bluuebunny/crossref_metadata_2025 huggingface dataset:
The efficiency of an array of tidal turbines partially blocking a wide channel
Authors: Nishino Takafumi , Willden Richard H. J.
Published: August 2012

A new theoretical model is proposed to explore the efficiency of a long array of tidal turbines partially blocking a wide channel cross-section. An idea of scale separation is introduced between the flow around each device (or turbine) and that around the entire array to assume that all device-scale flow events, including ‘far-wake’ mixing behind each device, take place much faster than the horizontal expansion of the flow around the entire array. This assumption makes it possible to model the flow as a combination of two quasi-inviscid problems of different scales, in both of which the conservation of mass, momentum and energy is considered. The new model suggests the following: when turbines block only a small portion of the span of a shallow channel cross-section, there is an optimal intra-turbine spacing to maximize the efficiency (limit of power extraction) for a given channel height and width. The efficiency increases as the spacing is reduced to the optimal value due to the effect of local blockage, but then decreases as the spacing is further reduced due to the effect of array-scale choking, i.e. reduced flow through the entire array. Also, when the channel is infinitely wide, the efficiency depends solely on the local area blockage rather than on the combination of the intra-turbine spacing and the channel height. As the local blockage is increased, the efficiency increases from the Lanchester–Betz limit of 0.593 to another limiting value of 0.798, but then decreases as the local blockage is further increased.
Energy decay of vortices in viscous fluids: an applied mathematics view
Authors: Nordström Jan , Lönn Björn
Published: August 2012

The energy decay of vortices in viscous fluids governed by the compressible Navier–Stokes equations is investigated. It is shown that the main reason for the slow decay is that zero eigenvalues exist in the matrix related to the dissipative terms. The theoretical analysis is purely mathematical and based on the energy method. To check the validity of the theoretical result in practice, numerical solutions to the Navier–Stokes equations are computed using a stable high-order finite difference method. The numerical computations corroborate the theoretical conclusion.
Antioxidative and immunomodulatory effects of tributyrin supplementation on experimental colitis
Authors: Leonel Alda J. , Teixeira Lílian G. , Oliveira Rafael P. , Santiago Andrezza F. , Batista Nathália V. , Ferreira Talita R. , Santos Rosana C. , Cardoso Valbert N. , Cara Denise C. , Faria Ana M. C. , Alvarez-Leite Jacqueline
Published: August 2012

Tributyrin (TBT) is a TAG composed of three butyric acids that has beneficial effects on ulcerative colitis due to its trophic, anti-inflammatory, pro-apoptotic and anti-carcinogenic properties. The goal of the present study was to evaluate the efficacy and mechanisms of action of TBT supplementation in the prevention of mucosal damage in experimental colitis. Mice received either a control diet or a TBT-supplemented diet for 15 d. Colitis was induced by dextran sodium sulphate administration during the last 7 d. Mucosal damage and the activation of immune cells and cytokines were determined by histological score, flow cytometry and ELISA. Leucocyte rolling and adhesion were assessed by intravital microscopy. Oxidative stress was determined by monitoring hydroperoxide concentration and evaluating superoxide dismutase (SOD) and catalase activities. Intestinal permeability was analysed using diethylenetriaminepentaacetate acid (99mTcDTPA). Compared with the colitis group, the animals in the colitis+TBT group had reduced mucosal damage and neutrophil and eosinophil mucosal infiltration, which were associated with a higher percentage of regulatory T cells (Treg) and higher levels of transforming growth factor β and IL-10 in the lamina propria. The level ofin vivoleucocyte adhesion in the colon microvasculature was reduced after TBT supplementation. A lower level of hydroperoxide and higher levels of SOD and catalase activities were associated with TBT supplementation. TBT-supplemented mice showed reduced intestinal permeability to the levels intermediate between the control and colitis groups. In conclusion, the present results show that TBT has positive effects on colonic restructuring in experimental colitis. Additionally, TBT supplementation changes the immune response by controlling inflammation and regulating the expression of anti-inflammatory cytokines and Treg.
Phylogeography ofTrichurispopulations isolated from different Cricetidae rodents
Authors: CALLEJÓN ROCÍO , DE ROJAS MANUEL , FELIÚ CARLOS , BALAO FRANCISCO , MARRUGAL ÁNGELA , HENTTONEN HEIKKI , GUEVARA DIEGO , CUTILLAS CRISTINA
Published: August 2012

The phylogeography ofTrichurispopulations (Nematoda) collected from Cricetidae rodents (Muroidea) from different geographical regions was studied. Ribosomal DNA (Internal Transcribed Spacers 1 and 2, and mitochondrial DNA (cytochrome c- oxidasesubunit 1 partial gene) have been used as molecular markers. The nuclear internal transcribed spacers (ITSs) 1 and 2 showed 2 clear-cut geographical and genetic lineages: one of the Nearctic region (Oregon), although the second was widespread throughout the Palaearctic region and appeared as a star-like structure in the minimum spanning network. The mitochondrial results revealed thatT. arvicolaepopulations from the Palaearctic region were separated into 3 clear-cut geographical and genetic lineages: populations from Northern Europe, populations from Southern (Spain) and Eastern Europe (Croatia, Belarus, Kazahstan), and populations from Italy and France (Eastern Pyrénean Mountains). Phylogenetic analysis obtained on the basis of ITS1-5·8S-ITS2 rDNA sequences did not show a differential geographical structure; however, these markers suggest a newTrichurisspecies parasitizingChionomys robertiandCricetulus barabensis. The mitochondrial results revealed thatTrichurispopulations from arvicolinae rodents show signals of a post-glacial northward population expansion starting from the Pyrenees and Italy. Apparently, the Pyrenees and the Alps were not barriers to the dispersal ofTrichurispopulations.
A functional study of nucleocytoplasmic transport signals of the EhNCABP166 protein from Entamoeba histolytica
Authors: URIBE R. , BARRERA MA DE J. ALMARAZ , ROBLES-FLORES M. , HERNÁNDEZ G. MENDOZA , GONZÁLEZ-ROBLES A. , HERNÁNDEZ-RIVAS R. , GUILLEN N. , VARGAS M.
Published: August 2012

