Energetics of ion competition in the DEKA selectivity filter of neuronal sodium channels

The energetics of ionic selectivity in the neuronal sodium channels is studied. A simple model constructed for the selectivity filter of the channel is used. The selectivity filter of this channel type contains aspartate (D), glutamate (E), lysine (K), and alanine (A) residues (the DEKA locus). We use Grand Canonical Monte Carlo simulations to compute equilibrium binding selectivity in the selectivity filter and to obtain various terms of the excess chemical potential from a particle insertion procedure based on Widom's method. We show that K$^{+}$ ions in competition with Na$^{+}$ are efficiently excluded from the selectivity filter due to entropic hard sphere exclusion. The dielectric constant of protein has no effect on this selectivity. Ca$^{2+}$ ions, on the other hand, are excluded from the filter due to a free energetic penalty which is enhanced by the low dielectric constant of protein.Comment: 14 pages, 7 figure

What Are Kinship Terminologies, and Why Do We Care? A Computational Approach to Analyzing Symbolic Domains

Kinship is a fundamental feature and basis of human societies. We describe a set of computational tools and services, the Kinship Algebra Modeler, and the logic that underlies these. These were developed to improve how we understand both the fundamental facts of kinship, and how people use kinship as a resource in their lives. Mathematical formalism applied to cultural concepts is more than an exercise in model building, as it provides a way to represent and explore logical consistency and implications. The logic underlying kinship is explored here through the kin term computations made by users of a terminology when computing the kinship relation one person has to another by referring to a third person for whom each has a kin term relationship. Kinship Algebra Modeler provides a set of tools, services and an architecture to explore kinship terminologies and their properties in an accessible manner

A dynamically adaptive multigrid algorithm for the incompressible Navier-Stokes equations: Validation and model problems

An algorithm is described for the solution of the laminar, incompressible Navier-Stokes equations. The basic algorithm is a multigrid based on a robust, box-based smoothing step. Its most important feature is the incorporation of automatic, dynamic mesh refinement. This algorithm supports generalized simple domains. The program is based on a standard staggered-grid formulation of the Navier-Stokes equations for robustness and efficiency. Special grid transfer operators were introduced at grid interfaces in the multigrid algorithm to ensure discrete mass conservation. Results are presented for three models: the driven-cavity, a backward-facing step, and a sudden expansion/contraction

Schwinger, Pegg and Barnett and a relationship between angular and Cartesian quantum descriptions

From a development of an original idea due to Schwinger, it is shown that it is possible to recover, from the quantum description of a degree of freedom characterized by a finite number of states (\QTR{it}{i.e}., without classical counterpart) the usual canonical variables of position/momentum \QTR{it}{and} angle/angular momentum, relating, maybe surprisingly, the first as a limit of the later.Comment: 7 pages, revised version, to appear on J. Phys. A: Math and Ge

Applications systems verification and transfer project. Volume 4: Operational applications of satellite snow cover observations. Colorado Field Test Center

The study was conducted on six watersheds ranging in size from 277 km to 3460 km in the Rio Grande and Arkansas River basins of southwestern Colorado. Six years of satellite data in the period 1973-78 were analyzed and snowcover maps prepared for all available image dates. Seven snowmapping techniques were explored; the photointerpretative method was selected as the most accurate. Three schemes to forecast snowmelt runoff employing satellite snowcover observations were investigated. They included a conceptual hydrologic model, a statistical model, and a graphical method. A reduction of 10% in the current average forecast error is estimated when snowcover data in snowmelt runoff forecasting is shown to be extremely promising. Inability to obtain repetitive coverage due to the 18 day cycle of LANDSAT, the occurrence of cloud cover and slow image delivery are obstacles to the immediate implementation of satellite derived snowcover in operational streamflow forecasting programs

Orthogonal, solenoidal, three-dimensional vector fields for no-slip boundary conditions

Viscous fluid dynamical calculations require no-slip boundary conditions. Numerical calculations of turbulence, as well as theoretical turbulence closure techniques, often depend upon a spectral decomposition of the flow fields. However, such calculations have been limited to two-dimensional situations. Here we present a method that yields orthogonal decompositions of incompressible, three-dimensional flow fields and apply it to periodic cylindrical and spherical no-slip boundaries.Comment: 16 pages, 2 three-part figure

