bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental study of a radial plasma source
Authors: Makrinich G. , Fruchtman A.
Published: April 2009

A radially outward acceleration of plasma in cylindrical geometry along an applied electric field and across an axial magnetic field is studied. The configuration, coined a radial plasma source, consists of two ceramic disks positioned parallel to each other, between which a cylindrical molybdenum anode is mounted. The electric field is generated by applying a voltage between the anode and a heated cathode neutralizer that is located away from the ceramic disks. The plasma diagnostic system includes Langmuir probes, an emissive probe, and a balance force meter. The discharge voltage is found to increase when the magnetic field is increased or when the mass flow rate (and the pressure) is decreased. For a discharge current of 1.4 A, the discharge voltage increases from 55 to 120 V when the magnetic field is increased from 0 to 186 G. The azimuthal uniformity of the plasma flow is found to decrease with the increase in gas pressure. The force exerted on the balance force meter is found to be larger than the force exerted by the plasma flow. This disparity indicates that a considerable part of the force is exerted by the neutral gas, which has gained momentum from the plasma via ion-neutral collisions. The force is increased because the momentum delivered for a given deposited power is larger if the energy is deposited in a larger mass, as happens here through plasma collisions. We estimate theoretically the expected force at the collisionless and the collisional limits and find that the measured force is between the expected forces at the two limits.
Stress field analysis to understand the breakdown characteristics of stacked high-k dielectrics
Authors: Lee Byoung Hun , Kang Changyong , Choi Rino , Lee Hi-Deok , Bersuker Gennadi
Published: April 2009

The validity of the stress biases used in reliability studies of high-k dielectric is discussed by analyzing the stress biases used in previous works. For single layer dielectrics, stress biases near the time zero dielectric breakdown point have been used to reduce the test time. However, stacked dielectrics need a more careful approach to avoid overstress. We show that the majority of earlier work on the reliability of high-k dielectric used high electric field and those results may not be optimal for predicting intrinsic reliability characteristics. A simple guideline to avoid overstress is provided.
Observation of chiral quantum-Hall edge states in graphene
Authors: Ki Dong-Keun , Jo Sanghyun , Lee Hu-Jong
Published: April 2009

In this study, we determined the chiral direction of the quantum-Hall (QH) edge states in graphene by adopting simple two-terminal conductance measurements while grounding different edge positions of the sample. The edge state with a smaller filling factor is found to more strongly interact with the electric contacts. This simple method can be conveniently used to investigate the chirality of the QH edge state with zero filling factor in graphene, which is important to understand the symmetry breaking sequence in high magnetic fields (≳25 T).
Enhancement of the magnetic field sensitivity in Al2O3 encapsulated NiFe films with anisotropic magnetoresistance
Authors: Ding Lei , Teng Jiao , Zhan Qian , Feng Chun , Li Ming-hua , Han Gang , Wang Li-jin , Yu Guang-hua , Wang Shu-yun
Published: April 2009

The anisotropic magnetoresistance value (ΔR/R) and magnetic field sensitivity (Sv) of NiFe films can be remarkably enhanced by using Al2O3 encapsulation, and the Sv is comparable to that of a spin valve. For an ultrathin NiFe film with the structure of Ta/Al2O3/NiFe/Al2O3/Ta, the Al2O3 layers suppress the formation of the magnetic dead layers and the interdiffusions between the NiFe layer and Ta layers, and decrease the current shunting of the Ta layers. More importantly, the flatter Al2O3/NiFe and NiFe/Al2O3 interfaces can significantly enhance the specular reflection of conduction electrons and lead to a higher ΔR/R. In addition, the formations of the NiFe (111) texture and the columnar grains by annealing can also increase the ΔR/R.
The Influence of Facing Direction on the Haptic Identification of Two-Dimensional Raised Pictures
Authors: Scocchia Lisa , Stucchi Natale , Loomis Jack M
Published: April 2009

It has been hypothesized (Lederman et al, 1990 Perception & Psychophysics47 54–64) that sighted people adopt a visual translation process when attempting to identify 2-D raised images by touch—they employ a visual image as a mediator between haptic sensory information and the object representation. If this hypothesis is correct, the performance in identifying pictures by touch (with eyes closed) ought to be better when the head is facing the picture than when facing in a very different direction. In this study, thirty-six blindfolded participants were required to identify raised pictures of common objects with their head facing either in the same direction as the raised picture or in an orthogonal direction. Identification performance was measured in terms of accuracy and response latencies. Overall, participants were more accurate and faster when their heads faced in the same direction as the picture. This finding is discussed in terms of spatial congruency between haptic representations of pictures and visual (or spatial) imagery created during exploration of haptic pictures.
Rapid Orienting toward Face-like Stimuli with Gaze-Relevant Contrast Information
Authors: Tomalski Przemyslaw , Csibra Gergely , Johnson Mark H
Published: April 2009