EhNCABP166 is an Entamoeba histolytica actin-binding protein that localizes to the nucleus and cytoplasm. Bioinformatic analysis of the EhNCABP166 amino acid sequence shows the presence of 3 bipartite nuclear localization signals (NLS) and a nuclear export signal (NES). The present study aimed to investigate the functionality of these signals in 3 ways. First, we fused each potential NLS to a cytoplasmic domain of ehFLN to determine whether the localization of this domain could be altered by the presence of the NLSs. Furthermore, the localization of each domain of EhNCABP166 was determined. Similarly, we generated mutations in the first block of bipartite signals from the domains that contained these signals. Additionally, we added an NES to 2 constructs that were then evaluated. We confirmed the intranuclear localization of EhNCABP166 using transmission electron microscopy. Fusion of each NLS resulted in shuttling of the cytoplasmic domain to the nucleus. With the exception of 2 domains, all of the evaluated domains localized within the nucleus. A mutation in the first block of bipartite signals affected the localization of the domains containing an NLS. The addition of an NES shifted the localization of these domains to the cytoplasm. The results presented here establish EhNCABP166 as a protein containing functional nuclear localization signals and a nuclear export signal.
Suppression of predation on the intermediate host by two trophically-transmitted parasites when uninfective
Authors: WEINREICH F. , BENESH D. P. , MILINSKI M.
Published: August 2012

Trophically-transmitted parasites generally need to undergo a period of development in the intermediate host before reaching infectivity. During this vulnerable period, manipulation of the host to reduce susceptibility to predation would be advantageous for parasites, because it increases the probability of surviving until infectivity and thus the probability of transmission. We tested this ‘predation suppression’ hypothesis in 2 parasite species that use copepods as first hosts: the tapewormSchistocephalus solidusand the nematodeCamallanus lacustris. In a series of prey choice experiments, we found that copepods harbouring uninfective, still-developing worm larvae were less frequently consumed by stickleback predators than uninfected copepods. The levels of predation suppression were similar in the two parasite species, suggestive of convergent evolution. Additionally, copepods harbouring 2 worms of a given species were not more susceptible to predation than those with 1 worm, suggesting that excessive larval parasite growth does not increase host susceptibility to predation. Our results support the idea that parasites can suppress intermediate host susceptibility to predation while uninfective, but we also note that the available studies suggest that this effect is weaker than the frequently observed enhancement of host predation by infective helminth larvae.
On the plurality of gods
Authors: STEINHART ERIC
Published: August 2012

Ordinal polytheism is motivated by the cosmological and design arguments. It is also motivated by Leibnizian–Lewisian modal realism. Just as there are many universes, so there are many gods. Gods are necessary concrete grounds of universes. The god-universe relation is one-to-one. Ordinal polytheism argues for a hierarchy of ranks of ever more perfect gods, one rank for every ordinal number. Since there are no maximally perfect gods, ordinal polytheism avoids many of the familiar problems of monotheism. It links theology with counterpart theory, mathematics and computer science. And it entails that the system of universes has an attractive axiological structure.
The Semantics of the Dutch Gender System
Authors: Kraaikamp Margot
Published: August 2012

In this paper, it is argued that, although Dutch gender assignment is not systematically organized along semantic lines in the lexicon, the gender system has a semantic basis. This semantic basis involves a distinction between masculine/common gender associated with a high degree of individuation on the one hand, and neuter gender associated with a low degree of individuation, on the other hand. This is in line with Audring (2006, 2009), who found that Dutch pronouns often show semantic agreement along these lines. It is shown that the same semantic distinction between the genders can also be found in the nominal domain. It surfaces particularly in cases where lexically stored gender does not play a role. The semantic distinction arguably goes back to Proto-Indo-European. It is argued that, since nominal gender has become an invariable, lexically stored feature of nouns, the semantic basis of nominal gender assignment has become disrupted. This causes a con-flict between lexical and semantic gender agreement in pronouns. It is suggested that the surfacing of semantic agreement in this conflict is connected with a reduced marking of lexical gender on adnominal elements.
Hyperspectral remote sensing data maps minerals in Afghanistan
Authors: King Trude V. V. , Kokaly Raymond F. , Hoefen Todd M. , Johnson Michaela R.
Published: August 2012

