bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleation theory with delayed interactions: An application to the early stages of the receptor-mediated adhesion/fusion kinetics of lipid vesicles
Authors: Raudino Antonio , Pannuzzo Martina
Published: January 2010

A semiquantitative theory aimed to describe the adhesion kinetics between soft objects, such as living cells or vesicles, has been developed. When rigid bodies are considered, the adhesion kinetics is successfully described by the classical Derjaguin, Landau, Verwey, and Overbeek (DLVO) picture, where the energy profile of two approaching bodies is given by a two asymmetrical potential wells separated by a barrier. The transition probability from the long-distance to the short-distance minimum defines the adhesion rate. Conversely, soft bodies might follow a different pathway to reach the short-distance minimum: thermally excited fluctuations give rise to local protrusions connecting the approaching bodies. These transient adhesion sites are stabilized by short-range adhesion forces (e.g., ligand-receptor interactions between membranes brought at contact distance), while they are destabilized both by repulsive forces and by the elastic deformation energy. Above a critical area of the contact site, the adhesion forces prevail: the contact site grows in size until the complete adhesion of the two bodies inside a short-distance minimum is attained. This nucleation mechanism has been developed in the framework of a nonequilibrium Fokker–Planck picture by considering both the adhesive patch growth and dissolution processes. In addition, we also investigated the effect of the ligand-receptor pairing kinetics at the adhesion site in the time course of the patch expansion. The ratio between the ligand-receptor pairing kinetics and the expansion rate of the adhesion site is of paramount relevance in determining the overall nucleation rate. The theory enables one to self-consistently include both thermodynamics (energy barrier height) and dynamic (viscosity) parameters, giving rise in some limiting cases to simple analytical formulas. The model could be employed to rationalize fusion kinetics between vesicles, provided the short-range adhesion transition is the rate-limiting step to the whole adhesion process. Approximate relationships between the experimental fusion rates reported in the literature and parameters such as membrane elastic bending modulus, repulsion strength, temperature, osmotic forces, ligand-receptor binding energy, solvent and membrane viscosities are satisfactory explained by our model. The present results hint a possible role of the initial long-distance→short-distance transition in determining the whole fusion kinetics.
Experimental observation of the transition from nonlocal to local electron kinetics in inductively coupled plasmas
Authors: Lee Hyo-Chang , Lee Min-Hyong , Chung Chin-Wook
Published: January 2010

The transition from nonlocal to local kinetics was observed through the spatially resolved measurements of electron energy distribution functions in inductively coupled plasmas. As gas pressures increase, the spatial profiles of the effective electron temperatures (Teff) from the electron energy distribution functions changed dramatically from hollow shapes to flat shapes. With further increases in gas pressures, the Teff had saddle-shaped profiles with the highest Teff in the vicinity of an antenna coil. These changes in the radial profiles of the Teff show a transition of the electron kinetics from nonlocal to local regimes. This transition occurred when the electron energy relaxation lengths became smaller than the antenna half size.
Nearly complete isobar suppression by photodetachment
Authors: Andersson P. , Lindahl A. O. , Hanstorp D. , Havener C. C. , Liu Yun , Liu Yuan
Published: January 2010

The efficiency of selective suppression of negative ions by photodetachment in a gas-filled radio frequency quadrupole ion cooler was investigated with a new detection method. A neodymium doped yttrium aluminum garnet laser beam at 1064 nm was used to remove Co− ions in the radio frequency quadrupole cooler and the remaining ions were then probed by photodetachment and neutral particle detection. More than 99.99% suppression of the Co− ions was observed. Under identical conditions, only 20% of a Ni− beam was suppressed. The results demonstrate that this isobar suppression technique can lead to nearly complete elimination of certain isobaric contaminants in negative ion beams, opening up new experimental possibilities in nuclear and atomic research and accelerator mass spectrometry.
The influence of aluminum grain size on alumina nanoporous structure
Authors: Feil A. F. , da Costa M. V. , Amaral L. , Teixeira S. R. , Migowski P. , Dupont J. , Machado G. , Peripolli S. B.
Published: January 2010

An approach to control the interpore distances and nanopore diameters of 150-nm-thick thin aluminum films is reported here. The Al thin films were grown by sputtering on p-type silicon substrate and anodized with a conventional anodization process in a phosphoric acid solution. It was found that interpore distance and pore diameter are related to the aluminum grain size and can be controlled by annealing. The grain contours limit the sizes of alumina cells. This mechanism is valid for grain sizes supporting only one alumina cell and consequently only one pore.
Bistable effect in the liquid crystal blue phase
Authors: Wang Chun-Ta , Liu Hu-Yi , Cheng Hsin-Hui , Lin Tsung-Hsien
Published: January 2010

This study investigates the bistable effect and transition mechanism between various lattice orientations in the negative liquid crystal blue phase. The blue phase exists over a wide temperature range ∼16 °C, and three lattices (110), (112), and (200) are confirmed with Kossel diagrams. The red platelet (110) lattice and blue platelet (200) lattice can be stabilized and switched to each other by particular pulse voltages. An electric field induced planar state and electrohydrodynamatic effect in the blue phase is also investigated. Additionally, the reflected color of the (200) lattice can be adjusted from 455 to 545 nm by temperature induced lattice distortions and provided with reversibility.
Evidence for random networks of diodes in thin films of LaVO3 on SrTiO3 substrates
Authors: Razavi F. S. , Gharetape S. Jamali , Crandles D. A. , Christiani G. , Kremer R. K. , Habermeier H.-U.
Published: January 2010

