bluuebunny/crossref_metadata_2025 huggingface dataset:
Analytical evaluation of Fukui functions and real-space linear response function
Authors: Yang Weitao , Cohen Aron J. , De Proft Frank , Geerlings Paul
Published: April 2012

Many useful concepts developed within density functional theory provide much insight for the understanding and prediction of chemical reactivity, one of the main aims in the field of conceptual density functional theory. While approximate evaluations of such concepts exist, the analytical and efficient evaluation is, however, challenging, because such concepts are usually expressed in terms of functional derivatives with respect to the electron density, or partial derivatives with respect to the number of electrons, complicating the connection to the computational variables of the Kohn-Sham one-electron orbitals. Only recently, the analytical expressions for the chemical potential, one of the key concepts, have been derived by Cohen, Mori-Sánchez, and Yang, based on the potential functional theory formalism. In the present work, we obtain the analytical expressions for the real-space linear response function using the coupled perturbed Kohn-Sham and generalized Kohn-Sham equations, and the Fukui functions using the previous analytical expressions for chemical potentials of Cohen, Mori-Sánchez, and Yang. The analytical expressions are exact within the given exchange-correlation functional. They are applicable to all commonly used approximate functionals, such as local density approximation (LDA), generalized gradient approximation (GGA), and hybrid functionals. The analytical expressions obtained here for Fukui function and linear response functions, along with that for the chemical potential by Cohen, Mori-Sánchez, and Yang, provide the rigorous and efficient evaluation of the key quantities in conceptual density functional theory within the computational framework of the Kohn-Sham and generalized Kohn-Sham approaches. Furthermore, the obtained analytical expressions for Fukui functions, in conjunction with the linearity condition of the ground state energy as a function of the fractional charges, also lead to new local conditions on the exact functionals, expressed in terms of the second-order functional derivatives. We implemented the expressions and demonstrate the efficacy with some atomic and molecular calculations, highlighting the importance of relaxation effects.
An orbital and electron density analysis of weak interactions in ethanol-water, methanol-water, ethanol and methanol small clusters
Authors: Mejía Sol M. , Flórez Elizabeth , Mondragón Fanor
Published: April 2012

A computational study of (ethanol)n-water, n = 1 to 5 heteroclusters was carried out employing the B3LYP/6-31+G(d) approach. The molecular (MO) and atomic (AO) orbital analysis and the topological study of the electron density provided results that were successfully correlated. Results were compared with those obtained for (ethanol)n, (methanol)n, n = 1 to 6 clusters and (methanol)n-water, n = 1 to 5 heteroclusters. These systems showed the same trends observed in the (ethanol)n-water, n = 1 to 5 heteroclusters such as an O---O distance of 5 Å to which the O–H---O hydrogen bonds (HBs) can have significant influence on the constituent monomers. The HOMO of the hetero(clusters) is less stable than the HOMO of the isolated alcohol monomer as the hetero(cluster) size increases, that destabilization is higher for linear geometries than for cyclic geometries. Changes of the occupancy and energy of the AO are correlated with the strength of O–H---O and C–H---O HBs as well as with the proton donor and/or acceptor character of the involved molecules. In summary, the current MO and AO analysis provides alternative ways to characterize HBs. However, this analysis cannot be applied to the study of H---H interactions observed in the molecular graphs.
Bound state for the fractional Schrödinger equation with unbounded potential
Authors: Cheng Ming
Published: April 2012

This paper considers the fractional Schrödinger equation with unbounded potential. We prove the existence of ground state by Lagrange multiplier method. The standing wave with prescribed frequency is also obtained by Nehari's manifold approach. In the last part, we obtain that the standing wave is bound state.
Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations
Authors: Liu Fu-Feng , Liu Zhen , Bai Shu , Dong Xiao-Yan , Sun Yan
Published: April 2012

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ17-42 are identified to provide interaction energy lower than −2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.
Relating composition, structural order, entropy and transport in multi-component molten salts
Authors: Jabes B. Shadrack , Chakravarty Charusita
Published: April 2012

Molecular dynamics simulations of the LiF-BeF2 molten salt mixture are used to establish relationships between composition, structural order, entropy, and transport properties of multi-component ionic liquids. A sharp rise in tetrahedral order associated with formation of the fluoroberyllate network occurs for compositions with BeF2 concentrations greater than that of the Li2BeF4-BeF2 eutectic. The excess entropy of the liquid in this regime, within the pair correlation approximation, is strongly correlated with the local tetrahedral order. The different degree of participation of beryllium, fluorine, and lithium ions in the cooperative dynamics of the fluoroberyllate network can be related to the degree of deviation from Rosenfeld-type excess entropy scaling, with the lithium ions remaining essentially unaffected by the liquid state network. We demonstrate that the deviations from Nernst-Einstein and Stokes-Einstein behaviour emerge only in temperature-composition regimes where tetrahedral order strongly correlates with the pair entropy. Implications for understanding structure-property relationships in other ionic liquids, such as molten salts, oxide melts, and RTILs are considered.
Microwave-induced transformation of rice husks to SiC
Authors: Qadri S. B. , Imam M. A. , Fliflet A. W. , Rath B. B. , Goswami R. , Caldwell J. D.
Published: April 2012