Human faces under natural illumination, and human eyes in their unique morphology, include specific contrast polarity relations that face-detection mechanisms could capitalise on. Newborns have been shown to preferentially orient to simple face-like patterns only when they contain face- or gaze-relevant contrast. We investigated whether human adults show similar preferential orienting towards schematic face-like stimuli, and whether this effect depends on the contrast polarity of the stimuli. In two experiments we demonstrate that upright schematic face-like patterns elicit faster eye movements in adult humans than inverted ones, and that this occurs only if they contain face- or gaze-relevant contrast information in the whole stimulus or in the eye region only. These results suggest that primitive mechanisms underlying the orienting bias towards faces and eyes influence and modulate social cognition not just in infants but in adults as well.
Viewpoint Dependence in the Recognition of Non-Elongated Familiar Objects: Testing the Effects of Symmetry, Front-Back Axis, and Familiarity
Authors: Niimi Ryosuke , Yokosawa Kazuhiko
Published: April 2009

Visual recognition of three-dimensional (3-D) objects is relatively impaired for some particular views, called accidental views. For most familiar objects, the front and top views are considered to be accidental views. Previous studies have shown that foreshortening of the axes of elongation of objects in these views impairs recognition, but the influence of other possible factors is largely unknown. Using familiar objects without a salient axis of elongation, we found that a foreshortened symmetry plane of the object and low familiarity of the viewpoint accounted for the relatively worse recognition for front views and top views, independently of the effect of a foreshortened axis of elongation. We found no evidence that foreshortened front–back axes impaired recognition in front views. These results suggest that the viewpoint dependence of familiar object recognition is not a unitary phenomenon. The possible role of symmetry (either 2-D or 3-D) in familiar object recognition is also discussed.
Seeded growth of β-amyloid fibrils from Alzheimer's brain-derived fibrils produces a distinct fibril structure
Authors: Paravastu Anant K. , Qahwash Isam , Leapman Richard D. , Meredith Stephen C. , Tycko Robert
Published: April 2009

Studies by solid-state nuclear magnetic resonance (NMR) of amyloid fibrils prepared
in vitro
from synthetic 40-residue β-amyloid (Aβ
1–40
) peptides have shown that the molecular structure of Aβ
1–40
fibrils is not uniquely determined by amino acid sequence. Instead, the fibril structure depends on the precise details of growth conditions. The molecular structures of β-amyloid fibrils that develop in Alzheimer's disease (AD) are therefore uncertain. We demonstrate through thioflavin T fluorescence and electron microscopy that fibrils extracted from brain tissue of deceased AD patients can be used to seed the growth of synthetic Aβ
1–40
fibrils, allowing preparation of fibrils with isotopic labeling and in sufficient quantities for solid-state NMR and other measurements. Because amyloid structures propagate themselves in seeded growth, as shown in previous studies, the molecular structures of brain-seeded synthetic Aβ
1–40
fibrils most likely reflect structures that are present in AD brain. Solid-state
13
C NMR spectra of fibril samples seeded with brain material from two AD patients were found to be nearly identical, indicating the same molecular structures. Spectra of an unseeded control sample indicate greater structural heterogeneity.
13
C chemical shifts and other NMR data indicate that the predominant molecular structure in brain-seeded fibrils differs from the structures of purely synthetic Aβ
1–40
fibrils that have been characterized in detail previously. These results demonstrate a new approach to detailed structural characterization of amyloid fibrils that develop in human tissue, and to investigations of possible correlations between fibril structure and the degree of cognitive impairment and neurodegeneration in AD.
STIM protein coupling in the activation of Orai channels
Authors: Wang Youjun , Deng Xiaoxiang , Zhou Yandong , Hendron Eunan , Mancarella Salvatore , Ritchie Michael F. , Tang Xiang D. , Baba Yoshihiro , Kurosaki Tomohiro , Mori Yasuo , Soboloff Jonathan , Gill Donald L.
Published: April 2009

STIM proteins are sensors of endoplasmic reticulum (ER) luminal Ca
2+
changes and rapidly translocate into near plasma membrane (PM) junctions to activate Ca
2+
entry through the Orai family of highly Ca
2+
-selective “store-operated” channels (SOCs). Dissecting the STIM–Orai coupling process is restricted by the abstruse nature of the ER–PM junctional domain. To overcome this problem, we studied coupling by using STIM chimera and cytoplasmic C-terminal domains of STIM1 and STIM2 (S1ct and S2ct) and identifying a fundamental action of the powerful SOC modifier, 2-aminoethoxydiphenyl borate (2-APB), the mechanism of which has eluded recent scrutiny. We reveal that 2-APB induces profound, rapid, and direct interactions between S1ct or S2ct and Orai1, effecting full Ca
2+
release-activated Ca
2+
(CRAC) current activation. The short 235-505 S1ct coiled-coil region was sufficient for functional Orai1 coupling. YFP-tagged S1ct or S2ct fragments cleared from the cytosol seconds after 2-APB addition, binding avidly to Orai1-CFP with a rapid increase in FRET and transiently increasing CRAC current 200-fold above basal levels. Functional S1ct–Orai1 coupling occurred in STIM1/STIM2
−/−
DT40 chicken B cells, indicating ct fragments operate independently of native STIM proteins. The 2-APB-induced S1ct–Orai1 and S2-ct–Orai1 complexes undergo rapid reorganization into discrete colocalized PM clusters, which remain stable for >100 s, well beyond CRAC activation and subsequent deactivation. In addition to defining 2-APB's action, the locked STIMct–Orai complex provides a potentially useful probe to structurally examine coupling.
The development of skill and tactical competencies during a season of badminton
Authors: Hastie Peter A. , Sinelnikov Oleg A. , Guarino A. J.
Published: April 2009