Highly conducting interfaces of transition metal oxide heterolayers could provide a promising access to transition metal oxide based electronic devices similar to those based on semiconductor heterostructures. Recently, metallic conductivity has been reported at the LaAlO3/SrTiO3 heterointerface. Here we report the observation of diodelike behavior and the formation of a random diode network in thin films of LaVO3 deposited on as-polished SrTiO3 substrates. Depending on films annealing conditions we observed linear or nonlinear I-V characteristic below 50 K.
Mechanism and reduction of temporal image sticking in ac plasma display panel
Authors: Park Choon-Sang , Tae Heung-Sik
Published: January 2010

It is found that temporal image sticking in ac plasma display panels (PDPs) is predominantly induced by organic impurities, such as CxHy, on the MgO surface. The vacuum ultraviolet produced during a short sustain discharge dissociates these organic impurities, such as CxHy, into C and H, where the latter then combines with the O from the MgO surface, resulting in the production of chemical compounds, including H2O, that lower the luminance by hindering the visible conversion of the phosphor layer. Thus, according to this mechanism, minimizing the residual organic impurities, such as CxHy, on the MgO surface is a key factor for removing temporal image sticking. Therefore, to reduce the residual impurity level on the MgO layer of a 50 in. full-high definition (HD) ac-PDP with an He (35%)-Xe (11%) content, the MgO layer is given rf-plasma treatment using various gases, and the experimental results show that Ar plasma treatment was most effective in eliminating the residual impurities on the MgO layer and thereby improving the temporal image sticking.
Tunable zero field ferromagnetic resonance in arrays of bistable magnetic nanowires
Authors: De La Torre Medina Joaquín , Piraux Luc , Encinas Armando
Published: January 2010

The tunability of the zero field resonance frequency in arrays of bistable nanowires is demonstrated. Analysis of the resonance spectra for different remanent states show that the signal results from the superposition of the double absorption related to wires magnetized in both the positive and negative direction. An analytical model is proposed and validated which depends of the configuration dependent dipolar interaction and the peak amplitude of the superposing signals. The range over which the zero field resonance frequency can be tuned has a lower bound at remanence equal to one and a maxima when remanence vanishes.
Control of direct band gap emission of bulk germanium by mechanical tensile strain
Authors: El Kurdi M. , Bertin H. , Martincic E. , de Kersauson M. , Fishman G. , Sauvage S. , Bosseboeuf A. , Boucaud P.
Published: January 2010

We show that the recombination energy of the direct band gap photoluminescence (PL) of germanium can be controlled by an external mechanical stress. The stress is provided by an apparatus commonly used for bulge or blister test. An energy redshift up to 60 meV is demonstrated for the room temperature PL of a thin germanium membrane (125 nm wavelength shift from 1535 to 1660 nm). This PL shift is correlated with the in-plane tensile strain generated in the film. A biaxial tensile strain larger than 0.6% is achieved by this method. This mechanical strain allows to approach the direct band gap condition for germanium which is of tremendous importance to achieve lasing with this material.
Three-dimensional manipulation of gold nanoparticles with electro-enhanced capillary forces
Authors: Toset J. , Gomila G.
Published: January 2010

We demonstrate the possibility to manipulate 25 nm radius gold nanoparticles in the three spatial dimensions with an atomic force microscope with the use of electroenhanced capillary forces. We show that an enhanced water-bridge can be electrostatically induced between a conducting probe and a metallic nanoparticle by the application of a voltage pulse, which is able to exert a pulling capillary force on the nanoparticle strong enough to detach it from the substrate. The nanoparticle can then be moved, attached to the probe, and placed back to the desired location on the substrate simply by contacting it.
Efficient generation and transportation of energetic electrons in a carbon nanotube array target
Authors: Ji Yanling , Jiang Gang , Wu Weidong , Wang Chaoyang , Gu Yuqiu , Tang Yongjian
Published: January 2010

Laser-driven energetic electron propagation in a carbon nanotube-array target is investigated using two-dimensional particle-in-cell simulations. Energetic electrons are efficiently generated when the array is irradiated by a short intense laser pulse. Confined and guided transportation of energetic electrons in the array is achieved by exploiting strong transient electromagnetic fields created at the wall surfaces of nanotubes. The underlying mechanisms are discussed in detail. Our investigation shows that the laser energy can be transferred more effectively to the target electrons in the array than that of in the flat foil due to the hole structures in the array.
Electrical transport properties of perpendicular magnetized Mn-Ga epitaxial films
Authors: Wu Feng , Sajitha E. P. , Mizukami Shigemi , Watanabe Daisuke , Miyazaki Terunobu , Naganuma Hiroshi , Oogane Mikihiko , Ando Yasuo
Published: January 2010

