bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real‐Time Investigation of Referential Domains in Unscripted Conversation: A Targeted Language Game Approach
Authors: Brown‐Schmidt Sarah , Tanenhaus Michael K. 
Published: June 2008

AbstractTwo experiments examined the restriction of referential domains during unscripted conversation by analyzing the modification and online interpretation of referring expressions. Experiment 1 demonstrated that from the earliest moments of processing, addressees interpreted referring expressions with respect to referential domains constrained by the conversation. Analysis of eye movements during the conversation showed elimination of standard competition effects seen with scripted language. Results from Experiment 2 pinpointed two pragmatic factors responsible for restriction of the referential domains used by speakers to design referential expressions and demonstrated that the same factors predict whether addressees consider local competitors to be potential referents during online interpretation of the same expressions. These experiments demonstrate, for the first time, that online interpretation of referring expressions in conversation is facilitated by referential domains constrained by pragmatic factors that predict when addressees are likely to encounter temporary ambiguity in language processing.
Understanding Mortality and the Life of the Ancestors in Rural Madagascar
Authors: Astuti Rita , Harris Paul L. 
Published: June 2008

AbstractAcross two studies, a wide age range of participants was interviewed about the nature of death. All participants were living in rural Madagascar in a community where ancestral beliefs and practices are widespread. In Study 1, children (8–17 years) and adults (19–71 years) were asked whether bodily and mental processes continue after death. The death in question was presented in the context of a narrative that focused either on the corpse or on the ancestral practices associated with the afterlife. Participants aged 8 years and older claimed that death brings an end to most bodily and mental processes. Nevertheless, particularly in the context of the religious narrative, they claimed that certain mental processes continue even after death. This assertion of an afterlife was more evident among adults than children, especially with respect to cognitive processes, such as knowing and remembering. In Study 2, 5‐ and 7‐year‐olds were asked similar questions in connection with the death of a bird and a person. Seven‐year‐olds consistently claimed that bodily and mental processes cease at death, whereas 5‐year‐olds were unsystematic in their replies. Together, the two studies replicate and extend findings obtained with Western children showing that, in the course of development, different conceptions of death are elaborated—a biological conception in which death terminates living processes and a religious conception in which death marks the beginning of a new form of spiritual existence.
Large‐Scale Modeling of Wordform Learning and Representation
Authors: Sibley Daragh E. , Kello Christopher T. , Plaut David C. , Elman Jeffrey L. 
Published: June 2008

AbstractThe forms of words as they appear in text and speech are central to theories and models of lexical processing. Nonetheless, current methods for simulating their learning and representation fail to approach the scale and heterogeneity of real wordform lexicons. A connectionist architecture termed the sequence encoder is used to learn nearly 75,000 wordform representations through exposure to strings of stress‐marked phonemes or letters. First, the mechanisms and efficacy of the sequence encoder are demonstrated and shown to overcome problems with traditional slot‐based codes. Then, two large‐scale simulations are reported that learned to represent lexicons of either phonological or orthographic wordforms. In doing so, the models learned the statistics of their lexicons as shown by better processing of well‐formed pseudowords as opposed to ill‐formed (scrambled) pseudowords, and by accounting for variance in well‐formedness ratings. It is discussed how the sequence encoder may be integrated into broader models of lexical processing.
Bigrams and the Richness of the Stimulus
Authors: Kam Xuân‐Nga Cao , Stoyneshka Iglika , Tornyova Lidiya , Fodor Janet D. , Sakas William G. 
Published: June 2008

AbstractRecent challenges to Chomsky's poverty of the stimulus thesis for language acquisition suggest that children's primary data may carry “indirect evidence” about linguistic constructions despite containing no instances of them. Indirect evidence is claimed to suffice for grammar acquisition, without need for innate knowledge. This article reports experiments based on those of , who demonstrated that a simple bigram language model can induce the correct form of auxiliary inversion in certain complex questions. This article investigates the nature of the indirect evidence that supports this learning, and assesses how reliably it is available. Results confirm the original finding for one specific sentence type but show that the model's success is highly circumscribed. It performs poorly on inversion in related constructions in English and Dutch. Because other, more powerful statistical models have so far been shown to succeed only on the same limited subset of cases as the bigram model, it remains to be seen whether stimulus richness can be substantiated more generally.
Gelatinization and Retrogradation Kinetics of High‐Fiber Wheat Flour Blends: A Calorimetric Approach
Authors: Santos E. , Rosell C. M. , Collar C. 
Published: June 2008