In this study, we examined the development of skill competence and tactical knowledge of 41 eighth‐grade students (mean age 13.6 years) as they completed a season of badminton conducted following the features of Sport Education. Using data from students’ performance on badminton skills tests, their competence in game play, and their tactical knowledge, it was determined that these students made significant improvements in their ability to not only control the shuttle, but also to hit it more aggressively. This resulted in improvements in both the selection (what shot to make) and execution (ability to produce the desired shot) dimensions of their game play. In addition, the students demonstrated significant improvements in their ability to select tactical solutions and make arguments for those decisions when watching videotaped performances of badminton games. The key explanation for the development of competence in this setting was that the structure of the Sport Education season allowed for significant practice opportunities, and that the authenticity and consequential nature of the game play helped move all but weak novice students from a more cooperative version of net‐game play to one where tactical decision making and execution was valued.
A motivational model of performance in the sport domain
Authors: Gillet Nicolas , Berjot Sophie , Gobancé Lucie
Published: April 2009

The aim of the present study was to propose and test a motivational model of sport performance based on the hierarchical model of intrinsic and extrinsic motivation (Vallerand, 1997). Tennis players completed the French version of the Sport Motivation Scale (Brière et al., 1995) at the beginning of the season. Two years later, they completed the same instrument and also a questionnaire designed to assess their perceptions of competence, autonomy, and relatedness. Their performances during three seasons were obtained via the French Tennis Federation. First, the present results reveal that self‐determined motivation has a positive impact on sport performance both during one and two seasons. The results also provide support for the mediating role of psychological need satisfaction in the relationship between sport performance and athletes’ motivation. Results are discussed in light of self‐determination theory (Deci & Ryan, 1985).
The influence of instructions and body‐scaling as constraints on decision‐making processes in team sports
Authors: Cordovil Rita , Araújo Duarte , Davids Keith , Gouveia Luís , Barreiros João , Fernandes Orlando , Serpa Sidónio
Published: April 2009

Team games conceptualized as dynamical systems engender a view of emergent decision‐making behaviour under constraints, although specific effects of instructional and body‐scaling constraints have yet to be verified empirically. For this purpose, we studied the effects of task and individual constraints on decision‐making processes in basketball. Eleven experienced female players performed 350 trials in 1 vs. 1 sub‐phases of basketball in which an attacker tried to perturb the stable state of a dyad formed with a defender (i.e. break the symmetry). In Experiment 1, specific instructions (neutral, risk taking or conservative) were manipulated to observe effects on emergent behaviour of the dyadic system. When attacking players were given conservative instructions, time to cross court mid‐line and variability of the attacker's trajectory were significantly greater. In Experiment 2, body‐scaling of participants was manipulated by creating dyads with different height relations. When attackers were considerably taller than defenders, there were fewer occurrences of symmetry‐breaking. When attackers were considerably shorter than defenders, time to cross court mid‐line was significantly shorter than when dyads were composed of athletes of similar height or when attackers were considerably taller than defenders. The data exemplify how interacting task and individual constraints can influence emergent decision‐making processes in team ball games.
Causal conjunction fallacies: The roles of causal strength and mental resources
Authors: Crisp Aimée Kay , Feeney Aidan
Published: April 2009

In two experiments we tested the prediction derived from Tversky and Kahneman's (1983) work on the causal conjunction fallacy that the strength of the causal connection between constituent events directly affects the magnitude of the causal conjunction fallacy. We also explored whether any effects of perceived causal strength were due to graded output from heuristic Type 1 reasoning processes or the result of analytic Type 2 reasoning processes. As predicted, Experiment 1 demonstrated that fallacy rates were higher for strongly than for weakly related conjunctions. Weakly related conjunctions in turn attracted higher rates of fallacious responding than did unrelated conjunctions. Experiment 2 showed that a concurrent memory load increased rates of fallacious responding for strongly related but not for weakly related conjunctions. We interpret these results as showing that manipulations of the strength of the perceived causal relationship between the conjuncts result in graded output from heuristic reasoning process and that additional mental resources are required to suppress strong heuristic output.
Timely Septation Requires SNAD-dependent Spindle Pole Body Localization of the Septation Initiation Network Components in the Filamentous FungusAspergillus nidulans
Authors: Kim Jung-Mi , Zeng Cui Jing Tracy , Nayak Tania , Shao Rongzhong , Huang An-Chi , Oakley Berl R. , Liu Bo
Published: April 2009

