Essential Constraints of Edge-Constrained Proximity Graphs

Given a plane forest $F = (V, E)$ of $|V| = n$ points, we find the minimum set $S \subseteq E$ of edges such that the edge-constrained minimum spanning tree over the set $V$ of vertices and the set $S$ of constraints contains $F$. We present an $O(n \log n )$-time algorithm that solves this problem. We generalize this to other proximity graphs in the constraint setting, such as the relative neighbourhood graph, Gabriel graph, $\beta$-skeleton and Delaunay triangulation. We present an algorithm that identifies the minimum set $S\subseteq E$ of edges of a given plane graph $I=(V,E)$ such that $I \subseteq CG_\beta(V, S)$ for $1 \leq \beta \leq 2$, where $CG_\beta(V, S)$ is the constraint $\beta$-skeleton over the set $V$ of vertices and the set $S$ of constraints. The running time of our algorithm is $O(n)$, provided that the constrained Delaunay triangulation of $I$ is given.Comment: 24 pages, 22 figures. A preliminary version of this paper appeared in the Proceedings of 27th International Workshop, IWOCA 2016, Helsinki, Finland. It was published by Springer in the Lecture Notes in Computer Science (LNCS) serie

Gabriel Triangulations and Angle-Monotone Graphs: Local Routing and Recognition

A geometric graph is angle-monotone if every pair of vertices has a path between them that---after some rotation---is $x$- and $y$-monotone. Angle-monotone graphs are $\sqrt 2$-spanners and they are increasing-chord graphs. Dehkordi, Frati, and Gudmundsson introduced angle-monotone graphs in 2014 and proved that Gabriel triangulations are angle-monotone graphs. We give a polynomial time algorithm to recognize angle-monotone geometric graphs. We prove that every point set has a plane geometric graph that is generalized angle-monotone---specifically, we prove that the half-$\theta_6$-graph is generalized angle-monotone. We give a local routing algorithm for Gabriel triangulations that finds a path from any vertex $s$ to any vertex $t$ whose length is within $1 + \sqrt 2$ times the Euclidean distance from $s$ to $t$. Finally, we prove some lower bounds and limits on local routing algorithms on Gabriel triangulations.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Spanning Properties of Theta-Theta Graphs

We study the spanning properties of Theta-Theta graphs. Similar in spirit with the Yao-Yao graphs, Theta-Theta graphs partition the space around each vertex into a set of k cones, for some fixed integer k > 1, and select at most one edge per cone. The difference is in the way edges are selected. Yao-Yao graphs select an edge of minimum length, whereas Theta-Theta graphs select an edge of minimum orthogonal projection onto the cone bisector. It has been established that the Yao-Yao graphs with parameter k = 6k' have spanning ratio 11.67, for k' >= 6. In this paper we establish a first spanning ratio of $7.82$ for Theta-Theta graphs, for the same values of $k$. We also extend the class of Theta-Theta spanners with parameter 6k', and establish a spanning ratio of $16.76$ for k' >= 5. We surmise that these stronger results are mainly due to a tighter analysis in this paper, rather than Theta-Theta being superior to Yao-Yao as a spanner. We also show that the spanning ratio of Theta-Theta graphs decreases to 4.64 as k' increases to 8. These are the first results on the spanning properties of Theta-Theta graphs.Comment: 20 pages, 6 figures, 3 table

An optimized TOPS+ comparison method for enhanced TOPS models

This article has been made available through the Brunel Open Access Publishing Fund.Background Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+. Results We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method. Conclusions Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy. Software Availability: The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/.This article is available through the Brunel Open Access Publishing Fun

Respiratory viral pathogens among Singapore military servicemen 2009 - 2012: Epidemiology and clinical characteristics

10.1186/1471-2334-14-204BMC Infectious Diseases141-BIDM

Use of intravitreal bevacizumab in a patient with a Von Hippel-Lindau-associated retinal haemangioblastoma of the optic nerve head: a case report

<p>Abstract</p> <p>Introduction</p> <p>The optimum management of a capillary haemangioblastoma affecting the optic nerve head is not clear. A number of treatment modalities have been used to treat the tumours and their consequences. Ocular haemangioblastomas express high levels of vascular endothelial growth factor and levels have been correlated with tumour growth and activity. Treatment with vascular endothelial growth factor inhibitors would therefore seem a logical approach.</p> <p>Case presentation</p> <p>We describe a 23-year-old man with an exophytic capillary haemangioblastoma of the optic nerve head that was treated with intravitreal bevacizumab injections.</p> <p>Conclusion</p> <p>Unfortunately, treatment with intravitreal bevacizumab on three occasions had no effect on either tumour size or exudation in this patient.</p

Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists. © 2011 Hatfull et al

Gaps in cancer care in a multi-ethnic population in Sarawak, Borneo: A central referral centre study.