ABSTRACTThe impact of dietary fiber (DF) mixtures on dough thermal properties needs to be investigated when designing high‐fiber wheat bread. Effects of flour replacement at different levels (6–34%) by soluble (inuline [FN]), partially soluble (sugar beet [FX], pea cell wall [SW]), and insoluble (pea hull [EX]) DF on wheat dough thermal profiles have been investigated by simulating baking, cooling, and storage in differential scanning calorimetry (DSC) pans. In general, DF incorporation into water‐flour systems delayed endothermic transition temperatures for both gelatinization and retrogradation phenomena except for the peak temperature (Tp) of retrogradation. With some exception, the pattern of the enthalpy of amylopectin retrogradation was lower and slower (lower constant of proportion, k) over 10 days of storage in gelatinized hydrated flour‐fiber blends when compared with control without DF. FX, a partially soluble fiber, provided major effects on gelatinization (Tp decrease and ΔH increase) and retrogradation kinetics (the Avrami exponent, n, increase). Single presence of EX allowed a significant reduction in the Avrami exponent n leading to slower kinetics for amylopectin retrogradation when included in the blends.
Effect of Moisture Content and Soluble Level on the Physical, Chemical, and Flow Properties of Distillers Dried Grains with Solubles (DDGS)
Authors: Ganesan V. , Muthukumarappan K. , Rosentrater K. A. 
Published: June 2008

ABSTRACTDistillers dried grains with solubles (DDGS) is a bulk material that has been widely used as a protein source for ruminants and nonruminants for more than two decades. DDGS is the nonfermentable processing residue (i.e., protein, fiber, fat, and ash) from fuel ethanol manufacturing. With the exponential growth of the fuel ethanol industry in the past several years, significant quantities (≈13.0 million tons in 2007) of distillers grains are now being produced. To effectively utilize these coproduct streams in the domestic market, DDGS must be transported greater distances and must be stored until final use. DDGS flow is often problematic as it can become restricted by caking and bridging that occur during shipping and storage. This flowability problem can present itself during dynamic and static flow conditions. This issue most likely results from physical or chemical interactions between particles (including particle size and shape), storage moisture, temperature, and relative humidity variations, as well as storage time. The objective of this study was to examine the effect of five moisture content levels (10, 15, 20, 25, and 30% db) on the resulting physical and chemical properties of DDGS with four soluble levels (10, 15, 20, and 25% db). To produce these materials, condensed distillers solubles (CDS) were combined with DDG, and appropriate quantities of water were added to adjust moisture contents. Carr indices were used to quantify the flowability of the DDGS samples. The results showed that both soluble level and moisture content had noticeable effects on physical and flow properties (e.g., aerated bulk density, packed bulk density, and compressibility). According to dispersibility, flowability index, and floodability index, flowability generally declined significantly (P < 0.05) with an increase in moisture content for most of the soluble levels under consideration. The color values and protein content of the DDGS were significantly affected (P < 0.05) as soluble level increased as well.
Effects of Growing Location and Irrigation on Attributes and Ethanol Yields of Selected Grain Sorghums
Authors: Wu X. , Zhao R. , Liu L. , Bean S. , Seib P. A. , McLaren J. , Madl R. , Tuinstra M. , Lenz M. , Wang D. 
Published: June 2008

