Grid-based state space exploration for molecular binding

Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is heavily limited by state space dimensionality. Here, we make the first steps towards a low-dimensional grid-based model of molecular binding. We discretise the state space of relative positions and orientations of the two molecules under the rigid body assumption.The corresponding program is published as the Python package molgri. For the rotational component of the grids, we test algorithms based on Euler angles, polyhedra and quaternions, of which the polyhedra-based are the most uniform. The program outputs a sequence of molecular structures that can be easily processed by standard MD programs to calculate grid point energies. We demonstrate the grid-based approach on two molecular systems: a water dimer and a coiled-coil protein interacting with a chloride anion. For the second system we relax the rigid-body assumption and improve the accuracy of the grid point energies by an energy minimisation. In both cases, oriented bonding patterns and energies confirm expectations from chemical intuition and MD simulations. We also demonstrate how analysis of energy contributions on a grid can be performed and demonstrate that electrostatically-driven association is sufficiently resolved by point-energy calculations. Overall, grid-based models of molecular binding are potentially a powerful complement to molecular sampling approaches, and we see the potential to expand the method to quantum chemistry and flexible docking applications.Comment: 13 pages, 7 figure

Visualization of the medial forebrain bundle using diffusion tensor imaging

Diffusion tensor imaging is a technique that enables physicians the portrayal of white matter tracts in vivo. We used this technique in order to depict the medial forebrain bundle (MFB) in 15 consecutive patients between 2012 and 2015. Men and women of all ages were included. There were six women and nine men. The mean age was 58.6 years (39–77). Nine patients were candidates for an eventual deep brain stimulation. Eight of them suffered from Parkinson‘s disease and one had multiple sclerosis. The remaining six patients suffered from different lesions which were situated in the frontal lobe. These were 2 metastasis, 2 meningiomas, 1 cerebral bleeding, and 1 glioblastoma. We used a 3DT1-sequence for the navigation. Furthermore T2- and DTI- sequences were performed. The FOV was 200 × 200 mm2, slice thickness 2 mm, and an acquisition matrix of 96 × 96 yielding nearly isotropic voxels of 2 × 2 × 2 mm. 3-Tesla-MRI was carried out strictly axial using 32 gradient directions and one b0-image. We used Echo-Planar-Imaging (EPI) and ASSET parallel imaging with an acceleration factor of 2. b-value was 800 s/mm2. The maximal angle was 50°. Additional scanning time was < 9 min. We were able to visualize the MFB in 12 of our patients bilaterally and in the remaining three patients we depicted the MFB on one side. It was the contralateral side of the lesion. These were 2 meningiomas and one metastasis. Portrayal of the MFB is possible for everyday routine for neurosurgical interventions. As part of the reward circuitry it might be of substantial importance for neurosurgeons during deep brain stimulation in patients with psychiatric disorders. Surgery in this part of the brain should always take the preservation of this white matter tract into account

A Study of Analysis PB1-F2 Protein of Influenza Viruses A/H1N1pdm09, a/ H3N2, and A/H5N1

Aim. Influenza virus PB1-F2 (polymerase basic 1-frame 2) protein is a novel protein previously shown to be involved in cell death induction and pathogenesis. Here we analysis the PB1-F2 protein of Influenza virus A/H5N1 and A/H1N1pdm09 Methods. We conducted Gen Bank National Center for Biotechnology Information (NCBI) for A/H5N1 and A/H1N1pdm09 Influenza virus sequences database search started from 1997 until 2015. Data pertinent to this study is PB1 gene of A/H5N1 and A/H1N1pdm09 Influenza viruses. We conducted the multiple alignments to determine the various length and important mutation. Results. The PB1-F2 sequences from the 3262 Influenza A/H5N1 and 2472 Influenza A/H1N1pdm09 were studied. The analysis showed that all Influenza A/H5N1 carrying the full length 90 amino acids of PB2-F1 sequences, except the Influenza pandemic A/H1N1 2009, only 87 amino acids. In addition, the mutation indicates the presence of a significant correlation with the virulence shown by Serine at nucleotide number 66 which replaces Asparagines (N66S). The mutation occurs in 8.5% of Influenza A/H5N1 and 0.5% of Influenza A/H1N1pdm09. Conclusion. Several varying length and important mutation of PB2-F1 sequences from different subtype of A/H5N1 and A/H1N1pdm09 were obtained which are indicating the positively selected in specific subtype due to introduction and adaptation into different host. The further studies are required to understanding this variability and contribution of PB1-F2 proteins in virulence and pathogenesis of influenza viruses

