bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid Growth, High Feeding Rates, and Early Piscivory in Young-of-the-Year Bluefish (Pomatomus saltatrix)
Authors: Juanes Francis , Conover David O.
Published: May 2008

The bluefish (Pomatomus saltatrix) is an offshore-spawning estuarine-dependent fish that is abundant along the east coast of North America. Young-of-the-year bluefish undergo a habitat shift from offshore waters to inshore nursery areas at about 40–70 mm total length which coincides with an increased growth rate and a diet shift from planktivory to piscivory. Here, we measure growth of young-of-the-year bluefish on different diets and estimate consumption rates both in the field and in the laboratory. Growth on a fish diet is significantly higher than that on a zooplanktivorous diet. Bluefish have among the highest evacuation (5–7 h), consumption (20–30% body weight/d), and specific growth rates (1–2 mm/d) reported for temperate fishes and are similar to those for pelagic tropical species. These results suggest that bluefish may exhibit a tropical feeding physiology in temperate estuarine nurseries as a way to achieve rapid growth rates.
Genetic Analysis of Striped Marlin (Tetrapturus audax) Population Structure in the Pacific Ocean
Authors: Graves John E. , McDowell Jan R.
Published: May 2008

Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) was used to determine the magnitude of intraspecific genetic differentiation among samples of striped marlin (Tetrapturus audax). Composite genotypes, representing information from 11 restriction endonucleases, were generated for samples of approximately 40 striped marlin each from Mexico, Ecuador, Australia, and Hawaii. Genotypic variation was relatively high in all samples: the pooled nucleon diversity was 0.82 (sample range 0.69–0.84), and the pooled nucleotide sequence diversity was 0.30% (sample range 0.20–0.32%). Values of corrected mean nucleotide sequence divergence between samples were low (0.01–0.06%, mean 0.03%). Despite low intersample divergences, significant heterogeneity was observed in the distribution of composite mtDNA genotypes among samples. Each location was characterized by the presence of unique genotypes at elevated frequencies. Samples taken from the same location 1 yr apart demonstrated temporal stability of the distribution of genotypes at that site. These results demonstrate significant spatial partitioning of genetic variation within striped marlin, a situation that sharply contrasts with similar studies of several species of tuna. Management should focus on units smaller than those currently used to conserve unique genetic variation within the species.
An Index of Biotic Integrity (IBI) for Fish Assemblages in the Littoral Zone of Great Lakes' Areas of Concern
Authors: Minns Charles K. , Cairns Victor W. , Randall Robert G. , Moore James E.
Published: May 2008

Karr's Index of Biotic Integrity (IBI) approach provides a biological measure of ecosystem health using a wide spectrum of metrics which can be extracted from fish catch data obtained using standardized methods. Extensive electrofishing surveys of littoral fish assemblages, conducted in three Great Lakes' Areas of Concern, provided the basis for developing a lacustrine IBI that was 12 metrics of three broad types: (i) species composition, (ii) trophic composition, and (iii) abundance and condition. In contrast with lotic IBIs where diversity and abundance metrics have mostly been used, several biomass metrics were adopted to accommodate the large size range of lentic fishes. The variability of repeated measures was low enough to allow valid testing of intertransect differences with three to five samples per transect. Comparisons among survey areas showed significant differences consistent with the varying levels of ecosystem degradation. Analyses of mean IBI values with measures of submerged vegetation density and cover by transect produced significant positive correlations. This IBI developed for the Great Lakes' littoral zone, both by design and by demonstrated correlations, integrates the effects of four main factors influencing fish assemblages and hence revealing ecosystem health: exotic fishes, water quality, physical habitat supply, and piscivore abundance.
Bayesian and Related Approaches to Fitting Surplus Production Models
Authors: Hoenig John M. , Warren William G. , Stocker Max
Published: May 2008

The Schaefer surplus production model relates equilibrium yield to fishing effort and can be fitted using just information on catch and fishing effort. Sometimes, the fitted model predicts a maximum sustainable yield (height of the parabola) that is clearly unrealistic. In this case, one may wish to use prior information on maximum sustainable yield either to constrain the height of the parabola or to provide a prior distribution for Bayesian estimation. To construct a Bayes estimator, one would generally specify a noninformative prior on the residual error variance and, possibly, on the width of the parabola; the prior distribution for height could be obtained by examining fisheries for similar stocks or species on a per unit area basis. Another possibility is to use an empirical Bayes estimator when data from several fisheries (e.g., individual lakes) are available for several years. The methodology is illustrated on catch and effort data for big-eye tuna (Thunnus obesus) and Dungeness crab (Cancer magister). The approach can be extended to other fishery models, including nonequilibrium production models. The prior distribution parameters can be allowed to depend on covariates.
Influence of Cover on the Spatial Distribution of Littoral-zone Fishes
Authors: Hosn Wafa Aboul , Downing John A.
Published: May 2008

Littoral-zone fish are thought to reduce predation pressure by seeking refuge within macrophyte beds or near the lake bottom, or by aggregating. We used underwater video to measure the spatial aggregation of prey fishes in the littoral habitat. At low density, fish were more aggregated off the bottom in open habitats than when found off the bottom within macrophyte beds. At high densities, fish were primarily observed near the lake bottom, and the presence or absence of macrophyte beds had little influence on spatial behavior. No difference could be detected in the degree of aggregation seen in fish on the lake bottom inside or outside macrophyte beds. Our results lend field support to theoretical and laboratory research that suggests aggregative behavior in littoral-zone fish is strongly influenced by fish density and by habitat structure.
Evaluation of the Depensatory Fishing Hypothesis as an Explanation for Population Cycles in Fraser River Sockeye Salmon (Oncorhynchus nerka)
Authors: Cass A. J. , Wood C. C.
Published: May 2008

