bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-dimensional patterning of bacterial light-harvesting 2 complexes on lipid-modified gold surface
Authors: Yajima Shunsuke , Furukawa Rei A. , Nagata Morio , Sakai Shunsuke , Kondo Masaharu , Iida Kouji , Dewa Takehisa , Nango Mamoru
Published: June 2012

In a photosynthetic membrane, nano-scale patterns of light-harvesting (LH) pigment-protein complexes play an essential role in capturing photons and ensuring efficient excitation energy transfer. LH complexes 1 and 2 have drawn attention as building blocks of a nano-scale photoelectric device. For obtaining a device with efficiency comparable to that of the natural photosynthesis, a method has to be established for forming a two-dimensional assembly of LH complexes around a metal electrode. In this study, LH2 complexes isolated from Rb. sphaeroides were immobilized on a patterned gold surface. Quenching of photo-excitation energy by gold was prevented through the placement of a self-assembled phospholipid monolayer between the LH2 complexes and the gold surface.
Flexible resistive switching memory using inkjet printing of a solid polymer electrolyte
Authors: Mohapatra Saumya R. , Tsuruoka T. , Hasegawa T. , Terabe K. , Aono M.
Published: June 2012

Resistive switching memory cells were fabricated on a plastic substrate via inkjet printing (IJP) of a solid polymer electrolyte (SPE). Using the high contrast between the surface energy of a metal electrode and the substrate, a thin SPE film could be deposited over the electrode by IJP. The fabricated Ag/SPE/Pt cells showed bipolar resistive switching behavior under electrical bias in vacuum and in air, which is attributed to the formation and dissolution of a metal filament between the electrodes. From the standpoint of the switching mechanism, our cell can be referred to as a ‘gapless-type atomic switch’. The cells also exhibited stable switching behavior under substrate bending. This device fabrication technique has great potential for flexible switch/memory applications.
Microwave plasma-assisted photoluminescence enhancement in nitrogen-doped ultrananocrystalline diamond film
Authors: Liu Yu Lin , Sun Kien Wen , Lin Yi Jie , Fong Shih-Chieh , Lin I Nan , Tai Nyan Hwa
Published: June 2012

Optical properties and conductivity of nitrogen-doped ultrananocrystal diamond (UNCD) films were investigated following treatment with low energy microwave plasma at room temperature. The plasma also generated vacancies in UNCD films and provided heat for mobilizing the vacancies to combine with the impurities, which formed the nitrogen-vacancy defect centers. The generated color centers were distributed uniformly in the samples. The conductivity of nitrogen-doped UNCD films treated by microwave plasma was found to decrease slightly due to the reduced grain boundaries. The photoluminescence emitted by the plasma treated nitrogen-doped UNCD films was enhanced significantly compared to the untreated films.
Response of woody species to different fire frequencies in semiarid rangelands of central Argentina
Authors: Peláez Daniel V. , Andrioli Romina J. , Elia Omar R. , Bontti Eliana E. , Tomas María A.
Published: June 2012

The aim of the study was to assess the effect of different controlled fire frequencies on cover, density and mortality of the most common woody species in semiarid rangelands of the Caldenal district of central Argentina over a 20-year period. The study comprised three fire treatments: (1) high fire frequency (controlled burns every 3–4 years; HFF); (2) low fire frequency (controlled burns every 8 years; LFF); and (3) unburned control. Repeated burns of moderate intensity, regardless of frequency, reduced the cover and the individual height and canopy area of the most common woody species. Their density was barely affected and the mortality rates were negligible with woody species producing new sprouts after each burn. The woody species under study had a similar response to the high- and low fire frequency treatments. A controlled burn every 3–4 years, permitted the control of woody species cover, height and canopy area, which in turn may favour the production of desirable perennial grasses. The important managerial implication is that the repeated use of controlled fires of moderate intensities in the autumn, given appropriate grazing management, is likely to be essential to maintain these rangelands.
Rho GTP exchange factor ARHGEF11 regulates the integrity of epithelial junctions by connecting ZO-1 and RhoA-Myosin II signaling
Authors: Itoh Masahiko , Tsukita Sachiko , Yamazaki Yuji , Sugimoto Hiroyuki
Published: June 2012

The organization of the apical junctional complex and its association with the cytoskeleton is essential for the function of epithelial cells. However, knowledge about the signaling pathways that regulate these processes is still fragmentary. Here we found that ARHGEF11, a member of the RGS-RhoGEF family, associates with tight junctions (TJs) by binding to ZO-1, but not to the highly homologous ZO-2, in polarized epithelial cells. In the early phases of cell–cell contact, ARHGEF11 was located at primordial adherens junctions, and then its localization was altered to TJs as epithelial polarity was established, much like ZO-1. Knockdown of ARHGEF11 reduced the phosphorylation of myosin light chain, retarding the assembly of cell–cell junctions and the development of the paracellular barrier. Furthermore, the simultaneous knockdown of ARHGEF11 and ZO-2 resulted in significant impairment of TJs and of the perijunctional actomyosin ring; similar defects arise when both ZO-1 and ZO-2 are depleted. These results suggest that ARHGEF11 mediates RhoA–myosin light chain signaling pathways at cell–cell junctions, functioning in cooperation with ZO-1, to regulate the paracellular barrier and the organization of the apical junctional complex and perijunctional actomyosin ring of epithelial cells.
Temperature dependence of protein folding kinetics in living cells
Authors: Guo Minghao , Xu Yangfan , Gruebele Martin
Published: June 2012