In the filamentous fungus Aspergillus nidulans, cytokinesis/septation is triggered by the septation initiation network (SIN), which first appears at the spindle pole body (SPB) during mitosis. The coiled-coil protein SNAD is associated with the SPB and is required for timely septation and conidiation. We have determined that SNAD acted as a scaffold protein that is required for the localization of the SIN proteins of SIDB and MOBA to the SPB. Another scaffold protein SEPK, whose localization at the SPB was dependent on SNAD, was also required for SIDB and MOBA localization to the SPB. In the absence of either SEPK or SNAD, SIDB/MOBA successfully localized to the septation site, indicating that their earlier localization at SPB was not essential for their later appearance at the division site. Unlike their functional counterparts in fission yeast, SEPK and SNAD were not required for vegetative growth but only for timely septation. Furthermore, down-regulation of negative regulators of the SIN suppressed the septation and conidiation phenotypes due to the loss of SNAD. Therefore, we conclude that SPB localization of SIN components is not essential for septation per se, but critical for septation to take place in a timely manner in A. nidulans.
MeSH Up: effective MeSH text classification for improved document retrieval
Authors: Trieschnigg Dolf , Pezik Piotr , Lee Vivian , de Jong Franciska , Kraaij Wessel , Rebholz-Schuhmann Dietrich
Published: April 2009

Motivation: Controlled vocabularies such as the Medical Subject Headings (MeSH) thesaurus and the Gene Ontology (GO) provide an efficient way of accessing and organizing biomedical information by reducing the ambiguity inherent to free-text data. Different methods of automating the assignment of MeSH concepts have been proposed to replace manual annotation, but they are either limited to a small subset of MeSH or have only been compared with a limited number of other systems.

Results: We compare the performance of six MeSH classification systems [MetaMap, EAGL, a language and a vector space model-based approach, a K-Nearest Neighbor (KNN) approach and MTI] in terms of reproducing and complementing manual MeSH annotations. A KNN system clearly outperforms the other published approaches and scales well with large amounts of text using the full MeSH thesaurus. Our measurements demonstrate to what extent manual MeSH annotations can be reproduced and how they can be complemented by automatic annotations. We also show that a statistically significant improvement can be obtained in information retrieval (IR) when the text of a user's query is automatically annotated with MeSH concepts, compared to using the original textual query alone.

Conclusions: The annotation of biomedical texts using controlled vocabularies such as MeSH can be automated to improve text-only IR. Furthermore, the automatic MeSH annotation system we propose is highly scalable and it generates improvements in IR comparable with those observed for manual annotations.

Contact:  trieschn@ewi.utwente.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Application and evaluation of automated semantic annotation of gene expression experiments
Authors: French Leon , Lane Suzanne , Law Tamryn , Xu Lydia , Pavlidis Paul
Published: April 2009

Motivation: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets.

Results: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments. We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references. The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise. We have integrated this annotation pipeline into Gemma.

Availability: The source code, documentation and Supplementary Materials are available at http://www.chibi.ubc.ca/GEOMMTX. The results of the manual evaluations are provided as Supplementary Material. Both manual and predicted annotations can be viewed and searched via the Gemma website at http://www.chibi.ubc.ca/Gemma. The complete set of predicted annotations is available as a machine readable resource description framework graph.

Contact:  paul@chibi.ubc.ca
A stochastic model for the evolution of metabolic networks with neighbor dependence
Authors: Mithani Aziz , Preston Gail M. , Hein Jotun
Published: April 2009

Motivation: Most current research in network evolution focuses on networks that follow a Duplication Attachment model where the network is only allowed to grow. The evolution of metabolic networks, however, is characterized by gain as well as loss of reactions. It would be desirable to have a biologically relevant model of network evolution that could be used to calculate the likelihood of homologous metabolic networks.

Results: We describe metabolic network evolution as a discrete space continuous time Markov process and introduce a neighbor-dependent model for the evolution of metabolic networks where the rates with which reactions are added or removed depend on the fraction of neighboring reactions present in the network. We also present a Gibbs sampler for estimating the parameters of evolution without exploring the whole search space by iteratively sampling from the conditional distributions of the paths and parameters. A Metropolis–Hastings algorithm for sampling paths between two networks and calculating the likelihood of evolution is also presented. The sampler is used to estimate the parameters of evolution of metabolic networks in the genus Pseudomonas.

Availability: An implementation of the Gibbs sampler in Java is available at http://www.stats.ox.ac.uk/∼mithani/networkGibbs/

Contact:  mithani@stats.ox.ac.uk

Supplementary information:  Supplementary data are available at the Bioinformatics online.
Domain Interaction Footprint: a multi-classification approach to predict domain–peptide interactions
Authors: Schillinger Christian , Boisguerin Prisca , Krause Gerd
Published: April 2009

Motivation: The flow of information within cellular pathways largely relies on specific protein–protein interactions. Discovering such interactions that are mostly mediated by peptide recognition modules (PRM) is therefore a fundamental step towards unravelling the complexity of varying pathways. Since peptides can be recognized by more than one PRM and high-throughput experiments are both time consuming and expensive, it would be preferable to narrow down all potential peptide ligands for one specific PRM by a computational method. We at first present Domain Interaction Footprint (DIF) a new approach to predict binding peptides to PRMs merely based on the sequence of the peptides. Second, we show that our method is able to create a multi-classification model that assesses the binding specificity of a given peptide to all examined PRMs at once.