Causes of cyclic fluctuations in the abundance of Fraser River sockeye (Oncorhynchus nerka) have been the focus of considerable debate for much of this century. Most hypotheses to explain cyclic behaviour in Fraser River sockeye centre on identifying agents of depensatory mortality, and several recent papers argue that sockeye cycles are maintained primarily by depensatory fishing patterns. We assess the evidence for depensatory fishing as an explanation for these cycles. Using simulations, we demonstrate that empirical evidence for depensatory fishing is likely an artifact caused by bias in estimating stock composition of catches in mixed-stock fisheries. Moreover, recent trends in harvest rates among comigrating stocks with asynchronous cycles are inconsistent with the depensatory fishing hypothesis. It also seems very unlikely that aboriginal and early commercial fisheries were intensive enough to maintain cycles that persisted prior to 1860. Only during the unregulated, early commercial fishery prior to the collapse of the upriver runs following the 1913–14 disaster at Hell's Gate is there any convincing evidence of depensatory fishing.
Oocyte Recruitment in First-Time Spawning Atlantic Cod (Gadus morhua) in Relation to Feeding Regime
Authors: Kjesbu O. S. , Holm J. C.
Published: May 2008

Adolescent (10-mo-old, ≈165 g) Atlantic cod (Gadus morhua) hatched and reared in the laboratory were transferred to three different feeding regimes (groups) for a full year, high–high (HH), low–high (LH), or high–low (HL), switching the ration size after 5 mo in July (i.e., before vitellogenesis). Subsequent analysis of fecundity before the first spawning season revealed that adolescent body weight was most important for fecundity followed by growth rate in the autumn, while growth rate in the spring contributed insignificantly. There existed a significant positive correlation between individual, starting (adolescent), and final body weight. All groups were characterized by high individual variability in both fecundity and oocyte development, suggesting strong genetic influences. The groups showed different final mean body weights (HH: 1265 g, LH: 1199 g, and HL: 886 g) but, unexpectedly, the same mean relative fecundities (number of oocytes per gram of ovary-free fish) (≈1200). The study on oocyte sizes provided evidence that HH fish will commence spawning earliest in the year followed by LH fish and then HL fish.
Skeletal patterns in the autopodium of native and regenerated limbs of the larval axolotl, Ambystoma mexicanum
Authors: Scadding Steven R.
Published: May 2008

The purpose of this investigation was to study the autopodial skeletal patterns that are observed in native (never regenerated) and regenerated limbs of the larval axolotl, Ambystoma mexicanum. The axolotl is used widely in limb regeneration studies, and in the regenerating axolotl limb mesopodial patterns can be modified by such factors as vitamin A administration. It is also known that other salamander species show significant variation in autopodial skeletal patterning. Hence, it seemed important to determine the type and frequency of autopodial variants in both native limbs and those that have regenerated after amputation at either the stylopodial and zeugopodial levels. The results showed that native limbs exhibited a complete skeletal pattern in the majority of cases, but that variants involving loss of a phalange or reduction in the number of carpals or tarsals occurred frequently. Regenerated limb patterns were more variable than those seen in native limbs, and limbs regenerating from zeugopodial level amputations were more variable than those regenerating from stylopodial level amputation. The significance of these observations for the development and regeneration of limb pattern is discussed.
Plumage variation and dominance in captive female Red-winged Blackbirds
Authors: Muma Katherine E. , Weatherhead Patrick J.
Published: May 2008

Flocks of female Red-winged Blackbirds (Agelaius phoeniceus) were maintained in aviaries to determine whether variation in brightness of epaulette or chin plumage correlated with dominance status in nonbreeding situations. No correlation was found between natural plumage variation and dominance in eight control groups, although dominant females were heavier and in better condition. In two groups in which epaulettes were experimentally brightened on some birds and two groups where some chins were brightened, brightening an individual's plumage had no consistent effect on dominance status. Thus, we did not find any evidence that there is direct selection on female plumage brightness for signalling competitive ability outside the breeding season. We propose that bright plumage in females could be an indirect consequence of genetic correlation with a trait selected for in males.
Modification of stream ecosystem structure and function by beaver (Castor canadensis) in the Adirondack Mountains, New York
Authors: Smith Michael E. , Driscoll Charles T. , Wyskowski Barbara J. , Brooks Carol M. , Cosentini Christina C.
Published: May 2008