We report electrical transport properties of perpendicular magnetized Mn-Ga epitaxial films with various thicknesses. The maximum extraordinary Hall resistivity and Hall angle is 11.5 μΩ cm and 5.7%, respectively, which is comparable to the highest value reported in amorphous Fe0.79Gd0.21 alloy. In the low temperature region, resistivity was proportional to T2.9 owing to the unconventional one-magnon scattering processes, indicating high spin polarization of this material.
Direct-current-like phase space manipulation using chirped alternating current fields
Authors: Schmit P. F. , Fisch N. J.
Published: January 2010

Waves in plasmas can accelerate particles that are resonant with the wave. A dc electric field also accelerates particles, but without a resonance discrimination, which makes the acceleration mechanism profoundly different. Whereas wave-particle acceleration mechanisms have been widely discussed in the literature, this work discusses the direct analogy between wave acceleration and dc field acceleration in a particular parameter regime explored in previous works. Apart from the academic interest of this correspondence, there may be practical advantages in using waves to mimic dc electric fields, for example, in driving plasma current with high efficiency.
An intrinsic formation mechanism for midgap electronic states in semiconductor glasses
Authors: Zhugayevych Andriy , Lubchenko Vassiliy
Published: January 2010

We argue that semiconducting quenched liquids and frozen glasses may exhibit a set of peculiar electronic states of topological origin. These states reside at strained regions arising during structural reconfigurations between distinct aperiodic states intrinsic to quenched melts. The strained regions are domain walls separating the distinct aperiodic states; their number is about 1020 cm−3 in all glassformers owing to the universal dynamics of deeply supercooled melts. Even though located near the middle of the forbidden gap, the topological states are rather extended in one direction while being centered at under- and overcoordinated atoms. The states exhibit the reverse charge-spin relation, the majority of states being diamagnetic and charged. The topological states may be sufficient to account for a number of irradiation-induced phenomena in amorphous semiconductors, including electron spin resonance signal, midgap absorption, photoluminescence, and the fatigue of photoluminescence. We propose experiments to test the present microscopic picture.
Enhancement and de-enhancement effects in vibrational resonance Raman optical activity
Authors: Luber Sandra , Neugebauer Johannes , Reiher Markus
Published: January 2010

In this study, we investigate interference between several excited electronic states in resonance enhanced vibrational Raman optical activity (RROA) spectra. A gradient Franck–Condon model for the excited-state potential energy surface is applied in order to include vibronic effects in the description of the RROA intensities. Both sum-over-states and time-dependent expressions for the RROA intensities in case of close-lying excited states are given. As an example, we compare the calculated RROA and resonance Raman spectra of (S)-(+)-naproxen-OCD3 to the experimental ones. Subsequently, we examine the excitation profiles of (S)-(+)-naproxen and study the vibration at 1611 cm−1 in more detail in order to demonstrate how the consideration of a second excited electronic state can lead to significant changes in the RROA intensities.
Optical to ultraviolet spectra of sandwiches of benzene and transition metal atoms: Time dependent density functional theory and many-body calculations
Authors: Martínez J. I. , García-Lastra J. M. , López M. J. , Alonso J. A.
Published: January 2010

The optical spectra of sandwich clusters formed by transition metal atoms (titanium, vanadium, and chromium) intercalated between parallel benzene molecules have been studied by time-dependent density functional theory (TDDFT) and many-body perturbation theory. Sandwiches with different number of layers, including infinite chains, are considered. The lowest excitation energy peaks in the spectra are characteristic of the robust bonding in these complexes. The excitation energies vary in a systematic way with the metal atoms and with the cluster size, and so these materials could be used to tune the optical properties according to specific functionality targets. The differences in the spectra could be used to identify relative abundances of isomers with different spins in experimental studies. As a salient feature, this theoretical spectroscopic analysis predicts the metallization of the infinite (TiBz)∞ chain, which is not the case of (CrBz)∞.
Statistical analysis of time resolved single molecule fluorescence data without time binning
Authors: Hinze G. , Basché T.
Published: January 2010

We depict two algorithms to calculate correlation functions from two different time resolved single molecule fluorescence experiments without the need of time binning. Our first procedure allows to calculate the reduced linear dichroism from polarization resolved fluorescence data. Since we process single photon counts instead of time binned data, considerably faster fluctuations of the dichroism can be analyzed than with conventional methods. With our second procedure time resolved fluorescence obtained with a time correlated single photon counting setup can be analyzed with respect to fluorescence lifetime fluctuations. Again this new algorithm processes single photon events making time binning of photon counts obsolete. Both methods presented are characterized by enhanced time resolution thus allowing to study fast fluctuations of either single molecular orientation or fluorescence life times, respectively.
Delivery of foreign antigens by engineered outer membrane vesicle vaccines
Authors: Chen David J. , Osterrieder Nikolaus , Metzger Stephan M. , Buckles Elizabeth , Doody Anne M. , DeLisa Matthew P. , Putnam David
Published: January 2010