ABSTRACTNine sorghum cultivars (five inbred lines and four hybrids) were grown in 2006 in three locations (Mount Hope, KS, Halstead, KS, and Plainview, TX) under different irrigation conditions and were evaluated for composition and ethanol fermentation efficiency. The objective was to study, in one growing season, the effects of genotype, growing location, and irrigation on the physical and chemical properties and fermentation efficiencies of grain sorghum. Genotype had a significant effect on chemical composition, physical properties, and ethanol yield. The cultivars showed a large variation in starch (61.0–74.8%), protein (7.56–16.35%), crude fat (2.79–4.77%), crude fiber (0.58–2.57%), ash (1.25–2.26%), kernel weight (20.0–35.9 mg), kernel hardness (49.6–97.5), and kernel size (1.9–2.7 mm) and were the most important factors affecting ethanol fermentation efficiency (87.5–93.9%). Starch and protein contents were significantly affected by growing location but not by irrigation. Environment had a significant effect on ethanol yields. Unexpectedly, irrigation somewhat reduced fermentation efficiency.
Pharmacogenomic studies of the anticancer and immunosuppressive thiopurines mercaptopurine and azathioprine
Authors: Hawwa Ahmed F. , Millership Jeff S. , Collier Paul S. , Vandenbroeck Koen , McCarthy Anthony , Dempsey Sid , Cairns Carole , Collins John , Rodgers Colin , McElnay James C. 
Published: June 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• 6‐Mercaptopurine (6‐MP) and azathioprine (AZA) are both inactive prodrugs that require intracellular activation into the active 6‐thioguanine nucleotides (6‐TGNs).• This metabolic process undergoes three different competitive pathways that are catalysed by three different enzymes; xanthine oxidase (XO), thiopurine methyltransferase (TPMT) and inosine triphosphatase (ITPA), all of which exhibit genetic polymorphisms.• Although the impact of genetic variation in theTPMTgene on treatment outcome and toxicity has been demonstrated, the role of other polymorphisms remains less well known.WHAT THIS STUDY ADDS• New information on the allelic variation of these three enzymes (XO, TPMT and ITPA) and their influence on 6‐MP/AZA metabolism and toxicity.• Confirmation of the association ofTPMTpolymorphism with haematological toxicity.• Identified potential genetic characteristics that may contribute to higher risk of adverse events (such asITPA IVS2+21A→Cmutation).AIMSTo examine the allelic variation of three enzymes involved in 6‐mercaptopurine/azathioprine (6‐MP/AZA) metabolism and evaluate the influence of these polymorphisms on toxicity, haematological parameters and metabolite levels in patients with acute lymphoblastic leukaemia (ALL) or inflammatory bowel disease (IBD).METHODSClinical data and blood samples were collected from 19 ALL paediatric patients and 35 IBD patients who were receiving 6‐MP/AZA therapy. All patients were screened for seven genetic polymorphisms in three enzymes involved in mercaptopurine metabolism [xanthine oxidase,inosine triphosphatase(C94→AandIVS2+21A→C) andthiopurine methyltransferase]. Erythrocyte and plasma metabolite concentrations were also determined. The associations between the various genotypes and myelotoxicity, haematological parameters and metabolite concentrations were determined.RESULTSThiopurine methyltransferasevariant alleles were associated with a preferential metabolism away from 6‐methylmercaptopurine nucleotides (P = 0.008 in ALL patients,P = 0.038 in IBD patients) favouring 6‐thioguanine nucleotides (6‐TGNs) (P = 0.021 in ALL patients). Interestingly, carriers ofinosine triphosphatase IVS2+21A→Cvariants among ALL and IBD patients had significantly higher concentrations of the active cytotoxic metabolites, 6‐TGNs (P = 0.008 in ALL patients,P = 0.047 in IBD patients). The study confirmed the association ofthiopurine methyltransferaseheterozygosity with leucopenia and neutropenia in ALL patients and reported a significant association betweeninosine triphosphatase IVS2+21A→Cvariants with thrombocytopenia (P = 0.012).CONCLUSIONSPharmacogenetic polymorphisms in the 6‐MP pathway may help identify patients at risk for associated toxicities and may serve as a guide for dose individualization.
Betalains: properties, sources, applications, and stability – a review
Authors: Azeredo Henriette M.C. 
Published: June 2008

SummaryConsumers are increasingly avoiding foods containing synthetic colourants, which lead food industries to replace them by natural pigments, such as carotenoids, betalains, anthocyanins and carminic acid. Betalains are water‐soluble nitrogen‐containing pigments, composed of two structural groups: the red‐violet betacyanins and the yellow‐orange betaxanthins. This review synthesises the published literature on basic chemistry of betalains, their sources and chemical stability. Moreover, several works are mentioned which have demonstrated the potent antioxidant activity of betalains, which has been associated with protection against degenerative diseases.
Antioxidative activity of rosemary extract using connective tissue proteins as carriers
Authors: Waszkowiak Katarzyna 
Published: June 2008