We measure the stability and folding rate of a mutant of the enzyme phosphoglycerate kinase (PGK) inside bone tissue cells as a function of temperature from 38 to 48 °C. To facilitate measurement in individual living cells, we developed a rapid laser temperature stepping method capable of measuring complete thermal melts and kinetic traces in about two min. We find that this method yields improved thermal melts compared to heating a sample chamber or microscope stage. By comparing results for six cells with in vitro data, we show that the protein is stabilized by about 6 kJ/mole in the cytoplasm, but the temperature dependence of folding kinetics is similar to in vitro. The main difference is a slightly steeper temperature dependence of the folding rate in some cells that can be rationalized in terms of temperature-dependent crowding, local viscosity, or hydrophobicity. The observed rate coefficients can be fitted within measurement uncertainty by an effective two-state model, even though PGK folds by a multistate mechanism. We validate the effective two-state model with a three-state free energy landscape of PGK to illustrate that the effective fitting parameters can represent a more complex underlying free energy landscape.
Interaction of structure-specific and promiscuous G-protein–coupled receptors mediates small-molecule signaling in
Caenorhabditis elegans
Authors: Park Donha , O'Doherty Inish , Somvanshi Rishi K. , Bethke Axel , Schroeder Frank C. , Kumar Ujendra , Riddle Donald L.
Published: June 2012

A chemically diverse family of small-molecule signals, the ascarosides, control developmental diapause (dauer), olfactory learning, and social behaviors of the nematode model organism,
Caenorhabditis elegans
. The ascarosides act upstream of conserved signaling pathways, including the insulin, TGF-β, serotonin, and guanylyl cyclase pathways; however, the sensory processes underlying ascaroside function are poorly understood. Because ascarosides often are multifunctional and show strongly synergistic effects, characterization of their receptors will be essential for understanding ascaroside biology and may provide insight into molecular mechanisms that produce synergistic outcomes in small-molecule sensing. Based on DAF-8 immunoprecipitation, we here identify two G-protein–coupled receptors, DAF-37 and DAF-38, which cooperatively mediate ascaroside perception.
daf-37
mutants are defective in all responses to ascr#2, one of the most potent dauer-inducing ascarosides, although this mutant responds normally to other ascarosides. In contrast,
daf-38
mutants are partially defective in responses to several different ascarosides. Through cell-specific overexpression, we show that DAF-37 regulates dauer when expressed in ASI neurons and adult behavior when expressed in ASK neurons. Using a photoaffinity-labeled ascr#2 probe and amplified luminescence assays (AlphaScreen), we demonstrate that ascr#2 binds to DAF-37. Photobleaching fluorescent energy transfer assays revealed that DAF-37 and DAF-38 form heterodimers, and we show that heterodimerization strongly increases cAMP inhibition in response to ascr#2. These results suggest that that the ascarosides' intricate signaling properties result in part from the interaction of highly structure-specific G-protein–coupled receptors such as DAF-37 with more promiscuous G-protein–coupled receptors such as DAF-38.
Environmental and biotic controls on the evolutionary history of insect body size
Authors: Clapham Matthew E. , Karr Jered A.
Published: June 2012

Giant insects, with wingspans as large as 70 cm, ruled the Carboniferous and Permian skies. Gigantism has been linked to hyperoxic conditions because oxygen concentration is a key physiological control on body size, particularly in groups like flying insects that have high metabolic oxygen demands. Here we show, using a dataset of more than 10,500 fossil insect wing lengths, that size tracked atmospheric oxygen concentrations only for the first 150 Myr of insect evolution. The data are best explained by a model relating maximum size to atmospheric environmental oxygen concentration (pO
2
) until the end of the Jurassic, and then at constant sizes, independent of oxygen fluctuations, during the Cretaceous and, at a smaller size, the Cenozoic. Maximum insect size decreased even as atmospheric pO
2
rose in the Early Cretaceous following the evolution and radiation of early birds, particularly as birds acquired adaptations that allowed more agile flight. A further decrease in maximum size during the Cenozoic may relate to the evolution of bats, the Cretaceous mass extinction, or further specialization of flying birds. The decoupling of insect size and atmospheric pO
2
coincident with the radiation of birds suggests that biotic interactions, such as predation and competition, superseded oxygen as the most important constraint on maximum body size of the largest insects.
Mode change of millennial CO
2
variability during the last glacial cycle associated with a bipolar marine carbon seesaw
Authors: Bereiter Bernhard , Lüthi Dieter , Siegrist Michael , Schüpbach Simon , Stocker Thomas F. , Fischer Hubertus
Published: June 2012