As new disease threats arise and existing pathogens grow resistant to conventional interventions, attention increasingly focuses on the development of vaccines to induce protective immune responses. Given their admirable safety records, protein subunit vaccines are attractive for widespread immunization, but their disadvantages include poor immunogenicity and expensive manufacture. We show here that engineered
Escherichia coli
outer membrane vesicles (OMVs) are an easily purified vaccine-delivery system capable of greatly enhancing the immunogenicity of a low-immunogenicity protein antigen without added adjuvants. Using green-fluorescent protein (GFP) as the model subunit antigen, genetic fusion of GFP with the bacterial hemolysin ClyA resulted in a chimeric protein that elicited strong anti-GFP antibody titers in immunized mice, whereas immunization with GFP alone did not elicit such titers. Harnessing the specific secretion of ClyA to OMVs, the ClyA-GFP fusion was found localized in OMVs, resulting in engineered recombinant OMVs. The anti-GFP humoral response in mice immunized with the engineered OMV formulations was indistinguishable from the response to the purified ClyA-GFP fusion protein alone and equal to purified proteins absorbed to aluminum hydroxide, a standard adjuvant. In a major improvement over current practice, engineered OMVs containing ClyA-GFP were easily isolated by ultracentrifugation, effectively eliminating the need for laborious antigen purification from cell-culture expression systems. With the diverse collection of heterologous proteins that can be functionally localized with OMVs when fused with ClyA, this work signals the possibility of OMVs as a robust and tunable technology platform for a new generation of prophylactic and therapeutic vaccines.
An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily
Authors: van Loo Bert , Jonas Stefanie , Babtie Ann C. , Benjdia Alhosna , Berteau Olivier , Hyvönen Marko , Hollfelder Florian
Published: January 2010

We report a catalytically promiscuous enzyme able to efficiently promote the hydrolysis of six different substrate classes. Originally assigned as a phosphonate monoester hydrolase (PMH) this enzyme exhibits substantial second-order rate accelerations ((
k
cat
/
K
M
)/
k
w
), ranging from 10
7
to as high as 10
19
, for the hydrolyses of phosphate mono-, di-, and triesters, phosphonate monoesters, sulfate monoesters, and sulfonate monoesters. This substrate collection encompasses a range of substrate charges between 0 and -2, transition states of a different nature, and involves attack at two different reaction centers (P and S). Intrinsic reactivities (half-lives) range from 200 days to 10
5
 years under near neutrality. The substantial rate accelerations for a set of relatively difficult reactions suggest that efficient catalysis is not necessarily limited to efficient stabilization of just one transition state. The crystal structure of PMH identifies it as a member of the alkaline phosphatase superfamily. PMH encompasses four of the native activities previously observed in this superfamily and extends its repertoire by two further activities, one of which, sulfonate monoesterase, has not been observed previously for a natural enzyme. PMH is thus one of the most promiscuous hydrolases described to date. The functional links between superfamily activities can be presumed to have played a role in functional evolution by gene duplication.
Role of microRNA-23b in flow-regulation of Rb phosphorylation and endothelial cell growth
Authors: Wang Kuei-Chun , Garmire Lana Xia , Young Angela , Nguyen Phu , Trinh Andrew , Subramaniam Shankar , Wang Nanping , Shyy John YJ , Li Yi-Shuan , Chien Shu
Published: January 2010

MicroRNAs (miRs) can regulate many cellular functions, but their roles in regulating responses of vascular endothelial cells (ECs) to mechanical stimuli remain unexplored. We hypothesize that the physiological responses of ECs are regulated by not only mRNA and protein signaling networks, but also expression of the corresponding miRs. EC growth arrest induced by pulsatile shear (PS) flow is an important feature for flow regulation of ECs. miR profiling showed that 21 miRs are differentially expressed (8 up- and 13 downregulated) in response to 24-h PS as compared to static condition (ST). The mRNA expression profile indicates EC growth arrest under 24-h PS. Analysis of differentially expressed miRs yielded 68 predicted mRNA targets that overlapped with results of microarray mRNA profiling. Functional analysis of miR profile indicates that the cell cycle network is highly regulated. The upregulation of miR-23b and miR-27b was found to correlate with the PS-induced EC growth arrest. Inhibition of miR-23b using antagomir-23b oligonucleotide (AM23b) reversed the PS-induced E2F1 reduction and retinoblastoma (Rb) hypophosphorylation and attenuated the PS-induced G1/G0 arrest. Antagomir AM27b regulated E2F1 expression, but did not affect Rb and growth arrest. Our findings indicate that PS suppresses EC proliferation through the regulation of miR-23b and provide insights into the role of miRs in mechanotransduction.
Nigerian English in informal email messages
Authors: Chiluwa Innocent
Published: January 2010

This study applies a sociolinguistic and discourse-analytical methodology to the study of features and manifestations of Nigerian English in computer-mediated communication, particularly informal emails. The data comprise 133 email samples consisting of messages received or sent within a seven-year period, i.e. between 2002 and 2009, from typical Nigerian environments, as well as by the youth, adults and the elderly. Analyses reveal that the rise of new media technologies and digital communication has provided a resource for the use and dissemination of Nigerian English alongside Nigerian cultures. The study shows that Nigerian English in informal emails comprises the construction of local thoughts through a range of characteristic properties. In non-standard Nigerian English features like misuse of words, grammatical inconsistencies and a mixture of local pidgin also exist. The study of Nigerian English in informal emails reveals that email samples provide resourceful data for the study of English regional varieties in computer-mediated communication. It also shows that a variety of English is a cultural medium for expressing language habits and socio-cultural practices.
Effects of gender-identity and gender-congruence on levels of politeness among young Japanese and Koreans
Authors: Tamaoka Katsuo , Yamaguchi Hyunjung Lim , Miyaoka Yayoi , Kiyama Sachiko
Published: January 2010

