The Jones polynomial of an almost alternating link

A link is almost alternating if it is non-alternating and has a diagram that can be transformed into an alternating diagram via one crossing change. We give formulas for the first two and last two potential coefficients of the Jones polynomial of an almost alternating link. Using these formulas, we show that the Jones polynomial of an almost alternating link is nontrivial. We also show that either the first two or last two coefficients of the Jones polynomial of an almost alternating link alternate in sign. Finally, we describe conditions that ensure an almost alternating diagram has the fewest number of crossings among all almost alternating diagrams of the link.Comment: 24 pages, 16 figures; minor changes throughou

Belted sum decompositions of fully augmented links

Given two orientable, cusped hyperbolic 3-manifolds containing certain thrice-punctured spheres, Adams gave a diagrammatic definition for a third such manifold, their belted sum. Fully augmented links, or FALs, are hyperbolic links constructed by augmenting a link diagram. This work considers belted sum decompositions in which all manifolds involved are FAL complements. To do so, we provide explicit classifications of thrice punctured spheres in FAL complements, making them easily recognizable. These classifications are used to characterize belted sum prime FALs geometrically, combinatorially and diagrammatically. Finally we prove that, in the context of belted sums, every FAL complement canonically decomposes into FALs which are either prime or two-fold covers of the Whitehead link

Introductory programming: a systematic literature review

As computing becomes a mainstream discipline embedded in the school curriculum and acts as an enabler for an increasing range of academic disciplines in higher education, the literature on introductory programming is growing. Although there have been several reviews that focus on specific aspects of introductory programming, there has been no broad overview of the literature exploring recent trends across the breadth of introductory programming. This paper is the report of an ITiCSE working group that conducted a systematic review in order to gain an overview of the introductory programming literature. Partitioning the literature into papers addressing the student, teaching, the curriculum, and assessment, we explore trends, highlight advances in knowledge over the past 15 years, and indicate possible directions for future research

Molecular adaptation of ammonia monooxygenase during independent pH specialization in Thaumarchaeota

Acknowledgements This work was funded by Natural Environment Research Council Fellowship NE/J019151/1 and by institutional funding from within the University of Aberdeen. Both authors designed and performed the research, analysed data and equally contributed to the writing of the manuscript.Peer reviewedPublisher PD

Prediction of second neurological attack in patients with clinically isolated syndrome using support vector machines

The aim of this study is to predict the conversion from clinically isolated syndrome to clinically definite multiple sclerosis using support vector machines. The two groups of converters and non-converters are classified using features that were calculated from baseline data of 73 patients. The data consists of standard magnetic resonance images, binary lesion masks, and clinical and demographic information. 15 features were calculated and all combinations of them were iteratively tested for their predictive capacity using polynomial kernels and radial basis functions with leave-one-out cross-validation. The accuracy of this prediction is up to 86.4% with a sensitivity and specificity in the same range indicating that this is a feasible approach for the prediction of a second clinical attack in patients with clinically isolated syndromes, and that the chosen features are appropriate. The two features gender and location of onset lesions have been used in all feature combinations leading to a high accuracy suggesting that they are highly predictive. However, it is necessary to add supporting features to maximise the accuracy. © 2013 IEEE

Predominant Distribution of the RNAi Machinery at Apical Adherens Junctions in Colonic Epithelia Is Disrupted in Cancer

The RNA interference (RNAi) machinery is an essential component of the cell, regulating miRNA biogenesis and function. RNAi complexes were thought to localize either in the nucleus, such as the microprocessor, or in the cytoplasm, such as the RNA-induced silencing complex (RISC). We recently revealed that the core microprocessor components DROSHA and DGCR8, as well as the main components of RISC, including Ago2, also associate with the apical adherens junctions of well-differentiated cultured epithelial cells. Here, we demonstrate that the localization of the core RNAi components is specific and predominant at apical areas of cell-cell contact of human normal colon epithelial tissues and normal primary colon epithelial cells. Importantly, the apical junctional localization of RNAi proteins is disrupted or lost in human colon tumors and in poorly differentiated colon cancer cell lines, correlating with the dysregulation of the adherens junction component PLEKHA7. We show that the restoration of PLEKHA7 expression at adherens junctions of aggressively tumorigenic colon cancer cells restores the junctional localization of RNAi components and suppresses cancer cell growth in vitro and in vivo. In summary, this work identifies the apical junctional localization of the RNAi machinery as a key feature of the differentiated colonic epithelium, with a putative tumor suppressing function