bluuebunny/crossref_metadata_2025_split huggingface dataset:
Between Hoax and Hope: Miscegenation and Nineteenth‐Century Interracial Romance
Authors: Ings Katharine Nicholson 
Published: June 2006

AbstractThis essay surveys recent scholarship on interracial romance during the nineteenth century using the hoax Miscegenation pamphlet of 1863 as a lens. An anonymous and ironic piece of writing that promoted race‐mixing from a deceptively Republican perspective, Miscegenation coined the titular term, newly situating interracial relationships within a Latinate, pseudo‐scientific framework. It also encouraged romance between white women and black men, an endorsement that was designed to enrage its white male readership but in fact gave hope to some white women who were unable to articulate their interracial desire publicly. Using this double focus, I explore how nineteenth‐century authors of interracial romance borrowed the language of science, such as “hybridity” and “crossing”; how they employed the concept of “blood‐mixing” as both sexual and medicinal (via transfusions); and I read the Miscegenation pamphlet as a kind of scientific romance fiction itself.
Persistent patterns in accretion discs
Authors: Amin Mustafa A. , Frolov Andrei V. 
Published: June 2006

Abstract
We present a set of new characteristic frequencies associated with accretion discs around compact objects. These frequencies arise from persistent rotating patterns in the disc that are finite in radial extent and driven purely by the gravity of the central body. Their existence depends on general relativistic corrections to orbital motion and, if observed, could be used to probe the strong gravity region around a black hole. We also discuss a possible connection to the puzzle of quasi-periodic oscillations.
The late time evolution of gamma-ray bursts: ending hyperaccretion and producing flares
Authors: Proga Daniel , Zhang Bing 
Published: June 2006

Abstract
We consider the properties of a hyperaccretion model for gamma-ray bursts (GRBs) at late times when the mass supply rate is expected to decrease with time. We point out that the region in the vicinity of the accretor and the accretor itself can play an important role in determining the rate of accretion, and its time behaviour, and ultimately the energy output. Motivated by numerical simulations and theoretical results, we conjecture that the energy release can be repeatedly stopped and then restarted by the magnetic flux accumulated around the accretor. We propose that the episode or episodes when the accretion resumes correspond to X-ray flares discovered recently in a number of GRBs.
Atmospheric Fluidized Bed Combustion (AFBC) Plants: An Operations and Maintenance Study
Authors: Fuller Jack A. , Beavers Harvie , Bessette Robert 
Published: June 2006

AbstractThe authors analyzed data from a fluidized bed boiler survey distributed during the spring of 2003 to develop appropriate AFBC (Atmospheric Fluidized Bed Combustion) performance benchmarks. The survey was sent to members of CIBO (Council of Industrial Boiler Owners), who sponsored the survey, as well as to other firms who had an operating AFBC boiler on-site. There were three primary purposes for the collection and analysis of the data contained in this fluidized bed boiler survey: (1) To develop AFBC benchmarks on technical, cost, revenue, and environmental issues; (2) to inform AFBC owners and operators of contemporary concerns and issues in the industry; (3) to improve decision making in the industry with respect to current and future plant start-ups and ongoing operations.
Functional Characterization of
Aspergillus nidulans
Homologues of
Saccharomyces cerevisiae
Spa2 and Bud6
Authors: Virag Aleksandra , Harris Steven D. 
Published: June 2006

ABSTRACT

The importance of polarized growth for fungi has elicited significant effort directed at better understanding underlying mechanisms of polarization, with a focus on yeast systems. At sites of tip growth, multiple protein complexes assemble and coordinate to ensure that incoming building material reaches the appropriate destination sites, and polarized growth is maintained. One of these complexes is the polarisome that consists of Spa2, Bud6, Pea2, and Bni1 in
Saccharomyces cerevisiae
. Filamentous hyphae differ in their development and life style from yeasts and likely regulate polarized growth in a different way. This is expected to reflect on the composition and presence of protein complexes that assemble at the hyphal tip. In this study we searched for polarisome homologues in the model filamentous fungus
Aspergillus nidulans
and characterized the
S. cerevisiae
Spa2 and Bud6 homologues, SpaA and BudA. Compared to the
S. cerevisiae
Spa2, SpaA lacks domain II but has three additional domains that are conserved within filamentous fungi. Gene replacement strains and localization studies show that SpaA functions exclusively at the hyphal tip, while BudA functions at sites of septum formation and possibly at hyphal tips. We show that SpaA is not required for the assembly or maintenance of the Spitzenkörper. We propose that the core function of the polarisome in polarized growth is maintained but with different contributions of polarisome components to the process.
Disruption of a Nonribosomal Peptide Synthetase in
Aspergillus fumigatus
Eliminates Gliotoxin Production
Authors: Cramer Robert A. , Gamcsik Michael P. , Brooking Rhea M. , Najvar Laura K. , Kirkpatrick William R. , Patterson Thomas F. , Balibar Carl J. , Graybill John R. , Perfect John R. , Abraham Soman N. , Steinbach William J. 
Published: June 2006