SummaryIn the research the activity of rosemary extract introduced using connective tissue proteins was investigated, taking into consideration the effect of the type of carrier (collagen and elastin), carrier concentration (1%, 2%, 4%) and the method of its introduction to fat substrate (rehydrated or unhydrated). Antioxidative activity was assessed using the Oxidograph instrumental test. The activity of rosemary extract on protein preparations was significantly affected by the rehydration of these preparations. The application of collagen as carrier of rosemary extract had an advantageous effect on the activity of this antioxidant. In turn, under the adopted testing conditions the application of elastin resulted in partial masking of antioxidative activity of rosemary extract. Amounts of the carriers, onto which the antioxidant was introduced, did not have a statistically significant effect on this activity.
Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini
Authors: BARRETT LUKE G. , THRALL PETER H. , BURDON JEREMY J. , NICOTRA ADRIENNE B. , LINDE CELESTE C. 
Published: June 2008

AbstractMany pathogens undergo both sexual and asexual reproduction to varying degrees, yet the ecological, genetic and evolutionary consequences of different reproductive strategies remain poorly understood. Here we investigate the population genetic structure of wild populations of the plant pathogen Melampsora lini on its host Linum marginale, using amplified fragment length polymorphism (AFLP) markers, two genes underlying pathogen virulence, and phenotypic variation in virulence. In Australia, M. lini occurs as two genetically and geographically divergent lineages (AA and AB), one of which is completely asexual (AB), and the other able to reproduce both clonally and sexually (AA). To quantify the genetic and evolutionary consequences of these different life histories, we sampled five populations in each of two biogeographical regions. Analysis of AFLP data obtained for 275 isolates revealed largely disjunct geographical distributions for the two different lineages, low genetic diversity within lineages, and strong genetic structure among populations within each region. We also detected significant divergence among populations for both Avr genes and virulence phenotypes, although generally these values were lower than those obtained with AFLP markers. Furthermore, isolates belonging to lineage AA collectively harboured significantly higher genotypic and phenotypic diversity than lineage AB isolates. Together these results illustrate the important roles of reproductive modes and geographical structure in the generation and maintenance of virulence diversity in populations of M. lini.
Phylogeography of the Rhabditis (Pellioditis) marina species complex: evidence for long‐distance dispersal, and for range expansions and restricted gene flow in the northeast Atlantic
Authors: DERYCKE S. , REMERIE T. , BACKELJAU T. , VIERSTRAETE A. , VANFLETEREN J. , VINCX M. , MOENS T. 
Published: June 2008

AbstractPinpointing processes that structure the geographical distribution of genetic diversity of marine species and lead to speciation is challenging because of the lack of obvious dispersal barriers and the likelihood of substantial (passive) dispersal in oceans. In addition, cryptic radiations with sympatric distributions abound in marine species, challenging the allopatric speciation mechanism. Here, we present a phylogeographical study of the marine nematode species complex Rhabditis (Pellioditis) marina to investigate processes shaping genetic structure and speciation. Rhabditis (P.) marina lives on decaying macroalgae in the intertidal, and may therefore disperse over considerable distances. Rhabditis (P.) marina consists of several cryptic species sympatrically distributed at a local scale. Genetic variation in the COI gene was screened in 1362 specimens from 45 locations around the world. Two nuclear DNA genes (ITS and D2D3) were sequenced to infer phylogenetic species. We found evidence for ten sympatrically distributed cryptic species, seven of which show a strong genetic structuring. A historical signature showed evidence for restricted gene flow with occasional long‐distance dispersal and range expansions pre‐dating the last glacial maximum. Our data also point to a genetic break around the British Isles and a contact zone in the Southern Bight of the North Sea. We provide evidence for the transoceanic distribution of at least one cryptic species (PmIII) and discuss the dispersal capacity of marine nematodes. The allopatric distribution of some intraspecific phylogroups and of closely related cryptic species points to the potential for allopatric speciation in R. (P.) marina.
Helicobacter pylori AddAB helicase‐nuclease and RecA promote recombination‐related DNA repair and survival during stomach colonization
Authors: Amundsen Susan K. , Fero Jutta , Hansen Lori M. , Cromie Gareth A. , Solnick Jay V. , Smith Gerald R. , Salama Nina R. 
Published: June 2008