Stream ecosystem structure and function were studied in an acidic second-order Adirondack Mountain stream system with current beaver activity. Acid-neutralizing capacity, pH, dissolved organic carbon, Fe2+, and Mn2+ values were elevated and [Formula: see text], Aln−, and dissolved oxygen concentrations were decreased following water transport through the beaver impoundment. Upstream acidity was primarily ameliorated by [Formula: see text] and Fe retention in the impoundment during the low-flow summer period. High Fe and Al sediment concentrations were present during low-flow periods immediately downstream of the beaver dam. During the high-flow period, Fe and Al concentrations were highest 0.25 km downstream of the dam, owing to slow metal hydrolysis–oxidation kinetics during spring snowmelt. The immediate downstream site exhibited significantly lower invertebrate richness and diversity and collector–filterer, Plecoptera, and Trichoptera densities, but significantly higher total invertebrate, Diptera, Ephemeroptera, predator, and collector–gatherer densities. Significant differences were noted primarily during April and July. Our results indicate that beaver dams modify stream ecosystems longitudinally and temporally and ameliorate stream acidity. Current lotic ecosystem paradigms like the river continuum concept should incorporate "patch" occurrences such as those created by beaver.
Population regulation in white-footed mice (Peromyscus leucopus) in a suboptimal habitat
Authors: Linzey Alicia V. , Kesner Michael H.
Published: May 2008

A white-footed mouse (Peromyscus leucopus) population living in a suboptimal habitat was monitored weekly throughout the year over a 4-year period. Data obtained were used to examine the hypothesis that populations living in suboptimal habitats are not self-regulating. A total of 880 different mice were handled on 3023 occasions. Population density fluctuated on both a seasonal and an annual basis, and differences in demographic structure among years included shifts in predominance of subadults versus adults, proportion of the population composed of juveniles, survivorship of males, and reproductive effort. In general, the 2nd year was distinctive in that it was lower in density, dominated by subadults, had few juveniles, poor overwinter survival, and low reproductive effort. A phase space plot of density against proportion of females breeding indicated that reproductive effort was being regulated in response to density, suggesting that this suboptimal habitat population was self-regulating.
Levels of steroids, including cortisol and 17α,20β-dihydroxy-4-pregnen-3-one, in plasma, seminal fluid, and urine of Pacific herring (Clupea hareng us pallasi) and North Sea plaice (Pleuronectes platessa L.)
Authors: Scott A. P. , Canario A. V. M. , Sherwood Nancy M. , Warby Carol M.
Published: May 2008

In an accompanying paper we report that herring milt contains high concentrations of conjugated cortisol and 17α,20β-dihydroxy-4-pregnen-3-one. We suggest that one source of these steroids was the urine, which could have become mixed with the milt during the hand-stripping procedure. In the present study, samples of hand-stripped milt from several other species, plaice (Pleuronectes platessa), dab (Limanda limanda), flounder (Platichthys flesus), goldfish (Carassius auratus), and rainbow trout (Oncorhynchus mykiss, formerly Salmo gairdneri), were assayed for free and conjugated cortisol. Uncontaminated samples of plasma, seminal fluid, and urine of male herring and plaice were also assayed for free and conjugated cortisol (both species), 17α,20β-dihydroxy-4-pregnen-3-one (herring only), 17α,20α-dihydroxy-4-pregnen-3-one, and 3α,17α,21-trihydroxy-5β-pregnan-20-one (plaice only). The results showed that hand-stripped milt from these other species, excluding rainbow trout (from which it was possible to obtain urine-free milt), also had markedly high levels of conjugated cortisol (200–1000 ng∙mL−1). Urine of herring and plaice had particularly high levels of conjugated cortisol (ca. 5 μg∙mL−1). Uncontaminated seminal fluid from herring, but not from plaice, also had high levels of conjugated cortisol (ca. 2 μg∙mL−1). Urine and plasma, but not seminal fluid, of herring had elevated levels of conjugated 17α,20β-dihydroxy-4-pregnen-3-one. Urine, but not plasma or seminal fluid, of male plaice had elevated levels of 17α,20α -dihydroxy-4-pregnen-3-one and 3α,17α,21-trihydroxy-5β-pregnan-20-one. It would appear that fish urine is a rich source of conjugated steroids and that care must be taken, when collecting milt for pheromone studies, to avoid urine contamination.
Flexibility in foraging and roosting behaviour by the big brown bat (Eptesicus fuscus)
Authors: Brigham R. Mark
Published: May 2008

I used radiotelemetry to study the roosting and foraging behaviour of big brown bats (Eptesicus fuscus) in south central British Columbia. Maternity colonies were found in hollows of dead ponderosa pine trees (Pinus ponderosa) and colony members were not loyal to specific trees. Individuals consistently foraged above a 300-m stretch of the Okanagan River, travelling 1.8 km on average from day roosts to the foraging area. There were significant differences in the duration of foraging bouts among different sex and age-classes. The results are compared with data collected in a similar manner for a population in Ontario, where, in contrast to British Columbia, E. fuscus were highly loyal to man-made roost structures and on average travelled less than 1 km to foraging sites that varied nightly. I suggest that the marked difference in both roosting and foraging behaviour is due to differences in the availability and structure of roosts and in the distribution of insect prey.
An assessment of leeches (Hirudinea) as indicators of lake acidification
Authors: Bendell Barry E. , McNicol Donald K.
Published: May 2008

To assess their value as indicators of acidification, leeches (Hirudinea) were surveyed with baited traps in 40 small lakes covering a wide pH range near Sudbury, Ontario. Leeches were caught in all 20 lakes with pH >5.5, and represented nine species. Leeches, representing four species, were caught in only 4 of 20 lakes with pH <5.5, and none were caught in 8 of these in which pH was <4.9. Artificial surfaces made from Styrofoam® were provided on 20 lakes for cocoon deposition by Nephelopsis obscura. After 30 days, cocoons were deposited on surfaces on 10 of 13 lakes with pH ≥5.2, but were not deposited at lower pH.
Facial skin glands of ringed and grey seals, and their possible function as odoriferous organs
Authors: Hardy Margaret H. , Roff Elizabeth , Smith Thomas G. , Ryg Morten
Published: May 2008