Important elements of natural climate variations during the last ice age are abrupt temperature increases over Greenland and related warming and cooling periods over Antarctica. Records from Antarctic ice cores have shown that the global carbon cycle also plays a role in these changes. The available data shows that atmospheric CO
2
follows closely temperatures reconstructed from Antarctic ice cores during these variations. Here, we present new high-resolution CO
2
data from Antarctic ice cores, which cover the period between 115,000 and 38,000 y before present. Our measurements show that also smaller Antarctic warming events have an imprint in CO
2
concentrations. Moreover, they indicate that during Marine Isotope Stage (MIS) 5, the peak of millennial CO
2
variations lags the onset of Dansgaard/Oeschger warmings by 250 ± 190 y. During MIS 3, this lag increases significantly to 870 ± 90 y. Considerations of the ocean circulation suggest that the millennial variability associated with the Atlantic Meridional Overturning Circulation (AMOC) undergoes a mode change from MIS 5 to MIS 4 and 3. Ocean carbon inventory estimates imply that during MIS 3 additional carbon is derived from an extended mass of carbon-enriched Antarctic Bottom Water. The absence of such a carbon-enriched water mass in the North Atlantic during MIS 5 can explain the smaller amount of carbon released to the atmosphere after the Antarctic temperature maximum and, hence, the shorter lag. Our new data provides further constraints for transient coupled carbon cycle-climate simulations during the entire last glacial cycle.
Induction of a G
1
-S checkpoint in fission yeast
Authors: Bøe Cathrine A. , Krohn Marit , Rødland Gro Elise , Capiaghi Christoph , Maillard Olivier , Thoma Fritz , Boye Erik , Grallert Beáta
Published: June 2012

Entry into S phase is carefully regulated and, in most organisms, under the control of a G
1
-S checkpoint. We have previously described a G
1
-S checkpoint in fission yeast that delays formation of the prereplicative complex at chromosomal replication origins after exposure to UV light (UVC). This checkpoint absolutely depends on the Gcn2 kinase. Here, we explore the signal for activation of the Gcn2-dependent G
1
-S checkpoint in fission yeast. If some form of DNA damage can activate the checkpoint, deficient DNA repair should affect the length of the checkpoint-induced delay. We find that the cell-cycle delay differs in repair-deficient mutants from that in wild-type cells. However, the duration of the delay depends not only on the repair capacity of the cells, but also on the nature of the repair deficiency. First, the delay is abolished in cells that are deficient in the early steps of repair. Second, the delay is prolonged in repair mutants that fail to complete repair after the incision stage. We conclude that the G
1
-S delay depends on damage to the DNA and that the activating signal derives not from the initial DNA damage, but from a repair intermediate(s). Surprisingly, we find that activation of Gcn2 does not depend on the processing of DNA damage and that activated Gcn2 alone is not sufficient to delay entry into S phase in UVC-irradiated cells. Thus, the G
1
-S delay depends on at least two different inputs.
Extra-large letter spacing improves reading in dyslexia
Authors: Zorzi Marco , Barbiero Chiara , Facoetti Andrea , Lonciari Isabella , Carrozzi Marco , Montico Marcella , Bravar Laura , George Florence , Pech-Georgel Catherine , Ziegler Johannes C.
Published: June 2012

Although the causes of dyslexia are still debated, all researchers agree that the main challenge is to find ways that allow a child with dyslexia to read more words in less time, because reading more is undisputedly the most efficient intervention for dyslexia. Sophisticated training programs exist, but they typically target the component skills of reading, such as phonological awareness. After the component skills have improved, the main challenge remains (that is, reading deficits must be treated by reading more—a vicious circle for a dyslexic child). Here, we show that a simple manipulation of letter spacing substantially improved text reading performance on the fly (without any training) in a large, unselected sample of Italian and French dyslexic children. Extra-large letter spacing helps reading, because dyslexics are abnormally affected by crowding, a perceptual phenomenon with detrimental effects on letter recognition that is modulated by the spacing between letters. Extra-large letter spacing may help to break the vicious circle by rendering the reading material more easily accessible.
Casparian strip diffusion barrier in
Arabidopsis
is made of a lignin polymer without suberin
Authors: Naseer Sadaf , Lee Yuree , Lapierre Catherine , Franke Rochus , Nawrath Christiane , Geldner Niko
Published: June 2012

Casparian strips are ring-like cell-wall modifications in the root endodermis of vascular plants. Their presence generates a paracellular barrier, analogous to animal tight junctions, that is thought to be crucial for selective nutrient uptake, exclusion of pathogens, and many other processes. Despite their importance, the chemical nature of Casparian strips has remained a matter of debate, confounding further molecular analysis. Suberin, lignin, lignin-like polymers, or both, have been claimed to make up Casparian strips. Here we show that, in
Arabidopsis
, suberin is produced much too late to take part in Casparian strip formation. In addition, we have generated plants devoid of any detectable suberin, which still establish functional Casparian strips. In contrast, manipulating lignin biosynthesis abrogates Casparian strip formation. Finally, monolignol feeding and lignin-specific chemical analysis indicates the presence of archetypal lignin in Casparian strips. Our findings establish the chemical nature of the primary root-diffusion barrier in
Arabidopsis
and enable a mechanistic dissection of the formation of Casparian strips, which are an independent way of generating tight junctions in eukaryotes.
Soluble epoxide hydrolase regulates hematopoietic progenitor cell function via generation of fatty acid diols
Authors: Frömel Timo , Jungblut Benno , Hu Jiong , Trouvain Caroline , Barbosa-Sicard Eduardo , Popp Rüdiger , Liebner Stefan , Dimmeler Stefanie , Hammock Bruce D. , Fleming Ingrid
Published: June 2012