Samples of rice husks were transformed to β (3C)-SiC by microwave processing in controlled conditions of temperature and vacuum. This simple and fast way of producing powdered samples of silicon carbide is technologically important if this material is to be used for electronics, sensors, biotechnology, and other applications. Using x-ray diffraction it was found that the microwave processed sample at 1900 °C consists of β (3C)-SiC phase. Raman scattering measurements confirmed the formation of β (3C)-SiC phase. Transmission electron microscopy revealed the presence of stacking faults along the [111] direction. The presence of 6H/4H stacking faults in 3C phase is explained in terms of their total energies. The presence of these stacking faults with a ∼1 eV band offset between the host 3C and hexagonal stacking faults implies that these stacking faults provide a conduction barrier, and the interfaces between the stacking faults and host lattice act as a heterojunction that may provide potential utility for various optoelectronic applications.
The splitting of atomic orbitals with a common principal quantum number revisited: np vs. ns
Authors: Katriel Jacob
Published: April 2012

Atomic orbitals with a common principal quantum number are degenerate, as in the hydrogen atom, in the absence of interelectronic repulsion. Due to the virial theorem, electrons in such orbitals experience equal nuclear attractions. Comparing states of several-electron atoms that differ by the occupation of orbitals with a common principal quantum number, such as 1s2 2s vs. 1s2 2p, we find that although the difference in energies, ΔE, is due to the interelectronic repulsion term in the Hamiltonian, the difference between the interelectronic repulsions, ΔC, makes a smaller contribution to ΔE than the corresponding difference between the nuclear attractions, ΔL. Analysis of spectroscopic data for atomic isoelectronic sequences allows an extensive investigation of these issues. In the low nuclear charge range of pertinent isoelectronic sequences, i.e., for neutral atoms and mildly positively charged ions, it is found that ΔC actually reverses its sign. About 96% of the nuclear attraction difference between the 6p 2P and the 6s 2S states of the Cs atom is cancelled by the corresponding interelectronic repulsion difference. From the monotonic increase of ΔE with Z it follows (via the Hellmann-Feynman theorem) that ΔL > 0. Upon increasing the nuclear charge along an atomic isoelectronic sequence with a single electron outside a closed shell from Zc, the critical charge below which the outmost electron is not bound, to infinity, the ratio \documentclass[12pt]{minimal}\begin{document}$\frac{\Delta C}{\Delta L}$\end{document}ΔCΔL increases monotonically from \documentclass[12pt]{minimal}\begin{document}$\lim _{Z\rightarrow Z_c^+} \frac{\Delta C}{\Delta L}=-1$\end{document}limZ→Zc+ΔCΔL=−1 to \documentclass[12pt]{minimal}\begin{document}$\lim _{Z\rightarrow \infty } \frac{\Delta C}{\Delta L}=1$\end{document}limZ→∞ΔCΔL=1. These results should allow for a more nuanced discussion than is usually encountered of the crude electronic structure of many-electron atoms and the structure of the periodic table.
Tuning the properties of Ge-quantum dots superlattices in amorphous silica matrix through deposition conditions
Authors: Pinto S. R. C. , Buljan M. , Chahboun A. , Roldan M. A. , Bernstorff S. , Varela M. , Pennycook S. J. , Barradas N. P. , Alves E. , Molina S. I. , Ramos M. M. D. , Gomes M. J. M.
Published: April 2012

In this work, we investigate the structural properties of Ge quantum dot lattices in amorphous silica matrix, prepared by low-temperature magnetron sputtering deposition of (Ge+SiO2)/SiO2 multilayers. The dependence of quantum dot shape, size, separation, and arrangement type on the Ge-rich (Ge + SiO2) layer thickness is studied. We show that the quantum dots are elongated along the growth direction, perpendicular to the multilayer surface. The size of the quantum dots and their separation along the growth direction can be tuned by changing the Ge-rich layer thickness. The average value of the quantum dots size along the lateral (in-plane) direction along with their lateral separation is not affected by the thickness of the Ge-rich layer. However, the thickness of the Ge-rich layer significantly affects the quantum dot ordering. In addition, we investigate the dependence of the multilayer average atomic composition and also the quantum dot crystalline quality on the deposition parameters.
Temperature-dependent preferential formation of quantum structures upon the droplet epitaxy
Authors: Cao Y. Y. , Yang G. W.
Published: April 2012

A theoretical model has been established to pursue the stability of quantum rings (QRs) and quantum dots (QDs) with respect to thermal effects in the droplet epitaxy. Adding thermal fluctuations to the energetic model within the statistical mechanics frame, we found that a critical temperature provides a means to separate regimes of preferential QR and QD formation. Thermal fluctuations play a crucial role in the temperature-dependent shape evolution. These theoretical results are in good agreement with experiments, which implied that the developed theory can be used to control ring or dot formation in droplet epitaxy.
Intramolecular vibrational coupling contribution to temperature dependence of vibrational mode frequencies
Authors: Kasyanenko Valeriy M. , Keiffer Patrick , Rubtsov Igor V.
Published: April 2012