Results: We first applied our approach to a previously investigated dataset of different SH3 domains and predicted their appropriate peptide ligands with an exceptionally high accuracy. This result outperforms all recent methods trained on the same dataset. Furthermore, we used our technique to build two multi-classification models (SH3 and PDZ domains) to predict the interaction preference between a peptide and every single domain in the corresponding domain family at once. Predicting the domain specificity most reliably, our proposed approach can be seen as a first step towards a complete multi-domain classification model comprised of all domains of one family. Such a comprehensive domain specificity model would benefit the quest for highly specific peptide ligands interacting solely with the domain of choice.

Contact:  gkrause@fmp-berlin.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Informed Consent in Complementary and Alternative Medicine
Authors: Caspi Opher , Shalom Tamar , Holexa Joshua
Published: April 2009

The objective of this study was to examine complementary and alternative medicine (CAM) practitioners’ (i) attitudes toward informed consent and (ii) to assess whether standards of practice exist with respect to informed consent, and what these standards look like. The design and setting of the study constituted face‐to‐face qualitative interviews with 28 non‐MD, community‐based providers representing 11 different CAM therapeutic modalities. It was found that there is great deal of variability with respect to the informed consent process in CAM across providers and modalities. No unique profession‐based patterns were identified. The content analysis yielded five major categories related to (i) general attitude towards the informed consent process, (ii) type and amount of information exchange during that process, (iii) disclosure of risks, (iv) discussions of alternatives, and (v) potential benefits. There is a widespread lack of standards with respect to the practice of informed consent across a broad range of CAM modalities. Addressing this problem requires concerted and systematic educational, ethical and judicial remedial actions. Informed consent, which is often viewed as a pervasive obligation is medicine, must be reshaped to have therapeutic value. Acknowledging current conceptions and misconception surrounding the practice of informed consent may help to bring about this change. More translational research is needed to guide this process.
Decadal changes in surface carbon dioxide and related variables in the Mediterranean Sea as inferred from a coupled data-diagnostic model approach
Authors: Louanchi Ferial , Boudjakdji Meriem , Nacef Lamri
Published: April 2009

Louanchi, F., Boudjakdji, M, and Nacef, L. 2009. Decadal changes in surface carbon dioxide and related variables in the Mediterranean Sea as inferred from a coupled data-diagnostic model approach. – ICES Journal of Marine Science, 66: 1538–1546. A coupled approach based on available datasets of temperature, salinity, oxygen, nutrients, and chlorophyll, and a surface layer box model previously developed and modified for the present study, allowed us to reconstruct dissolved inorganic carbon (DIC), total alkalinity, and carbon dioxide fugacity (fCO2) mixed-layer fields for the Mediterranean Sea, from the 1960s to the 1990s. The approach used in this study resulted in a 7% relative error on reconstructed surface fCO2 fields. The Mediterranean Sea transformed from a source of 0.62 Tg C year−1 for atmospheric CO2 in the 1960s, to a net sink of −1.98 Tg C year−1 in the 1990s. The annual cycle in surface fCO2 was driven mainly by temperature variations in the Mediterranean Sea, whereas its decadal variations resulted from a balance between primary production and the thermal effect. According to our model results, the atmospheric CO2 increase of ∼40 µatm over the period of our investigation induced an increase in DIC of ∼30 µmol l−1 in surface waters. A 50% reduction in the magnitude of seasonal variations in surface temperature occurred during the 1990s relative to the earlier decades. Therefore, surface fCO2 only increased by 24 µatm from the 1960s to the 1990s. Changes in pH were not significant over this period.
Generalized Hooke's law for isotropic second gradient materials
Authors: dell'Isola F. , Sciarra G. , Vidoli S.
Published: April 2009

In the spirit of Germain the most general objective stored elastic energy for a second gradient material is deduced using a literature result of Fortuné & Vallée. Linear isotropic constitutive relations for stress and hyperstress in terms of strain and strain-gradient are then obtained proving that these materials are characterized by seven elastic moduli and generalizing previous studies by Toupin, Mindlin and Sokolowski. Using a suitable decomposition of the strain-gradient, it is found a necessary and sufficient condition, to be verified by the elastic moduli, assuring positive definiteness of the stored elastic energy. The problem of warping in linear torsion of a prismatic second gradient cylinder is formulated, thus obtaining a possible measurement procedure for one of the second gradient elastic moduli.
Do ants make direct comparisons?
Authors: Robinson Elva J.H. , Smith Faith D. , Sullivan Kathryn M.E. , Franks Nigel R.
Published: April 2009