ABSTRACT

The fungal secondary metabolite gliotoxin produced by
Aspergillus fumigatus
has been hypothesized to be important in the development of invasive aspergillosis. In this study, we addressed this hypothesis by disrupting a nonribosomal peptide synthetase (NRPS) (encoded by
gliP
) predicted to be involved in gliotoxin production. Mutants with a disrupted
gliP
locus failed to produce gliotoxin, which confirmed the role of the NRPS encoded by
gliP
in gliotoxin biosynthesis. We found no morphological, developmental, or physiological defects in Δ
gliP
mutant strains. In addition, disruption of
gliP
resulted in down regulation of gene expression in the gliotoxin biosynthesis gene cluster, which was restored with addition of exogenous gliotoxin. This interesting result suggests a role for gliotoxin in regulating its own production. Culture filtrates from the Δ
gliP
mutant were unable to inhibit ionomycin-dependent degranulation of mast cells, suggesting a role for gliotoxin in suppressing mast cell degranulation and possibly in disease development. However, the Δ
gliP
mutant did not have an impact on survival or tissue burden in a murine inhalational model of invasive aspergillosis. This result suggests that gliotoxin is not required for virulence in an immunosuppressed host with an invasive pulmonary infection.
Identification of the Major Spliceosomal RNAs in
Dictyostelium discoideum
Reveals Developmentally Regulated U2 Variants and Polyadenylated snRNAs
Authors: Hinas Andrea , Larsson Pontus , Avesson Lotta , Kirsebom Leif A. , Virtanen Anders , Söderbom Fredrik 
Published: June 2006

ABSTRACT

Most eukaryotic mRNAs depend upon precise removal of introns by the spliceosome, a complex of RNAs and proteins. Splicing of pre-mRNA is known to take place in
Dictyostelium discoideum
, and we previously isolated the U2 spliceosomal RNA experimentally. In this study, we identified the remaining major spliceosomal RNAs in
Dictyostelium
by a bioinformatical approach. Expression was verified from 17 small nuclear RNA (snRNA) genes. All these genes are preceded by a putative noncoding RNA gene promoter. Immunoprecipitation showed that snRNAs U1, U2, U4, and U5, but not U6, carry the conserved trimethylated 5′ cap structure. A number of divergent U2 species are expressed in
Dictyostelium
. These RNAs carry the U2 RNA hallmark sequence and structure motifs but have an additional predicted stem-loop structure at the 5′ end. Surprisingly, and in contrast to the other spliceosomal RNAs in this study, the new U2 variants were enriched in the cytoplasm and were developmentally regulated. Furthermore, all of the snRNAs could also be detected as polyadenylated species, and polyadenylated U1 RNA was demonstrated to be located in the cytoplasm.
Genetic diversity and distribution ofSarracenia purpurea(Sarraceniaceae) in the western Lake Superior basin
Authors: Karberg Jennifer M. , Gale Margaret R. 
Published: June 2006

