A user-friendly web portal for T-Coffee on supercomputers

Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results: In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions: The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.

Privacy-friendly Business Models for Location-Based Mobile Services

This paper presents a theoretical model to analyze the privacy issues around location based mobile business models. We report the results of an exploratory field experiment in Switzerland that assessed the factors driving user payoff in mobile business. We found that (1) the personal data disclosed has a negative effect on user payoff; (2) the amount of personalization available has a direct and positive effect, as well as a moderating effect on user payoff; (3) the amount of control over user's personal data has a direct and positive effect, as well as a moderating effect on user payoff. The results suggest that privacy protection could be the main value proposition in the B2C mobile market. From our theoretical model we derive a set of guidelines to design a privacy-friendly business model pattern for third-party services. We discuss four examples to show the mobile platform can play a key role in the implementation of these new business models.

Services "amis des jeunes": promouvoir des soins adaptés aux adolescents [Youth friendly health services: how to promote quality health care for adolescents].

Beaucoup de jeunes éprouvent des difficultés à demander une aide médicale et psychosociale alors qu'ils en auraient bien besoin. Cela est lié au processus d'autonomisation propre à cette période de la vie : les adolescents souhaitent résoudre leurs problèmes eux-mêmes. Pour améliorer la qualité des soins aux jeunes, l'Organisation mondiale de la santé, avec l'UNICEF et d'autres organismes, a développé le concept de youth friendly health services ; services amis des jeunes. Ce concept repose sur plusieurs principes, comme l'accessibilité, la flexibilité, une formation spécifique du personnel, le respect de la neutralité et de la confidentialité, compétences communicationnelles, etc. L'application de cette approche ne se limite pas aux centres spécialisés en médecine de l'adolescence, mais devra être progressivement implantée dans toutes les structures de soins accueillant des jeunes. Many young people have difficulties requesting medical or psychosocial support, although some badly need it. This difficulty is related to the fact that, as part of their search for autonomy, young people prefer to solve their problems by themselves. To improve the quality of care, the World Health Organization, UNICEF and allied organizations have developed the concept of "Youth friendly health services". This concept includes policies and strategies to improve the accessibility and flexibility, staff's competence and communication skills, etc. Such an approach should not be limited to specialized centers for adolescent health. It should be adopted by all health care institutions dealing with young people.

Development of an environmentally friendly method of starch oxidation by hydrogen peroxide and a complex water-soluble Iron catalyst

Oxidized starch is a key component in the paper industry, where it is used as both surfacing sizer and filler. Large quantities are annually used for this purpose; however, the methods for the oxidation are not environmentally friendly. In our research, we have studied the possibility to replace the harmful oxidation agents, such as hypochlorite or iodates and transition metal catalysts, with a more environmentally friendly oxidant, hydrogen peroxide (H2O2), and a special metal complex catalyst (FePcS), of which only a small amount is needed. The work comprised batch and semi-batch studies by H2O2, ultrasound studies of starch particles, determination of low-molecular by-products and determination of the decomposition kinetics of H2O2 in the presence of starch and the catalyst. This resulted in a waste-free oxidation method, which only produces water and oxygen as side products. The starch oxidation was studied in both semi-batch and batch modes in respective to the oxidant (H2O2) addition. The semi-batch mode proved to yield a sufficient degree of substitution (COOH groups) for industrial purposes. Treatment of starch granules by ultrasound was found to improve the reactivity of starch. The kinetic results were found out to have a rather complex pattern – several oxidation phases were observed, apparently due to the fact that the oxidation reaction in the beginning only took place on the surface, whereas after a prolonged reaction time, partial degradation of the solid starch granules allowed further reaction in the interior parts. Batch-mode experiments enabled a more detailed study of the mechanisms of starch in the presence of H2O2 and the catalyst, but yielded less oxidized starch due to rapid decomposition of H2O2 due to its high concentrations. The effect of the solid-liquid (S/L) ratio in the reaction system was studied in batch experiments. These studies revealed that the presence of the catalyst and the starch enhance the H2O2 decomposition.