The two factors of ‘gender-identity’ (whether the speaker is male or female) and ‘gender-congruence’ (whether or not the gender of speaker and listener is the same) can be assumed to act differently in determining levels of politeness. To investigate this assumption, the present study was designed to analyze university student politeness levels in Japan and South Korea when they (i.e., speakers) asked various people (i.e., listeners) to purchase a concert ticket. A decision tree analysis revealed hierarchies of factors predictive of politeness levels specific to young Japanese and Koreans. Among Japanese, distance (i.e., extent to which speaker and listener are acquainted) was the strongest followed by power (i.e., extent of disparity in social status) and gender-identity/gender-congruence. Among Koreans, however, power appeared to override distance, resulting in the descending order of power and gender-identity/gender-congruence. Regarding gender-related factors, the results of these parallel studies in Japan and South Korea generally suggested a distinctive influence of gender-identity on politeness levels when listeners held equal or lesser power than speakers, while gender-congruence was implicated when listeners held greater power.
Face goals in apology
Authors: Han Bing , Cai Deborah A.
Published: January 2010

This study investigated how the offender’s responsibility, offense severity, offender’s prior relationship with the offended person, and culture influence the offender’s concerns for self- and other-positive and negative face when apologizing to the offended person. The study hypothesized that responsibility, severity, and relationship have positive relationships with other-positive, other-negative, and self-positive face concerns but a negative relationship with self-negative face concern. Culture was expected to moderate the effect of relationship on the four face concerns. Results supported the main effects of responsibility and relationship on other-positive, other-negative, and self-positive face concerns, but these effects were moderated by culture such that the expected positive relationships were supported only among U.S. Americans but not among Chinese. U.S. Americans varied their face concerns when apologizing based on situational and relational cues whereas Chinese did not make such distinctions; Chinese maintained relatively high levels of face concerns across the different levels of responsibility and relationship type.
Diglossia in East Asia
Authors: Snow Don
Published: January 2010

This article examines the most extensive case of diglossia in history, that of diglossia in East Asia. In pre-modern times, Classical Chinese functioned as the high (H) language variety in not only China, but also Korea, Japan, and Vietnam, and this entire region can arguably be viewed as a single instance of diglossia in the sense that the rise and eventual decline of diglossia in these societies followed similar patterns, and changes in one society often affected the others. Examination of diglossia in East Asia shows that even during long centuries of apparent stability, gradual changes were always underway, hence supporting Hudson’s (2002) view that stability in diglossic patterns is at best relative. The East Asian case also supports Coulmas’ (2002) view that writing is pivotal to any theory of diglossia, in that the division of roles between H and L in East Asia was essentially one of written/spoken language. Finally, the case of East Asia suggests that there are two essentially different kinds of diglossia, a traditional kind which is common in pre-modern societies and in which H is what Anderson (2006) calls a “sacred language,” and a less common modern kind in which H is a modern standard language.
Factors Associated with Substance Use among Homeless Young Adults
Authors: Gomez Rebecca , Thompson Sanna J. , Barczyk Amanda N.
Published: January 2010

The purpose of this study was to investigate factors associated with substance use among homeless young adults. Multinomial logistic regression analyses examined the influence of social networks and economic factors among a group of homeless young adults with differing levels of alcohol and drug use. In addition, for those with an alcohol use disorder, the role of future time expectancies was examined. A sample ( n = 185) of homeless young adults aged 18 to 23 were recruited from a community drop-in center and interviewed utilizing self-report instruments. Findings suggest that social networks, economic factors, and future expectancies are significant predictors of the level of substance use among homeless young adults. Being able to identify those areas that place homeless young adults at risk for substance abuse and dependence has implications for effective intervention.
THE ‘ACTIVE WELFARE STATE’ AND ITS CONSEQUENCES
Authors: Holmqvist Mikael
Published: January 2010

This paper reports the findings of a longitudinal case study of sheltered employment for activating so-called occupationally disabled people in Sweden. Data consist of interviews, archival studies and participant observation on how occupationally disabled people's employability is to be promoted and the consequences of such activities. It is argued that those that, for one reason or another, are unable to live up to the norms of being a ‘normal’ and hence fully active citizen, are objectified as passive and unemployable persons through the same principles that aim to make them active. Through its emphasis on ability, strength, and competence, the ‘active society’ may raise the bar of employability higher than ever before. As a result, an increasing number of people risk disablement and indeed end up as ‘disabled’.
Exogenous and endogenous spatial attention effects on visuospatial working memory
Authors: Botta Fabiano , Santangelo Valerio , Raffone Antonino , Lupiáñez Juan , Belardinelli Marta Olivetti
Published: January 2010

