Computer-aided design of bus route maps

The bus route map is a diagram that aims to convey necessary information for map readers to find an appropriate way of moving from an origin to a destination. Design of bus route map is a complicated and time-consuming task that requires careful consideration of readability and aesthetics. This paper proposes a new computational method for designing bus route maps. The method helps us to reduce six types of undesirable elements in bus route maps, i.e., gap, shift, crossing, overlap, misalignment, and acute bend. The method consists of two phases: line layout phase determines the relative order of bus routes on each road segment and map layout phase calculates the actual position of bus routes drawn on a map. This paper applies the method to the design of bus route maps of Chiba City, Japan. The result supports the effectiveness of the method as well as reveals open topics for future research.     

A multiphysics and multiscale software environment for modeling astrophysical systems

We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a “Noah’s Ark” milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multiscale and multiphysics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe three examples calculated using MUSE: the merger of two galaxies, the merger of two evolving stars, and a hybrid N-body simulation. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.     

Vertical zonation and aggregated distribution of the Manila clam on subtidal sand flats in a coastal brackish lagoon along the Sea of Japan

The Manila clam, Ruditapes philippinarum, has maintained small‐sized populations in a semi‐enclosed brackish lake along the Sea of Japan, the Honjo area of Lake Nakaumi, although the environment and biota of this area have changed dramatically due to a large‐scale reclamation project. There should be underlying processes that enable the restoration of this species from small‐sized populations, such as the existence of source (i.e. reproductive) populations in other areas and depth zones of the lake. However, there has been no robust, properly designed evaluation of the distribution of the Manila clam in the subtidal sand flats. In order to elucidate the possible mechanisms that allow for the persistence of populations of the Manila clam, we examined the spatiotemporal and vertical variation in distributions of 0‐age clams in the subtidal zone of sand flats. Seasonal effects on population variations showed erratic changes among depth zones without a decreasing trend along the depth gradient. Further, many local populations became extinct even in the shallower zones due to seasonal (summer) hypoxia at deeper zones and hypoxia by the accumulation of key benthic species (Asian mussel and decaying macroalgae) in mats at shallower zones. A few surviving local populations were stable with a spatial‐fragmental (patchy) distribution, associated with fragmented accumulations of Asian mussels and macroalgae. Efforts to maintain stable populations and to restore this species in the subtidal area may depend on these small, restricted, patchy local populations. These findings suggest that high fertility and productivity of the Manila clam as well as patchy distribution of small populations may contribute to the maintenance of the population and the avoidance of extinction (by spatially diffusing the risk of extinction) in harsh environments resulting from the reclamation project.     

Experimental constraints on the effects of pressure and H2O on the fractional crystallization of high-Mg island arc basalt

H₂O-undersaturated melting experiments of synthesized basalt (SiO₂ = 50.7 wt.%, MgO = 8.3 wt.%, Mg# = 60) were conducted at fO₂ corresponding to NNO+1 and NNO−1 to clarify the effects of pressure (2–7 kbar) and H₂O on fractional crystallization in island arcs. H₂O content was ranged from nominally anhydrous to 4.4 wt.%. Differentiation trends, namely the liquid lines of descent, change sensitively according to pressure-H₂O relations. Tholeiitic differentiation trends are reproduced with H₂O ≤ ∼2 wt.% in primary magma. With such quantities of H₂O, fractional crystallization is controlled by olivine + plagioclase at 2 kbar. Increasing the pressure from 2 to ≥4 kbar induces early crystallization of orthopyroxene instead of olivine and therefore SiO₂ enrichment in the residual melts is suppressed. Increasing H₂O (≥ ∼2 wt.% in primary magma) stabilizes clinopyroxene relative to orthopyroxene and/or magnetite. Although the phase relations and proportions strongly depend on fO₂ and H₂O content, differentiation trends are always calc-alkaline.     

Nuclear field shift in natural environments

The nuclear field shift (NFS) is an isotope shift in atomic energy levels caused by a combination of differences in nuclear size and shape and electron densities at the nucleus. The effect of NFS in isotope fractionation was theoretically established by Bigeleisen in 1996 [Bigeleisen J. (1996) J. Am. Chem. Soc. 118:3676–3680] and has been analytically measured in laboratory chemical exchange reactions. More recently, some isotopic variations of heavy elements (Hg, Tl, U) measured in natural systems as well as isotopic anomalies measured for lower-mass elements in meteorites have been attributed to the NFS effect. These isotopic variations open up new and exciting fields of investigations in Earth sciences. In this paper, we review the different natural systems in which NFS has been proposed to be the origin of isotopic variations.     