Mature male ringed seals (Phoca hispida) have a very strong odour emanating from the facial region during the breeding season. The inner surface of the skin from the heads of three animals captured during the mating season revealed the distribution of closely packed, much enlarged sebaceous glands on the anterior muzzle skin and extending into the interorbital and postvibrissal regions. A histological study was made of facial skin from 22 animals of different ages and both sexes, taken from Svalbard, Norway, during the breeding season. In mature males the sebaceous glands on the face were 3–8 times larger in cross section and more actively secreting than glands on the neck. Melanin granules were concentrated in the sebum. These facial glands were also 2–10 times larger and more actively secreting than the facial glands of immature males, mature females, or immature females. The apocrine sweat glands on the face of mature males were also much larger and more active than those of the other groups. It was concluded that the greater size, secretory activity, and melanin production of the sebaceous glands of mature male ringed seals could account for the strong odour and dark colour that have been observed on the face in the breeding season. The enlarged and active apocrine sweat glands might also contribute to the odour. The facial skin of six dominant bull grey seals (Halichoerus grypus), killed during the breeding season, had sebaceous glands of intermediate size, but high activity and high melanin content in the sebum. Their apocrine sweat glands were very large and active, indicating that they also may have a role in sexual signalling.
The blood of Halicryptus spinulosus (Priapulida)
Authors: Schreiber Arnd , Storch Volker , Powilleit Martin , Higgins Robert P.
Published: May 2008

The blood of the priapulid Halicryptus spinulosus was investigated by protein electrophoresis and electron microscopy. Two cell types were encountered: irregularly shaped amoebocytes and spherical erythrocytes. In vitro, the former efficiently phagocytized bacteria and tended to coagulate. A 12-kilodalton polypeptide was the major molecule in erythrocytes, amounting to 20–30% of total erythrocytic proteins. It contained iron and probably formed complexes of higher molecular mass in the cells. These findings support suggestions that Halicryptus contains a haemerythrin-like pigment. Blood colour ranged from pink to black, probably depending on the hydrogen sulphide or oxygen concentration of the medium. Haematocrit values averaged 15.6%, and 58 000 erythrocytes were typically counted per microlitre of body fluid. The major blood constituent was a water-clear serum containing at least 20 proteins at very low and fairly variable concentrations; the molecular masses have been determined for 14 of these. A 46-kilodalton protein was prominent among serum proteins. Superoxide dismutase activity was demonstrated in erythrocyte lysates.
Evolutionary genetics of flycatchers. III. Variation in Empidonax hammondii (Aves: Tyrannidae)
Authors: Johnson Ned K. , Marten Jill A.
Published: May 2008

We assessed variability at 36 structural gene loci in 149 individuals from nine breeding populations of the Hammond's Flycatcher (Empidonax hammondii), a species showing striking morphologic homogeneity over a nesting distribution spanning 30 degrees of latitude. Although moderately polymorphic (44.4%) at these loci, the species demonstrated low levels of mean observed heterozygosity (0.026), mean percentage of polymorphic loci (9.56), and mean number of alleles per locus (1.19), perhaps as a result of past population bottlenecks. Geographic genetic structuring was minimal (FSt = 0.043) and paralleled the lack of morphologic variation. Six of the eight unique alleles recorded occurred in Oregon, near the center of present abundance. Gene flow, as estimated by the rare allele method, was moderately high to high at 8–31 individuals per generation. Because most or all of the modern distribution of the species in western Canada and Alaska was either covered by ice or otherwise unsuitable for occupancy until the post-Wisconsin – Holocene interval, recolonization of the high latitudes in recent millenia is indicated. Reduced genetic variability and extreme morphologic uniformity of present populations is in agreement with this hypothesis.
Pyruvate kinase from the earthworm Allolobophora calliginosa: modification of the enzyme during anaerobiosis
Authors: Papadopoulos Athanasios I. , Michaelidis Basile , Beis Isidoros
Published: May 2008

The relative activity of pyruvate kinase from the body-wall muscle of the earthworm Allolobophora calliginosa was found to drop dramatically within 6 h of exposure to N2, whereas the opposite was observed during recovery. Two forms of pyruvate kinase (designated as peak I and peak II) were separated chromatographically on DEAE-cellulose and eluted at 50 and 150 mM of KCl, respectively. They displayed different kinetic behaviour with respect to substrate phosphoenolpyruvate; peak I exhibited Michaelis–Menten kinetics whereas peak II showed sigmoidal kinetics. The ratio of the enzyme units (peak I/peak II) decreased from 3.38 under normoxic conditions to 0.09 under anoxic conditions. In vitro incubation of the aerobic form of pyruvate kinase in the presence of ATP and Mg++ resulted in a reduction of the enzyme activity by 64%, suggesting the presence of an endogenous cyclic-nucleotide-independent protein kinase capable of phosphorylating pyruvate kinase. After in vitro incubation, alkaline phosphatase from E. coli increased the depressed activity of anaerobic pyruvate kinase, indicating that the enzyme molecule is phosphorylated in vivo during exposure to anoxia.
Torpor patterns in food-deprived Myotis lucifugus (Chiroptera: Vespertilionidae) under simulated roost conditions
Authors: Kurta Allen
Published: May 2008