Manifestation of the pairing symmetry in the vortex core structure in iron-based superconductors

The superconducting gap is a basic character of a superconductor. While the cuprates and conventional phonon-mediated superconductors are characterized by distinct d- and s-wave pairing symmetries with nodal and nodeless gap distributions respectively, the superconducting gap distributions in iron-based superconductors are rather diversified. While nodeless gap distributions have been directly observed in Ba1–xKxFe2As2, BaFe2–xCoxAs2, LiFeAs, KxFe2–ySe2, and FeTe1–xSex, the signatures of a nodal superconducting gap have been reported in LaOFeP, LiFeP, FeSe, KFe2As2, BaFe2–xRuxAs2, and BaFe2(As1–xPx)2. Due to the multiplicity of the Fermi surface in these compounds s± and d pairing states can be both nodeless and nodal. A nontrivial orbital structure of the order parameter, in particular the presence of the gap nodes, leads to effects in which the disorder is much richer in dx2–y2-wave superconductors than in conventional materials. In contrast to the s-wave case, the Anderson theorem does not work, and nonmagnetic impurities exhibit a strong pair-breaking influence. In addition, a finite concentration of disorder produces a nonzero density of quasiparticle states at zero energy, which results in a considerable modification of the thermodynamic and transport properties at low temperatures. The influence of order parameter symmetry on the vortex core structure in iron-based pnictide and chalcogenide superconductors has been investigated in the framework of quasiclassical Eilenberger equations. The main results of the thesis are as follows. The vortex core characteristics, such as, cutoff parameter, ξh, and core size, ξ2, determined as the distance at which density of the vortex supercurrent reaches its maximum, are calculated in wide temperature, impurity scattering rate, and magnetic field ranges. The cutoff parameter, ξh(B; T; Г), determines the form factor of the flux-line lattice, which can be obtained in _SR, NMR, and SANS experiments. A comparison among the applied pairing symmetries is done. In contrast to s-wave systems, in dx2–y2-wave superconductors, ξh/ξc2 always increases with the scattering rate Г. Field dependence of the cutoff parameter affects strongly on the second moment of the magnetic field distributions, resulting in a significant difference with nonlocal London theory. It is found that normalized ξ2/ξc2(B/Bc2) dependence is increasing with pair-breaking impurity scattering (interband scattering for s±-wave and intraband impurity scattering for d-wave superconductors). Here, ξc2 is the Ginzburg-Landau coherence length determined from the upper critical field Bc2 = Φ0/2πξ2 c2, where Φ0 is a flux quantum. Two types of ξ2/ξc2 magnetic field dependences are obtained for s± superconductors. It has a minimum at low temperatures and small impurity scattering transforming in monotonously decreasing function at strong scattering and high temperatures. The second kind of this dependence has been also found for d-wave superconductors at intermediate and high temperatures. In contrast, impurity scattering results in decreasing of ξ2/ξc2(B/Bc2) dependence in s++ superconductors. A reasonable agreement between calculated ξh/ξc2 values and those obtained experimentally in nonstoichiometric BaFe2–xCoxAs2 (μSR) and stoichiometric LiFeAs (SANS) was found. The values of ξh/ξc2 are much less than one in case of the first compound and much more than one for the other compound. This is explained by different influence of two factors: the value of impurity scattering rate and pairing symmetry.

Keskitehoestimaattorin lisääminen diesel-sähköiseen hybridijärjestelmään

Nykyajan jatkuvasti kiristyvät päästörajoitukset ja ilmastonmuutoksen uhka ovat ajavia voimia kehittämään voimalaitosten tekniikkaa energiatehokkaampaan ja ympäristöystävällisempään suuntaan. Polttomoottoritekniikan parantaminen on tärkeä osa tätä kehitystä, mutta jo nykyisiä moottoreita voitaisiin ajaa energiate-hokkaammin käyttämällä akustoa ja älykästä säätöjärjestelmää apuna. Työssä tutkitaan simulaatioiden avulla voidaanko ulkomerellä toimivan huolto-aluksen energiatehokkuutta parantaa muokkaamalla sen tehon tuottoa keskitehoes-timaattorin ja akuston avulla.