High-frequency vibrational modes in molecules in solution are sensitive to temperature and shift either to lower or higher frequencies with the temperature increase. These frequency shifts are often attributed to specific interactions of the molecule and to the solvent polarization effect. We found that a substantial and often dominant contribution to sensitivity of vibrational high-frequency modes to temperature originates from anharmonic interactions with other modes in the molecule. The temperature dependencies were measured for several modes in ortho-, meta-, and para-isomers of acetylbenzonitrile in solution and in a solid matrix and compared to the theoretical predictions originated from the intramolecular vibrational coupling (IVC) evaluated using anharmonic density functional theory calculations. It is found that the IVC contribution is essential for temperature dependencies of all high-frequency vibrational modes and is dominant for many modes. As such, the IVC contribution alone permits predicting the main trend in the temperature dependencies, especially for vibrational modes with smaller transition dipoles. In addition, an Onsager reaction field theory was used to describe the solvent contribution to the temperature dependencies.
Temperature and composition dependence of photoluminescence dynamics in CdSxSe1−x (0 ≤ x ≤ 1) nanobelts
Authors: Liu H. W. , Lu J. P. , Fan H. M. , Sow C. H. , Tang S. H. , Zhang X. H.
Published: April 2012

CdSxSe1−x nanobelts with uniform and controllable composition are successfully fabricated by a one-step vapor-liquid-solid process. Temperature-dependent steady and time-resolved transient photoluminescence (PL) are studied for the obtained CdSxSe1−x nanobelts as well as pure CdS and CdSe nanobelts prepared in same method. For all samples, both band edge and surface state emission are found to contribute to the observed PL spectra. However, the emission originated from surface state is quite weak for CdSxSe1−x nanobelts as compared to CdS and CdSe. The reduced surface state emission in CdSxSe1−x nanobelts is ascribed to exciton localization due to random potential fluctuations. This attribution is further confirmed by the time-decay PL profiles where a very fast process of exciton transfer from interior to surface of nanobelts, observed in CdS and CdSe nanobelts, is absent for CdSxSe1−x nanobelts. These observations reveal that the surface effect of CdSxSe1−x nanobelts is less significant than that in CdS and CdSe nanobelts, which consequently leads to enhanced band-edge emission in CdSxSe1−x nanobelts.
Zn doping-induced enhanced dielectric response of quantum paraelectric SrTiO3
Authors: Guo Y. Y. , Guo Y. J. , Liu J.-M.
Published: April 2012

The dielectric and ferroelectric behaviors of Zn2+-doped SrTiO3 (STO-Zn) have been investigated to explore the effects of Zn-doping on quantum fluctuations and ferroelectric instability. Structurally, the smaller Zn2+ ions occupy the Sr2+ sites at low substitution level up to 0.9% and an over-substitution may lead to impurity phase. It is found that no ferroelectric or relaxor-like anomaly emerges, while significantly enhanced dielectric constant and broad dielectric plateau are identified upon the substitution. These phenomena observed in Zn2+-doped STO are slightly different from well investigated Ca2+-doped STO and additional mechanism besides the off-centrality of Zn2+ ions at Sr2+ sites is possible. The transverse-field Ising model is consulted to explain self-consistently the observed effects.
Nanoscale magnetic field mapping with a single spin scanning probe magnetometer
Authors: Rondin L. , Tetienne J.-P. , Spinicelli P. , Dal Savio C. , Karrai K. , Dantelle G. , Thiaville A. , Rohart S. , Roch J.-F. , Jacques V.
Published: April 2012

We demonstrate quantitative magnetic field mapping with nanoscale resolution, by applying a lock-in technique on the electron spin resonance frequency of a single nitrogen-vacancy defect placed at the apex of an atomic force microscope tip. In addition, we report an all-optical magnetic imaging technique which is sensitive to large off-axis magnetic fields, thus extending the operation range of diamond-based magnetometry. Both techniques are illustrated by using a magnetic hard disk as a test sample. Owing to the non-perturbing and quantitative nature of the magnetic probe, this work should open up numerous perspectives in nanomagnetism and spintronics.
Suppression of threading defects formation during Sb-assisted metamorphic buffer growth in InAs/InGaAs/InP structure
Authors: Gocalinska A. , Manganaro M. , Pelucchi E.
Published: April 2012

A virtual substrate for high quality InAs epitaxial layer has been attained via metalorganic vapor-phase epitaxy growth of Sb-assisted InxGa1−xAs metamorphic buffers, following a convex compositional continuous gradient of the In content from x = 53% to 100%. The use of trimethylantimony (or its decomposition products) as a surfactant has been found to crucially enable the control over the defect formation during the relaxation process. Moreover, an investigation of the wafer offcut-dependence of the defect formation and surface morphology has enabled the achievement of a reliably uniform growth on crystals with offcut towards the [111]B direction.
Laser induced non-thermal deposition of ultrathin graphite
Authors: Reininghaus M. , Wortmann D. , Finger J. , Faley O. , Poprawe R. , Stampfer C.
Published: April 2012