Temperate insectivorous bats are commonly prevented from foraging by cold or wet weather. This study examines the effect of missing a single night of foraging on the energetics of pregnant and lactating little brown bats (Myotis lucifugus) under simulated roost conditions. After not foraging, the day-roosting metabolic rate of pregnant M. lucifugus was reduced by 61% and that of lactating bats by 46%. Although previous laboratory studies predicted that food-deprived bats should remain in torpor throughout the day-roosting period, M. lucifugus consistently aroused from torpor between 11:00 and 15:00 and maintained elevated metabolic rates for the rest of the day.
Effect of acute and chronic temperature transition on enzymes of cardiac metabolism in white perch (Morone americana), yellow perch (Perca flavescens), and smallmouth bass (Micropterus dolomieui)
Authors: Sephton Dawn H. , Driedzic William R.
Published: May 2008

White perch (Morone americana), yellow perch (Perca flavescens), and smallmouth bass (Micropterus dolomieui) were acclimated to 5 and 20 °C. There was an increase in ventricle mass relative to body mass in smallmouth bass only following acclimation to 5° C. Maximal in vitro activities of hexokinase, citrate synthase, carnitine acyl CoA transferase (with palmitoyl CoA, palmitoleoyl CoA, and oleoyl CoA as substrates), and total ATPase were assessed in crude heart homogenates. Tissues removed from warm-acclimated animals were tested at 20 and 5 °C; tissues removed from cold-acclimated animals were assessed at 5 °C. Acute temperature transitions were associated with decreases in the activities of hexokinase (Q10 ≈ 1.8), citrate synthase (Q10 ≈ 1.4), and ATPase (Q10 ≈ 1.7). The impact of temperature on carnitine acyl CoA transferases was generally less severe. This suggests that maximal fatty acid oxidation is conserved better than glucose oxidation during a warm to cold transition. Maximal enzyme activities were generally unaffected by the acclimation regime, with the exception of that of carnitine acyl CoA transferase in white perch heart. The substantial increase in carnitine acyl CoA transferase activity when unsaturated CoA derivatives were provided as substrate suggests an increased capacity to oxidize unsaturated fatty acids at low temperature following an acclimation period. Attempts to sustantiate this contention by offering labelled oleic acid to ventricle sheets were thwarted by a high rate of incorporation into the total lipid pool.
THE SECOND QUANTIZED QUANTUM TURING MACHINE AND KOLMOGOROV COMPLEXITY
Authors: ROGERS CAROLINE , VEDRAL VLATKO
Published: May 2008

The Kolmogorov complexity of a physical state is the minimal physical resources required to reproduce that state. We define a second quantized quantum Turing machine and use it to define second quantized Kolmogorov complexity. There are two advantages to our approach — our measure of the second quantized Kolmogorov complexity is closer to physical reality and unlike other quantum Kolmogorov complexities, it is continuous. We give examples where the second quantized and quantum Kolmogorov complexity differ.
PHOTOLUMINESCENCE, COMPOSITION AND MICROSTRUCTURE OF POROUS SILICON PREPARED BY DIFFERENT SUBSTRATES
Authors: ZHAO YUE , LI DONG-SHENG , SANG WEN-BIN , YANG DE-REN , JIANG MIN-HUA
Published: May 2008

In this paper, the microstructure of porous silicon was discussed by scanning electron microscopy and Raman spectra. The compositions of the samples were studied by X-ray diffraction and electron diffraction. The luminescent properties of porous silicon were explored by the PL measurements. The results showed that the structure of the top porous silicon prepared by epitaxial silicon consists of meso-pores and that of the underlying porous silicon consists of macro-pores. Furthermore, the structure of porous silicon prepared by heavily doped silicon is made of nano-pores. The composition of porous silicon consists of the single-crystal phase, poly-crystal phase and amorphous-crystal phase, respectively. In addition, the luminescence of porous silicon may come from the defects on the silicon-rod surface and in Si complexes including siloxene, Si oxide and Si hydrides, and may not be related to amorphous phase and nano-phase.
PERIODIC 3-MANIFOLDS AND MODULAR CATEGORIES
Authors: QAZAQZEH KHALED
Published: May 2008

A p-periodic 3-manifold is a 3-manifold that admits a ℤp-action whose fixed point set is a circle. We give a congruence that relates the quantum invariant of a p-periodic 3-manifold associated to any modular category over an integrally closed ground ring and the corresponding quantum invariant of its orbit space.
KNOTS WITH INFINITELY MANY INCOMPRESSIBLE SEIFERT SURFACES
Authors: WILSON ROBIN T.
Published: May 2008

We show that a knot in S3 with an infinite number of incompressible Seifert surfaces contains a closed non-peripheral incompressible surface in its complement.
POLYGONAL KNOT SPACE NEAR ROPELENGTH-MINIMIZED KNOTS
Authors: MILLETT KENNETH C. , PIATEK MICHAEL , RAWDON ERIC J.
Published: May 2008