Although Afghanistan has abundant mineral resources, including gold, silver, copper, rare earth elements, uranium, tin, iron ore, mercury, lead‐zinc, bauxite, and industrial minerals, most have not been successfully developed or explored using modern methods. The U.S. Geological Survey (USGS) with cooperation from the Afghan Geological Survey (AGS) and support from the Department of Defense's Task Force for Business and Stability Operations (TFBSO) has used new imaging spectroscopy surface material maps to help refine the geologic signatures of known but poorly understood mineral deposits and identify previously unrecognized mineral occurrences. To help assess the potential mineral deposit types, the high‐resolution hyperspectral data were analyzed to detect the presence of selected minerals that may be indicative of past mineralization processes. This legacy data set is providing tangible support for economic decisions by both the government of Afghanistan and other public and private sector parties interested in the development of the nation's natural resources.
Tropospheric gas at potentially toxic levels in air
Authors: Bhattacharya Atreyee
Published: August 2012

Forest fires and emission of air pollutants, such as fumes from vehicles running on diesel and slow burning of coal and charcoal, release isocyanic acid in the troposphere. In 2011, scientists first detected isocyanic acid in the ambient atmosphere at levels toxic to human populations; at concentrations exceeding 1 part per billion by volume (ppbv), human beings could experience tissue decay when exposed to the toxin. For the first time, using a chemical transport model designed to estimate the distribution and budget of isocyanic acid in the troposphere, Young et al. showed that in several parts of the world, local emissions may increase the concentration of isocyanic acid in the ambient atmosphere, thereby exposing large populations to potentially toxic levels of the acid.
Structural changes of filled ice Ic hydrogen hydrate under low temperatures and high pressures from 5 to 50 GPa
Authors: Hirai Hisako , Kagawa Shingo , Tanaka Takehiko , Matsuoka Takahiro , Yagi Takehiko , Ohishi Yasuo , Nakano Satoshi , Yamamoto Yoshitaka , Irifune Tetsuo
Published: August 2012

Low-temperature and high-pressure experiments were performed on the filled ice Ic structure of hydrogen hydrate at previously unexplored conditions of 5–50 GPa and 30–300 K using diamond anvil cells and a helium-refrigeration cryostat. In situ x-ray diffractometry revealed that the cubic filled ice Ic structure transformed to tetragonal at low temperatures and high pressures; the axis ratio of the tetragonal phase changed depending on the pressure and temperature. These results were consistent with theoretical predictions performed via first principle calculations. The tetragonal phase was determined to be stable above 20 GPa at 300 K, above 15 GPa at 200 K, and above 10 GPa at 100 K. Further changes in the lattice parameters were observed from about 45–50 GPa throughout the temperature region examined, which suggests the transformation to another high-pressure phase above 50 GPa. In our previous x-ray study that was performed up to 80 GPa at room temperature, a similar transformation was observed above 50 GPa. In this study, the observed change in the lattice parameters corresponds to the beginning of that transformation. The reasons for the transformation to the tetragonal structure are briefly discussed: the tetragonal structure might be induced due to changes in the vibrational or rotational modes of the hydrogen molecules under low temperature and high pressure.
Extending magnetohydrodynamics to the slow dynamics of collisionless plasmas
Authors: Passot T. , Sulem P. L. , Hunana P.
Published: August 2012

A fluid approach aimed to provide a consistent description of the slow dynamics of a collisionless plasma, is presented. In this regime, both Landau damping and finite Larmor radius effects cannot be ignored. Two models are discussed; one retains the dynamics at sub-ionic scales, while the other is restricted to scales larger than the ion gyroscale. Special attention is paid to the capability of these approaches to accurately reproduce the properties of linear waves that are known to play an important role, for example, in the small-scale dynamics of solar wind turbulence.
Numerical investigation of edge plasma phenomena in an enhanced D-alpha discharge at Alcator C-Mod: Parallel heat flux and quasi-coherent edge oscillations
Authors: Russell D. A. , D’Ippolito D. A. , Myra J. R. , LaBombard B. , Terry J. L. , Zweben S. J.
Published: August 2012

Reduced-model scrape-off layer turbulence (SOLT) simulations of an enhanced D-alpha (EDA) H-mode shot observed in the Alcator C-Mod tokamak were conducted to compare with observed variations in the scrape-off-layer (SOL) width of the parallel heat flux profile. In particular, the role of the competition between sheath- and conduction-limited parallel heat fluxes in determining that width was studied for the turbulent SOL plasma that emerged from the simulations. The SOL width decreases with increasing input power and with increasing separatrix temperature in both the experiment and the simulation, consistent with the strong temperature dependence of the parallel heat flux in balance with the perpendicular transport by turbulence and blobs. The particularly strong temperature dependence observed in the case analyzed is attributed to the fact that these simulations produce SOL plasmas which are in the conduction-limited regime for the parallel heat flux. A persistent quasi-coherent (QC) mode dominates the SOLT simulations and bears considerable resemblance to the QC mode observed in C-Mod EDA operation. The SOLT QC mode consists of nonlinearly saturated wave-fronts located just inside the separatrix that are convected poloidally by the mean flow, continuously transporting particles and energy and intermittently emitting blobs into the SOL.
Root biomass, root:shoot ratio and belowground carbon stocks in the open savannahs of Roraima, Brazilian Amazonia
Authors: Barbosa Reinaldo Imbrozio , Silva dos Santos Jhonson Reginaldo , Souza da Cunha Mariana , Pimentel Tania Pena , Fearnside Philip Martin
Published: August 2012

