Protein-RNA interactions: a structural analysis

A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level

Special colored Superpolynomials and their representation-dependence

We introduce the notion of "special superpolynomials" by putting q=1 in the formulas for reduced superpolynomials. In this way we obtain a generalization of special HOMFLY polynomials depending on one extra parameter t. Special HOMFLY are known to depend on representation R in especially simple way: as |R|-th power of the fundamental ones. We show that the same dependence persists for our special superpolynomials in the case of symmetric representations, at least for the 2-strand torus and figure-eight knots. For antisymmetric representations the same is true, but for t=1 and arbitrary q. It would be interesting to find an interpolation between these two relations for arbitrary representations, but no superpolynomails are yet available in this case.Comment: 5 page

Cladding strategies for building-integrated photovoltaics

Photovoltaic cladding on the surfaces of commercial buildings has the potential for considerable reductions in carbon emissions due to embedded renewable power generation displacing conventional power utilization. In this paper, a model is described for the optimization of photovoltaic cladding densities on commercial building surfaces. The model uses a modified form of the ‘fill factor’ method for photovoltaic power supply coupled to new regression-based procedures for power demand estimation. An optimization is included based on a defined ‘mean index of satisfaction’ for matched power supply and demand (i.e., zero power exportation to the grid). The mean index of satisfaction directly translates to the reduction in carbon emission that might be expected over conventional power use. On clear days throughout the year, reductions of conventional power use of at least 60% can be achieved with an optimum cladding pattern targeted to lighting and small power load demands

Disease prevention versus data privacy : using landcover maps to inform spatial epidemic models

The availability of epidemiological data in the early stages of an outbreak of an infectious disease is vital for modelers to make accurate predictions regarding the likely spread of disease and preferred intervention strategies. However, in some countries, the necessary demographic data are only available at an aggregate scale. We investigated the ability of models of livestock infectious diseases to predict epidemic spread and obtain optimal control policies in the event of imperfect, aggregated data. Taking a geographic information approach, we used land cover data to predict UK farm locations and investigated the influence of using these synthetic location data sets upon epidemiological predictions in the event of an outbreak of foot-and-mouth disease. When broadly classified land cover data were used to create synthetic farm locations, model predictions deviated significantly from those simulated on true data. However, when more resolved subclass land use data were used, moderate to highly accurate predictions of epidemic size, duration and optimal vaccination and ring culling strategies were obtained. This suggests that a geographic information approach may be useful where individual farm-level data are not available, to allow predictive analyses to be carried out regarding the likely spread of disease. This method can also be used for contingency planning in collaboration with policy makers to determine preferred control strategies in the event of a future outbreak of infectious disease in livestock

Internal and External Barriers to Effective Supply Chain Management Implementation in Malaysian Manufacturing Companies: A Priority List Based on Varying Demographic Perspectives

Successful implementation of supply-chain management in a developing country such as Malaysia is considered a major challenge due to lack of awareness and unclear missions and goals. Focusing on this idea, this article compares the ranking of various demographic groups in relation to the internal and external barriers experienced by Malaysian manufacturing companies. The identified lists of internal and external barriers are prioritised using the Analytic Hierarchy Process (AHP). Ten respondents with wide ranging experience in SCM provided the necessary information in the prioritisation exercise. The ranking of the respondents from different races, age groups, education levels, employment types, work experience and designations suggests significant variations between these groups in the ranking of the internal and external barriers. The findings of this research provide important information to company managers who desire to implement SCM in a multi-cultural setting such as Malaysia. The onus is on these managers to be cautious in developing a strategic plan for its effective implementation and also in designing programs to overcome SCM obstacles

Self-perceived competence correlates poorly with objectively measured competence in Evidence Based Medicine among medical students

<p>Abstract</p> <p>Background</p> <p>Previous studies report various degrees of agreement between self-perceived competence and objectively measured competence in medical students. There is still a paucity of evidence on how the two correlate in the field of Evidence Based Medicine (EBM). We undertook a cross-sectional study to evaluate the self-perceived competence in EBM of senior medical students in Malaysia, and assessed its correlation to their objectively measured competence in EBM.</p> <p>Methods</p> <p>We recruited a group of medical students in their final six months of training between March and August 2006. The students were receiving a clinically-integrated EBM training program within their curriculum. We evaluated the students' self-perceived competence in two EBM domains ("searching for evidence" and "appraising the evidence") by piloting a questionnaire containing 16 relevant items, and objectively assessed their competence in EBM using an adapted version of the Fresno test, a validated tool. We correlated the matching components between our questionnaire and the Fresno test using Pearson's product-moment correlation.</p> <p>Results</p> <p>Forty-five out of 72 students in the cohort (62.5%) participated by completing the questionnaire and the adapted Fresno test concurrently. In general, our students perceived themselves as moderately competent in most items of the questionnaire. They rated themselves on average 6.34 out of 10 (63.4%) in "searching" and 44.41 out of 57 (77.9%) in "appraising". They scored on average 26.15 out of 60 (43.6%) in the "searching" domain and 57.02 out of 116 (49.2%) in the "appraising" domain in the Fresno test. The correlations between the students' self-rating and their performance in the Fresno test were poor in both the "searching" domain (r = 0.13, p = 0.4) and the "appraising" domain (r = 0.24, p = 0.1).</p> <p>Conclusions</p> <p>This study provides supporting evidence that at the undergraduate level, self-perceived competence in EBM, as measured using our questionnaire, does not correlate well with objectively assessed EBM competence measured using the adapted Fresno test.</p> <p>Study registration</p> <p>International Medical University, Malaysia, research ID: IMU 110/06</p

Dynamics of the Tippe Top -- properties of numerical solutions versus the dynamical equations

We study the relationship between numerical solutions for inverting Tippe Top and the structure of the dynamical equations. The numerical solutions confirm oscillatory behaviour of the inclination angle $\theta(t)$ for the symmetry axis of the Tippe Top. They also reveal further fine features of the dynamics of inverting solutions defining the time of inversion. These features are partially understood on the basis of the underlying dynamical equations

Impact of maternal cigarette smoke exposure on brain and kidney health outcomes in female offspring

© 2016 John Wiley & Sons Australia, Ltd Increased oxidative stress in the brain can lead to increased sympathetic tone that may further induce kidney dysfunction. Previously we have shown that maternal cigarette smoke exposure (SE) leads to significantly increased oxidative stress and inflammation in both brain and kidney, as well as reduced brain and kidney mitochondrial activity. This is closely associated with significant kidney underdevelopment and abnormal function in adulthood in the male offspring. This study aimed to investigate the impact of maternal SE on brain and kidney health in the female offspring. In this study, the mouse dams were exposed to two cigarettes, twice daily for 6 weeks prior to gestation, during pregnancy and lactation. Brains and kidneys from the female offspring were collected at 20 days (P20) and 13 weeks (W13) and were subject to further analysis. We found that mRNA expression of brain inflammatory markers interleukin-1 receptor and Toll-like receptor 4 were significantly increased in the SE offspring at both P20 and W13. Their brain mitochondrial activity markers were however increased at W13 with increased antioxidant activity. Kidney development and function in the female SE offspring were not different from the control offspring. We concluded that although brain inflammatory markers were upregulated in the SE female offspring, they were protected from some of the indicators of brain oxidative stress, such as endogenous antioxidant and mitochondrial dysfunction, as well as abnormal kidney development and function in adulthood