A Universal Point Set for 2-Outerplanar Graphs

A point set $S \subseteq \mathbb{R}^2$ is universal for a class $\cal G$ if every graph of ${\cal G}$ has a planar straight-line embedding on $S$. It is well-known that the integer grid is a quadratic-size universal point set for planar graphs, while the existence of a sub-quadratic universal point set for them is one of the most fascinating open problems in Graph Drawing. Motivated by the fact that outerplanarity is a key property for the existence of small universal point sets, we study 2-outerplanar graphs and provide for them a universal point set of size $O(n \log n)$.Comment: 23 pages, 11 figures, conference version at GD 201

Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB

BACKGROUND: Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe(2+ )oxygenase superfamily. RESULTS: In this article, we report identification and sequence analysis of five human members of the (2OG-Fe(2+)) oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family (and specifically to the lineage that groups together hABH2 and hABH3) rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes. CONCLUSIONS: We hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes

Data intensive scientific analysis with grid computing

At the end of September 2009, a new Italian GPS receiver for radio occultation was launched from the Satish Dhawan Space Center (Sriharikota, India) on the Indian Remote Sensing OCEANSAT-2 satellite. The Italian Space Agency has established a set of Italian universities and research centers to implement the overall processing radio occultation chain. After a brief description of the adopted algorithms, which can be used to characterize the temperature, pressure and humidity, the contribution will focus on a method for automatic processing these data, based on the use of a distributed architecture. This paper aims at being a possible application of grid computing for scientific research

Superpatterns and Universal Point Sets

An old open problem in graph drawing asks for the size of a universal point set, a set of points that can be used as vertices for straight-line drawings of all n-vertex planar graphs. We connect this problem to the theory of permutation patterns, where another open problem concerns the size of superpatterns, permutations that contain all patterns of a given size. We generalize superpatterns to classes of permutations determined by forbidden patterns, and we construct superpatterns of size n^2/4 + Theta(n) for the 213-avoiding permutations, half the size of known superpatterns for unconstrained permutations. We use our superpatterns to construct universal point sets of size n^2/4 - Theta(n), smaller than the previous bound by a 9/16 factor. We prove that every proper subclass of the 213-avoiding permutations has superpatterns of size O(n log^O(1) n), which we use to prove that the planar graphs of bounded pathwidth have near-linear universal point sets.Comment: GD 2013 special issue of JGA

Periostin in exhaled breath condensate and in serum of asthmatic patients : relationship to upper and lower airway disease

PURPOSE: Periostin is considered a biomarker for eosinophilic airway inflammation and have been associated with NSAID-Exacerbated Respiratory Disease (NERD) and chronic rhinosinusitis (CRS). In this study, we aimed to evaluate periostin in exhaled breath condensate (EBC) and in serum of patients with various asthma phenotypes. METHODS: The study included 40 asthmatic patients (22 with NERD) and 17 healthy controls. All the procedures (questionnaire, spirometry, FeNO, nasal swabs, EBC collecting, and blood sampling) were performed on the same day. Periostin concentrations were measured using an ELISA kit. RESULTS: Periostin was detected in EBC from 37 of 40 asthmatics and in 16 from 17 of controls. The concentration of periostin in EBC did not differ between the study groups and was not associated with NERD or asthma severity. However, the EBC periostin was significantly higher in asthmatics with CRS as compared to those without (3.1 vs 2 ng/mL, P=0.046). Patients with positive bacterial culture from nasal swabs had higher EBC periostin concentrations than those without (3.2 vs 2.1 ng/mL; P=0.046). The mean serum periostin level was higher in asthmatics with a 1-year history of exacerbation than in those without (3.2 vs 2.3 ng/mL, P=0.045). Asthmatics with skin manifestation of NSAIDs hypersensitivity had higher serum periostin levels as compared to those without (3.5 vs 2.3 ng/mL; P=0.03). CONCLUSIONS: EBC periostin levels seem to reflect intensity of upper airway disease in asthmatics, while serum levels of periostin are associated with asthma activity (exacerbations or FeNO) or NERD subphenotypes

Universal and Non-Universal First-Passage Properties of Planar Multipole Flows

The dynamics of passive Brownian tracer particles in steady two-dimensional potential flows between sources and sinks is investigated. The first-passage probability, $p(t)$, exhibits power-law decay with a velocity-dependent exponent in radial flow and an order-dependent exponent in multipolar flows. For the latter, there also occur diffusive ``echo'' shoulders and exponential decays associated with stagnation points in the flow. For spatially extended dipole sinks, the spatial distribution of the collected tracer is independent of the overall magnitude of the flow field.Comment: 7 pages, LaTe

Dynamics of a faceted nematic-smectic B front in thin-sample directional solidification

We present an experimental study of the directional-solidification patterns of a nematic - smectic B front. The chosen system is C_4H_9-(C_6H_{10})_2CN (in short, CCH4) in 12 \mu m-thick samples, and in the planar configuration (director parallel to the plane of the sample). The nematic - smectic B interface presents a facet in one direction -- the direction parallel to the smectic layers -- and is otherwise rough, and devoid of forbidden directions. We measure the Mullins-Sekerka instability threshold and establish the morphology diagram of the system as a function of the solidification rate V and the angle theta_{0} between the facet and the isotherms. We focus on the phenomena occurring immediately above the instability threshold when theta_{0} is neither very small nor close to 90^{o}. Under these conditions we observe drifting shallow cells and a new type of solitary wave, called "faceton", which consists essentially of an isolated macroscopic facet traveling laterally at such a velocity that its growth rate with respect to the liquid is small. Facetons may propagate either in a stationary, or an oscillatory way. The detailed study of their dynamics casts light on the microscopic growth mechanisms of the facets in this system.Comment: 12 pages, 19 figures, submitted to Phys. Rev.

BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene

A mutant line, bifurcate flower truss (bif), was recovered from a tomato breeding program. Plants from the control line LAM183 produced a mean of 0.16 branches per truss, whereas the value for bif plants was 4.1. This increase in branching was accompanied by a 3.3-fold increase in flower number and showed a significant interaction with exposure to low temperature during truss development. The LAM183 and bif genomes were resequenced and the bif gene was mapped to a 2.01 Mbp interval on chromosome 12; all coding region polymorphisms in the interval were surveyed and five candidate genes displaying altered protein sequences were detected. One of these genes, SlMAPK1, encoding a MAP kinase, contained a leucine-to-stop codon mutation predicted to disrupt kinase function. SlMAPK1 is an excellent candidate for bif because knock-out mutations of an Arabidopsis orthologue MPK6 were reported to have increased flower number. An introgression browser was used to demonstrate that the origin of the bif genomic DNA at the BIF locus was Solanum galapagense and that the SlMAPK1 null mutant is a naturally occurring allele widespread only on the Galápagos Islands. This work strongly implicates SlMAPK1 as part of the network of genes controlling inflorescence branching in tomato

The factors of quality assessment in nursing care

Autorzy skupili sią na zagadnieniach związanych z działaniami zapewniającymi pożądany poziom jakości, a więc na systemie organizacyjny opieki, przepisach prawnych regulujących funkcjonowanie opieki zdrowotnej, środowisku czyli miejscu wykonywania opieki. Podkreślili znaczenie kwalifikacji pracowników, systemów informacyjnych oraz dokumentowania działalności medycznej.The authors focus on the matters related to the actions meant to ensure the desired quality level, namely on the care organization system, legal regulations pertaining to healthcare and envi-ronment, that is the location of healthcare provision. The significance of staff qualifications, information systems and medical record keeping were emphasized