Many individual decisions are informed by direct comparison of the alternatives. In collective decisions, however, only certain group members may have the opportunity to compare options. Emigrating ant colonies (
Temnothorax albipennis
) show sophisticated nest-site choice, selecting superior sites even when they are nine times further away than the alternative. How do they do this? We used radio-frequency identification-tagged ants to monitor individual behaviour. Here we show for the first time that switching between nests during the decision process can influence nest choice without requiring direct comparison of nests. Ants finding the poor nest were likely to switch and find the good nest, whereas ants finding the good nest were more likely to stay committed to that nest. When ants switched quickly between the two nests, colonies chose the good nest. Switching by ants that had the opportunity to compare nests had little effect on nest choice. We suggest a new mechanism of collective nest choice: individuals respond to nest quality by the decision either to commit or to seek alternatives. Previously proposed mechanisms, recruitment latency and nest comparison, can be explained as side effects of this simple rule. Colony-level comparison and choice can emerge, without direct comparison by individuals.
A feeding tube model for activation of a cell-specific transcription factor during sporulation in Bacillus subtilis
Authors: Camp Amy H. , Losick Richard
Published: April 2009

Spore formation by Bacillus subtilis takes place in a sporangium consisting of two chambers, the forespore and the mother cell, which are linked by pathways of intercellular communication. One pathway, which couples the activation of the forespore transcription factor σG to the action of σE in the mother cell, has remained mysterious. Traditional models hold that σE initiates a signal transduction pathway that specifically activates σG in the forespore. Recent experiments indicating that the mother cell and forespore are joined by a channel have led to the suggestion that a specific regulator of σG is transported from the mother cell into the forespore. As we report here, however, the requirement for the channel is not limited to σG. Rather, it is also required for the persistent activity of the early-acting forespore transcription factor σF as well as that of a heterologous RNA polymerase (that of phage T7). We infer that macromolecular synthesis in the forespore becomes dependent on the channel at intermediate stages of development. We propose that the channel is a gap junction-like feeding tube through which the mother cell nurtures the developing spore by providing small molecules needed for biosynthetic activity, including σG-directed gene activation.
Single cells (put a ring on it): Figure 1.
Authors: Wolfe Benjamin A. , Glotzer Michael
Published: April 2009

Proper spatial and temporal regulation of the small GTPase RhoA at the equatorial cortex represents a critical step in the specification of the division plane in eukaryotes. Despite increased understanding of the mechanisms whereby RhoA becomes active following chromosome segregation, far less is known about how RhoA is spatially regulated so that it concentrates precisely at the division site. In the April 1, 2009, issue of Genes & Development, Yoshida and colleagues (pp. 810–823) uncovered two genetically separable mechanisms whereby Rho1 is recruited to the bud neck in the budding yeast Saccharomyces cerevisiae to facilitate cytokinesis.
High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues
Authors: Huang Guo-Jen , Shifman Sagiv , Valdar William , Johannesson Martina , Yalcin Binnaz , Taylor Martin S. , Taylor Jennifer M. , Mott Richard , Flint Jonathan
Published: April 2009

A proportion of the genetic variants underlying complex phenotypes do so through their effects on gene expression, so an important challenge in complex trait analysis is to discover the genetic basis for the variation in transcript abundance. So far, the potential of mapping both quantitative trait loci (QTLs) and expression quantitative trait loci (eQTLs) in rodents has been limited by the low mapping resolution inherent in crosses between inbred strains. We provide a megabase resolution map of thousands of eQTLs in hippocampus, lung, and liver samples from heterogeneous stock (HS) mice in which 843 QTLs have also been mapped at megabase resolution. We exploit dense mouse SNP data to show that artifacts due to allele-specific hybridization occur in ∼30% of the cis-acting eQTLs and, by comparison with exon expression data, we show that alternative splicing of the 3′ end of the genes accounts for <1% of cis-acting eQTLs. Approximately one third of cis-acting eQTLs and one half of trans-acting eQTLs are tissue specific. We have created an important systems biology resource for the genetic analysis of complex traits in a key model organism.
Cytochrome P450 Monooxygenases as Reporters for Circadian-Regulated Pathways
Authors: Pan Yinghong , Michael Todd P. , Hudson Matthew E. , Kay Steve A. , Chory Joanne , Schuler Mary A.
Published: April 2009