A model of fish preference and mortality under hypoxic water in the coastal environment

Eutrophication and associated occurrence of hypoxic condition could cause significant damage to marine ecosystems, resulting in considerable economic losses to fisheries and aquaculture and is a major source of stress that fish often have to contend with in order to survive. This problem is likely to be exacerbated in the coming years, since the wastewater treatment facilities is unlikely to catch up with increasing human activities. Moreover, large-scale reclamation projects in coastal areas have recently been increased, and these activities certainly have adverse impacts on water quality and fisheries resources. Coastal construction has a significant role in the development of hypoxic water by changing the current and mixing pattern of water. Changes in species composition and decreases in species richness and diversity have been well documented in hypoxic systems. Hypoxia could cause endocrine disruption in fish and eliminate populations of sensitive species. Shallow coastal areas are of great importance for the special nursery of fish and shellfish and land reclamation in these areas cause strong damage to fisheries. Although the tolerance of aquatic life to hypoxia is known, there is no information about the mortality of fish caused by hypoxia because fish can swim around it and no modeling study has yet been carried out. Criteria that influence the movement of fish are: amounts of food, water temperature and depth, dissolved oxygen concentration and nature of seabed. However, among these, water temperature and dissolved oxygen are the most crucial parameters that affect survival, movement and growth of fish. In this paper, a model of fish preference and mortality for environmental conditions was developed and applied to the Hakata Bay where hypoxic water occurs every summer. For the purpose of this study, a field survey of fish behavior under hypoxic water was conducted by releasing marbled sale (Pleuronectes yokohamae) in the inner bay. Moreover, a series of preference tests for DO, salinity and temperature in the laboratory were conducted in order to decide preference parameters of fish. Using the results of both field and laboratory studies, a sub-module of fish preference and mortality was coded within an integrated hydrothermal and eutrophication model (CHEM) to predict the behavior and mortality of marbled sale when hypoxia would occur in the bay. The model could reasonably simulate the behavior of the fish under hypoxia. An assessment of the impact of the ongoing land reclamation project of about 401 ha in the Wajiro tidal flat zones at the head of the bay on the fisheries resources was also conducted using the model. The results showed that the artificial land lowered the mortality rate of fish under hypoxic condition in the bay during the summer period.     

Microbial responses using denaturing gradient gel electrophoresis to oil and chemical dispersant in enclosed ecosystems

Microbial responses to the addition of oil with or without a chemical dispersant were examined in mesocosm and microcosm experiments by using denaturing gradient gel electrophoresis of bacterial ribosomal DNA and direct cell counting. When a water-soluble fraction of oil was added to seawater, increases in cell density were observed in the first 24h, followed by a decrease in abundance and a change in bacterial species composition. After addition of an oil-dispersant mixture, increases in cell density and changes in community structure coincided, and the amount of bacteria remained high. These phenomena also occurred in response to addition of only dispersant. Our results suggest that the chemical dispersant may be used as a nutrient source by some bacterial groups and may directly or indirectly prevent the growth of other bacterial groups.     

Latest Jurassic–earliest Cretaceous radiolarian fauna from the Xialu chert in the Yarlung Zangbo suture zone, southern Tibet: Comparison with coeval western Pacific radiolarian faunas and paleoceanographic implications

Abstract The Xialu chert radiolarian fauna is latest Jurassic–earliest Cretaceous in age (Pseudodictyomitra carpatica zone) and contains many taxa in common with coeval northern hemisphere middle‐latitude (temperate) radiolarian faunas represented by the Torinosu fauna in southwest Japan. Common elements include Eucyrtidiellum pyramis (Aita), Protunuma japonicus Matsuoka & Yao, Sethocapsa pseudouterculus Aita, Sethocapsa (?) subcrassitestata Aita, Archaeodictyomitra minoensis (Mizutani), Stichocapsa praepulchella Hori and Xitus gifuensis (Mizutani). The Xialu fauna is less similar to low‐latitude (tropical) assemblages represented by the Mariana fauna. For this reason, the Xialu fauna is regarded as representative of a southern hemisphere middle‐latitude (temperate) fauna. A mirror‐image bi‐temperate provincialism to the equator in radiolarian faunas is reconstructed for the Ceno‐Tethys and Pacific Ocean in latest Jurassic–earliest Cretaceous time.