FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies

Improved Semileptonic Form Factor Calculations in Lattice QCD

We investigate the computational efficiency of two stochastic based alternatives to the Sequential Propagator Method used in Lattice QCD calculations of heavy-light semileptonic form factors. In the first method, we replace the sequential propagator, which couples the calculation of two of the three propagators required for the calculation, with a stochastic propagator so that the calculations of all three propagators are independent. This method is more flexible than the Sequential Propagator Method but introduces stochastic noise. We study the noise to determine when this method becomes competitive with the Sequential Propagator Method, and find that for any practical calculation it is competitive with or superior to the Sequential Propagator Method. We also examine a second stochastic method, the so-called ``one-end trick", concluding it is relatively inefficient in this context. The investigation is carried out on two gauge field ensembles, using the non-perturbatively improved Wilson-Sheikholeslami-Wohlert action with N_f=2 mass-degenerate sea quarks. The two ensembles have similar lattice spacings but different sea quark masses. We use the first stochastic method to extract ${\mathcal O}(a)$-improved, matched lattice results for the semileptonic form factors on the ensemble with lighter sea quarks, extracting f_+(0)

Pengaruh Store Atmosphere Dan Faktor Psikologis Terhadap Keputusan Pembelian Pada Matahari Departemen Store Mega Trade Center Manado

Penelitian ini bertujuan untuk mengetahui seberapa besar pengaruh suasana toko dan faktor psikologis terhadap keputusan pembelian konsumen. Sampel pada penelitian ini diambil sebanyak 100 responden dengan teknik Non-probability sampling dengan pendekatan Accidental Sampling. Data dalam penelitian ini menggunakan metode survey melalui kuesioner yang diisi oleh pelanggan. Data diperoleh dengan menggunakan analisis regresi berganda dengan meliputi Uji Validitas, Uji Reliabilitas, Uji Asumsi Klasik, Analisis Regresi Berganda, Uji Hipotesis melalui Uji t dan Uji F. Pengujian hipotesis menggunakan uji t menunjukkan bahwa kedua variabel independen yang diteliti yaitu variabel suasana toko, dan Faktor Psikologis terbukti berpengaruh positif dan signifikan terhadap variabel dependen Keputusan pembelian. Kemudian hasil analisis menggunakan uji F dapat diketahui bahwa kedua variabel independen yaitu suasana toko, dan faktor psikologis secara bersama-sama berpengaruh signifikan terhadap variabel dependen yaitu Keputusan pembelian

Uji Daya Hambat Jamur Endofit Rimpang Lengkuas (Alpinia Galanga L.) Terhadap Pertumbuhan Bakteri Escherichia Coli Dan Staphylococcus Aureus

: Endophytic fungi could be used as an alternative antibiotic because it produced bioactive compounds, which are developed as basic ingredients for medicine such as antibiotic, antioxcide, anticancer. Endophytic fungi can be isolated from Rhizome of Alpinia galanga L. which is abundant in Indonesia. The aim of this study was to find the inhibiting zone of endophytic fungi rhizome of Alpinia galanga L. to the growth of Staphylococcus aueus and Escherichia coli. This was an experimental laboratory study using modified Kirby-Bauer well diffusion technique in Marine Pharmaceutical and Biology Molecular laboratory of FPIK faculty in Sam Ratulangi University. Endophytic fungi were produced by Rhizome of Alpinia galanga L. which are cultured in carbohydrate-rich media. Then, it produced various fungi isolate, which is being used for testing its bioactiy to Staphylococcus aureus and Escherichia coli. The results showed that only 2 isolates of endophytic fungi that have inhibitory and the range of the average value of inhibition zone endophytic fungi rhizome of Alpinia galanga L. against Staphylococcus aureus 19 mm to 21.3 mm, while the Escherichia coli 21.3 mm to 22.3 mm. Conclusion: Endophytic fungi Rhizome of Alpinia galanga L. could inhibit the bacterial growth of Staphylococcus aureus and Escherichia coli

Water Chemisorption and Reconstruction of the MgO Surface

The observed reactivity of MgO with water is in apparent conflict with theoretical calculations which show that molecular dissociation does not occur on a perfect (001) surface. We have performed ab-initio total energy calculations which show that a chemisorption reaction involving a reconstruction to form a (111) hydroxyl surface is strongly preferred with Delta E = -90.2kJ/mol. We conclude that protonation stabilizes the otherwise unstable (111) surface and that this, not the bare (001), is the most stable surface of MgO under ambient conditions.Comment: RevTeX, 4 pages, 1 Encapsulated Postscript Figur

Non-spherical shapes of capsules within a fourth-order curvature model

We minimize a discrete version of the fourth-order curvature based Landau free energy by extending Brakke's Surface Evolver. This model predicts spherical as well as non-spherical shapes with dimples, bumps and ridges to be the energy minimizers. Our results suggest that the buckling and faceting transitions, usually associated with crystalline matter, can also be an intrinsic property of non-crystalline membranes.Comment: 6 pages, 4 figures (LaTeX macros EPJ), accepted for publication in EPJ

Temperature control in molecular dynamic simulations of non-equilibrium processes

Thermostats are often used in various condensed matter problems, e.g. when a biological molecule undergoes a transformation in a solution, a crystal surface is irradiated with energetic particles, a crack propagates in a solid upon applied stress, two surfaces slide with respect to each other, an excited local phonon dissipates its energy into a crystal bulk, and so on. In all of these problems, as well as in many others, there is an energy transfer between different local parts of the entire system kept at a constant temperature. Very often, when modelling such processes using molecular dynamics simulations, thermostatting is done using strictly equilibrium approaches serving to describe the NV T ensemble. In this paper we critically discuss the applicability of such approaches to non-equilibrium problems, including those mentioned above, and stress that the correct temperature control can only be achieved if the method is based on the generalized Langevin equation (GLE). Specifically, we emphasize that a meaningful compromise between computational efficiency and a physically appropriate implementation of the NV T thermostat can be achieved, at least for solid state and surface problems, if the so-called stochastic boundary conditions (SBC), recently derived from the GLE (Kantorovich and Rompotis 2008 Phys. Rev. B 78 094305), are used. For SBC, the Langevin thermostat is only applied to the outer part of the simulated fragment of the entire system which borders the surrounding environment (not considered explicitly) serving as a heat bath. This point is illustrated by comparing the performance of the SBC and some of the equilibrium thermostats in two problems: (i) irradiation of the Si(001) surface with an energetic CaF2 molecule using an ab initio density functional theory based method, and (ii) the tribology of two amorphous SiO2 surfaces coated with self-assembled monolayers of methyl-terminated hydrocarbon alkoxylsilane molecules using a classical atomistic force field. We discuss the differences in behaviour of these systems due to applied thermostatting, and show that in some cases a qualitatively different physical behaviour of the simulated system can be obtained if an equilibrium thermostat is used