Scientist-friendly policies for non-native English-speaking authors: timely and welcome

That English is the lingua franca of today's science is an indisputable fact. Publication in English in international journals is a pre-requisite for a research paper to gain visibility in academia. However, English proficiency appears to be taken for granted in the scientific community, though this language can be a hurdle for a number of authors, particularly from non-native English-speaking countries. The influence of English proficiency on the publication output of Brazilian authors has never been assessed. We report our preliminary data on the relationship between the English proficiency of 51,223 researchers registered in the CNPq database and their publication output in international journals. We have found that publication rates are higher for those authors with good command of English, particularly written English. Although our research is still underway and our results are preliminary, they suggest that the correlation between written English proficiency and research productivity should not be underestimated. We also present the comments of some Brazilian scientists with high publication records on the relevance of communication skills to the scientific enterprise.

Investigations on Eco-friendly Natural Insecticides

Instead of developing easily degradable, and low-priced insecticides, we are going after highly sophisticated chemicals. Here, an attempt is being made to develop safer formulations of insecticides of botanical origin. Different parts of the plants were chosen based on their use in countryside and villages The dried plant materials were extracted with petroleum ether, and were applied on Tribolium castaneum. The results were statistically analysed. The active principles from Croton tigilium and Leea sambucina, the most potential plants, were isolated using Column Chromatography, TLC, and Hydrolysis. The isolated principles were analysed spectroscopically ( UV-Vis., IR, NMR, and MS ) to identify their chemical nature. The active principles from Leea and Croton were identified as a cholisterate derivative and a phorbol derivative respectively. In order to ascertain the environmental combatibility of the principles, degradation by soil bacteria was studied. The isolated principles were made into three type of formulations using stabilizers .The formulations were applied on Snake gourd semilooper, Pulse beetle, and mosquito larvae. Also the biocidal activity of the formulations was studied. Both Leea derivative and Croton derivative could be formulated effectively and were effective against a variety of pests. They are eco-friendly, as there is no artificial chemicals involved.

Characterization of laccase from Streptomyces psammoticus: an enzyme for eco-friendly treatment of environmental pollutants

The present study has identified an actinomycete culture (S. psammoticus) which was capable of producing all the three major ligninolytic enzymes. The study revealed that least explored mangrove regions are potential sources for the isolation of actinomycetes with novel characteristics. The laccase production by the strain in SmF and SSF was found to be much higher than the reported values. The growth of the organism was favoured by alkaline pH and salinity of the medium. The enzyme also exhibited novel characteristics such as activity and stability at alkaline pH and salt tolerance. These two characters are quite significant from the industrial point of view making the enzyme an ideal candidate for industrial applications. Many of the application studies to date are focused on enzymes from fungal sources. However, the fungal laccases, which are mostly acidic in nature, could not be used universally for all application purposes especially, for the treatment of effluents from different industries, largely due to the alkaline nature of the effluents. Under such situations the enzymes from organisms like S. psammoticus with wide pH range could play a better role than the fungal counterparts. In the present study, the ability of the isolated strain and laccase in the degradation of dyes and phenolic compounds was successfully proved. The reusability of the immobilized enzyme system made the entire treatment process inexpensive. Thus it can be concluded from the present study that the laccase from this organism could be hopefully employed for the eco-friendly treatment of dye or phenol containing industrial effluents from various sources.

Generic finite-size enhancement of pairing in mesoscopic Fermi systems

The finite-size-dependent enhancement of pairing in mesoscopic Fermi systems is studied under the assumption that the BCS approach is valid and that the two-body force is size independent. Different systems are investigated such as superconducting metallic grains and films as well as atomic nuclei. It is shown that the finite size enhancement of pairing in these systems is in part due to the presence of a surface which accounts quite well for the data of nuclei and explains a good fraction of the enhancement in Al grains.

Pairing with polarization effects in low-density neutron matter

We study the properties of the 1S0 pairing gap in low-density neutron matter. Different corrections to the lowest-order scattering length approximation are explored, resulting in a strong suppression with respect to the BCS result.

Nuclear pairing: surface or bulk?

We analyze how the spatial localization properties of pairing correlations are changing in a major neutron shell of heavy nuclei. It is shown that the radial distribution of the pairing density depends strongly on whether the chemical potential is close to a low or a high angular momentum level and has little sensitivity to whether the pairing force acts at the surface or in the bulk. The pairing density averaged over one major shell is, however, rather flat, exhibiting little dependence on the pairing force. Hartree-Fock-Bogoliubov calculations for the isotopic chain 100-132Sn are presented for demonstration purposes.