Restoring plant populations requires an understanding of plant morphological adaptation to site locations and population genetic diversity and relatedness. This study examined the genetic and morphological diversity of Sarracenia purpurea L. within the natural fragmentation of western Lake Superior. Populations of S. purpurea were compared among three locations: Isle Royale National Park, the Keweenaw Peninsula, Michigan, USA, and Sleeping Giant Provincial Park, Ontario, Canada. Analysis of genetic and demographic data showed Canadian populations to be less robust with smaller plant sizes. Canadian populations were also slightly distinct genetically. Overall genetic diversity appears moderate (H = 0.30–0.36) and populations genetically similar. Analysis of molecular variance showed only 3.83% of variation among the three locations (p = 0.0049). Fragmentation did not have a distinguishable effect on genetic diversity and morphological characters but the limestone bedrock geology of the Canadian region may be starting to influence plant morphology and genetic differentiation. This indicates that restoration can take place within the western basin of Lake Superior using a variety of seed sources but regional geology may influence observed plant morphology.
Cryptic characteristics distinguish diploid and triploid varieties of Pteris fauriei (Pteridaceae)
Authors: Huang Yao-Moan , Chou Hsueh-Mei , Hsieh Tsung-Hsin , Wang Jenn-Che , Chiou Wen-Liang 
Published: June 2006

There are two varieties of Pteris fauriei Hieron. in Taiwan: P. fauriei var. fauriei and P. fauriei var. minor Hieron. Their mature sporophytes are virtually indistinguishable based on gross morphology. To better understand these two varieties and the differences between them, and to determine whether they are based on different ploidies, we examined and compared the sporophytes and gametophytes of both varieties in detail. Each variety exhibited distinct, constant cryptic characteristics and cytotype. Based on the diameter of spores from type specimens, we confirmed that P. fauriei var. minor is diploid and that P. fauriei var. fauriei is triploid. Diploid sporophytes produced 64-spore sporangia. Their haploid gametophytes produced archegonia and antheridia containing 64 sperm each. Gametophytes cultured for 10 weeks formed sexual sporophytes, the first fronds of which lacked midribs. Triploid sporophytes produced 32-spore sporangia. Triploid spores were significantly larger in diameter than haploid spores. Triploid gametophytes did not produce archegonia but did produce 32-sperm antheridia, which were significantly larger in diameter than antheridia produced by haploid gametophytes. The life span of triploid gametophytes was 4 weeks shorter than that of haploid gametophytes. After 6 weeks in culture, apomictic triploid sporophytes arose directly from gametophyte cells. Each of their first fronds had three pinnae and a midrib. These data are useful for delimiting P. fauriei var. fauriei and P. fauriei var. minor.
Molecular evidence for the systematic positions of two enigmatic mosses: Pterogonidium pulchellum (Sematophyllaceae, Musci) and Piloecium pseudorufescens (Myuriaceae, Musci)
Authors: Chang Ying , Khiong Chan Woon , Graham Sean W. , Tan Benito C. 
Published: June 2006

The systematic position of Pterogonidium pulchellum (W.J. Hooker) Muell. Hal. in the Sematophyllaceae and Piloecium pseudorufescens (Hampe) Muell. Hal. in the Myuriaceae is reexamined with new evidence derived from rbcL gene sequences. A total of 18 taxa from Sematophyllaceae, Hypnaceae, Myuriaceae, and Hookeriaceae were included, 11 of which were newly sequenced for the rbcL gene. Analyses were done using maximum parsimony, maximum likelihood (TrN + Γ + I model and GTR + Γ + I model), and Bayesian inference (GTR + Γ + I model). The results show that Pterogonidium pulchellum has a closer relationship with members of Hypnaceae than with Sematophyllaceae, while Piloecium pseudorufescens forms a clade with the Sematophyllaceae in all phylogenetic analyses, with robust branch support. Two SOWH tests were carried out and the results show that it is not appropriate to classify Pterogonidium pulchellum in Sematophyllaceae and it is also not appropriate to classify Piloecium pseudorufescens in Myuriaceae.
Stand age influence on litter mass ofPinus nigraplantations on dolomite hills in Hungary
Authors: Cseresnyés Imre , Csontos Péter , Bózsing Erika 
Published: June 2006