Temporal Dynamics of Lipid and Fatty Acid Characteristics of Gulf Menhaden, \u3ci\u3eBrevoortia patronus\u3c/i\u3e in the Northern Gulf of Mexico

Gulf Menhaden, Brevoortia patronus, in the northern Gulf of Mexico support a large commercial fishery and are thought to play an important trophic role in the coastal ecosystem. The temporal dynamics of both fatty acid and oil content have a direct impact on the value of Gulf Menhaden to predators and to the fishery. In this work, we describe how oil content of Gulf Menhaden varies with season, sex, age, condition, and tissue and investigate how fatty acid composition of mature (137.5 mm FL) female tissues varies with season, month, and tissue type. We found pronounced temporal (January to October) variation in mean oil content ranging from 0.062 to 0.579 mg g−1 that exhibited a significant (p \u3c 0.001) seasonal pattern. We observed significant differences in oil content between tissue (muscle vs. ovary) of mature females and these exhibited a significant seasonal contrast, indicating that females were provisioning eggs in the fall. PERMANOVA analysis indicated the existence of significant differences (p \u3c 0.001) in the composition of fatty acids of muscle tissue collected in different months. Mean eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and long chain polyunsaturated fatty acid (LC-PUFA) levels exhibited significant seasonal differences (p \u3c 0.05), and in the case of DHA and LC-PUFA, both exhibited mean tissue-specific differences (p \u3c 0.05). This work indicates that the value of Gulf Menhaden as prey and a fishery resource in the region varies during the year and we propose that trophic models of the Gulf of Mexico ecosystem should account for this variation

Reproductive Dynamics of Gulf Menhaden (\u3ci\u3eBrevoortia patronus\u3c/i\u3e) in the Northern Gulf of Mexico: Effects On Stock Assessments

Gulf menhaden (Brevoortia patronus) produce one of the largest U.S. fisheries, yet information on reproductive dynamics of the stock is sparse. Males and females reach 50% maturity at 140.8 and 137.2 mm fork length, respectively and recruit into the commercial fishery at this size. Analysis of fishery-dependent data from 1964 through 2014 indicated that somatic condition was lower during the late 1980s and late 2000s and that reproductively active fish from 2014 were significantly larger and had greater gonadosomatic index values than those from 1964 through 1970. Histological analysis performed on fish from 2014 through 2016 revealed spawning-capable and actively spawning fish of both sexes from early October through midMarch. Females have indeterminate fecundity, are batch spawners, and spawn every 2.1-4.3 days, although oocyte recruitment shows some characteristics of determinate fecundity. Mean relative batch fecundity was 107.8 eggs/g ovary-free body weight (standard error 17.1). Estimates from age-structured assessment models based on updated fecundity and maturity measures resulted in a 100-1000x greater production of eggs than previous estimates. Model output, including the number-at-age, age-specific fishing-induced mortality, and spawners-per-recruit are sensitive to alterations in age-specific annual fecundity. Therefore, updated estimates of Gulf menhaden reproductive dynamics can affect assessments of the stock

Application of the matched nested case-control design to the secondary analysis of trial data

Background: A nested case-control study is an efficient design that can be embedded within an existing cohort study or randomised trial. It has a number of advantages compared to the conventional case-control design, and has the potential to answer important research questions using untapped prospectively collected data. Methods: We demonstrate the utility of the matched nested case-control design by applying it to a secondary analysis of the Abnormal Doppler Enteral Prescription Trial. We investigated the role of milk feed type and changes in milk feed type in the development of necrotising enterocolitis in a group of 398 high risk growth-restricted preterm infants. Results: Using matching, we were able to generate a comparable sample of controls selected from the same population as the cases. In contrast to the standard case-control design, exposure status was ascertained prior to the outcome event occurring and the comparison between the cases and matched controls could be made at the point at which the event occurred. This enabled us to reliably investigate the temporal relationship between feed type and necrotising enterocolitis. Conclusions: A matched nested case-control study can be used to identify credible associations in a secondary analysis of clinical trial data where the exposure of interest was not randomised, and has several advantages over a standard case-control design. This method offers the potential to make reliable inferences in scenarios where it would be unethical or impractical to perform a randomised clinical trial.</br