On pairwise distances and median score of three genomes under DCJ

In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a resulting genome is called median genome). In contrast to the rearrangement distance between two genomes which can be computed in linear time, computing the median score for three genomes is NP-hard. This inspires a quest for simpler and faster approximations for the median score, the most natural of which appears to be the halved sum of pairwise distances which in fact represents a lower bound for the median score. In this work, we study relationship and interplay of pairwise distances between three genomes and their median score under the model of Double-Cut-and-Join (DCJ) rearrangements. Most remarkably we show that while a rearrangement may change the sum of pairwise distances by at most 2 (and thus change the lower bound by at most 1), even the most "powerful" rearrangements in this respect that increase the lower bound by 1 (by moving one genome farther away from each of the other two genomes), which we call strong, do not necessarily affect the median score. This observation implies that the two measures are not as well-correlated as one's intuition may suggest. We further prove that the median score attains the lower bound exactly on the triples of genomes that can be obtained from a single genome with strong rearrangements. While the sum of pairwise distances with the factor 2/3 represents an upper bound for the median score, its tightness remains unclear. Nonetheless, we show that the difference of the median score and its lower bound is not bounded by a constant.Comment: Proceedings of the 10-th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG), 2012. (to appear

New strategies for human papillomavirus-based cervical screening.

Author manuscript; published in final edited form as: Womens Health (Lond Engl). 2013 September; 9(5):. doi:10.2217/whe.13.48Human papillomavirus testing has been shown to be far more sensitive and robust in detecting cervical intraepithelial neoplasia 2 and above (and cervical intraepithelial neoplasia 3 and above) for cervical screening than approaches based on either cytology or visual inspection; however, there are a number of issues that need to be overcome if it is to substantially reduce the morbidity and mortality associated with cervical cancer at the population level. The two main issues are coverage (increasing the number of women who participate in screening) and the management of women who test positive for high-risk human papillomavirus. This article will review the potential for vaginal self-collection to improve coverage and the options for triage of high-risk human papillomavirus-positive women in high-resource and low-resource settings

Instruction Set Architectures for Quantum Processing Units

Progress in quantum computing hardware raises questions about how these devices can be controlled, programmed, and integrated with existing computational workflows. We briefly describe several prominent quantum computational models, their associated quantum processing units (QPUs), and the adoption of these devices as accelerators within high-performance computing systems. Emphasizing the interface to the QPU, we analyze instruction set architectures based on reduced and complex instruction sets, i.e., RISC and CISC architectures. We clarify the role of conventional constraints on memory addressing and instruction widths within the quantum computing context. Finally, we examine existing quantum computing platforms, including the D-Wave 2000Q and IBM Quantum Experience, within the context of future ISA development and HPC needs.Comment: To be published in the proceedings in the International Super Computing Conference 2017 publicatio

The relationship between dental status, food selection, nutrient intake, nutritional status, and body mass index in older people

This paper reviewed the findings from a national survey in Great Britain which assessed whether dental status affected older people's food selection, nutrient intake, and nutritional status. The survey analyzed national random samples of free-living and institution subjects for dental examination, interview, and four-day food diary as well as blood and urine tests In the free-living sample, intakes of non-starch polysaccharides, protein, calcium, non-heme iron, niacin, and vitamin C were significantly lower in edentulous as compared to dentate subjects. People with 21 or more teeth consumed more of most nutrients, particularly non-starch polysaccharides. This relationship in intake was not apparent in the hematological analysis. Plasma ascorbate and retinol were the only analytes significantly associated with dental status. Having 21 or more teeth increased the likelihood of having an acceptable body mass index (BMI). Thus, maintaining a natural and functional dentition defined as having more than twenty teeth into old age plays an important role in having a healthy diet rich in fruits and vegetables, a satisfactory nutritional status, and an acceptable BMI

Chlorination and oxidation of heparin and hyaluronan by hypochlorous acid and hypochlorite anions: effect of sulfate groups on reaction pathways and kinetics.

Hypochlorous acid (HOCl), produced in inflammatory conditions by the enzyme myeloperoxidase, and its anion hypochlorite (OCl(-)) exist in vivo at almost equal concentrations. Their reactions with hyaluronan and heparin (as a model for sulfated glycosaminoglycans in the extracellular matrix) have been studied as a function of pH. The major product in these reactions is the chloramide derivative of the glycosaminoglycans. Spectral, chloramide yield, and kinetic measurements show sharply contrasting behavior of heparin and hyaluronan and the data allow the calculation of second-order rate constants for the reactions of both HOCl and OCl(-) for all reaction pathways leading to the formation of chloramides and also oxidation products. By comparison with hyaluronan, it can be demonstrated that both N-sulfate and O-sulfate groups in heparin influence the proportions of these pathways in this glycosaminoglycan. Evidence is also given for further oxidation pathways involving a reaction of HOCl with the chloramide product of hyaluronan but not with heparin. The significance of these results for the mechanisms of inflammation, particularly for fragmentation of extracellular matrix glycosaminoglycans, is discussed

Dyspraxia in a patient with corticobasal degeneration: the role of visual and tactile inputs to action