In this study, we investigate how exogenous and endogenous orienting of spatial attention affect visuospatial working memory (VSWM). Specifically, we focused on two attentional effects and their consequences on storage in VSWM, when exogenous (Experiment 1) or endogenous (Experiment 2) orienting cues were used. The first effect, known as the meridian effect, is given by a decrement in behavioural performance when spatial cues and targets are presented in locations separated by vertical and/or horizontal meridians. The second effect, known as the distance effect, is given by a decrement in the orienting effects as a function of the spatial distance between cues and targets. Our results revealed a dissociation between exogenous and endogenous orienting mechanisms in terms of both meridian and distance effects. We found that meridian crossing affects performance only when endogenous cues were used. Specifically, VSWM performance with endogenous cueing depended more on the number of meridian crossings than on distance between cue and target. By contrast, a U-shaped distance dependency was observed using exogenous cues. Our findings therefore suggest that exogenous and endogenous orienting mechanisms lead to different forms of attentional bias for storage in VSWM.
FineStr: a web server for single-base-resolution nucleosome positioning
Authors: Gabdank Idan , Barash Danny , Trifonov Edward N.
Published: January 2010

Summary: The DNA in eukaryotic cells is packed into the chromatin that is composed of nucleosomes. Positioning of the nucleosome core particles on the sequence is a problem of great interest because of the role nucleosomes play in different cellular processes including gene regulation.

Using the sequence structure of 10.4 base DNA repeat presented in our previous works and nucleosome core DNA sequences database, we have derived the complete nucleosome DNA bendability matrix of Caenorhabditis elegans.

We have developed a web server named FineStr that allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them.

Availability: FineStr server is freely available for use on the web at http:/www.cs.bgu.ac.il/~nucleom. The site contains a help file with explanation regarding the exact usage.

Contact:  gabdank@cs.bgu.ac.il
Building a home from foam—túngara frog foam nest architecture and three-phase construction process
Authors: Dalgetty Laura , Kennedy Malcolm W.
Published: January 2010

Frogs that build foam nests floating on water face the problems of over-dispersion of the secretions used and eggs being dangerously exposed at the foam : air interface. Nest construction behaviour of túngara frogs,
Engystomops pustulosus
, has features that may circumvent these problems. Pairs build nests in periodic bursts of foam production and egg deposition, three discrete phases being discernible. The first is characterized by a bubble raft without egg deposition and an approximately linear increase in duration of mixing events with time. This phase may reduce initial over-dispersion of foam precursor materials until a critical concentration is achieved. The main building phase is marked by mixing events and start-to-start intervals being nearly constant in duration. During the final phase, mixing events do not change in duration but intervals between them increase in an exponential-like fashion. Pairs joining a colonial nesting abbreviate their initial phase, presumably by exploiting a pioneer pair's bubble raft, thereby reducing energy and material expenditure, and time exposed to predators. Finally, eggs are deposited only in the centre of nests with a continuously produced, approximately 1 cm deep egg-free cortex that protectively encloses hatched larvae in stranded nests.
Efficiency of coding in macaque vocal communication
Authors: Semple Stuart , Hsu Minna J. , Agoramoorthy Govindasamy
Published: January 2010

A key characteristic of human language efficiency is that more frequently used words tend to be shorter in length—the ‘law of brevity’. To date, no test of this relationship between frequency of use and length has been carried out on non-human animal vocal communication. We show here that the vocal repertoire of the Formosan macaque (
Macaca cyclopis
) conforms to the pattern predicted by the law of brevity, with an inverse relationship found between call duration and rate of utterance. This finding provides evidence for coding efficiency in the vocal communication system of this species, and indicates commonality in the basic structure of the coding system between human language and vocal communication in this non-human primate.
Magnetoreception in eusocial insects: an update
Authors: Wajnberg Eliane , Acosta-Avalos Daniel , Alves Odivaldo Cambraia , de Oliveira Jandira Ferreira , Srygley Robert B. , Esquivel Darci M. S.
Published: January 2010

Behavioural experiments for magnetoreception in eusocial insects in the last decade are reviewed. Ants and bees use the geomagnetic field to orient and navigate in areas around their nests and along migratory paths. Bees show sensitivity to small changes in magnetic fields in conditioning experiments and when exiting the hive. For the first time, the magnetic properties of the nanoparticles found in eusocial insects, obtained by magnetic techniques and electron microscopy, are reviewed. Different magnetic oxide nanoparticles, ranging from superparamagnetic to multi-domain particles, were observed in all body parts, but greater relative concentrations in the abdomens and antennae of honeybees and ants have focused attention on these segments. Theoretical models for how these specific magnetosensory apparatuses function have been proposed. Neuron-rich ant antennae may be the most amenable to discovering a magnetosensor that will greatly assist research into higher order processing of magnetic information. The ferromagnetic hypothesis is believed to apply to eusocial insects, but interest in a light-sensitive mechanism is growing. The diversity of compass mechanisms in animals suggests that multiple compasses may function in insect orientation and navigation. The search for magnetic compasses will continue even after a magnetosensor is discovered in eusocial insects.
Muscle performance during frog jumping: influence of elasticity on muscle operating lengths
Authors: Azizi Emanuel , Roberts Thomas J.
Published: January 2010