Cytochrome P450 monooxygenases (P450s) play important roles in the synthesis of diverse secondary compounds in Arabidopsis (Arabidopsis thaliana). Comparison of four data sets analyzing seedlings harvested over a 2-d period of constant conditions after growth with varying photoperiods and thermocycles recorded a total of 98 P450 loci as circadian regulated for at least one of the four conditions. Here, we further describe the circadian-regulated pathways using, as reporters, individual P450 loci that are likely to be rate limiting in secondary metabolic pathways. Reverse transcription-polymerase chain reaction gel blot analyses have confirmed circadian regulation of P450s in phenylpropanoid, carotenoid, oxylipin, glucosinolate, and brassinosteroid biosyntheses and have shown that both P450 and non-P450 genes in the many branches of the phenylpropanoid pathway have similar circadian patterns of expression. In silico analyses of the subsets of coregulated promoters have identified overrepresented promoter elements in various biosynthetic pathway genes, including MYB and MYB4 elements that are significantly more abundant in promoters for the core and lignin sections of phenylpropanoid metabolism. Interactions with these elements important for circadian regulation do not involve the MYB transcription factor PAP1, as previously proposed, since the expression patterns of circadian-regulated P450s are the same in pap1-D mutant seedlings as in wild-type seedlings. Further analysis of circadian-regulated promoters in other biochemical pathways provides us with the opportunity to identify novel promoter motifs that might be important in P450 circadian regulation.
CIA2 Coordinately Up-Regulates Protein Import and Synthesis in Leaf Chloroplasts
Authors: Sun Chih-Wen , Huang Yen-Chiao , Chang Hsin-Yen
Published: April 2009

Plastid biogenesis and maintenance depend on the coordinated assembly of proteins imported from the cytosol with proteins translated within plastids. Chloroplasts in leaf cells have a greater need for protein import and protein synthesis than plastids in other organs due to the large amount of proteins required for photosynthesis. We previously reported that the Arabidopsis (Arabidopsis thaliana) transcription factor CIA2 specifically up-regulates leaf expression of genes encoding protein translocons Toc33 and Toc75, which are essential for protein import into chloroplasts. Protein import efficiency was therefore reduced in cia2 mutant chloroplasts. To further understand the function of CIA2, gene expression profiles of the wild type and a cia2 mutant were compared by microarray analysis. Interestingly, in addition to genes encoding protein translocon components, other genes down-regulated in cia2 almost exclusively encode chloroplast ribosomal proteins. Isolated cia2 mutant chloroplasts showed reduced translation efficiency and steady-state accumulation of plastid-encoded proteins. When CIA2 was ectopically expressed in roots, expression of both the protein translocon and ribosomal protein genes increased. Further analyses in vivo revealed that CIA2 up-regulated these genes by binding directly to their promoter regions. We propose that CIA2 is an important factor responsible for fulfilling the higher protein demands of leaf chloroplasts by coordinately increasing both protein import and protein translation efficiencies.
Anatomical and Transcriptomic Studies of the Coleorhiza Reveal the Importance of This Tissue in Regulating Dormancy in Barley
Authors: Barrero José M. , Talbot Mark J. , White Rosemary G. , Jacobsen John V. , Gubler Frank
Published: April 2009

The decay of seed dormancy during after-ripening is not well understood, but elucidation of the mechanisms involved may be important for developing strategies for modifying dormancy in crop species and, for example, addressing the problem of preharvest sprouting in cereals. We have studied the germination characteristics of barley (Hordeum vulgare ‘Betzes’) embryos, including a description of anatomical changes in the coleorhiza and the enclosed seminal roots. The changes that occur correlate with abscisic acid (ABA) contents of embryo tissues. To understand the molecular mechanisms involved in dormancy loss, we compared the transcriptome of dormant and after-ripened barley embryos using a tissue-specific microarray approach. Our results indicate that in the coleorhiza, ABA catabolism is promoted and ABA sensitivity is reduced and that this is associated with differential regulation by after-ripening of ABA 8′-hydroxylase and of the LIPID PHOSPHATE PHOSPHATASE gene family and ABI3-INTERACTING PROTEIN2, respectively. We also identified other processes, including jasmonate responses, cell wall modification, nitrate and nitrite reduction, mRNA stability, and blue light sensitivity, that were affected by after-ripening in the coleorhiza that may be downstream of ABA signaling. Based on these results, we propose that the coleorhiza plays a major role in causing dormancy by acting as a barrier to root emergence and that after-ripening potentiates molecular changes related to ABA metabolism and sensitivity that ultimately lead to degradation of the coleorhiza, root emergence, and germination.
Large-Scale Arabidopsis Phosphoproteome Profiling Reveals Novel Chloroplast Kinase Substrates and Phosphorylation Networks
Authors: Reiland Sonja , Messerli Gaëlle , Baerenfaller Katja , Gerrits Bertran , Endler Anne , Grossmann Jonas , Gruissem Wilhelm , Baginsky Sacha
Published: April 2009