BACKGROUND: The state of Sarawak on the island of Borneo in East Malaysia, in working towards developing and strengthening cancer services through a holistic patient-centred approach, must focus on the comprehensive needs of cancer patients by taking into account the psycho-social, cultural and spiritual aspects of Sarawak's multi-ethnic, multi-cultural population. METHODS: A 42-item survey questionnaire was developed and validated with a total of 443 patients. The perceived importance of information provided and level of patient satisfaction were assessed with a 5-point Likert scale in 10 domains (Diagnosis, Surgery, Radiotherapy, Systemic therapy, Clinical trials, Pain management, Treatment monitoring, Psychosocial support, Sexual care and fertility issues, and Financial support). A Spearman's rank correlation test was applied to determine the correlation between response in both item and domain categories for perceived importance and satisfaction. RESULTS: Overall, patients were more satisfied with information related to cancer diagnosis, treatment and surgery but less satisfied with information pertaining to sexual aspects of care and family planning, psycho-social support and financial support. The majority of patients were satisfied with the level of treatment-related information received but preferred the information to be delivered in more easily comprehendible formats. Sexual aspects of care and family planning, psychosocial support and treatment monitoring post-discharge were perceived as important but seldom addressed by health care professionals due to lack of professional counsellors, social workers and clinical nurse specialists. Many patients face financial toxicity following a cancer diagnosis, particularly when diagnosed with advanced cancer requiring complex multi-modality treatment. CONCLUSION: Cancer patients in Sarawak have various unmet information needs. Written information and educational videos in local indigenous languages may be more suitable for Sarawak's multi-ethnic population. Sexual aspects of care and family planning are challenging but essential topics to discuss, in particular due to the high prevalence of breast and cervical cancer amongst young women of reproductive age in Sarawak. Financial assessment and information on support services offered by government and non-government organisations should be provided to eligible patients. A holistic needs assessment of each patient at time of diagnosis and support through their cancer journey requires a multi-disciplinary team of medical, nursing and allied health professionals including clinical nurse specialists, pharmacists, counsellors, physiotherapists, occupational therapists, speech and language therapists, dieticians and social workers

Gliders2d: Source Code Base for RoboCup 2D Soccer Simulation League

We describe Gliders2d, a base code release for Gliders, a soccer simulation team which won the RoboCup Soccer 2D Simulation League in 2016. We trace six evolutionary steps, each of which is encapsulated in a sequential change of the released code, from v1.1 to v1.6, starting from agent2d-3.1.1 (set as the baseline v1.0). These changes improve performance by adjusting the agents' stamina management, their pressing behaviour and the action-selection mechanism, as well as their positional choice in both attack and defense, and enabling riskier passes. The resultant behaviour, which is sufficiently generic to be applicable to physical robot teams, increases the players' mobility and achieves a better control of the field. The last presented version, Gliders2d-v1.6, approaches the strength of Gliders2013, and outperforms agent2d-3.1.1 by four goals per game on average. The sequential improvements demonstrate how the methodology of human-based evolutionary computation can markedly boost the overall performance with even a small number of controlled steps.Comment: 12 pages, 1 figure, Gliders2d code releas

Multiple structure alignment and consensus identification for proteins

<p>Abstract</p> <p>Background</p> <p>An algorithm is presented to compute a multiple structure alignment for a set of proteins and to generate a consensus (pseudo) protein which captures common substructures present in the given proteins. The algorithm represents each protein as a sequence of triples of coordinates of the alpha-carbon atoms along the backbone. It then computes iteratively a sequence of transformation matrices (i.e., translations and rotations) to align the proteins in space and generate the consensus. The algorithm is a heuristic in that it computes an approximation to the optimal alignment that minimizes the sum of the pairwise distances between the consensus and the transformed proteins.</p> <p>Results</p> <p>Experimental results show that the algorithm converges quite rapidly and generates consensus structures that are visually similar to the input proteins. A comparison with other coordinate-based alignment algorithms (MAMMOTH and MATT) shows that the proposed algorithm is competitive in terms of speed and the sizes of the conserved regions discovered in an extensive benchmark dataset derived from the HOMSTRAD and SABmark databases.</p> <p>The algorithm has been implemented in C++ and can be downloaded from the project's web page. Alternatively, the algorithm can be used via a web server which makes it possible to align protein structures by uploading files from local disk or by downloading protein data from the RCSB Protein Data Bank.</p> <p>Conclusions</p> <p>An algorithm is presented to compute a multiple structure alignment for a set of proteins, together with their consensus structure. Experimental results show its effectiveness in terms of the quality of the alignment and computational cost.</p