Fatty acid epoxides are important lipid signaling molecules involved in the regulation of vascular tone and homeostasis. Tissue and plasma levels of these mediators are determined by the activity of cytochrome P450 epoxygenases and the soluble epoxide hydrolase (sEH), and targeting the latter is an effective way of manipulating epoxide levels in vivo. We investigated the role of the sEH in regulating the mobilization and proliferation of progenitor cells with vasculogenic/reparative potential. Our studies revealed that sEH down-regulation/inhibition impaired the development of the caudal vein plexus in zebrafish, and decreased the numbers of lmo2/cmyb-positive progenitor cells therein. In mice sEH inactivation attenuated progenitor cell proliferation (spleen colony formation), but the sEH products 12,13-dihydroxyoctadecenoic acid (12,13-DiHOME) and 11,12- dihydroxyeicosatrienoic acid stimulated canonical Wnt signaling and rescued the effects of sEH inhibition. In murine bone marrow, the epoxide/diol content increased during G-CSF–induced progenitor cell expansion and mobilization, and both mobilization and spleen colony formation were reduced in sEH
−/−
mice. Similarly, sEH
−/−
mice showed impaired functional recovery following hindlimb ischemia, which was rescued following either the restoration of bone marrow sEH activity or treatment with 12,13-DiHOME. Thus, sEH activity is required for optimal progenitor cell proliferation, whereas long-term sEH inhibition is detrimental to progenitor cell proliferation, mobilization, and vascular repair.
Hydrophobic forces and the length limit of foldable protein domains
Authors: Lin Milo M. , Zewail Ahmed H.
Published: June 2012

To find the native conformation (fold), proteins sample a subspace that is typically hundreds of orders of magnitude smaller than their full conformational space. Whether such fast folding is intrinsic or the result of natural selection, and what is the longest foldable protein, are open questions. Here, we derive the average conformational degeneracy of a lattice polypeptide chain in water and quantitatively show that the constraints associated with hydrophobic forces are themselves sufficient to reduce the effective conformational space to a size compatible with the folding of proteins up to approximately 200 amino acids long within a biologically reasonable amount of time. This size range is in general agreement with the experimental protein domain length distribution obtained from approximately 1,200 proteins. Molecular dynamics simulations of the Trp-cage protein confirm this picture on the free energy landscape. Our analytical and computational results are consistent with a model in which the length and time scales of protein folding, as well as the modular nature of large proteins, are dictated primarily by inherent physical forces, whereas natural selection determines the native state.
Reciprocal uniparental disomy in yeast
Authors: Andersen Sabrina L. , Petes Thomas D.
Published: June 2012

In the diploid cells of most organisms, including humans, each chromosome is usually distinguishable from its partner homolog by multiple single-nucleotide polymorphisms. One common type of genetic alteration observed in tumor cells is uniparental disomy (UPD), in which a pair of homologous chromosomes are derived from a single parent, resulting in loss of heterozygosity for all single-nucleotide polymorphisms while maintaining diploidy. Somatic UPD events are usually explained as reflecting two consecutive nondisjunction events. Here we report a previously undescribed mode of chromosome segregation in
Saccharomyces cerevisiae
in which one cell division produces daughter cells with reciprocal UPD for the same pair of chromosomes without an aneuploid intermediate. One pair of sister chromatids is segregated into one daughter cell and the other pair is segregated into the other daughter cell, mimicking a meiotic chromosome segregation pattern. We term this process “reciprocal uniparental disomy.”
Cold but not sympathomimetics activates human brown adipose tissue in vivo
Authors: Cypess Aaron M. , Chen Yih-Chieh , Sze Cathy , Wang Ke , English Jeffrey , Chan Onyee , Holman Ashley R. , Tal Ilan , Palmer Matthew R. , Kolodny Gerald M. , Kahn C. Ronald
Published: June 2012

As potential activators of brown adipose tissue (BAT), mild cold exposure and sympathomimetic drugs have been considered as treatments for obesity and diabetes, but whether they activate the same pathways is unknown. In 10 healthy human volunteers, we found that the sympathomimetic ephedrine raised blood pressure, heart rate, and energy expenditure, and increased multiple circulating metabolites, including glucose, insulin, and thyroid hormones. Cold exposure also increased blood pressure and energy expenditure, but decreased heart rate and had little effect on metabolites. Importantly, cold increased BAT activity as measured by18F-fluorodeoxyglucose PET-CT in every volunteer, whereas ephedrine failed to stimulate BAT. Thus, at doses leading to broad activation of the sympathetic nervous system, ephedrine does not stimulate BAT in humans. In contrast, mild cold exposure stimulates BAT energy expenditure with fewer other systemic effects, suggesting that cold activates specific sympathetic pathways. Agents that mimic cold activation of BAT could provide a promising approach to treating obesity while minimizing systemic effects.
Temporalia, maxime respectu aeternorum, nihil sunt
Authors: Quero-Sánchez Andrés
Published: June 2012