Biomass of roots, the root : shoot ratio (ratio of below- to aboveground biomass) and carbon stocks belowground (to 100-cm depth) were estimated in different open savannah environments in the extreme north of the Brazilian Amazon. Sampling was conducted in permanent plots established in two open savannah areas in the state of Roraima. We identified four phytopedounits in the 27 plots sampled in two areas: four in dry grasslands on Argisol/Ultisol soils (DG-Arg), eight in dry grasslands on Latosol/Oxisol soils (DG-Lts), five in a mosaic of grasslands with savannah-parkland on Latosol/Oxisol soils (GP-Lts) and 10 in seasonally flooded (wet) grasslands on Hydromorphic/Entisol soils (WG-Hyd). Fine roots (<2 mm diameter) dominated the 0–100-cm vertical profile in the four phytopedounits (>92.5%). Biomass of the roots in WG-Hyd (29.52 ± 7.15 Mg ha–1) was significantly higher as compared with the other phytopedounits studied, although the carbon stocks did not differ among the phytopedounits (6.20–7.21 MgC ha–1). The largest concentration of roots was found in the upper three 10-cm sections of the soil profile, ranging from 56.3 to 82.9% in the four environments. The root : shoot ratio based only on living biomass of roots with diameter ≥2 mm (standard Intergovernmental Panel on Climate Change methodology) ranged from 0 for seasonally flooded grasslands to 0.07–0.20 for unflooded grasslands on clay soils. The results indicate that the root : shoot ratio (expansion factor) for belowground biomass in open savannah ecosystems in the northern Amazon are low and differ from the default values used in Brazil’s reference report to the Climate Convention.
Antitropical distribution of Lobelia species (Campanulaceae) between the Ryukyu Archipelago of Japan and Oceania as indicated by molecular data
Authors: Kokubugata Goro , Nakamura Koh , Forster Paul I. , Hirayama Yumiko , Yokota Masatsugu
Published: August 2012

We tested the antitropical distribution of Lobelia loochooensis, endemic to the Ryukyu Archipelago of Japan, and its putative sister species of the same section Hypsela in Oceania (Australia and New Zealand). Molecular phylogenetic analyses based on cpDNA sequences were conducted for 41 Lobelia species of 11 sections including all the species of sect. Hypsela investigated in Asia and Malesia and 32 species of 16 allied genera of family Campanulaceae, because the genus Lobelia is known to be polyphyletic. In the result, L. loochooensis and an Australian endemic L. fluviatilis formed a clade, and this clade was sister to a clade of four New Zealand endemics: L. carens, L. fatiscens, L. fugax and L. ionantha. These two clades were nested in a clade with two other Australian congeners. We conclude that: (1) the lineage of L. loochooensis and the five Lobelia species occurring in Oceania demonstrate an antitropical distribution pattern; and (2) L. loochooensis has likely originated from a dispersal event from Australia to the Ryukyu Archipelago.
Uniform Chrysanthemum-Like Bi2S3 Microspheres for Dye-Sensitised Solar Cells
Authors: Wang Junfeng , Liu Zhao , Yuan Shuming , Liu Lu , Zhou Zhen , Chen Wei
Published: August 2012

3D uniform Bi2S3 chrysanthemum-like microspheres with 1D nanowire-assembly were prepared through a facile one-step hydrothermal route, using poly(vinylpyrrolidone) (PVP) as a soft template, and Bi(NO3)3 and thiourea as Bi and S sources, respectively. PVP molecules played an important role in the formation of uniform 3D Bi2S3 nanostructures. The reasonable formation mechanism of uniform chrysanthemum-shaped Bi2S3 microspheres was also proposed. Photovoltaic properties were studied preliminarily to demonstrate potential application in dye-sensitised solar cells for the replacement of scarce platinum as counter electrode.
Selective Transport of Water-Soluble Proteins from Aqueous to Ionic Liquid Phase via a Temperature-Sensitive Phase Change of These Mixtures
Authors: Kohno Yuki , Nakamura Nobuhumi , Ohno Hiroyuki
Published: August 2012

Mixtures of some ionic liquids (ILs) and water show reversible phase change between a homogeneous mixture and phase-separated state by a small change in temperature. Some water-soluble proteins have been migrated from the aqueous to the IL phase. When tetrabutylphosphonium 2,4,6-trimethylbenzenesulfonate was used as an IL, cytochrome c (Cyt.c) was found to be extracted from the water phase to the IL phase. Conversely, both horseradish peroxidase (HRP) and azurin remained in the aqueous phase. This selective extraction was comprehended to be due to the difference in solubility of these proteins in both phases. The separated aqueous phase contained a small amount of IL, which induced the salting-out of Cyt.c. On the other hand, condensed IL phase promoted the salting-in of Cyt.c. As a result, Cyt.c was preferably dissolved in the hydrated IL phase rather than aqueous phase. In the case of HRP, there was only a salting-out profile upon increasing the concentration of IL, which induced selective dissolution of HRP in the aqueous phase. These results clearly suggest that the profile of salting-out and salting-in for proteins is the key factor to facilitate the selective extraction of proteins from aqueous to the IL phase.
The fate of mercury in Arctic terrestrial and aquatic ecosystems, a review
Authors: Douglas Thomas A. , Loseto Lisa L. , Macdonald Robie W. , Outridge Peter , Dommergue Aurélien , Poulain Alexandre , Amyot Marc , Barkay Tamar , Berg Torunn , Chételat John , Constant Philippe , Evans Marlene , Ferrari Christophe , Gantner Nikolaus , Johnson Matthew S. , Kirk Jane , Kroer Niels , Larose Catherine , Lean David , Nielsen Torkel Gissel , Poissant Laurier , Rognerud Sigurd , Skov Henrik , Sørensen Søren , Wang Feiuye , Wilson Simon , Zdanowicz Christian M.
Published: August 2012