Objectives-To investigate the roles of visual and tactile information in a dyspraxic patient with corticobasal degeneration (CBD) who showed dramatic facilitation in miming the use of a tool or object when he was given a tool to manipulate; and to study the nature of the praxic and neuropsychological deficits in CBD. Methods-The subject had clinically diagnosed CBD, and exhibited alien limb behaviour and striking ideomotor dyspraxia. General neuropsychological evaluation focused on constructional and visuospatial abilities, calculation, verbal fluency, episodic and semantic memory, plus spelling and writing because impairments in this domain were presenting complaints. Four experiments assessed the roles of visual and tactile information in the facilitation of motor performance by tools. Experiment I evaluated the patient's performance of six limb transitive actions under six conditions: (1) after he described the relevant tool from memory, (2) after he was shown a Line drawing of the tool, (3) after he was shown a real exemplar of the tool, (4) after he watched the experimenter perform the action, (5) while he was holding the tool, and (6) immediately after he had performed the action with the tool but with the tool removed from his grasp. Experiment 2 evaluated the use of the same six tools when the patient had tactile but no visual information (while he was blindfolded). Experiments 3 and 4 assessed performance of actions appropriate to the same six tools when the patient had either neutral or inappropriate tactile feedback-that is, while he was holding a non-tool object or a different tool. Results-Miming of tool use was not facilitated by visual input; moreover, lack of visual information in the blindfolded condition did not reduce performance. The principal positive finding was a dramatic facilitation of the patient's ability to demonstrate object use when he was holding either the appropriate tool or a neutral object. Tools inappropriate to the requested action produced involuntary performance of the stimulus relevant action. Conclusions-Tactile stimulation was paramount in the facilitation of motor performance in tool use by this patient with CBD. This outcome suggests that tactile information should be included in models which hypothesise modality specific inputs to the action production system. Significant impairments in spelling and letter production that have not previously been reported in CBD have also been documented

Wave intensity analysis: A novel non-invasive method for determining arterial wave transmission

Wave intensity analysis is a novel technique for assessing wavelet transmission in the cardiovascular system. Using this tool, we have developed non-invasive techniques to study wave transmission in both central & peripheral arteries in man. The aim of this study was to determine the reproducibility of various haemodynamic measures in the carotid, brachial and radial arteries. 12 treated hypertensive men underwent applanation tonometry and pulsed Doppler ultrasound studies of the carotid, brachial and radial arteries on 2 occasions. Coefficients of variation for the local wave speed, cardiac compression wave intensity and main reflected wave intensity ranged between 3.7-6.6%, 8.2-11.4% and 12.5-19.6% respectively. We conclude that non-invasive methods used for wave intensity analysis are reproducible & provide additional information regarding the complex phenomenon of arterial wave transmission in man

Factors influencing in vivo transduction by recombinant adeno-associated viral vectors expressing the human factor IX cDNA.

Long-term expression of coagulation factor IX (FIX) has been observed in murine and canine models following administration of recombinant adeno-associated viral (rAAV) vectors into either the portal vein or muscle. These studies were designed to evaluate factors that influence rAAV-mediated FIX expression. Stable and persistent human FIX (hFIX) expression (> 22 weeks) was observed from 4 vectors after injection into the portal circulation of immunodeficient mice. The level of expression was dependent on promoter with the highest expression, 10% of physiologic levels, observed with a vector containing the cytomegalovirus (CMV) enhancer/beta-actin promoter complex (CAGG). The kinetics of expression after injection of vector particles into muscle, tail vein, or portal vein were similar with hFIX detectable at 2 weeks and reaching a plateau by 8 weeks. For a given dose, intraportal administration of rAAV CAGG-FIX resulted in a 1.5-fold or 4-fold higher level of hFIX compared to tail vein or intramuscular injections, respectively. Polymerase chain reaction analysis demonstrated predominant localization of the rAAV FIX genome in liver and spleen after tail vein injection with a higher proportion in liver after portal vein injection. Therapeutic levels of hFIX were detected in the majority of immunocompetent mice (21 of 22) following intravenous administration of rAAV vector without the development of anti-hFIX antibodies, but hFIX was not detected in 14 immunocompetent mice following intramuscular administration, irrespective of strain. Instead, neutralizing anti-hFIX antibodies were detected in all the mice. These observations may have important implications for hemophilia B gene therapy with rAAV vectors

Abstract Interpretation of Stateful Networks

Modern networks achieve robustness and scalability by maintaining states on their nodes. These nodes are referred to as middleboxes and are essential for network functionality. However, the presence of middleboxes drastically complicates the task of network verification. Previous work showed that the problem is undecidable in general and EXPSPACE-complete when abstracting away the order of packet arrival. We describe a new algorithm for conservatively checking isolation properties of stateful networks. The asymptotic complexity of the algorithm is polynomial in the size of the network, albeit being exponential in the maximal number of queries of the local state that a middlebox can do, which is often small. Our algorithm is sound, i.e., it can never miss a violation of safety but may fail to verify some properties. The algorithm performs on-the fly abstract interpretation by (1) abstracting away the order of packet processing and the number of times each packet arrives, (2) abstracting away correlations between states of different middleboxes and channel contents, and (3) representing middlebox states by their effect on each packet separately, rather than taking into account the entire state space. We show that the abstractions do not lose precision when middleboxes may reset in any state. This is encouraging since many real middleboxes reset, e.g., after some session timeout is reached or due to hardware failure

System-adapted correlation energy density functionals from effective pair interactions

We present and discuss some ideas concerning an ``average-pair-density functional theory'', in which the ground-state energy of a many-electron system is rewritten as a functional of the spherically and system-averaged pair density. These ideas are further clarified with simple physical examples. We then show that the proposed formalism can be combined with density functional theory to build system-adapted correlation energy functionals. A simple approximation for the unknown effective electron-electron interaction that enters in this combined approach is described, and results for the He series and for the uniform electron gas are briefly reviewed.Comment: to appear in Phil. Mag. as part of Conference proceedings for the "Electron Correlations and Materials Properties", Kos Greece, July 5-9, 200