We present a laser induced ablation process to fabricate ultrathin graphitic flakes. By varying the fluence of the ablating pulsed fs-laser radiation, we identify distinct values for "thermal" evaporation and so-called "non-thermal" ablation of graphitic flakes. The presence of the non-thermal ablation is a direct consequence of the strong asymmetry of the bonding strength in normal and in-plane direction in layered materials, such as graphite. The experimentally extracted non-thermal ablation threshold for graphite of 250 mJ/cm2 agrees well with theoretical predictions. Finally, we deposited ultrathin graphitic flakes of 50 μm2 in size, which we characterize by Raman spectroscopy and scanning force microscopy.
Spatiotemporal patterns of elephant poaching in south-eastern Kenya
Authors: Maingi John K. , Mukeka Joseph M. , Kyale Daniel M. , Muasya Robert M.
Published: April 2012

Context Poaching of the African elephant for ivory had been on the increase since 1997 when the Convention on International Trade in Endangered Species (CITES) allowed a one-off legal sale of ivory by several southern Africa countries. In Kenya, reports indicate continuous year-to-year increase in elephant poaching since 2003. Aims The goals of the study were to describe the temporal and spatial patterns of elephant poaching in south-eastern Kenya between 1990 and 2009, and examine relationships between observed patterns of poaching, and human and biophysical variables. The study aimed to answer the following questions: (1) how has elephant poaching varied seasonally and annually; (2) what are the spatial patterns of elephant poaching in the Tsavo Conservation Area (TCA); and (3) what are the relationships between observed patterns of poaching and human and biophysical variables? Methods The study used elephant-poaching data and various GIS-data layers representing human and environmental variables to describe the spatial and temporal patterns of elephant poaching. The observed patterns were then related to environmental and anthropogenic variables using correlation and regression analyses. Key results Elephant poaching was clustered, with a majority of the poaching occurring in the dry season. Hotspots of poaching were identified in areas with higher densities of roads, waterholes, rivers and streams. The Tsavo East National Park and the Tsavo National Park accounted for 53.7% and 44.8% of all poached elephants, respectively. The best predictors for elephant poaching were density of elephants, condition of vegetation, proximity to ranger bases and outposts, and densities of roads and rivers. Conclusions Predictor variables used in the study explained 61.5–78% of the total variability observed in elephant poaching. The location of the hotspots suggests that human–wildlife conflicts in the area may be contributing to poaching and that factors that quantify community attitudes towards elephant conservation may provide additional explanation for observed poaching patterns. Implications The poaching hotpots identified can be a used as starting point by the Kenya Wildlife Service (KWS) to begin implementing measures that ensure local-community support for conservation, whereas on other hotspots, it will be necessary to beef-up anti-poaching activities. There is a need for Kenya to legislate new anti-poaching laws that are a much more effective deterrence to poaching than currently exist.
Antarctic and Southern Ocean influences on Late Pliocene global cooling
Authors: McKay Robert , Naish Tim , Carter Lionel , Riesselman Christina , Dunbar Robert , Sjunneskog Charlotte , Winter Diane , Sangiorgi Francesca , Warren Courtney , Pagani Mark , Schouten Stefan , Willmott Veronica , Levy Richard , DeConto Robert , Powell Ross D.
Published: April 2012

The influence of Antarctica and the Southern Ocean on Late Pliocene global climate reconstructions has remained ambiguous due to a lack of well-dated Antarctic-proximal, paleoenvironmental records. Here we present ice sheet, sea-surface temperature, and sea ice reconstructions from the ANDRILL AND-1B sediment core recovered from beneath the Ross Ice Shelf. We provide evidence for a major expansion of an ice sheet in the Ross Sea that began at ∼3.3 Ma, followed by a coastal sea surface temperature cooling of ∼2.5 °C, a stepwise expansion of sea ice, and polynya-style deep mixing in the Ross Sea between 3.3 and 2.5 Ma. The intensification of Antarctic cooling resulted in strengthened westerly winds and invigorated ocean circulation. The associated northward migration of Southern Ocean fronts has been linked with reduced Atlantic Meridional Overturning Circulation by restricting surface water connectivity between the ocean basins, with implications for heat transport to the high latitudes of the North Atlantic. While our results do not exclude low-latitude mechanisms as drivers for Pliocene cooling, they indicate an additional role played by southern high-latitude cooling during development of the bipolar world.
Being prepared for acculturation: On the importance of the first months after immigrants enter a new culture
Authors: Ramelli Marcella , Florack Arnd , Kosic Ankica , Rohmann Anette
Published: April 2012

We hypothesized that perceived communication effectiveness at arrival and initial friendships with members of the receiving society during the first months after arrival in a new country have a long‐term effect on the development of acculturation orientations and that this effect is pronounced for individuals with a high need for cognitive closure (NCC). We examined the hypotheses in a study with Spanish‐speaking immigrants in Switzerland (n = 146) and in Italy (n = 147). We asked participants to indicate their current attitude to contact with the receiving society and cultural maintenance and report retrospectively their perceived communication effectiveness at arrival and initial friendships. In line with the predictions, the perceptions of high communication effectiveness at arrival and friendships with members of the receiving society during the initial phase in the new culture were positively correlated with the current attitude to contact with the receiving society assessed 7 years after arrival on average. Also, initial friendships with members of the receiving society were negatively correlated with present cultural maintenance. Moreover, with an increase in NCC, these correlations increased.
Transposed-letter priming effect in Hebrew in the same–different task
Authors: Kinoshita Sachiko , Norris Dennis , Siegelman Noam
Published: April 2012