Environmental contextMercury, in its methylated form, is a neurotoxin that biomagnifies in marine and terrestrial foodwebs leading to elevated levels in fish and fish-eating mammals worldwide, including at numerous Arctic locations. Elevated mercury concentrations in Arctic country foods present a significant exposure risk to Arctic people. We present a detailed review of the fate of mercury in Arctic terrestrial and marine ecosystems, taking into account the extreme seasonality of Arctic ecosystems and the unique processes associated with sea ice and Arctic hydrology. AbstractThis review is the result of a series of multidisciplinary meetings organised by the Arctic Monitoring and Assessment Programme as part of their 2011 Assessment ‘Mercury in the Arctic’. This paper presents the state-of-the-art knowledge on the environmental fate of mercury following its entry into the Arctic by oceanic, atmospheric and terrestrial pathways. Our focus is on the movement, transformation and bioaccumulation of Hg in aquatic (marine and fresh water) and terrestrial ecosystems. The processes most relevant to biological Hg uptake and the potential risk associated with Hg exposure in wildlife are emphasised. We present discussions of the chemical transformations of newly deposited or transported Hg in marine, fresh water and terrestrial environments and of the movement of Hg from air, soil and water environmental compartments into food webs. Methylation, a key process controlling the fate of Hg in most ecosystems, and the role of trophic processes in controlling Hg in higher order animals are also included. Case studies on Eastern Beaufort Sea beluga (Delphinapterus leucas) and landlocked Arctic char (Salvelinus alpinus) are presented as examples of the relationship between ecosystem trophic processes and biologic Hg levels. We examine whether atmospheric mercury depletion events (AMDEs) contribute to increased Hg levels in Arctic biota and provide information on the links between organic carbon and Hg speciation, dynamics and bioavailability. Long-term sequestration of Hg into non-biological archives is also addressed. The review concludes by identifying major knowledge gaps in our understanding, including: (1) the rates of Hg entry into marine and terrestrial ecosystems and the rates of inorganic and MeHg uptake by Arctic microbial and algal communities; (2) the bioavailable fraction of AMDE-related Hg and its rate of accumulation by biota and (3) the fresh water and marine MeHg cycle in the Arctic, especially the marine MeHg cycle.
The importance of live coral for small-sized herbivorous reef fishes in physically challenging environments
Authors: Johansson C. L. , Bellwood D. R. , Depczynski M.
Published: August 2012

Tropical coral reefs are facing increasing levels of disturbance, with predictions of ongoing reductions in live coral cover. The response of herbivorous fishes to loss of coral cover was investigated by analysing the relationship between the abundance of different sized herbivorous fishes and live coral cover, on a high flow reef slope and a sheltered back reef on Ningaloo Reef, Western Australia. We found positive relationships between coral cover and the abundance of small (10–20 cm) excavating and scraping parrotfishes on the slope, but a negative relationship between corals and small (10–15 cm) grazers. These relationships were not evident on back reefs. Generally, the abundance of large individuals were not correlated with live coral in either habitat. We suggest that in physically demanding environments small parrotfishes may utilise the structural complexity of corals to resist strong water flow and/or to reduce predation. Small acanthurid grazers may school to reduce energy costs and minimise predation risk. The loss of coral cover appears to be particularly important for small fishes in high energy habitats, especially non-schooling species.
Do invasive eastern gambusia (Gambusia holbrooki) shape wetland fish assemblage structure in south-eastern Australia?
Authors: Macdonald Jed I. , Tonkin Zeb D. , Ramsey David S. L. , Kaus Andrew K. , King Alison K. , Crook David A.
Published: August 2012

Defining the ecological impacts conferred by invasive fishes provides a framework for evaluating the feasibility of control efforts in invaded waterways, and for predicting the consequences of future incursions. Eastern gambusia (Gambusia holbrooki) is a remarkably successful invader of freshwater systems worldwide, with the capacity to detrimentally impact native fishes both directly (e.g. competition, predation, agonistic interactions) and indirectly (e.g. triggering trophic cascades). Here, we modelled the influence of eastern gambusia and several environmental covariates on fish species diversity, abundance and condition based on quantitative survey data collected from 93 wetlands in south-eastern Australia. We predicted that small-bodied, wetland specialist species sharing dietary- and habitat-niches with eastern gambusia would be most severely impacted, and that environmental stressors associated with wetland drying during late summer would magnify these impacts. Eastern gambusia influenced the occurrence, abundance and/or body condition of most common wetland species; however, the direction and level of impact appeared dependent on both biotic and environmental forces. From these results, we postulate that generalist life-history strategies that permit niche-segregation may release some native species from competitive/predatory pressures, allowing coexistence with eastern gambusia in resource-limited, environmentally harsh habitats, whilst specialist species that occupy narrower ecological niches may be less resistant.
Morphology of twin and triplet equine conceptuses during Weeks 3 and 4 of pregnancy
Authors: Waelchli Rudolf O. , Betteridge Keith J.
Published: August 2012