In Hungary, plantations of Pinus nigra Arn. (Austrian pine) involve large areas of dolomite rock grasslands and have caused the impoverishment or local extinction of the original flora. In addition to these conservation concerns, an important economic problem is the flammability of these forests. Fire risk depends on the amount of accumulated flammable organic components. Thus, the purpose of our research was to quantify the mass of litter accumulated in Austrian pine stands and to examine the correlation between litter mass, stand age, and slope aspect. Forty-eight sampling sites were selected with stand ages ranging from 21 to 108 years. Stands represented four age classes and three exposure types. At each sampling site, litter mass was determined in the following three fractions: needles, branches, and cones. The litter fractions showed their maximum quantities in age class 61–80 years (needles = 17 560 kg/ha, branches = 2764 kg/ha, and cones = 2960 kg/ha). For the needle litter, a significant increase with age was detected through the age classes of 21–40, 41–60, and 61–80 years, and then a significant decrease occurred in stands above 80 years. In the case of branch litter, the age-dependent increase was again significant to its maximum quantity, but the decrease in old stands proved to be insignificant. With cone litter, age dependence could not be detected. Exposure of the stands had no effect on the quantities of the three litter fractions. The amount of accumulated litter of Austrian pine stands many times exceed the litter quantity of the rock grasslands (the original vegetation prior to afforestation). Furthermore, it is two or three times higher than the amount of litter reported from native zonal forests of Hungary. Therefore, the Austrian pine stands are subjected to an increased risk of fire, especially in age class 61–80 years.
Impacts of Lythrum salicaria invasion on plant community and soil properties in two wetlands in central New York, USA
Authors: Mahaney Wendy M. , Smemo Kurt A. , Yavitt Joseph B. 
Published: June 2006

While the spread of the exotic Lythrum salicaria L. across wetlands in North America is thought to negatively affect the performance and diversity of native species, the actual impacts of L. salicaria invasion on community dynamics and ecosystem properties are not well understood. To determine whether L. salicaria affects community aboveground biomass, native species biomass, or soil properties, we studied two common situations in central New York State where L. salicaria invaded (i) an abandoned agricultural field and (ii) a relatively pristine wetland with low species diversity. In the agricultural site, nearly monospecific stands of L. salicaria and Phalaris arundinacea L. had nearly identical shoot mass (approx. 850 g·m–2) but divergent soil characteristics. Inorganic nitrogen was significantly higher under L. salicaria than under P. arundinacea. The low-diversity site is dominated by Carex lacustris Willd., with distinct areas codominated by either L. salicaria or Typha latifolia L. In this site, we found that areas with a codominant species had significantly more total aboveground biomass than those dominated by C. lacustris, suggesting that L. salicaria invasion does not significantly lower native species biomass. However, most soil nutrient levels did not differ among vegetation zones, indicating that species composition changes did not alter soil properties in the short term. This study supports a growing literature suggesting that L. salicaria invasion may not negatively impact relatively pristine wetlands as previously believed.
Size-dependent reproductive effort in Amaranthus retroflexus: the influence of planting density and sowing date
Authors: Wang Tianhui , Zhou Daowei , Wang Ping , Zhang Hongxiang 
Published: June 2006

Size-dependent reproductive effort is an important component of plant fitness. The responses of reproductive effort to environmental factors in Amaranthus retroflexus L. were measured in two experiments. A wide range of selection pressures were generated by manipulating the sowing date (29 April, 23 May, 18 June, and 14 July) and planting density (13.4, 36, 121, and 441 plants·m–2). Allometric analysis between reproductive biomass and vegetative biomass across treatments showed that reproductive effort increased with size in response to different planting densities but decreased with size in sowing dates experiment. The allometric exponent between treatments was not influenced by planting densities but had significant variation with sowing date. Total branch length could explain most of the variation of reproductive accumulation and allocation in planting density experiments. For the plants with different sowing dates, total branch length was the main determinant of reproductive biomass, while reproductive effort mainly depended on the number of primary branches per unit stem mass. Architectural constraints with size result in size-dependent reproduction. Size-dependent reproduction in A. retroflexus was influenced by available resources and environmental conditions through the mechanisms of self-regulation of architectural traits.
Competition ofScleroconidioma sphagnicolawith fungi decomposing spruce litter needles
Authors: Koukol O. , Mrnka L. , Kulhánková A. , Vosátka M. 
Published: June 2006