We investigated the interaction between morphological structure and transposed-letter priming using the same–different task with Hebrew, a Semitic language in which morphology has been shown to play a key role in visual word recognition. In contrast to the results observed with lexical decision (e.g., Velan & Frost, 2009, 2011), a transposed-letter priming effect was observed irrespective of the morphological structure of the words. We take these results to suggest that morphological decomposition occurs only in the service of lexical access. We discuss further a unique feature of written Arabic, another Semitic language, to explain the apparent conflict between our findings and those reported by Perea, Abu Mallouh, García-Orza, and Carreiras (2010).
The effect of explanation in simple binary decision tasks
Authors: Taylor Eric G. , Landy David H. , Ross Brian H.
Published: April 2012

Many studies of explanation have focused on higher level tasks and on how explanations draw upon relevant prior knowledge, which then helps in understanding some event or observation. However, explanations may also affect performance in simple tasks even when they include no task-relevant information. In three experiments, we show that explanations adding no task-relevant information alter performance in a sequential binary decision task. Whereas people with no explanation for why two events occurred at different rates tended to predict each outcome in proportion to their probability of occurrence (to “probability match”), people with an explanation tended to predict the more likely event more often (to “overmatch,” a better strategy). These results suggest a broader view of explanation, which includes a role in shaping simple tasks outside of higher level reasoning.
Autophagy modulates dynamics of connexins at the plasma membrane in a ubiquitin-dependent manner
Authors: Bejarano Eloy , Girao Henrique , Yuste Andrea , Patel Bindi , Marques Carla , Spray David C. , Pereira Paulo , Cuervo Ana Maria
Published: April 2012

Different pathways contribute to the turnover of connexins, the main structural components of gap junctions (GJs). The cellular pool of connexins targeted to each pathway and the functional consequences of degradation through these degradative pathways are unknown. In this work, we focused on the contribution of macroautophagy to connexin degradation. Using pharmacological and genetic blockage of macroautophagy both in vitro and in vivo, we found that the cellular pool targeted by this autophagic system is primarily the one organized into GJs. Interruption of connexins' macroautophagy resulted in their retention at the plasma membrane in the form of functional GJs and subsequent increased GJ-mediated intercellular diffusion. Up-regulation of macroautophagy alone is not sufficient to induce connexin internalization and degradation. To better understand what factors determine the autophagic degradation of GJ connexins, we analyzed the changes undergone by the fraction of plasma membrane connexin 43 targeted for macroautophagy and the sequence of events that trigger this process. We found that Nedd4-mediated ubiquitinylation of the connexin molecule is required to recruit the adaptor protein Eps15 to the GJ and to initiate the autophagy-dependent internalization and degradation of connexin 43. This study reveals a novel regulatory role for macroautophagy in GJ function that is directly dependent on the ubiquitinylation of plasma membrane connexins.
An interdomain binding site on HIV-1 Nef interacts with PACS-1 and PACS-2 on endosomes to down-regulate MHC-I
Authors: Dikeakos Jimmy D. , Thomas Laurel , Kwon Grace , Elferich Johannes , Shinde Ujwal , Thomas Gary
Published: April 2012

The human immunodeficiency virus type 1 (HIV-1) accessory protein Nef directs virus escape from immune surveillance by subverting host cell intracellular signaling and membrane traffic to down-regulate cell-surface major histocompatibility complex class I (MHC-I). The interaction of Nef with the sorting proteins PACS-1 and PACS-2 mediates key signaling and trafficking steps required for Nef-mediated MHC-I down-regulation. Little is known, however, about the molecular basis underlying the Nef–PACS interaction. Here we identify the sites on Nef and the PACS proteins required for their interaction and describe the consequences of disrupting this interaction for Nef action. A previously unidentified cargo subsite on PACS-1 and PACS-2 interacted with a bipartite site on Nef formed by the EEEE65acidic cluster on the N-terminal domain and W113in the core domain. Mutation of these sites prevented the interaction between Nef and the PACS proteins on Rab5 (PACS-2 and PACS-1)- or Rab7 (PACS-1)-positive endosomes as determined by bimolecular fluorescence complementation and caused a Nef mutant defective in PACS binding to localize to distorted endosomal compartments. Consequently, disruption of the Nef–PACS interaction repressed Nef-induced MHC-I down-regulation in peripheral blood mononuclear cells. Our results provide insight into the molecular basis of Nef action and suggest new strategies to combat HIV-1.
Regulation of myosin activation during cell–cell contact formation by Par3-Lgl antagonism: entosis without matrix detachment
Authors: Wan Qingwen , Liu Jing , Zheng Zhen , Zhu Huabin , Chu Xiaogang , Dong Zheng , Huang Shuang , Du Quansheng
Published: April 2012