Twin ovulations are common in horses, but twin pregnancies are rarely carried to term. Theories of how one or both twins is/are naturally eliminated in early pregnancy, termed ‘embryo reduction’, have been based on ultrasonographic, not morphological, studies. Here we describe conceptuses recovered transcervically between Days 15 and 28 from 31 twin and two triplet pregnancies. Signs of contact between conceptuses were deduced from those seen in one pair that remained attached by their capsules on Day 18. Signs were found on capsules in two of 10 pairs before or during fixation (immobilisation) at Days 16–17 even though contact had not been seen by ultrasound. After fixation, the signs became stronger in seven of nine unilateral pregnancies, indicated adhesion between pairs and included effects on the vitelline circulation and/or degeneration of one twin. Conceptuses recovered from five of seven unilateral twin pregnancies after the time of capsule disruption (~Day 21) evidenced embryo reduction; in the two surviving pairs, attachment between twins was near the trilaminar/bilaminar yolk-sac wall border. The findings are consistent with the notions that: (1) the capsule plays a role in initiating adhesion between twins; and (2) twin survival depends on an unencumbered trilaminar yolk-sac wall and a functional vitelline circulation.
Geographical clustering of anal cancer incidence in Australia
Authors: Poynten I. Mary , Stein Alicia N. , Conway E. Lynne , Prestage Garrett , Regan David G. , Jin Fengyi , Hocking Jane , Grulich Andrew E.
Published: August 2012

Introduction: Homosexual men are at an increased risk of anal cancer. We aimed to establish the burden of anal squamous cell carcinoma (SCC) in those parts of Australia where homosexual men are most likely to live. Methods: Data on the proportion of homosexual male residents were obtained from published estimates. Men were categorised into three postcode groups by prevalence of men reporting homosexual identity. Male population data in age groups were extracted for each postcode group and analyses of cancer incidence were performed by postcode group. The analyses were restricted to 2000–2005. Results: Eight postcodes had populations where more than 10% of males reported homosexual identity (high prevalence) and 4–10% of men reported homosexual activity in a further 19 postcodes (medium prevalence). From 2000 to 2005, the average annual age-standardised incidence rates of anal SCC in males was 7.61 per 100 000 (95% confidence interval (CI): 4.68–10.55) and 2.21 per 100 000 (95% CI: 1.05–3.37) in high and medium prevalence postcodes, respectively. The corresponding incidence rate ratios compared with low prevalence postcodes (less than 4% of males reported homosexual identity) were 9.6 (95% CI: 6.6–14.1) for the high prevalence and 2.4 (95% CI: 1.4–4.1) for the medium prevalence postcodes. Conclusion: A substantial concentration of the burden of anal cancer occurred among areas where large proportions of homosexual men reside. These results should guide the prioritisation of health service investment in anal cancer treatment and prevention to appropriate geographical areas.
Fast rebinding increases dwell time of Src homology 2 (SH2)-containing proteins near the plasma membrane
Authors: Oh Dongmyung , Ogiue-Ikeda Mari , Jadwin Joshua A. , Machida Kazuya , Mayer Bruce J. , Yu Ji
Published: August 2012

Receptor tyrosine kinases (RTKs) control a host of biological functions by phosphorylating tyrosine residues of intracellular proteins upon extracellular ligand binding. The phosphotyrosines (p-Tyr) then recruit a subset of ∼100 Src homology 2 (SH2) domain-containing proteins to the cell membrane. The in vivo kinetics of this process are not well understood. Here we use total internal reflection (TIR) microscopy and single-molecule imaging to monitor interactions between SH2 modules and p-Tyr sites near the cell membrane. We found that the dwell time of SH2 modules within the TIR illumination field is significantly longer than predictions based on chemical dissociation rate constants, suggesting that SH2 modules quickly rebind to nearby p-Tyr sites after dissociation. We also found that, consistent with the rebinding model, the effective diffusion constant is negatively correlated with the respective dwell time for different SH2 domains and the dwell time is positively correlated with the local density of RTK phosphorylation. These results suggest a mechanism whereby signal output can be regulated through the spatial organization of multiple binding sites, which will prompt reevaluation of many aspects of RTK signaling, such as signaling specificity, mechanisms of spatial control, and noise suppression.
Targeted deletion of
Sost
distal enhancer increases bone formation and bone mass
Authors: Collette Nicole M. , Genetos Damian C. , Economides Aris N. , Xie LiQin , Shahnazari Mohammad , Yao Wei , Lane Nancy E. , Harland Richard M. , Loots Gabriela G.
Published: August 2012

The Wnt antagonist Sost has emerged as a key regulator of bone homeostasis through the modulation of Lrp4/5/6 Wnt coreceptors. In humans, lack of Sclerostin causes sclerosteosis and van Buchem (VB) disease, two generalized skeletal hyperostosis disorders that result from hyperactive Wnt signaling. Unlike sclerosteosis, VB patients lack
SOST
coding mutations but carry a homozygous 52 kb noncoding deletion that is essential for the transcriptional activation of
SOST
in bone. We recently identified a putative bone enhancer,
ECR5
, in the VB deletion region, and showed that the transcriptional activity of
ECR5
is controlled by Mef2C transcription factor in vitro. Here we report that mice lacking
ECR5
or
Mef2C
through
Col1-Cre
osteoblast/osteocyte-specific ablation result in high bone mass (HBM) due to elevated bone formation rates. We conclude that the absence of the
Sost
-specific long-range regulatory element
ECR5
causes VB disease in rodents, and that Mef2C is the main transcription factor responsible for
ECR5
-dependent
Sost
transcriptional activation in the adult skeleton.
Identification of two functionally redundant RNA elements in the coding sequence of poliovirus using computer-generated design
Authors: Song Yutong , Liu Ying , Ward Charles B. , Mueller Steffen , Futcher Bruce , Skiena Steven , Paul Aniko V. , Wimmer Eckard
Published: August 2012