For a polygonal knot K, it is shown that a tube of radius R(K), the polygonal thickness radius, is an embedded torus. Given a thick configuration K, perturbations of size r < R(K) define satellite structures, or local knotting. We explore knotting within these tubes both theoretically and numerically. We provide bounds on perturbation radii for which one can obtain small trefoil and figure-eight summands and use Monte Carlo simulations to estimate the relative probabilities of these structures as a function of the number of edges.
A POLYNOMIAL INVARIANT FOR FLAT VIRTUAL LINKS
Authors: KAUFFMAN LOUIS H. , RICHTER R. BRUCE
Published: May 2008

This paper gives a polynomial invariant for flat virtual links. In the case of one component, the polynomial specializes to Turaev's virtual string polynomial. We show that Turaev's polynomial has the property that it is non-zero precisely when there is no filamentation of the knot, as described by Hrencecin and Kauffman. Schellhorn has provided a version of filamentations for flat virtual links. Our polynomial has the property that if there is a filamentation, then the polynomial is 0. The converse fails, although if the polynomial is 0, then it turns out to be easy to determine if there is a filamentation.
On the complexity of partially-flow-sensitive alias analysis
Authors: Rinetzky N. , Ramalingam G. , Sagiv M. , Yahav E.
Published: May 2008

We introduce the notion of apartially-flow-sensitive analysis based on the number of read and write operations that are guaranteed to be analyzed in a sequential manner. We study the complexity of partially-flow-sensitive alias analysis and show that precise alias analysis with a very limited flow-sensitivity is as hard as precise flow-sensitive alias analysis, both when dynamic memory allocation is allowed, as well as in the absence of dynamic memory allocation.
AspectML
Authors: Dantas Daniel S. , Walker David , Washburn Geoffrey , Weirich Stephanie
Published: May 2008

This article defines AspectML, a typed functional, aspect-oriented programming language. The main contribution of AspectML is the seamless integration of polymorphism, run-time type analysis and aspect-oriented programming language features. In particular, AspectML allows programmers to define type-safe polymorphic advice using pointcuts constructed from a collection of polymorphic join points. AspectML also comes equipped with a type inference algorithm that conservatively extends Hindley--Milner type inference. To support first-class polymorphic point-cut designators, a crucial feature for developing aspect-oriented profiling or logging libraries, the algorithm blends the conventional Hindley--Milner type inference algorithm with a simple form of local type inference.

We give our language operational meaning via a type-directed translation into an expressive type-safe intermediate language. Many complexities of the source language are eliminated in this translation, leading to a modular specification of its semantics. One of the novelties of the intermediate language is the definition of polymorphic labels for marking control-flow points. When a set of labels is assembled as a pointcut, the type of each label is an instance of the type of the pointcut.
Size-change termination with difference constraints
Authors: Ben-Amram Amir M.
Published: May 2008

This article considers an algorithmic problem related to the termination analysis of programs. More specifically, we are given bounds on differences in sizes of data values before and after every transition in the program's control-flow graph. Our goal is to infer program termination via the following reasoning (“the size-change principle”): if in any infinite (hypothetic) execution of the program, some size must descend unboundedly, the program must always terminate, since infinite descent of a natural number is impossible.

The problem of inferring termination from such abstract information is not the halting problem for programs and may well be decidable. If this is the case, the decision algorithm forms a “back end” of a termination verifier, and it is interesting to find out the computational complexity of the problem.

A restriction of the problem described above, which only uses monotonicity information (but not difference bounds), is already known to be decidable. We prove that the unrestricted problem is undecidable, which gives a theoretical argument for studying restricted cases. We consider a case where the termination proof is allowed to make use of at most one bound per target variable in each transition. For this special case, which we claim is practically significant, we give (for the first time) an algorithm and show that the problem is in PSPACE, in fact that it is PSPACE-complete. The algorithm is based on combinatorial arguments and results from the theory of integer programming not previously used for similar problems.

The algorithm has interesting connections to other work in termination, in particular to methods for generating linear ranking functions or invariants.
PEAK—a fast and effective performance tuning system via compiler optimization orchestration
Authors: Pan Zhelong , Eigenmann Rudolf
Published: May 2008

Compile-time optimizations generally improve program performance. Nevertheless, degradations caused by individual compiler optimization techniques are to be expected. Feedback-directed
optimization orchestration
systems generate optimized code versions under a series of optimization combinations, evaluate their performance, and search for the best version. One challenge to such systems is to tune program performance quickly in an exponential search space. Another challenge is to achieve high program performance, considering that optimizations interact. Aiming at these two goals, this article presents an automated performance tuning system,
PEAK
, which searches for the best compiler optimization combinations for the important code sections in a program. The major contributions made in this work are as follows: (1) An algorithm called
Combined Elimination (CE)
is developed to explore the optimization space quickly and effectively; (2) Three fast and accurate rating methods are designed to evaluate the performance of an optimized code section based on a partial execution of the program; (3) An algorithm is developed to identify important code sections as candidates for performance tuning by trading off tuning speed and tuned program performance; and (4) A set of compiler tools are implemented to automate optimization orchestration. Orchestrating optimization options in SUN Forte compilers at the whole-program level, our CE algorithm improves performance by 10.8% over the SPEC CPU2000 FP baseline setting, compared to 5.6% improved by manual tuning. Orchestrating GCC O3 optimizations, CE improves performance by 12% over O3, the highest optimization level. Applying the rating methods, PEAK reduces tuning time from 2.19 hours to 5.85 minutes on average, while achieving equal or better program performance.
Note on array-valued functions
Authors: Markus Arjen
Published: May 2008