Cell–cell contact formation following cadherin engagement requires actomyosin contraction along the periphery of cell–cell contact. The molecular mechanisms that regulate myosin activation during this process are not clear. In this paper, we show that two polarity proteins, partitioning defective 3 homologue (Par3) and mammalian homologues of Drosophila Lethal (2) Giant Larvae (Lgl1/2), antagonize each other in modulating myosin II activation during cell–cell contact formation in Madin-Darby canine kidney cells. While overexpression of Lgl1/2 or depletion of endogenous Par3 leads to enhanced myosin II activation, knockdown of Lgl1/2 does the opposite. Intriguingly, altering the counteraction between Par3 and Lgl1/2 induces cell–cell internalization during early cell–cell contact formation, which involves active invasion of the lateral cell–cell contact underneath the apical-junctional complexes and requires activation of the Rho–Rho-associated, coiled-coil containing protein kinase (ROCK)–myosin pathway. This is followed by predominantly nonapoptotic cell-in-cell death of the internalized cells and frequent aneuploidy of the host cells. Such effects are reminiscent of entosis, a recently described process observed when mammary gland epithelial cells were cultured in suspension. We propose that entosis could occur without matrix detachment and that overactivation of myosin or unbalanced myosin activation between contacting cells may be the driving force for entosis in epithelial cells.
Expression of the inclusion body myopathy 3 mutation in Drosophila depresses myosin function and stability and recapitulates muscle inclusions and weakness
Authors: Wang Yang , Melkani Girish C. , Suggs Jennifer A. , Melkani Anju , Kronert William A. , Cammarato Anthony , Bernstein Sanford I.
Published: April 2012

Hereditary myosin myopathies are characterized by variable clinical features. Inclusion body myopathy 3 (IBM-3) is an autosomal dominant disease associated with a missense mutation (E706K) in the myosin heavy chain IIa gene. Adult patients experience progressive muscle weakness. Biopsies reveal dystrophic changes, rimmed vacuoles with cytoplasmic inclusions, and focal disorganization of myofilaments. We constructed a transgene encoding E706K myosin and expressed it in Drosophila (E701K) indirect flight and jump muscles to establish a novel homozygous organism with homogeneous populations of fast IBM-3 myosin and muscle fibers. Flight and jump abilities were severely reduced in homozygotes. ATPase and actin sliding velocity of the mutant myosin were depressed >80% compared with wild-type myosin. Light scattering experiments and electron microscopy revealed that mutant myosin heads bear a dramatic propensity to collapse and aggregate. Thus E706K (E701K) myosin appears far more labile than wild-type myosin. Furthermore, mutant fly fibers exhibit ultrastructural hallmarks seen in patients, including cytoplasmic inclusions containing aberrant proteinaceous structures and disorganized muscle filaments. Our Drosophila model reveals the unambiguous consequences of the IBM-3 lesion on fast muscle myosin and fibers. The abnormalities observed in myosin function and muscle ultrastructure likely contribute to muscle weakness observed in our flies and patients.
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
Authors: Xie Zhong-Ru , Hwang Ming−Jing
Published: April 2012

Motivation: Knowledge about the site at which a ligand binds provides an important clue for predicting the function of a protein and is also often a prerequisite for performing docking computations in virtual drug design and screening. We have previously shown that certain ligand-interacting triangles of protein atoms, called protein triangles, tend to occur more frequently at ligand-binding sites than at other parts of the protein.

Results: In this work, we describe a new ligand-binding site prediction method that was developed based on binding site-enriched protein triangles. The new method was tested on 2 benchmark datasets and on 19 targets from two recent community-based studies of such predictions, and excellent results were obtained. Where comparisons were made, the success rates for the new method for the first predicted site were significantly better than methods that are not a meta-predictor. Further examination showed that, for most of the unsuccessful predictions, the pocket of the ligand-binding site was identified, but not the site itself, whereas for some others, the failure was not due to the method itself but due to the use of an incorrect biological unit in the structure examined, although using correct biological units would not necessarily improve the prediction success rates. These results suggest that the new method is a valuable new addition to a suite of existing structure-based bioinformatics tools for studies of molecular recognition and related functions of proteins in post-genomics research.

Availability: The executable binaries and a web server for our method are available from http://sourceforge.net/projects/msdock/ and http://lise.ibms.sinica.edu.tw, respectively, free for academic users.

Contact:  mjhwang@ibms.sinica.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Characterization of the Plasma Membrane H+-ATPase in the Liverwort Marchantia polymorpha
Authors: Okumura Masaki , Inoue Shin-ichiro , Takahashi Koji , Ishizaki Kimitsune , Kohchi Takayuki , Kinoshita Toshinori
Published: April 2012

The plasma membrane H+-ATPase generates an electrochemical gradient of H+ across the plasma membrane that provides the driving force for solute transport and regulates pH homeostasis and membrane potential in plant cells. Recent studies have demonstrated that phosphorylation of the penultimate threonine in H+-ATPase and subsequent binding of a 14-3-3 protein is the major common activation mechanism for H+-ATPase in vascular plants. However, there is very little information on the plasma membrane H+-ATPase in nonvascular plant bryophytes. Here, we show that the liverwort Marchantia polymorpha, which is the most basal lineage of extant land plants, expresses both the penultimate threonine-containing H+-ATPase (pT H+-ATPase) and non-penultimate threonine-containing H+-ATPase (non-pT H+-ATPase) as in the green algae and that pT H+-ATPase is regulated by phosphorylation of its penultimate threonine. A search in the expressed sequence tag database of M. polymorpha revealed eight H+-ATPase genes, designated MpHA (for M. polymorpha H+-ATPase). Four isoforms are the pT H+-ATPase; the remaining isoforms are non-pT H+-ATPase. An apparent 95-kD protein was recognized by anti-H+-ATPase antibodies against an Arabidopsis (Arabidopsis thaliana) isoform and was phosphorylated on the penultimate threonine in response to the fungal toxin fusicoccin in thalli, indicating that the 95-kD protein contains pT H+-ATPase. Furthermore, we found that the pT H+-ATPase in thalli is phosphorylated in response to light, sucrose, and osmotic shock and that light-induced phosphorylation depends on photosynthesis. Our results define physiological signals for the regulation of pT H+-ATPase in the liverwort M. polymorpha, which is one of the earliest plants to acquire pT H+-ATPase.
DDX39 acts as a suppressor of invasion for bladder cancer
Authors: Kato Minoru , Wei Min , Yamano Shotaro , Kakehashi Anna , Tamada Satoshi , Nakatani Tatsuya , Wanibuchi Hideki
Published: April 2012