Genomes of RNA viruses contain multiple functional RNA elements required for translation or RNA replication. We use unique approaches to identify functional RNA elements in the coding sequence of poliovirus (PV), a plus strand RNA virus. The general method is to recode large segments of the genome using synonymous codons, such that protein sequences, codon use, and codon pair bias are conserved but the nucleic acid sequence is changed. Such recoding does not affect the growth of PV unless it destroys the sequence/structure of a functional RNA element. Using genetic analyses and a method called “signal location search,” we detected two unique functionally redundant RNA elements (α and β), each about 75 nt long and separated by 150 nt, in the 3′-terminal coding sequence of RNA polymerase, 3D
pol
. The presence of wild type (WT) α or β was sufficient for the optimal growth of PV, but the alteration of both segments in the same virus yielded very low titers and tiny plaques. The nucleotide sequences and predicted RNA structures of α and β have no apparent resemblance to each other. In α, we narrowed down the functional domain to a 48-nt-long, highly conserved segment. The primary determinant of function in β is a stable and highly conserved hairpin. Reporter constructs showed that the α- and β-segments are required for RNA replication. Recoding offers a unique and effective method to search for unknown functional RNA elements in coding sequences of RNA viruses, particularly if the signals are redundant in function.
Grammatical variation in Bequia (St Vincent and the Grenadines)
Authors: Meyerhoff Miriam , Walker James A.
Published: August 2012

Despite the publication of Aceto & Williams (2003), the languages spoken in the Eastern Caribbean remain underdescribed. In this paper, we outline a project examining language use in Bequia (St Vincent and the Grenadines), based on fieldwork between 2003 and 2005, comprising over 100 hours of sociolinguistic interviews conducted and recorded by community-member researchers. We present quantitative analysis of three aspects of the grammatical system that exhibit variation: absence of the verb BE, verbal negation, and tense-aspect marking. We focus on three communities characterized by different sociodemographic histories. This paper fills a gap in our knowledge of the Eastern Caribbean and provides a descriptive sociolinguistic analysis as a starting point for future work. The findings contribute more generally to our understanding of (post-)colonial and contact varieties of English.
Multi-verb constructions in Sri Lanka Malay
Authors: Nordhoff Sebastian
Published: August 2012

This paper investigates serial verbs and related constructions in Sri Lanka Malay and shows that at least four types have to be distinguished (Motion Verb Serialization, Vector Verb Serialization, Compound Verbs, Clause Chains). The constructions found are quite different from those found in Atlantic or Pacific Creoles. This is due to the different input languages: Two of the constructions can be traced to influence from the local languages Tamil and/or Sinhala; one is of Indonesian origin, and one is mixed. Sri Lanka Malay is thus not a simple combination of South Asian Grammar and Malay lexicon but also shows retentions of Malay grammar, as already demonstrated by Slomanson (2006). This recombination of features can only be explained with an account which acknowledges the possibility of grammatical contributions from all input languages, whether substrate, superstrate, or any other.
Poetic dialogue analysis of Chinese–English poetry translation
Authors: Xu Jianzhong , Chang Chengxia
Published: August 2012

The translation of ancient Chinese Poetry into English is considered to be one of the most challenging tasks not only because of the different features between the two languages, especially as they belong to different linguistic families, but also the unique features of the ancient Chinese poetry itself.. This paper, by applying poetry dialogue analysis based on dialogism, explores the operation of its elements such as context, subject, sense, image, the reader and text form, and tries to seek out the mechanism for understanding the source text and reproducing what the source contains in the target language, thus shedding light on poetry translation studies.
Bruce Nicklas: Pioneering studies on spindle forces
Authors: Sedwick Caitlin
Published: August 2012

Nicklas performed innovative studies on the forces that drive cell division.
T granules in human platelets function in TLR9 organization and signaling
Authors: Thon Jonathan N. , Peters Christopher G. , Machlus Kellie R. , Aslam Rukhsana , Rowley Jesse , Macleod Hannah , Devine Matthew T. , Fuchs Tobias A. , Weyrich Andrew S. , Semple John W. , Flaumenhaft Robert , Italiano Joseph E.
Published: August 2012

Human and murine platelets (PLTs) variably express toll-like receptors (TLRs), which link the innate and adaptive immune responses during infectious inflammation and atherosclerotic vascular disease. In this paper, we show that the TLR9 transcript is specifically up-regulated during pro-PLT production and is distributed to a novel electron-dense tubular system-related compartment we have named the T granule. TLR9 colocalizes with protein disulfide isomerase and is associated with either VAMP 7 or VAMP 8, which regulates its distribution in PLTs on contact activation (spreading). Preincubation of PLTs with type IV collagen specifically increased TLR9 and CD62P surface expression and augmented oligodeoxynucleotide (ODN) sequestration and PLT clumping upon addition of bacterial/viral ODNs. Collectively, this paper (a) tracks TLR9 to a new intracellular compartment in PLTs and (b) describes a novel mechanism of TLR9 organization and signaling in human PLTs.
PKA and PDE4D3 anchoring to AKAP9 provides distinct regulation of cAMP signals at the centrosome
Authors: Terrin Anna , Monterisi Stefania , Stangherlin Alessandra , Zoccarato Anna , Koschinski Andreas , Surdo Nicoletta C. , Mongillo Marco , Sawa Akira , Jordanides Niove E. , Mountford Joanne C. , Zaccolo Manuela
Published: August 2012