Master Eckhart’s metaphysics is an idealistic one: Being is not what there
is, but only and exclusively what is truthful, i. e. the normativity which reason (God Himself) sets. Further: What is truthful comes about by negation of what there is, because this is itself nothing, pure negation as such. What is truthful is therefore the negation of negation. This is an idealistic thesis which cannot be described as being thomistic, but rather which corresponds to the metaphysics of German Idealism, especially of Fichte. This essay shows that the thesis that Eckhart was thomistic until his Parisian idealistic turn at the beginning of the 14th century is not correct. It argues that Eckhart’s metaphysics is unambiguously idealistic, i. e. non-thomistic, and that this is also the case in works which he certainly wrote before the Parisian Questions. This applies especially to the Rede der underscheidunge und the Tractatus super oratione dominica.
Kenntnis und Erkenntnis: Der innere Zusammenhang von Philosophiegeschichte und Geschichtsphilosophie
Authors: Hutter Axel
Published: June 2012

A specifically rational understanding of the philosophical tradition (“Erkenntnis”), which addresses the question of truth, is opposed to a purely historical understanding of philosophy (“Kenntnis”). Nevertheless this rational understanding of philosophy remains critically related to history: It frees the philosophy of the past from solidification into an antiquity, while it integrates earlier thought into an autonomous re-thinking, and it frees the thinking of the present from its prejudices, while it confronts its comfortable ways of understanding with the unsatisfied truth of the tradition.
Attention
Authors: Pettersson Rune
Published: June 2012

We do not become conscious of all the stimuli detected by our sensory organs. The selective process that controls our awareness of events in the environment is called attention. The process of attention determines which events we become conscious of. Attention may be controlled (1) automatically, (2) by instructions, and (3) by the specific demands of the particular task at hand. The information designer may use various design principles and guidelines in order to facilitate the reader’s attention processes, and subsequent processes for understanding and learning.
Evasive actions in top-down communication
Authors: Dieltjens Sylvain , Heynderickx Priscilla
Published: June 2012

The ambiguity of the we-referent in internal communication documents can make text interpretation difficult. We analyzed the 1999 issues of the ’Maxi Guide’, the weekly top-down briefing of a large Belgian distribution chain. In relational and hybrid texts in particular, the referent of the pronoun often changes within the same text without any textual or graphic indicator.

This article will first describe how the use of we is avoided. In total seven strategies were detected (e.g., perspective changes, non-finite clauses, elliptical sentences). They will be explained and illustrated with examples translated from both French and Dutch. Next, the article will outline how we itself operates as an evasive strategy. The examples will demonstrate how similar strategies are used in the two languages.
Restoring reputation with direct mail
Authors: van Wijk Carel
Published: June 2012

A company can consider a disastrous incident from several perspectives. The pervasive ones are ‘Who did it ?’ and ‘How could it happen’ How the public reacts to these perspectives has been determined in a field experiment. Subjects read a direct-mail letter in which an international chain of hotels commented on two recent fires from either the who or the how perspective on their causes. Evaluative responses to the text versions interacted with gender; persuasive effects depended on both gender and value-relevant involvement. Gender determined the direction of the preference; men reacted more positively to the how version, women tended to do so to the who version. Involvement determined the magnitude of these differences; the more concerned about personal safety, the greater the differences. These results can be understood in terms of certain moral beliefs and behaviors derived from crisis management theory.
Stylistic dilemmas in document design
Authors: Lassen Inger
Published: June 2012

In technical discourse, the majority of texts are found to be accessible only to a specialist audience, and the feeling is prevalent with some technical genres that they would lose their generic integrity if part of their complexity was removed, since such a change would jeopardize the acceptability of the texts. Technical translators, on the other hand, often feel a strong need to simplify conventional technical writing style, which by convention has a high frequency of passives, nominalizations, nonfinite clauses and compound noun clusters, and omits some definite articles. Halliday (1994) and Halliday and Matthiessen (1999) have referred to some of these configurations (nominalizations, nominal groups, and nonfinite clauses) as grammatical metaphor (GM). Following Halliday’s argumentation, I have suggested an extension of the GM range to also include the passive and definite article omission (see, for example, Lassen, 1997, pp. 67–83), making possible a discussion of the characteristic stylistic features in technical discourse under the umbrella term GM. This article discusses the stylistic dilemmas involved in negotiating between the two conflicting aims of observing genre conventions and facilitating comprehen- sion. The empirical basis of the discussion is a survey in which the attitudes of different audiences to text accessibility and acceptability were investigated by means of a questionnaire distributed to a variety of professional groupings, including technical writers, translators, engi- neers, and technical language instructors, as well as a nonspecialist group of respondents with mixed occupations who were unfamiliar with technical writing style. The respondents were encouraged to state their attitudes to accessibility and acceptability on the basis of three text versions. One version was an original text, the second a text from which the grammatical metaphors had been removed, and the third was a version with short sentences.
An experimental view of language comprehension
Authors: Zwaan Rolf A.
Published: June 2012