One feature of Fortran that deserves more attention in my opinion is the use of
array-valued functions
. In particular this feature can be used to achieve a high-level programming style, much like what John Backus advocated in his ACM speech (Backus, 1978). Many of the intrinsic functions return arrays and Fortran's array operations are further examples, be it implicit.
Absoft tools Fortran integrated development environment
Authors: Goelz Tony
Published: May 2008

Although the roots of the Fortran language go back to the days of punch cards, it is still very much in use today and Integrated Development Environments are becoming increasingly popular with Fortran developers. An Integrated Development Environment (IDE) is a software tool that is used during all phases of program development. By combining the separate tasks of source code editing, compiling, linking, and debugging in a single unified interface, an IDE minimizes the amount of time spent learning separate tools. This article is an introduction to Absoft's Absoft Tools Integrated Development Environment for Fortran and C©++ programming. It provides an overview of the key features and presents an example of using the IDE to build an open source Fortran subroutine library.
Nutrigenomics and Selenium: Gene Expression Patterns, Physiological Targets, and Genetics
Authors: Hesketh John
Published: May 2008

Dietary selenium intake is regarded as an important factor in determining optimal health and susceptibility to disease. Therefore, it is critical to understand the interaction between selenium intake and molecular events at the genetic and cellular level. This article addresses two facets of this interaction. The first facet is how genomics is contributing to understanding the molecular mechanisms by which selenium affects cell function through selenoproteins and downstream targets of Se supply in other metabolic pathways. The contribution of transgenic animals in this field is emphasized, and the more recent studies using transcriptomics are discussed. The second facet is the extent to which single nucleotide polymorphisms (SNPs) in genes encoding selenoproteins and components of the selenoprotein synthetic machinery affect individual dietary requirements for optimal health. The state of knowledge of known functional SNPs in selenoprotein genes is presented, and a strategy for future studies is discussed.
Pharmacological activation of PPARβ promotes rapid and calcineurin-dependent fiber remodeling and angiogenesis in mouse skeletal muscle
Authors: Gaudel Céline , Schwartz Chantal , Giordano Christian , Abumrad Nada A. , Grimaldi Paul A.
Published: May 2008

Recent studies have shown that administration of peroxisome proliferator-activated receptor-β (PPARβ) agonists enhances fatty acid oxidation in rodent and human skeletal muscle and that muscle-restricted PPARβ overexpression affects muscle metabolic profile by increasing oxidative myofiber number, which raises the possibility that PPARβ agonists alter muscle morphology in adult animals. This possibility was examined in this study in which adult mice were treated with a PPARβ agonist, and the resulting changes in myofiber metabolic phenotype and angiogenesis were quantified in tibialis anterior muscles. The findings indicate a muscle remodeling that is completed within 2 days and is characterized by a 1.63-fold increase in oxidative fiber number and by a 1.55-fold increase in capillary number. These changes were associated with a quick and transient upregulation of myogenic and angiogenic markers. Both myogenic and angiogenic responses were dependent on the calcineurin pathway, as they were blunted by cyclosporine A administration. In conclusion, the data indicate that PPARβ activation is associated with a calcineurin-dependent effect on muscle morphology that enhances the oxidative phenotype.
Maximal Exercise Electrocardiography Responses and Coronary Heart Disease Mortality Among Men With Diabetes Mellitus
Authors: Lyerly G. William , Sui Xuemei , Church Timothy S. , Lavie Carl J. , Hand Gregory A. , Blair Steven N.
Published: May 2008

Background—

An abnormal ECG during maximal exercise testing has been shown to be a powerful predictor of future coronary heart disease (CHD) mortality in asymptomatic men. However, little is known about the relationship between exercise ECG responses and CHD risk in men with diabetes mellitus.

Methods and Results—

We examined the association between exercise ECG responses and mortality in 2854 men with documented diabetes mellitus (mean age 49.5 years) who completed a maximal treadmill exercise test during the period from 1974 to 2001 and who were without a previous cardiovascular disease (CVD) event at baseline. Mortality due to all causes, CHD, and CVD were the main outcome measures across categories of exercise ECG responses, with stratification by cardiorespiratory fitness, quantified as treadmill test duration. During an average follow-up of 16 years, 441 deaths (210 CVD and 133 CHD) were identified. Across normal, equivocal, and abnormal exercise ECG groups, age- and examination year–adjusted CHD mortality rates per 10 000 person-years were 23.0, 48.6, and 69.0, respectively (
P
trend
<0.001). After further adjustment for fasting plasma glucose level, smoking, body mass index, hypercholesterolemia, hypertension, family history of CVD or diabetes mellitus, abnormal resting ECG responses, and cardiorespiratory fitness, hazard ratios (95% confidence intervals) were 1.00 (referent), 1.68 (1.01 to 2.77), and 2.21 (1.41 to 3.46;
P
trend
<0.001). Similar patterns of associations were noted between exercise ECG testing and both CVD and all-cause mortality risk.