A fundamental feature of vertebrate muscle is that maximal force can be generated only over a limited range of lengths. It has been proposed that locomotor muscles operate over this range of lengths in order to maximize force production during movement. However, locomotor behaviours like jumping may require muscles to shorten substantially in order to generate the mechanical work necessary to propel the body. Thus, the muscles that power jumping may need to shorten to lengths where force production is submaximal. Here we use direct measurements of muscle lengthin vivoand muscle force–length relationshipsin vitroto determine the operating lengths of the plantaris muscle in bullfrogs (Rana catesbeiana) during jumping. We find that the plantaris muscle operates primarily on the descending limb of the force–length curve, resting at long initial lengths (1.3 ± 0.06Lo) before shortening to muscle's optimal length (1.03 ± 0.05Lo). We also compare passive force–length curves from frogs with literature values for mammalian muscle, and demonstrate that frog muscles must be stretched to much longer lengths before generating passive force. The relatively compliant passive properties of frog muscles may be a critical feature of the system, because it allows muscles to operate at long lengths and improves muscles' capacity for force production during a jump.
Molecular markers reveal spatially segregated cryptic species in a critically endangered fish, the common skate (Dipturus batis)
Authors: Griffiths Andrew M. , Sims David W. , Cotterell Stephen P. , El Nagar Aliya , Ellis Jim R. , Lynghammar Arve , McHugh Matthew , Neat Francis C. , Pade Nicolas G. , Queiroz Nuno , Serra-Pereira Bárbara , Rapp Toby , Wearmouth Victoria J. , Genner Martin J.
Published: January 2010

Many sharks and skates are particularly vulnerable to overfishing because of their large size, slow growth, late maturity and low fecundity. In Europe dramatic population declines have taken place in common skate (Dipturus batisL.), one of the largest demersal fish in regional shelf seas, leading to extirpations from substantial parts of its former range. Here we report the discovery of cryptic species in common skate collected from the northeast Atlantic continental shelf. Data from nuclear microsatellite markers indicated two clearly distinct clades and phylogenetic analysis of mitochondrial DNA sequences demonstrated monophyly of each one of them. Capture locations showed evidence of strong spatial segregation, with one taxon occurring mainly in waters off the southern British Isles and around Rockall, while the other was restricted to more northerly shelf waters. These apparently cryptic species showed overlapping substrate and depth preferences, but distributional limits were closely related to temperature gradients, potentially indicating thermal limits to their distributions. This discovery of hidden diversity within a large, critically endangered marine vertebrate demonstrates how marine biodiversity can be underestimated, even in such a relatively well-studied and heavily exploited region.
Unparalleled rates of species diversification in Europe
Authors: Valente Luis M. , Savolainen Vincent , Vargas Pablo
Published: January 2010

The most rapid species radiations have been reported from ‘evolutionary laboratories’, such as the Andes and the Cape of South Africa, leading to the prevailing view that diversification elsewhere has not been as dramatic. However, few studies have explicitly assessed rates of diversification in northern regions such as Europe. Here, we show that carnations (
Dianthus
, Caryophyllaceae), a well-known group of plants from temperate Eurasia, have diversified at the most rapid rate ever reported in plants or terrestrial vertebrates. Using phylogenetic methods, we found that the majority of species of carnations belong to a lineage that is remarkably species-rich in Europe, and arose at the rate of 2.2–7.6 species per million years. Unlike most previous studies that have inferred rates of diversification in young diverse groups, we use a conservative approach throughout that explicitly incorporates the uncertainties associated with phylogenetic inference, molecular dating and incomplete taxon sampling. We detected a shift in diversification rates of carnations coinciding with a period of increase in climatic aridity in the Pleistocene, suggesting a link between climate and biodiversity. This explosive radiation suggests that Europe, the continent with the world's best-studied flora, has been underestimated as a cradle of recent and rapid speciation.
Widespread and tissue specific age-related DNA methylation changes in mice
Authors: Maegawa Shinji , Hinkal George , Kim Hyun Soo , Shen Lanlan , Zhang Li , Zhang Jiexin , Zhang Nianxiang , Liang Shoudan , Donehower Lawrence A. , Issa Jean-Pierre J.
Published: January 2010