The consensus view in cognitive psychology is that the construction of situation models is an integral part of language comprehension. A great deal of empirical evidence supports this view. Moreover, recent theorizing and empirical evidence suggest that situation models are best viewed as experiential simulations of the narrated events, actions, people, objects, and places. In this Experiential View, language is a set of cues guiding the simulation processes, by activating perceptual representations stored in the brain areas that are also active during the direct experience of the referent object, person, or event. In this article I discuss the empirical evidence for the Experiential view from cognitive psychology and cognitive neuroscience. In addition, I consider some of the implications of this view for the design of instructional documents.
Short and mid-term effects of an earlier start
Authors: Celaya M. Luz , Torras Maria Rosa , Pérez-Vidal Carmen
Published: June 2012

Most studies concerning the issue of age have focused on the language outcomes of subjects who started acquiring a second language during childhood, or later on during adolescence or adulthood in naturalistic contexts. However, relatively few studies have been concerned with school contexts where a foreign language is a compulsory subject in the early stages of the curriculum. The aim of the present study is to address the question of the effects of starting age (8 versus 11) on the acquisition of English as a foreign language in a school context, with specific reference to written production. Data are analysed after 200 and 416 hours of instruction, that is, when learners are 10 and 12, and 12 and 14 respectively. Results suggest that an earlier start does not have clear benefits in the acquisition of EFL as reflected in written language.
I-learning
Authors: Carroll Susanne Elizabeth
Published: June 2012

This paper outlines the Autonomous Induction Theory, a theory of learning which is compatible with the hypothesis that Universal Grammar constrains the nature of natural languages. Based on Jackendoff’s architecture of the language faculty and Representational Modularity Hypothesis, it defines a trigger for the acquisition mechanisms and states a number of formal and psycholinguistic constraints on how they can operate. Finally, it argues that the theory is a necessary adjunct to purely formal learnability research.
Multiple subject constructions in Japanese and the development of AGRP in L2 English
Authors: Zobl Helmut
Published: June 2012

Starting from the assumption that Japanese has no subject–verb agreement, this paper focuses on the acquisition of agreement, specifically on structure building of a functional category AGRP (agreement phrase) which provides a configuration in which nominative case is licensed/checked in a bi-unique SpecAGR relation. L2 clausal structures corresponding to Japanese multiple subject sentences receive particular scrutiny since the possibility of licensing more than one subject phrase is expected to influence L2 implementation of an AGRP in this context. Relying on a written corpus, the paper outlines a transition to a grammar with AGR, drawing on lexical learning (Clahsen, Eisenbeiss and Penke 1996), structure-building (Vainikka and Young-Scholten 1996, 1998) and elements of constructionism (Herschensohn 2000). The data indicate that Japanese speakers create a bi-unique spec-head relation for agreement. However, in clauses corresponding to multiple subject sentences, instances of failed agreement suggest that co-indexing is not yet consistently carried out with the phrase in SpecAGR. Also, instances of inappropriate predication and caseless DPs indicate that creation of AGRP does not bring about an immediate solution to the problem of integrating the multiple subject phrases in Japanese into English clausal structure.
The mental processing of L2 English lexical compounds
Authors: Kırkıcı Bilal
Published: June 2012

A number of SLA studies in the past decade (e.g. Lardiere, 1995; Murphy, 2000) have attempted to answer the question of whether the Dual-Mechanism Model can be extended to L2 English processing. These studies have found that the clear regular-irregular dissociation in compounds observed for L1 users is not the case for L2 users, who tend to include regular plurals in compounds to varying degrees. The present study reports on further efforts to investigate this issue with Turkish learners of English as a Foreign Language (EFL) in Turkey. An elicited written production task, similar to that used by Murphy (2000), was administered to high and low proficiency L1 Turkish users of EFL and native English speakers. The results, it is claimed, indicate that both the L1 controls and the L2 participants dissociate between regular and irregular nouns within English compounds. However, in contrast to most previous studies, the L2 dissociation was found to be stronger at higher levels of L2 proficiency, which speaks for a developmental restructuring in L2 inflectional processing that could be explained under a weak version of the Dual-Mechanism Model.
Modularity in SLA
Authors: Miličević Maja
Published: June 2012

This paper reports on a study of the acquisition of reflexive and reciprocal forms in L2 Italian from the point of view of their argument structure. The results are interpreted with respect to the debate about whether transfer is monolithic (Schwartz and Sprouse 1996, Whong-Barr 2005) or modular (Montrul 1997), considering at the same time other relevant factors — innate mechanisms and L2 input. On the basis of the acceptability judgements of Serbian and English learners, compared to native speakers of Italian, it is argued that a modular approach is more realistic, as different types of transfer were identified for morphology (direct transfer of L1 marking) and argument structure (indirect influence of L1 general properties). Possible reliance on innate knowledge was detected at the argument structure level, while the input (examined through a corpus study) was found to influence both domains in different ways. It is also suggested that the three factors should be looked at jointly rather than in isolation.
Fundamental issues in the study of second language acquisition
Authors: Hulstijn Jan H.
Published: June 2012

The study of second language acquisition (SLA) forms a young academic discipline, emerging from fundamental paradigm shifts in SLA’s parent disciplines, linguistics and psychology. This paper gives a brief overview of how the study of SLA came into existence, formulates the fundamental questions concerning SLA, reviews some recent developments, and identifies possibilities and challenges for SLA theory construction and empirical research in the near future. To tackle the fundamental issues of SLA successfully, it is mandatory that SLA researchers, of whom the majority currently has a linguistic background, collaborate with researchers in psychology and other disciplines.
The nature of the L2 user
Authors: Cook Vivian
Published: June 2012

Three of the basic issues raised by the multi-competence perspective for SLA research are:

(1) who are the L2 users? Both as the possession of the individual and of the community, L1 and L2 are diverse and flexible, ranging from developing to relatively static to reducing. SLA research has to recognise the shifting flux of L1 and L2 systems.