Conclusions—

Among men with diabetes mellitus, equivocal and abnormal exercise ECG responses were associated with higher risk of all-cause, CVD, and CHD mortality.
A Novel Method of Expressing Left Ventricular Mass Relative to Body Size in Children
Authors: Foster Bethany J. , Mackie Andrew S. , Mitsnefes Mark , Ali Huma , Mamber Silvia , Colan Steven D.
Published: May 2008

Background—

Left ventricular (LV) hypertrophy (LVH) in children is widely defined as a left ventricular mass index (LVMI, g/m
2.7
) >95th percentile. However, LVMI increases with decreasing height in young children; thus, the 95th percentile LVMI will depend on the height distribution of the reference population. The objective of this study was to compare the performance of a novel method of expressing LV mass relative to body size (centile curves) with the LVMI method.

Methods and Results—

LV mass was estimated by M-mode echocardiography in 440 healthy nonobese reference children (birth to 21 years) and 239 children at risk for LVH; the LVMI was calculated for all children. Three samples of 270 children, each with different height distributions, were drawn from the reference population. A sample-specific 95th percentile LVMI was determined for each reference sample. At-risk children were classified as having LVH or not based on each sample-specific 95th percentile. Four LV mass-for-height centile curves were constructed with the Cole lambda-mu-sigma method and data from each reference sample. At-risk children were each assigned an LV mass-for-height percentile with these curves and were reclassified as having LVH if LV mass-for-height was >95th percentile. The centile method provided a stable estimate of the proportion of at-risk children with LVH regardless of reference group, whereas proportion estimates varied significantly depending on the reference population when the LVMI method was used.

Conclusions—

LV mass-for-height centile curves are superior to LVMI as a method of normalizing LV mass to body size in children.
Cardiomyocyte Expression of a Polyglutamine Preamyloid Oligomer Causes Heart Failure
Authors: Pattison J. Scott , Sanbe Atsushi , Maloyan Alina , Osinska Hanna , Klevitsky Raisa , Robbins Jeffrey
Published: May 2008

Background—

To determine whether soluble preamyloid oligomers (PAOs) are toxic when expressed internally in the cardiomyocyte, we tested the hypothesis that cardiomyocyte-restricted expression and accumulation of a known PAO is cytotoxic and sufficient to cause heart failure.

Methods and Results—

Intracellular PAOs, the entities believed to cause toxicity in many neurodegenerative diseases, have been observed in cardiomyocytes derived from mouse and human heart failure samples. Long (>50) polyglutamine (PQ) repeats form PAOs and cause neurotoxicity in Huntington disease and other neurodegenerative diseases, whereas shorter PQ peptides are benign. We created transgenic mice in which cardiomyocyte-autonomous expression of an 83 residue–long PQ repeat (PQ83) or a non–amyloid-forming peptide of 19 PQ repeats (PQ19) as a nonpathological control was expressed. A PQ83 line with relatively low levels of expression was generated, along with a PQ19 line that expressed ≈9-fold the levels observed in the PQ83 line. Hearts expressing PQ83 exhibited reduced cardiac function and dilation by 5 months, and all mice died by 8 months, whereas PQ19 mice had normal cardiac function, morphology, and life span. PQ83 protein accumulated within aggresomes with PAO-specific staining. The PQ83 hearts showed increased autophagosomal and lysosomal content but also showed markers of necrotic death, including inflammatory cell infiltration and increased sarcolemmal permeability.

Conclusions—

The data confirm the hypothesis that expression of an exogenous PAO-forming peptide is toxic to cardiomyocytes and is sufficient to cause cardiomyocyte loss and heart failure in a murine model.
Inhibition of GSK3β by Postconditioning Is Required to Prevent Opening of the Mitochondrial Permeability Transition Pore During Reperfusion
Authors: Gomez Ludovic , Paillard Mélanie , Thibault Hélène , Derumeaux Geneviève , Ovize Michel
Published: May 2008

Background—

Opening of the mitochondrial permeability transition pore (mPTP) is a crucial event in lethal reperfusion injury. Phosphorylation (inhibition) of glycogen synthase kinase-3β (GSK3β) has been involved in cardioprotection. We investigated whether phosphorylated GSK3β may protect the heart via the inhibition of mPTP opening during postconditioning.

Methods and Results—

Wild-type and transgenic GSK3β-S9A mice (the cardiac GSK3β activity of which cannot be inactivated) underwent 60 minutes of ischemia and 24 hours of reperfusion. At reperfusion, wild-type and GSK3β-S9A mice received no intervention (control), postconditioning (3 cycles of 1 minute ischemia and 1 minute of reperfusion), the mPTP inhibitor cyclosporine A (CsA; 10 mg/kg IV), or the GSK3β inhibitor SB216763 (SB21; 70 μg/kg IV). Infarct size was assessed by triphenyltetrazolium chloride staining. The resistance of the mPTP to opening after Ca
2+
loading was assessed by spectrofluorometry on mitochondria isolated from the area at risk. In wild-type mice, infarct size was significantly reduced by postconditioning, CsA, and SB21, averaging 39±2%, 35±5%, and 37±4%, respectively, versus 58±5% of the area at risk in control mice (
P
<0.05). In GSK3β-S9A mice, only CsA, but not postconditioning or SB21, reduced infarct size. Postconditioning, CsA, and SB21 all improved the resistance of the mPTP in wild-type mice, but only CsA did so in GSK3β-S9A mice.

Conclusion—

These results suggest that S9-phosphorylation of GSK3β is required for postconditioning and likely acts by inhibiting the opening of the mitochondrial permeability transition pore.