Aberrant methylation of promoter CpG islands in cancer is associated with silencing of tumor-suppressor genes, and age-dependent hypermethylation in normal appearing mucosa may be a risk factor for human colon cancer. It is not known whether this age-related DNA methylation phenomenon is specific to human tissues. We performed comprehensive DNA methylation profiling of promoter regions in aging mouse intestine using methylated CpG island amplification in combination with microarray analysis. By comparing C57BL/6 mice at 3-mo-old versus 35-mo-old for 3627 detectable autosomal genes, we found 774 (21%) that showed increased methylation and 466 (13%) that showed decreased methylation. We used pyrosequencing to quantitatively validate the microarray data and confirmed linear age-related methylation changes for all 12 genomic regions examined. We then examined 11 changed genomic loci for age-related methylation in other tissues. Of these, three of 11 showed similar changes in lung, seven of 11 changed in liver, and six of 11 changed in spleen, though to a lower degree than the changes seen in colon. There was partial conservation between age-related hypermethylation in human and mouse intestines, and Polycomb targets in embryonic stem cells were enriched among the hypermethylated genes. Our findings demonstrate a surprisingly high rate of hyper- and hypomethylation as a function of age in normal mouse small intestine tissues and a strong tissue-specificity to the process. We conclude that epigenetic deregulation is a common feature of aging in mammals.
Imaging and Analysis Platform for Automatic Phenotyping and Trait Ranking of Plant Root Systems
Authors: Iyer-Pascuzzi Anjali S. , Symonova Olga , Mileyko Yuriy , Hao Yueling , Belcher Heather , Harer John , Weitz Joshua S. , Benfey Philip N.
Published: January 2010

The ability to nondestructively image and automatically phenotype complex root systems, like those of rice (Oryza sativa), is fundamental to identifying genes underlying root system architecture (RSA). Although root systems are central to plant fitness, identifying genes responsible for RSA remains an underexplored opportunity for crop improvement. Here we describe a nondestructive imaging and analysis system for automated phenotyping and trait ranking of RSA. Using this system, we image rice roots from 12 genotypes. We automatically estimate RSA traits previously identified as important to plant function. In addition, we expand the suite of features examined for RSA to include traits that more comprehensively describe monocot RSA but that are difficult to measure with traditional methods. Using 16 automatically acquired phenotypic traits for 2,297 images from 118 individuals, we observe (1) wide variation in phenotypes among the genotypes surveyed; and (2) greater intergenotype variance of RSA features than variance within a genotype. RSA trait values are integrated into a computational pipeline that utilizes supervised learning methods to determine which traits best separate two genotypes, and then ranks the traits according to their contribution to each pairwise comparison. This trait-ranking step identifies candidate traits for subsequent quantitative trait loci analysis and demonstrates that depth and average radius are key contributors to differences in rice RSA within our set of genotypes. Our results suggest a strong genetic component underlying rice RSA. This work enables the automatic phenotyping of RSA of individuals within mapping populations, providing an integrative framework for quantitative trait loci analysis of RSA.
The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2/ERF Transcription Factors
Authors: Jung Ki-Hong , Seo Young-Su , Walia Harkamal , Cao Peijian , Fukao Takeshi , Canlas Patrick E. , Amonpant Fawn , Bailey-Serres Julia , Ronald Pamela C.
Published: January 2010

We previously characterized the rice (Oryza sativa) Submergence1 (Sub1) locus encoding three ethylene-responsive factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1-mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1-containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene. We identified 898 genes displaying Sub1A-1-dependent regulation. Integration of the expression data with publicly available metabolic pathway data identified submergence tolerance-associated pathways governing anaerobic respiration, hormone responses, and antioxidant systems. Of particular interest were a set of APETALA2 (AP2)/ERF family transcriptional regulators that are associated with the Sub1A-1-mediated response upon submergence. Visualization of expression patterns of the AP2/ERF superfamily members in a phylogenetic context resolved 12 submergence-regulated AP2/ERFs into three putative functional groups: (1) anaerobic respiration and cytokinin-mediated delay in senescence via ethylene accumulation during submergence (three ERFs); (2) negative regulation of ethylene-dependent gene expression (five ERFs); and (3) negative regulation of gibberellin-mediated shoot elongation (four ERFs). These results confirm that the presence of Sub1A-1 impacts multiple pathways of response to submergence.
Validated annual band‐pair periodicity and growth parameters of blue‐spotted maskray Neotrygon kuhlii from south‐east Queensland, Australia
Authors: Pierce S. J. , Bennett M. B.
Published: January 2010

Age and growth parameters were derived for blue‐spotted maskray Neotrygon kuhlii from Moreton Bay in subtropical eastern Australia. Maximum age estimates of 13 and 10 years were obtained from female (n = 76) and male (n = 44) N. kuhlii, respectively. Estimated ages at maturity for 50% of females and males were 6·32 and 3·95 years, respectively. A three‐parameter power function provided the best statistical fit to size at age data in both sexes, providing parameter estimates of y0 = 163·13, a = 58·52 and b = 0·58 for females and y0 = 165·13, a = 59·02 and b = 0·54 in males. The two‐parameter von Bertalanffy growth function was used to estimate biological parameters based on disc width (WD) for both female (WD∞ = 465·81 mm, K = 0·13 year−1, b = 0·63) and male N. kuhlii (WD∞ = 385·19 mm, K = 0·20 year−1, b = 0·54). Annual band‐pair deposition was observed in three calcein‐injected N. kuhlii after periods of liberty ranging from 631 to 1081 days. Centrum edge analysis indicated that annual band‐pair formation was generally consistent within this population, with translucent bands formed over spring and summer and opaque bands formed in autumn and winter. Individual growth rates obtained from tagged specimens were similar to power function growth predictions. These results support previous characterizations of this common trawl by‐catch species as comparatively resilient to non‐targeted catches, although higher catch rates outside Australia infer a need for cautious management.