(2) what is the language that the L2 user knows? Five meanings of ‘language’ are discussed: human representation system, institutional object, set of sentences, community and individual possession, concluding that the language systems of the individual and of the community need to be treated as a whole.

(3) What is the community the L2 user belongs to? L2 users belong to diverse communities of their own, both local and global. SLA research needs to explore the nature of these communities rather than assuming L2 users wish to be part of native monolingual communities.
SPLLOC: A new database for Spanish second language acquisition research
Authors: Mitchell Rosamond , Domínguez Laura , Arche María J. , Myles Florence , Marsden Emma
Published: June 2012

The contribution of Spanish to the field of SLA continues to grow (Lafford & Salaberry 2003; Montrul 2004), and the need for good L2 Spanish datasets is becoming increasingly evident. In this paper we introduce a newly created database titled Spanish Learner Language Oral Corpus (SPLLOC), describing the rationale underlying the database design and methodology used for its construction. This project applying CHILDES tools to L2 Spanish follows successful creation of a collection of French L2 oral corpora (Rule et al. 2003), already available at www.flloc.soton.ac.uk. Creating a successful oral corpus is costly and available corpora are often built somewhat opportunistically from available material rather than designed in a balanced way to facilitate SLA research. The SPLLOC database has been designed to fill the existing gap in Spanish L2 resources and also to support a focused research agenda investigating learner development with respect to the verb phrase, clitic pronouns, and word order, from an interface perspective.
Theme in discourse
Authors: Crompton Peter
Published: June 2012

Fries (1981) hypothesises that the textual phenomena of ‘thematic progression’ (TP) (Danesˇ 1974) and ‘method of development’ (MOD) provide discourse evidence for the function proposed by Halliday (1967) for Theme, in particular that ‘initial position in the sentence, or sentence-level Theme, means “point of departure of the sentence as message”‘. This paper discusses the theoretical basis for this hypothesis, in particular the relation between TP and MOD, and reviews previous empirical research. Further research conducted by the author is described, into global proportions of TP, TP patterning, and the relation between TP and rhematic progression (RP) in a small corpus of 80 short argumentative texts. It was found that only small proportions of either argumentative text, or high-quality argumentative text could be considered as having a MOD. It was also found that texts had comparable levels of TP and RP. It is concluded that MOD is not a universal feature of discourse organisation, and therefore not conclusive evidence for Fries’s original hypothesis.
Diachronic construction grammar and grammaticalization theory
Authors: Noël Dirk
Published: June 2012

Grammaticalization theorists are becoming increasingly aware of the relevance of constructions to their discipline, to the point that one of its leading exponents has recently defined grammaticalization as the creation of new constructions. This is precisely the problem which construction grammarians engaging in diachronic research are addressing — or one they should be addressing, because to date diachronic construction grammar has not really taken off as a discipline. The question arises of whether grammaticalization theory could simply be turned into the historical branch of construction grammar, or whether diachronic construction grammar has its own raison d’être as a separate discipline. Since grammaticalization theoretical practice is fairly narrowly focused on the change of extant constructions along a path towards the grammatical end of the meaning continuum, there is a need for a wider discipline that also concerns itself with the primary emergence of constructions. Though grammaticalization presupposes ‘constructionalization’, the two developments need to be kept apart because not all constructions go on to grammaticalize.
UNG shapes the specificity of AID-induced somatic hypermutation
Authors: Pérez-Durán Pablo , Belver Laura , de Yébenes Virginia G. , Delgado Pilar , Pisano David G. , Ramiro Almudena R.
Published: June 2012

Secondary diversification of antibodies through somatic hypermutation (SHM) and class switch recombination (CSR) is a critical component of the immune response. Activation-induced deaminase (AID) initiates both processes by deaminating cytosine residues in immunoglobulin genes. The resulting U:G mismatch can be processed by alternative pathways to give rise to a mutation (SHM) or a DNA double-strand break (CSR). Central to this processing is the activity of uracil-N-glycosylase (UNG), an enzyme normally involved in error-free base excision repair. We used next generation sequencing to analyze the contribution of UNG to the resolution of AID-induced lesions. Loss- and gain-of-function experiments showed that UNG activity can promote both error-prone and high fidelity repair of U:G lesions. Unexpectedly, the balance between these alternative outcomes was influenced by the sequence context of the deaminated cytosine, with individual hotspots exhibiting higher susceptibility to UNG-triggered error-free or error-prone resolution. These results reveal UNG as a new molecular layer that shapes the specificity of AID-induced mutations and may provide new insights into the role of AID in cancer development.
Runx1–Cbfβ facilitates early B lymphocyte development by regulating expression of Ebf1
Authors: Seo Wooseok , Ikawa Tomokatsu , Kawamoto Hiroshi , Taniuchi Ichiro
Published: June 2012