Previous work has shown that the protein kinase A (PKA)–regulated phosphodiesterase (PDE) 4D3 binds to A kinase–anchoring proteins (AKAPs). One such protein, AKAP9, localizes to the centrosome. In this paper, we investigate whether a PKA–PDE4D3–AKAP9 complex can generate spatial compartmentalization of cyclic adenosine monophosphate (cAMP) signaling at the centrosome. Real-time imaging of fluorescence resonance energy transfer reporters shows that centrosomal PDE4D3 modulated a dynamic microdomain within which cAMP concentration selectively changed over the cell cycle. AKAP9-anchored, centrosomal PKA showed a reduced activation threshold as a consequence of increased autophosphorylation of its regulatory subunit at S114. Finally, disruption of the centrosomal cAMP microdomain by local displacement of PDE4D3 impaired cell cycle progression as a result of accumulation of cells in prophase. Our findings describe a novel mechanism of PKA activity regulation that relies on binding to AKAPs and consequent modulation of the enzyme activation threshold rather than on overall changes in cAMP levels. Further, we provide for the first time direct evidence that control of cell cycle progression relies on unique regulation of centrosomal cAMP/PKA signals.
RWM control studies on RFX-mod with a limited set of active coils*
Authors: Baruzzo M. , Bolzonella T. , Liu Y.Q. , Manduchi G. , Marchiori G. , Soppelsa A. , Takechi M. , Villone F.
Published: August 2012

In this paper, the results of resistive wall mode (RWM) control experiments using several sets of active coils are presented.

The control effectiveness as a function of coil number and covered torus surface is studied in the RFX-mod device, thanks to the powerful and flexible MHD active control system. Active control is tried using similar coil number and size both in the reversed field pinch (RFP) and in the tokamak configurations, giving a good experimental set to exploit the differences between the two cases.

The experimental results are compared with predictions by a new integrated simulator for closed loop RWM growth. The numerical tool couples, in a self-consistent way, a full 3D finite element description of the machine boundaries, a 2D toroidal model of RFP plasma stability and a model of the RFX-mod control system, producing an overall dynamic model cast in the state variable space. In this way a full dynamic flight simulator of RWM control experiments is implemented, where coil coverage and experimental proportional–integral–derivative gains are explored in simulations.

Both in the performed experiments and in simulations wall mode active control is proven to be possible in both the configurations with a very reduced set of active control coils.
Generalization of Atkin’s orthogonal polynomials and supersingular elliptic curves
Authors: Tran Ying-Ying
Published: August 2012

In a 1998 paper, Kaneko and Zagier explain unpublished work of Atkin which exhibits an infinite sequence of polynomials with the property that when suitable polynomials are reduced mod

p
p

for a prime

p
p

, one gets the locus of supersingular elliptic curves. Here we generalize this phenomenon by considering the continued fraction expansions of modular and quasimodular forms.
Global rigidity of higher rank Anosov actions on tori and nilmanifolds
Authors: Fisher David , Kalinin Boris , Spatzier Ralf
Published: August 2012

We show that sufficiently irreducible Anosov actions of higher rank abelian groups on tori and nilmanifolds are

C

∞

C^{\infty }

-conjugate to affine actions.
PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data
Authors: Sükösd Zsuzsanna , Knudsen Bjarne , Kjems Jørgen , Pedersen Christian N.S.
Published: August 2012

Summary: PPfold is a multi-threaded implementation of the Pfold algorithm for RNA secondary structure prediction. Here we present a new version of PPfold, which extends the evolutionary analysis with a flexible probabilistic model for incorporating auxiliary data, such as data from structure probing experiments. Our tests show that the accuracy of single-sequence secondary structure prediction using experimental data in PPfold 3.0 is comparable to RNAstructure. Furthermore, alignment structure prediction quality is improved even further by the addition of experimental data. PPfold 3.0 therefore has the potential of producing more accurate predictions than it was previously possible.

Availability and implementation: PPfold 3.0 is available as a platform-independent Java application and can be downloaded from http://birc.au.dk/software/ppfold.

Contact: Zsuzsanna Sükösd or zs@birc.au.dk.
BioJava: an open-source framework for bioinformatics in 2012
Authors: Prlić Andreas , Yates Andrew , Bliven Spencer E. , Rose Peter W. , Jacobsen Julius , Troshin Peter V. , Chapman Mark , Gao Jianjiong , Koh Chuan Hock , Foisy Sylvain , Holland Richard , Rimša Gediminas , Heuer Michael L. , Brandstätter–Müller H. , Bourne Philip E. , Willis Scooter
Published: August 2012

Motivation: BioJava is an open-source project for processing of biological data in the Java programming language. We have recently released a new version (3.0.5), which is a major update to the code base that greatly extends its functionality.

Results: BioJava now consists of several independent modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.

Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.6 or higher. All inquiries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists

Contact: andreas.prlic@gmail.com