased to 50% when asked about feedback at university (z=-8.326; p<0.05).Conclusion: Students appear to be insufficiently prepared for the demands of higher education. They desire various aspects of their university educational experience to be more akin to that of school, including: a greater level of individual attention, increased access to teaching staff, and further clarification and transparency about the standard required to pass exams. Further work can now be done by academic staff to aid the transition and improve the learning experience.

Developing mathematics support for first-year engineering students with non-traditional mathematics backgrounds

A maths support system for first-year engineering students with non-traditional entry qualifications has involved students working through practice questions structured to correspond with the maths module which runs in parallel. The setting was informal and there was significant one-to-one assistance. The non-traditional students (who are known to be less well prepared mathematically) were explicitly contacted in the first week of their university studies regarding the maths support and they generally seemed keen to participate. However, attendance at support classes was relatively low, on average, but varied greatly between students. Students appreciated the personal help and having time to ask questions. It seemed that having a small group of friends within the class promoted attendance – perhaps the mutual support or comfort that they all had similar mathematical difficulties was a factor. The classes helped develop confidence. Attendance was hindered by the class being timetabled too soon after the relevant lecture and students were reluctant to come with no work done beforehand. Although students at risk due to their mathematical unpreparedness can easily be identified at an early stage of their university career, encouraging them to partake of the maths support is an ongoing, major problem.

Mathematical anxiety is linked to reduced cognitive reflection: A potential road from discomfort in the mathematics classroom to susceptibility to biases

Background
When asked to solve mathematical problems, some people experience anxiety and threat, which can lead to impaired mathematical performance (Curr Dir Psychol Sci 11:181–185, 2002). The present studies investigated the link between mathematical anxiety and performance on the cognitive reflection test (CRT; J Econ Perspect 19:25–42, 2005). The CRT is a measure of a person’s ability to resist intuitive response tendencies, and it correlates strongly with important real-life outcomes, such as time preferences, risk-taking, and rational thinking.

Methods
In Experiments 1 and 2 the relationships between maths anxiety, mathematical knowledge/mathematical achievement, test anxiety and cognitive reflection were analysed using mediation analyses. Experiment 3 included a manipulation of working memory load. The effects of anxiety and working memory load were analysed using ANOVAs.

Results
Our experiments with university students (Experiments 1 and 3) and secondary school students (Experiment 2) demonstrated that mathematical anxiety was a significant predictor of cognitive reflection, even after controlling for the effects of general mathematical knowledge (in Experiment 1), school mathematical achievement (in Experiment 2) and test anxiety (in Experiments 1–3). Furthermore, Experiment 3 showed that mathematical anxiety and burdening working memory resources with a secondary task had similar effects on cognitive reflection.

Conclusions
Given earlier findings that showed a close link between cognitive reflection, unbiased decisions and rationality, our results suggest that mathematical anxiety might be negatively related to individuals’ ability to make advantageous choices and good decisions.

M level Inquiry Across Disciplinary Boundaries: Using Reflective Sketchbooks

Debates unfolding around the recent development of M Level programmes for teacher education are not unfamiliar to those being addressed in other professional disciplines such as business. A strong theme in our analysis is that reflective practitioners could be provided with a wider range of tools and methods to support them in their reflection. Considerable energies have been expended on e portfolios, but our experience of use of paper based reflective
sketchbooks suggests that they may have some distinct advantages over text-dominated electronic media. In fact such sketchbooks challenge typed text as the dominant route to learning and communication (Gilbert 1998), (New, 2005), (Hickman, 2007). Professionals in teacher education are currently exploring ways in which M level can be conceived in terms of professional learning. This is also important terrain in other professions. For example, best practice in business management involves constant innovation so that students do not experience a split between the research context of the business faculty and the experience of operating in the business situation. This is paralleled in education by the concern that trainees do not experience a split between the research or scholarly informed approach of university tutors, and the experience of practical teaching in school. Our research question is concerned with how a consciously developed reflective sketchbook method can generate levels of critical thought that are both postgraduate and professionally valued in the workplace. We are also interested in the contribution this form of enquiry at M Level can make in terms of life long learning.

Development of an app to support learning in A-level maths

This project involved producing an app for smart devices to enable modernised learning for A-level maths students. Research in a stakeholder school showed that 94% of pupils surveyed within the upper-secondary level owned a smartphone and most owned a tablet also, emphasising the opportunity for using apps to support learning. The app was developed using iBuildApp, an online app-creation programme which requires no programming. Past exam questions and solutions, notes and video tutorials were included and the topic was vectors, identified by teachers as problematic. Pupils generally found the app easy to use and wanted further development. The videos were popular despite this not ranking highly as a preferred method of revision previously. Teachers were happy for pupils to use the app to supplement their learning, both in the classroom and outside.

Suppression of the high affinity phosphate uptake system:A mechanism of arsenate tolerance in Holcus lanatus L.

In Holcus lanatus L. phosphate and arsenate are taken up by the same transport system. Short-term uptake kinetics of the high affinity arsenate transport system were determined in excised roots of arsenate-tolerant and non-tolerant genotypes. In tolerant plants the V_max of ion uptake in plants grown in phosphate-free media was decreased compared to non-tolerant plants, and the affinity of the uptake system was lower than in the non-tolerant plants. Both the reduction in V_max and the increase in K_m led to reduced arsenate influx into tolerant roots. When the two genotypes were grown in nutrient solution containing high levels of phosphate, there was little change in the uptake kinetics in tolerant plants. In non-tolerant plants, however, there was a marked decrease in the V_max to the level of the tolerant plants but with little change in the K_m. This suggests that the low rate of arsenate uptake over a wide range of differing root phosphate status is due to loss of induction of the synthesis of the arsenate (phosphate) carrier. © 1992 Oxford University Press.

Empathy in UK pharmacy students: assessing differences by gender, level in the degree programme, part-time employment and medical status

Background: Empathy is an important aspect of patient–healthcare professional interactions.Aims: To investigate whether gender, level in the degree programme, employment and health status affected empathy scores of undergraduate pharmacy students.Method: All undergraduate pharmacy students (n=529) at Queen’s University Belfast were invited via email to completean online validated empathy questionnaire. Empathy scores were calculated and non-parametric tests used to determine associations between factors.Results: Response rate was 60.1% (318/529) and the mean empathy score was 106.19. Scores can range from 20 to 140,with higher scores representing a greater degree of empathy. There was no significant difference between genders (p=0.211). There was a significant difference in scores across the four levels of the programme (p<0.001); scores were lowest at Level 1 and greatest at Level 4 (final year). There were no significant differences in scores for respondents who had a part-time job, a chronic condition, or took regular medication in comparison to those who did not (p=0.028,p=0.880, p=0.456, respectively).Conclusion: A reasonable level of empathy was found relative to other studies; this could be further enhanced at lower levels of the degree pathway.