Although Runx and Cbfβ transcription factor complexes are involved in the development of multiple hematopoietic lineages, their precise roles in early mouse B lymphocyte differentiation remain elusive. In this study, we examined mouse strains in which Runx1, Runx3, or Cbfβ were deleted in early B lineage progenitors by an mb1-cre transgene. Loss of Runx1, but not Runx3, caused a developmental block during early B lymphopoiesis, resulting in the lack of IgM+ B cells and reduced VH to DJH recombination. Expression of core transcription factors regulating early B cell development, such as E2A, Ebf1, and Pax5, was reduced in B cell precursors lacking Runx1. We detected binding of Runx1–Cbfβ complexes to the Ebf1 proximal promoter, and these Runx-binding motifs were essential to drive reporter gene expression. Runx1-deficient pro-B cells harbored excessive amounts of the repressive histone mark H3K27 trimethylation in the Ebf1 proximal promoter. Interestingly, retroviral transduction of Ebf1, but not Pax5, into Runx1-deficient progenitors restored not only development of B220+ cells that underwent VH to DJH rearrangement but also expression of B lineage signature genes. Collectively, these results demonstrate that Runx1–Cbfβ complexes are essential to facilitate B lineage specification, in part via epigenetic activation of the Ebf1 gene.
Neural reflexes in inflammation and immunity
Authors: Andersson Ulf , Tracey Kevin J.
Published: June 2012

The mammalian immune system and the nervous system coevolved under the influence of infection and sterile injury. Knowledge of homeostatic mechanisms by which the nervous system controls organ function was originally applied to the cardiovascular, gastrointestinal, musculoskeletal, and other body systems. Development of advanced neurophysiological and immunological techniques recently enabled the study of reflex neural circuits that maintain immunological homeostasis, and are essential for health in mammals. Such reflexes are evolutionarily ancient, dating back to invertebrate nematode worms that possess primitive immune and nervous systems. Failure of these reflex mechanisms in mammals contributes to nonresolving inflammation and disease. It is also possible to target these neural pathways using electrical nerve stimulators and pharmacological agents to hasten the resolution of inflammation and provide therapeutic benefit.
Classical dendritic cells as a unique immune cell lineage
Authors: Reizis Boris
Published: June 2012

Despite the critical role of classical dendritic cells (cDCs) in the initiation of adaptive immune responses, the genetic and phenotypic definition of cDCs remains moot. Two new studies designate Zbtb46 as a novel transcription factor that is specifically expressed in all cDCs in both humans and mice. Although Zbtb46 appears dispensable for cDC development, its specific pattern of expression supports the notion that cDCs constitute a unique immune cell lineage. Furthermore, these two studies provide novel tools that will aid in the study of cDC progenitors, visualization of cDCs in vivo, and depletion of cDCs for functional analysis.
Association ofBacillus cereusInfection with Contaminated Alcohol Prep Pads
Authors: Dolan Susan A. , Littlehorn Cynthia , Glodé Mary P. , Dowell Elaine , Xavier Karen , Nyquist Ann-Christine , Todd James K.
Published: June 2012

Background.

Bacillusspecies have caused healthcare-associated outbreaks of invasive disease as well as pseudo-outbreaks. We report an outbreak investigation of blood cultures positive forBacillus cereusassociated with alcohol prep pads (APPs) contaminated withB. cereusandBacillusspecies resulting in a rapid internal product recall and subsequent international product recall.

Design.

Epidemiologic and microbiologic outbreak investigation.

Setting.

A 300-bed tertiary care children's hospital in Aurora, Colorado.

Patients.

Patients with blood or cerebrospinal fluid cultures positive forB. cereus.

Methods.

Three patients with blood cultures positive forB. cereuswere identified in late 2010. Breaches in procedural and surgical techniques, common interventions, and products were explored. The following 3 common products were cultured: sterile saline syringes, chlorhexidine/alcohol skin preparation solution, and APPs. Repetitive sequence-based polymerase chain reaction (Rep-PCR) was used to compare isolates obtained from patients and from APPs and was confirmed by independent pulsed-field gel electrophoresis.

Results.

There appeared to be a significant increase in blood cultures positive forB. cereusduring 2009-2010.B. cereusand otherBacillusspecies were cultured from the internal contents of 63.3% of APPs not labeled as sterile, and 8 of the 10 positive lots were manufactured after 2007. None of the isolates obtained from the patients matched strains isolated from the APPs. However, some lots of APPs had strains that were indistinguishable from one another.

Conclusions.

APPs that were not labeled as sterile were contaminated withBacillusspecies. The product was immediately recalled internally and replaced with APPs from another manufacturer that were labeled as sterile. On January 3, 2011, the manufacturer voluntarily recalled its APPs. Healthcare facilities, healthcare providers, and users of APPs should avoid the use of APPs not specifically labeled as sterile.