This study addressed competition of Scleroconidioma sphagnicola Tsuneda, Currah & Thormann with saprotrophic ascomycetes and basidiomycetes. We isolated this fungus, previously considered as a preferentially necrotrophic parasite of moss, from spruce needle litter. Competition of Scleroconidioma sphagnicola was simulated with strains of the autochthonous litter colonizers Ceuthospora pinastri (Fr.) Höhn., Chalara longipes (Preus) Cooke, Setulipes androsaceus (L.) Antonín ( Marasmius androsaceus (L.) Fr.), and Mollisia minutella (Sacc.) Rehm and the wood-decaying fungus Hypholoma fasciculare (Huds.) Quél. Pairings were performed on agar plates with two types of low-nutrient medium made from spruce litter needles. Reisolation on nutritionally rich agar medium following the competition revealed that Sleroconidioma sphagnicola was mostly successfully reisolated even though apparently being replaced by the mycelium of other fungi. It formed strongly melanised mycelium and microsclerotia that seem to be responsible for its resistance to fungal competition. All tested strains of needle litter colonizers were outcompeted by Hypholoma fasciculare. Enzymatic screening aimed at semiquantitative assay of polyphenol oxidase, peroxidase, and tyrosinace revealed that Scleroconidioma sphagnicola, together with other strains, was able to produce polyphenol oxidase and peroxidase on various nutritional media. Activity of tyrosinase was detected only for Hypholoma fasciculare. Previous records of Scleroconidioma sphagnicola from moss, wood, and our isolations from spruce litter suggest that this species possesses an ability to occupy a wide spectrum of niches.
UNAMBIGUOUS MORPHIC IMAGES OF STRINGS
Authors: FREYDENBERGER DOMINIK D. , REIDENBACH DANIEL , SCHNEIDER JOHANNES C. 
Published: June 2006

We study a fundamental combinatorial problem on morphisms in free semigroups: With regard to any string α over some alphabet we ask for the existence of a morphism σ such that σ(α) is unambiguous, i.e. there is no morphism τ with τ(i) ≠ σ(i) for some symbol i in α and, nevertheless, τ(α) = σ(α). As a consequence of its elementary nature, this question shows a variety of connections to those topics in discrete mathematics which are based on finite strings and morphisms such as pattern languages, equality sets and, thus, the Post Correspondence Problem. Our studies demonstrate that the existence of unambiguous morphic images essentially depends on the structure of α: We introduce a partition of the set of all finite strings into those that are decomposable (referred to as prolix) in a particular manner and those that are indecomposable (called succinct). This partition, that is also known to be of major importance for the research on pattern languages and on finite fixed points of morphisms, allows to formulate our main result according to which a string α can be mapped by an injective morphism onto an unambiguous image if and only if α is succinct.
Gene Designer: a synthetic biology tool for constructing artificial DNA segments
Authors: Villalobos Alan , Ness Jon E , Gustafsson Claes , Minshull Jeremy , Govindarajan Sridhar 
Published: June 2006

Abstract

Background
Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi resistant genes and protein engineering. Here we introduce a software tool that drastically facilitates the design of synthetic genes.

Results
Gene Designer is a stand-alone software for fast and easy design of synthetic DNA segments. Users can easily add, edit and combine genetic elements such as promoters, open reading frames and tags through an intuitive drag-and-drop graphic interface and a hierarchical DNA/Protein object map. Using advanced optimization algorithms, open reading frames within the DNA construct can readily be codon optimized for protein expression in any host organism. Gene Designer also includes features such as a real-time sliding calculator of oligonucleotide annealing temperatures, sequencing primer generator, tools for avoidance or inclusion of restriction sites, and options to maximize or minimize sequence identity to a reference.

Conclusion
Gene Designer is an expandable Synthetic Biology workbench suitable for molecular biologists interested in the de novo creation of genetic constructs.
An analysis of intra array repeats: the good, the bad and the non informative
Authors: Elbez Yedid , Farkash-Amar Shlomit , Simon Itamar 
Published: June 2006

AbstractBackgroundOn most common microarray platforms many genes are represented by multiple probes. Although this is quite common no one has systematically explored the concordance between probes mapped to the same gene.ResultsHere we present an analysis of all the cases of multiple probe sets measuring the same gene on the Affymetrix U133a GeneChip and found that although in the majority of cases both measurements tend to agree there are a significant number of cases in which the two measurements differ from each other. In these cases the measurements can not be simply averaged but rather should be handled individually.ConclusionOur analysis allows us to provide a comprehensive list of the correlation between all pairs of probe sets that are mapped to the same gene and thus allows microarray users to sort out the cases that deserve further analysis. Comparison between the set of highly correlated pairs and the set of pairs that tend to differ from each other reveals potential factors that may affect it.