We have characterized the phosphoproteome of Arabidopsis (Arabidopsis thaliana) seedlings using high-accuracy mass spectrometry and report the identification of 1,429 phosphoproteins and 3,029 unique phosphopeptides. Among these, 174 proteins were chloroplast phosphoproteins. Motif-X (motif extractor) analysis of the phosphorylation sites in chloroplast proteins identified four significantly enriched kinase motifs, which include casein kinase II (CKII) and proline-directed kinase motifs, as well as two new motifs at the carboxyl terminus of ribosomal proteins. Using the phosphorylation motifs as a footprint for the activity of a specific kinase class, we connected the phosphoproteins with their putative kinases and constructed a chloroplast CKII phosphorylation network. The network topology suggests that CKII is a central regulator of different chloroplast functions. To provide insights into the dynamic regulation of protein phosphorylation, we analyzed the phosphoproteome at the end of day and end of night. The results revealed only minor changes in chloroplast kinase activities and phosphorylation site utilization. A notable exception was ATP synthase β-subunit, which is found phosphorylated at CKII phosphorylation sites preferentially in the dark. We propose that ATP synthase is regulated in cooperation with 14-3-3 proteins by CKII-mediated phosphorylation of ATP synthase β-subunit in the dark.
Leucine Aminopeptidase Regulates Defense and Wound Signaling in Tomato Downstream of Jasmonic Acid
Authors: Fowler Jonathan H. , Narváez-Vásquez Javier , Aromdee Dale N. , Pautot Véronique , Holzer Frances M. , Walling Linda L.
Published: April 2009

Leucine aminopeptidase A (LapA) is a late wound-response gene of tomato (Solanum lycopersicum). To elucidate the role of LapA, transgenic plants that overexpressed or abolished LapA gene expression were used. The early wound-response gene RNA levels were similar in wild-type and Lap-silenced (LapA-SI), -antisense (LapA-AS), and -overexpressing (LapA-OX) plants. By contrast, late wound-response gene RNA levels and protection against Manduca sexta damage were influenced by LapA RNA and protein levels. While LapA-OX plants had elevated levels of LapA RNAs and protein, ectopic expression of LapA was not sufficient to induce Pin (Ser proteinase inhibitor) or PPO (polyphenol oxidase) transcripts in nonwounded leaves. M. sexta larvae damaged less foliage and displayed delays in growth and development when feeding on LapA-OX plants. By contrast, LapA-SI and LapA-AS lines had lower levels of Pin and PPO RNAs than wild-type controls. Furthermore, larvae consumed more foliage and attained larger masses when feeding on LapA-SI plants. Jasmonic acid (JA) did not complement the wound-signaling phenotype of LapA-SI plants. Based on root elongation in the presence of JA, JA perception appeared to be intact in LapA-SI lines. Collectively, these data suggested that LAP-A has a role in modulating essential defenses against herbivores by promoting late wound responses and acting downstream of JA biosynthesis and perception.
GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis
Authors: Waters Mark T. , Wang Peng , Korkaric Muris , Capper Richard G. , Saunders Nigel J. , Langdale Jane A.
Published: April 2009

Chloroplasts of photosynthetic organisms harness light energy and convert it into chemical energy. In several land plants, GOLDEN2-LIKE (GLK) transcription factors are required for chloroplast development, as glk1 glk2 double mutants are pale green and deficient in the formation of the photosynthetic apparatus. We show here that glk1 glk2 double mutants of Arabidopsis thaliana accumulate abnormal levels of chlorophyll precursors and that constitutive GLK gene expression leads to increased accumulation of transcripts for antenna proteins and chlorophyll biosynthetic enzymes. To establish the primary targets of GLK gene action, an inducible expression system was used in combination with transcriptome analysis. Following induction, transcript pools were substantially enriched in genes involved in chlorophyll biosynthesis, light harvesting, and electron transport. Chromatin immunoprecipitation experiments confirmed the direct association of GLK1 protein with target gene promoters, revealing a putative regulatory cis-element. We show that GLK proteins influence photosynthetic gene expression independently of the phyB signaling pathway and that the two GLK genes are differentially responsive to plastid retrograde signals. These results suggest that GLK genes help to coregulate and synchronize the expression of a suite of nuclear photosynthetic genes and thus act to optimize photosynthetic capacity in varying environmental and developmental conditions.
Members of the GCN5 Histone Acetyltransferase Complex Regulate PLETHORA-Mediated Root Stem Cell Niche Maintenance and Transit Amplifying Cell Proliferation inArabidopsis
Authors: Kornet Noortje , Scheres Ben
Published: April 2009

The PLETHORA (PLT) stem cell transcription factors form a developmentally instructive protein gradient in Arabidopsis thaliana roots. Histone acetylation is known to facilitate gene transcription and plays an important role in developmental processes. Here, we show that histone acetyltransferase GCN5 (for general control nonderepressible 5) attenuates the PLT gradient. Based on genetic evidence, we establish that GCN5 is essential for root stem cell niche maintenance and acts in the PLT pathway. The GCN5-associated factor ADA2b (for alteration/deficiency in activation 2b) is also positioned in the PLT pathway and regulates PLT expression, similar to GCN5. Both GCN5 and ADA2b mediate proliferation of the transit amplifying cells, but ADA2b does not affect stem cell niche maintenance. Overexpression of PLT2 rescues the stem cell niche defect of gcn5 mutants, indicating that GCN5 regulation of PLT expression is essential for maintenance of the root stem cell niche. We conclude that histone acetylation complexes play an important role in shaping a developmentally instructive gradient in the root.