Summary Helicobacter pylori colonization of the human stomach is characterized by profound disease‐causing inflammation. Bacterial proteins that detoxify reactive oxygen species or recognize damaged DNA adducts promote infection, suggesting that H. pylori requires DNA damage repair for successful in vivo colonization. The molecular mechanisms of repair remain unknown. We identified homologues of the AddAB class of helicase‐nuclease enzymes, related to the Escherichia coli RecBCD enzyme, which, with RecA, is required for repair of DNA breaks and homologous recombination. H. pylori mutants lacking addA or addB genes lack detectable ATP‐dependent nuclease activity, and the cloned H. pylori addAB genes restore both nuclease and helicase activities to an E. coli recBCD deletion mutant. H. pylori addAB and recA mutants have a reduced capacity for stomach colonization. These mutants are sensitive to DNA damaging agents and have reduced frequencies of apparent gene conversion between homologous genes encoding outer membrane proteins. Our results reveal requirements for double‐strand break repair and recombination during both acute and chronic phases of H. pylori stomach infection.
A Porphyromonas gingivalis tyrosine phosphatase is a multifunctional regulator of virulence attributes
Authors: Maeda Kazuhiko , Tribble Gena D. , Tucker Chelsea M. , Anaya Cecilia , Shizukuishi Satoshi , Lewis Janina P. , Demuth Donald R. , Lamont Richard J. 
Published: June 2008

SummaryLow Molecular Weight Tyrosine Phosphatases (LMWTP) are widespread in prokaryotes; however, understanding of the signalling cascades controlled by these enzymes is still emerging. Porphyromonas gingivalis, an opportunistic oral pathogen, expresses a LMWTP, Ltp1, that is differentially regulated in biofilm communities. Here we characterize the enzymatic activity of Ltp1 and, through the use of mutants that lack Ltp1 or expresses catalytically defective Ltp1, show that tyrosine phosphatase activity constrains both monospecies biofilm development and community development with the antecedent oral biofilm constituent Streptococcus gordonii. Exopolysaccharide production is downregulated by Ltp1 through transcriptional regulation of multiple genes involved in biosynthesis and transport. Furthermore, Ltp1 regulates transcriptional activity of luxS and thus impacts AI‐2‐dependent signalling in biofilm communities. In the absence of Ltp1 transcription across the hmu haemin uptake locus is reduced, and consequently uptake of haemin is impaired in the Ltp1 mutant. The gingipain proteinases Kgp and RgpA/B remain phosphorylated in the Ltp1 mutant. Phosphorylated Rgps are poorly secreted, whereas cell surface activity of phosphorylated Kgp is enhanced. By controlling the activity of several virulence‐associated properties, Ltp1 may restrain the pathogenic potential of P. gingivalis and maintain a commensal interaction with the host.
Activation mechanism, functional role and shedding of glycosylphosphatidylinositol‐anchored Yps1p at the Saccharomyces cerevisiae cell surface
Authors: Gagnon‐Arsenault Isabelle , Parisé Luc , Tremblay Jessy , Bourbonnais Yves 
Published: June 2008

SummaryYeast cell wall assembly is a highly regulated and dynamic process. A class of cell surface aspartic peptidases anchored by a glycosylphosphatidylinositol (GPI) group, collectively known as yapsins, was proposed to be involved in cell wall construction. The Saccharomyces cerevisiae Yps1p, the prototypal yapsin, is processed internally within a loop region to produce an α/β two‐subunit enzyme. Here we investigated the activation mechanism of GPI‐anchored Yps1p and identified some of its substrates. We report that all activation steps of GPI‐Yps1p take place at the cell surface and are regulated by the environmental pH. GPI‐Yps1p is active in vivo at pH 6.0 and pH 3.0 and functions as a sheddase for a subset of GPI‐anchored enzymes, including itself and the Gas1 glucanosyltransferase. Importantly, while native GPI‐Yps1p weakly suppresses many phenotypes associated with the yeast kex2Δ mutant, loop mutants that interfere with conversion into the two‐subunit enzyme restore the kex2Δ phenotypes to near wild type level. We propose that cleavage of this internal loop region plays an important regulatory function through stimulating its shedding activity. Collectively, our data provide a direct link between the pH regulation of yeast cell wall assembly and the activity of a yapsin.