The object of the present study was to identify markers for predicting urinary bladder cancer progression by comparative proteome analysis of bladder cancers and paired normal mucosas. We found that DDX39 was overexpressed in four of six bladder cancers examined compared with respective control tissues. Immunohistochemical analysis using 303 bladder cancer specimens revealed that DDX39 was inversely correlated to pT stage and histological grade progression. The incidence of DDX39high tumors (positive cells ≥50%) was 68.6%, 43.5%, 20.0%, and 5.3% in pTa, pT1, pTis, and ≥pT2 tumors, respectively, and 65.2%, 60.7%, and 19.6% in G1, G2, and G3 tumors, respectively. The incidence of DDX39high tumors was significantly lower in pT1 and ≥pT2 compared to pTa tumors, and also significantly lower in G3 compared to G1 and G2 tumors. Follow‐up analysis (n = 105) revealed that DDX39low tumors (positive cells <50%) were associated with disease progression (hazard ratio 7.485; P = 0.0083). Furthermore, DDX39‐knockdown bladder cancer cells increased their invasion ability compared to negative control cells. These results suggest that DDX39 is a suppressor of invasion and loss of its function predicts disease progression in bladder cancers. (Cancer Sci 2012; 103: 1363–1369)
Dysadherin expression promotes the motility and survival of human breast cancer cells by AKT activation
Authors: Lee Yoo‐Kyung , Lee Su‐Youn , Park Jeong‐Ran , Kim Ran‐Ju , Kim Soo‐Rim , Roh Kyung‐Jin , Nam Jeong‐Seok
Published: April 2012

High dysadherin expression has been recognized as a biological predictor of metastasis and poor prognosis for many different cancer types; however, the molecular mechanisms of how dysadherin affects cancer progression are still poorly understood. In this study, we examined whether AKT signaling could link dysadherin expression with downstream events that promote the metastatic potential of human breast cancer cells. Immunohistochemical analysis of breast cancer tissues showed that dysadherin expression was highly associated with elevated expression of phospho‐AKT. The introduction of dysadherin cDNA into BT‐474, MCF‐7 and T‐47D breast cancer cell lines enhanced their levels of AKT phosphorylation, while knockdown of dysadherin in MDA‐MB‐231 and Hs578T breast cancer cell lines suppressed AKT phosphorylation. Treatment with the AKT inhibitor triciribine suppressed dysadherin‐mediated pro‐metastatic effects, including epithelial–mesenchymal transition, cell motility and drug resistance. These findings suggest that dysadherin might contribute to breast cancer progression through AKT activation. (Cancer Sci 2012; 103: 1280–1289)
Ecotropic viral integration site 1, stem cell self‐renewal and leukemogenesis
Authors: Kataoka Keisuke , Kurokawa Mineo
Published: April 2012

It has become evident that acute myeloid leukemia (AML) is organized as a cellular hierarchy initiated and maintained by a subset of self‐renewing leukemia stem cells. Recent gene expression profile analysis of human leukemia stem cells and hematopoietic stem cell (HSC) populations identified a key transcriptional program shared by leukemia stem cells and HSC, which is associated with adverse outcomes in AML patients. One molecule that has been established as a pivotal regulator in fine‐tuning of stem cell properties as well as a potent oncogenic determinant is ecotropic viral integration site 1 (EVI1). EVI1 is a transcription factor that has stem cell‐specific expression pattern and is essential for the regulation of HSC self‐renewal. This gene is notorious for its involvement in AML, as its activation confers extremely poor prognosis in patients with AML. Molecular analysis has identified a variety of gene products that are involved in HSC regulation as downstream targets or interacting proteins of EVI1. Thus, exploration of the molecular pathogenesis underlying EVI1‐related leukemogenesis provides insight into how shared stemness transcriptional programs contribute to leukemia progression and therapeutic resistance in AML. Here, we review the current knowledge regarding the role of EVI1 in HSC self‐renewal and leukemogenesis and highlight the relationship between stem cell self‐renewal properties and adverse outcome in myeloid malignancies. (Cancer Sci, doi: 10.1111/j.1349‐7006.2012.02303.x, 2012)
Validating the impact of a molecular subtype in ovarian cancer on outcomes: A study of theOVCADConsortium
Authors: Pils Dietmar , Hager Gudrun , Tong Dan , Aust Stefanie , Heinze Georg , Kohl Maria , Schuster Eva , Wolf Andrea , Sehouli Jalid , Braicu Ioana , Vergote Ignace , Cadron Isabelle , Mahner Sven , Hofstetter Gerda , Speiser Paul , Zeillinger Robert
Published: April 2012