Bringing Age Back In: Accounting for Population Age Distribution in Forecasting Migration

The link between age and migration propensity is long established, but existing models of country-level net migration ignore the effect of population age distribution on past and projected migration rates. We propose a method to estimate and forecast international net migration rates for the 200 most populous countries, taking account of changes in population age structure. We use age-standardized estimates of country-level net migration rates and in-migration rates over quinquennial periods from 1990 through 2020 to decompose past net migration rates into in-migration rates and out-migration rates. We then recalculate historic migration rates on a scale that removes the influence of the population age distribution. This is done by scaling past and projected migration rates in terms of a reference population and period. We show that this can be done very simply, using a quantity we call the migration age structure index (MASI). We use a Bayesian hierarchical model to generate joint probabilistic forecasts of total and age- and sex- specific net migration rates over five-year periods for all countries from 2020 through 2100. We find that accounting for population age structure in historic and forecast net migration rates leads to narrower prediction intervals by the end of the century for most countries. Also, applying a Rogers & Castro-like migration age schedule to migration outflows reduces uncertainty in population pyramid forecasts. Finally, accounting for population age structure leads to less out-migration among countries with rapidly aging populations that are forecast to contract most rapidly by the end of the century. This leads to less drastic population declines than are forecast without accounting for population age structure.Comment: 29 pages, 8 figures, 3 table

Pupil Detection Based on Color Difference and Circular Hough Transfor

Human pupil eye detection is a significant stage in iris segmentation which is representing one of the most important steps in iris recognition. In this paper, we present a new method of highly accurate pupil detection. This method is consisting of many steps to detect the boundary of the pupil. First, the read eye image (R, G, B), then determine the work area which is consist of many steps to detect the boundary of the pupil. The determination of the work area contains many circles which are larger than pupil region. The work area is necessary to determine pupil region and neighborhood regions afterward the difference in color and intensity between pupil region and surrounding area is utilized, where the pupil region has color and intensity less than surrounding area. After the process of detecting pupil region many steps on the resulting image is applied in order to concentrate the pupil region and delete the others regions by using many methods such as dilation, erosion, canny filter, circle hough transforms to detect pupil region as well as apply optimization to choose the best circle that represents the pupil area. The proposed method is applied for images from palacky university, it achieves to 100 % accura

Multi-criteria governmental crop planning problem based on an integrated AHP-PROMETHEE approach

The study uses analytic hierarchy process (AHP) and preference ranking organisation method for enrichment evaluations (PROMETHEE) to deal with the crop planning problem as a multi-criteria decision-making problem, for governmental lands in Gaza Strip under two conditions: the normal economy condition and the resistant economy condition. These two conditions are studied from the governmental point of view. The study goal is to rank crops according to some considered criteria. Crops are divided into eight types that include vegetables, fruits, citrus, olives, palms, export crops, field crops and medical and aromatic crops. The developed AHP and PROMETHEE compare crops with respect to seven main criteria, namely; economical, financial, marketing, environmental, technical, political and social criteria. AHP is used to obtain criteria weights to be used as input for PROMETHEE to outrank alternatives. The

The Dynamics of Organic Farming Institution Towards Sustainable Development

The development of organic agriculture is significant both at local, national, regional, and global in the last two decades and organic farming has matured enough to offer lesson. In the process, these developments characterized by a variety of internal and external conflicts such as conflict of interest, the data conflicts, resource conflicts, and structural conflicts. Products from various conflicts between the actors who are related, ultimately forming institutional arrangements. This study aims to explain the mechanisms that made the actors involved in organic farming in managing conflicts by placing community as an important actor. This study uses a constructivist paradigm that seeks to understand the meaning construction management of conflicts of various actors. The study was conducted in three locations namely Tasikmalaya District, West Java, Boyolali, Central Java, and Malang in East Java. Conflict management model that has been built by the institutional organic farming in Tasikmalaya, Boyolali, and Malang a lesson learned for other lowland rice farming locations that could potentially be the location of the development of organic rice. In the development phase, while this institutional organic farming that have been built are encouraged to ensure food security where production is not only oriented to meet export demand, but also meet the needs of organic food at the local and national levels