A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

EPUAP classification system for pressure ulcers: European reliability study

‘The definitive version is available at www3.interscience.wiley.com .' Copyright Blackwell PublishingPeer reviewe

The floor in the interplanetary magnetic field: Estimation on the basis of relative duration of ICME observations in solar wind during 1976-2000

To measure the floor in interplanetary magnetic field and estimate the time- invariant open magnetic flux of Sun, it is necessary to know a part of magnetic field of Sun carried away by CMEs. In contrast with previous papers, we did not use global solar parameters: we identified different large-scale types of solar wind for 1976-2000 interval, obtained a fraction of interplanetary CMEs (ICMEs) and calculated magnitude of interplanetary magnetic field B averaged over 2 Carrington rotations. The floor of magnetic field is estimated as B value at solar cycle minimum when the ICMEs were not observed and it was calculated to be 4,65 \pm 6,0 nT. Obtained value is in a good agreement with previous results.Comment: 10 pages, 2 figures, submitted in GR

Survivorship data in Prostate Cancer : Where are we and where do we need to be?

Funding/Support and role of the sponsor: PIONEER is funded through the IMI2 Joint Undertaking and is listed under grant agreement 777492. IMI2 receives support from the European Union’s Horizon 2020 research and innovation programme and the European Federation of Pharmaceutical Industries and Associations (EFPIA). The funding bodies played no direct role in this study. The views communicated here are those of PIONEER. Neither the IMI nor the European Union, EFPIA, or any associated partners are responsible for any use that may be made of the information contained herein.Peer reviewedPublisher PD

A distance for partially labeled trees

In a number of practical situations, data have structure and the relations among its component parts need to be coded with suitable data models. Trees are usually utilized for representing data for which hierarchical relations can be defined. This is the case in a number of fields like image analysis, natural language processing, protein structure, or music retrieval, to name a few. In those cases, procedures for comparing trees are very relevant. An approximate tree edit distance algorithm has been introduced for working with trees labeled only at the leaves. In this paper, it has been applied to handwritten character recognition, providing accuracies comparable to those by the most comprehensive search method, being as efficient as the fastest.This work is supported by the Spanish Ministry projects DRIMS (TIN2009-14247-C02), and Consolider Ingenio 2010 (MIPRCV, CSD2007-00018), partially supported by EU ERDF and the Pascal Network of Excellence

Increased risk of lower limb osteoarthritis among former professional soccer (football) players

Background: Soccer is a high-speed contact sport with risk of injury. Despite long-standing concern, evidence to date remains inconsistent as to the association between playing professional-level soccer and lifelong musculoskeletal consequences. Aims: The objectives were to assess risk of osteoarthritis in former professional soccer players compared to matched general population controls, and subsequently assess associated musculoskeletal disorders which may contribute to, or result from, osteoarthritis—specifically meniscal injury and joint replacement. Methods: We conducted a retrospective cohort study using national electronic health records (EHRs) on a cohort of 7676 former professional soccer players aged 40 or over at recruitment, matched on year of birth, sex (all male) and socio-economic status with 23 028 general population controls. Outcomes of interest were obtained by utilizing individual-level record linkage to EHRs from general hospital inpatient and day-case admissions. Results: Compared to controls, former soccer players showed a greater risk of hospital admission for osteoarthritis (hazard ratio [HR] 3.01; 95% confidence interval [CI] 2.80–3.25; P < 0.001). This increased risk appeared age dependant, normalizing over age 80 years and reflective of increased risk of lower limb osteoarthritis. Further, risk of hospital admissions for meniscal injury (HR 2.73; 95% CI 2.42–3.08; P < 0.001) and joint replacement (HR 2.82; 95% CI 2.23–3.57; P < 0.001) were greater among former soccer players. Conclusions: We report an increased risk of lower limb osteoarthritis in former soccer players when compared with matched population controls. The results of this research add data in support of lower limb osteoarthritis among former soccer players representing a potential industrial injury

Probing Lorentz and CPT violation with space-based experiments

Space-based experiments offer sensitivity to numerous unmeasured effects involving Lorentz and CPT violation. We provide a classification of clock sensitivities and present explicit expressions for time variations arising in such experiments from nonzero coefficients in the Lorentz- and CPT-violating Standard-Model Extension.Comment: 15 page

Electric current circuits in astrophysics

Cosmic magnetic structures have in common that they are anchored in a dynamo, that an external driver converts kinetic energy into internal magnetic energy, that this magnetic energy is transported as Poynting fl ux across the magnetically dominated structure, and that the magnetic energy is released in the form of particle acceleration, heating, bulk motion, MHD waves, and radiation. The investigation of the electric current system is particularly illuminating as to the course of events and the physics involved. We demonstrate this for the radio pulsar wind, the solar flare, and terrestrial magnetic storms