Most patients with epithelial ovarian cancer (EOC) are diagnosed at advanced stage and have a poor prognosis. However, a small proportion of these patients will survive, whereas others will die very quickly. Clinicopathological factors do not allow precise identification of these subgroups. Thus, we have validated a molecular subclassification as new prognostic factor inEOC. One hundred and ninety‐four patients with StageII–IV EOCwere characterized by whole‐genome expression profiling of tumor tissues and were classified using a published 112 gene set, derived from an International Federation of Gynecology and Obstetrics (FIGO) stage‐directed supervised classification approach. The 194 tumor samples were classified into two subclasses comprising 95 (Subclass 1) and 99 (Subclass 2) tumors. All nineFIGO IItumors were grouped in Subclass 1 (P = 0.001). Subclass 2 (54% of advanced‐stage tumors) was significantly correlated with peritoneal carcinomatosis and non‐optimal debulking. Patients with Subclass 2 tumors had a worse overall survival for both serous and non‐serous histological subtypes, as revealed by univariate analysis (hazard ratios [HR] of 3.17 and 17.11, respectively;P ≤ 0.001) and in models corrected for relevant clinicopathologic parameters (HR2.87 and 12.42, respectively;P ≤ 0.023). Significance analysis of microarrays revealed 2082 genes that were differentially expressed in advanced‐grade serous tumors of both subclasses and the focal adhesion pathway as the most deregulated pathway. In the present validation study, we have shown that, in advanced‐stage serous ovarian cancer, two approximately equally large molecular subtypes exist, independent of classical clinocopathological parameters and presenting with highly different whole‐genome expression profiles and a markedly different overall survival. Similar results were obtained in a small cohort of patients with non‐serous tumors. (Cancer Sci2012; 103: 1334–1341)
Modulation of chlorophyll biosynthesis by water stress in rice seedlings during chloroplast biogenesis*
Authors: DALAL VIJAY K. , TRIPATHY BAISHNAB C.
Published: April 2012

To understand the impact of water stress on the greening process, water stress was applied to 6‐day‐old etiolated seedlings of a drought‐sensitive cultivar of rice (Oryza sativa), Pusa Basmati‐1 by immersing their roots in 40 mm polyethylene glycol (PEG) 6000 (−0.69 MPa) or 50 mm PEG 6000 (−1.03 MPa) dissolved in half‐strength Murashige and Skoog (MS)‐nutrient‐solution, 16 h prior to transfer to cool‐white‐fluorescent + incandescent light. Chlorophyll (Chl) accumulation substantially declined in developing water‐stressed seedlings. Reduced Chl synthesis was due to decreased accumulation of chlorophyll biosynthetic intermediates, that is, glutamate‐1‐semialdehyde (GSA), 5‐aminolevulinic acid, Mg‐protoporphyrin IX monomethylester and protochlorophyllide. Although 5‐aminolevulinic acid synthesis decreased, the gene expression and protein abundance of the enzyme responsible for its synthesis, GSA aminotransferase, increased, suggesting its crucial role in the greening process in stressful environment. The biochemical activities of Chl biosynthetic enzymes, that is, 5‐aminolevulinic acid dehydratase, porphobilinogen deaminase, coproporphyrinogen III oxidase, porphyrinogen IX oxidase, Mg‐chelatase and protochlorophyllide oxidoreductase, were down‐regulated due to their reduced protein abundance/gene expression in water‐stressed seedlings. Down‐regulation of protochlorophyllide oxidoreductase resulted in impaired Shibata shift. Our results demonstrate that reduced synthesis of early intermediates, that is, GSA and 5‐aminolevulinic acid, could modulate the gene expression of later enzymes of Chl biosynthesis pathway.
A distant magmatic source for Cretaceous karst bauxites of Southern Apennines (Italy), revealed through SHRIMP zircon age dating
Authors: Boni Maria , Reddy Steven M. , Mondillo Nicola , Balassone Giuseppina , Taylor Rich
Published: April 2012

Terra Nova, 24, 326–332, 2012

Karst bauxites occur at a Late Cretaceous hiatus on a Bahamian‐type platform in Southern Apennines, Italy. In contrast to the well‐defined stratigraphic context, their origin remains controversial. Detrital zircon grains preserve textures and Th/U ratios consistent with crystallization from a melt, occasionally around older cores. U‐Pb isotopic data, collected using SHRIMP II, record several age populations. The youngest (∼90 Ma) falls into the age interval of bauxite formation as defined by stratigraphic criteria. The zircons must therefore be derived from a contemporary Cretaceous volcanic source. The older zircons may be interpreted as xenocrysts associated with the Cretaceous magmas or derived from different sources. Because the bauxite occurs on a isolated carbonate platform, the grains must come from far away sources, most probably transported by wind. The age, palaeogeography and inferred Cretaceous wind pattern are consistent with a prevailing origin from the Dinaric and Carpatho‐Balkan orogenic belts, with its Cretaceous bimodal volcanism.