bluuebunny/crossref_metadata_2025 huggingface dataset:
Hcc‐2, a novel mammalian ER thioredoxin that is differentially expressed in hepatocellular carcinoma
Authors: Nissom Peter Morin , Lo Siaw Ling , Lo Jennifer Chi Yi , Ong Peh Fern , Lim Justin Wee Eng , Ou Keli , Liang Rosa Cynthia , Seow Teck Keong , Chung Maxey Ching Ming
Published: March 2006

Hepatocellular carcinoma (HCC) is the most common primary cancer of the liver. Thus there is great interest to identify novel HCC diagnostic markers for early detection of the disease and tumour specific associated proteins as potential therapeutic targets in the treatment of HCC. Currently, we are screening for early biomarkers as well as studying the development of HCC by identifying the differentially expressed proteins of HCC tissues during different stages of disease progression. We have isolated, by reverse transcriptase and polymerase chain reaction (RT‐PCR), a 1741 bp cDNA encoding a protein that is differentially expressed in HCC. This novel protein was initially identified by proteome analysis and we designate it as Hcc‐2. The protein is upregulated in poorly‐differentiated HCC but unchanged in well‐differentiated HCC. The full‐length transcript encodes a protein of 363 amino acids that has three thioredoxin (Trx) (CGHC) domains and an ER retention signal motif (KDEL). Fluorescence GFP tagging to this protein confirmed that it is localized predominantly to the cytoplasm when expressed in mammalian cells. Protein alignment analysis shows that it is a variant of the TXNDC5 gene, and the human variants found in Genbank all show close similarity in protein sequence. Functionally, it exhibits the anticipated reductase activity in the insulin disulfide reduction assay, but its other biological role in cell function remains to be elucidated. This work demonstrates that an integrated proteomics and genomics approach can be a very powerful means of discovering potential diagnostic and therapeutic protein targets for cancer therapy.
Reversible inhibition of caspase‐3 activity by iron(III)
Authors: Sliskovic Inga , Mutus Bulent
Published: March 2006

Desferoxamine is known to induce apoptosis in cancer cells, but the mechanisms are still not fully understood. We have shown that iron(III) is a potent caspase‐3 inhibitor, and the inhibition is reversible by the iron chelating agent desferoxamine. Also, protein disulfide isomerase (PDI) is capable of activating caspase‐3 inhibited by iron(III), likely by formation of iron–sulfur complex through its active site thiols. Data presented here suggests that iron(III) could be a potential inhibitor of apoptosis in vivo, by caspase‐3‐dependent inhibition with a possibility of recovery through PDI overexpression.
Post‐transcriptional downregulation of sarcolipin mRNA by triiodothyronine in the atrial myocardium
Authors: Minamisawa Susumu , Uemura Nobuyuki , Sato Yoji , Yokoyama Utako , Yamaguchi Teruhide , Inoue Kazuhide , Nakagome Masamichi , Bai Yunzhe , Hori Hideaki , Shimizu Mitsuyuki , Mochizuki Seibu , Ishikawa Yoshihiro
Published: March 2006

Thyroid hormone‐mediated positive cardiotropic effects are differently regulated between the atria and ventricles. This regulation is, at least in part, dependent on sarcoplasmic reticulum (SR) proteins. Sarcolipin, a homologue of phospholamban, has been recently identified as an atrium‐specific SR protein. The expression of sarcolipin mRNA was significantly decreased in the atria of mice with hyperthyroidism and in 3,5,3′‐triiodo‐l‐thyronine‐treated neonatal rat atrial myocytes. Promoter activity and mRNA stability analyses revealed that thyroid hormone post‐transcriptionally downregulated the expression of sarcolipin mRNA. The atrium‐specific effect of thyroid hormone may occur in part through the regulation of atrial sarcolipin gene expression.
Identification of the basement membrane protein nidogen as a candidate ligand for tumor endothelial marker 7 in vitro and in vivo
Authors: Lee Hyun Kyoung , Seo In Ae , Park Hye Kyung , Park Hwan Tae
Published: March 2006

Tumor endothelial marker 7 (TEM7) is a novel transmembrane protein that is highly expressed in the tumor endothelium. However, the ligands and functions of TEM7 are unknown at present. Using a recombinant ectodomain of TEM7 as a probe, we could identify the saturable interaction between nidogen and TEM7 in vitro. A cell overlay binding assay showed that recombinant nidogen interact with full length TEM7 on cell surface. Finally, nidogen/TEM7 interaction enhanced cell spreading in TEM7 transfected 293T cells. This novel nidogen/TEM7 interaction may provide an important molecular tool with potential therapeutic applications in the anti‐angiogenic therapies.
Synaptotagmin I and Ca2+ promote half fusion more than full fusion in SNARE‐mediated bilayer fusion
Authors: Lu Xiaobing , Xu Yibin , Zhang Fan , Shin Yeon-Kyun
Published: March 2006

Synaptic membrane fusion, which is necessary for neurotransmitter release, may be mediated by SNAREs and regulated by synaptotagmin (Syt) and Ca2+. Fusion of liposomes mediated by reconstituted SNAREs produces full fusion and hemifusion, a membrane structure in which outer leaflets are mixed but the inner leaflets remain intact. Here, using the liposome fusion assay, it is shown that Syt promoted both hemifusion and full fusion in a Ca2+‐dependent manner. Syt · Ca2+ increased hemifusion more than full fusion, modulating the ratio of hemifusion to full fusion. Unlike the case of neuronal SNAREs, stimulation of fusion by Syt · Ca2+ was not seen for other SNAREs involved in trafficking in yeast, indicating that the Syt · Ca2+ stimulation was SNARE‐specific. We constructed hybrid SNAREs in which transmembrane domains were swapped between neuronal and yeast SNAREs. With these hybrid SNAREs, we demonstrated that the interaction between the SNARE motifs of neuronal proteins and Syt · Ca2+ was required for the stimulation of fusion.
Prokaryotic and eukaryotic monothiol glutaredoxins are able to perform the functions of Grx5 in the biogenesis of Fe/S clusters in yeast mitochondria
Authors: Molina-Navarro Maria Micaela , Casas Celia , Piedrafita Lidia , Bellí Gemma , Herrero Enrique
Published: March 2006

The Saccharomyces cerevisiae monothiol glutaredoxin Grx5 participates in the mitochondrial biogenesis of iron–sulfur clusters. Grx5 homologues exist in organisms from bacteria to humans. Chicken (cGRX5) and human (hGRX5) homologues contain a mitochondrial targeting sequence, suggesting a mitochondrial localization for these two proteins. We have compartmentalized the Escherichia coli and Synechocystis sp. homologues, and also cGRX5 and hGRX5, in the mitochondrial matrix of a yeast grx5 mutant. All four heterologous proteins rescue the defects of the mutant. The chicken cGRX5 gene was significantly expressed throughout the embryo stages in different tissues. These results underline the functional conservation of Grx5 homologues throughout evolution.
Legality and legitimacy: the quest for principled flexibility and restraint
Authors: FALK RICHARD
Published: March 2006

What follows is an attempt to acknowledge the complexity and relevance of debates about the relation between legality and legitimacy as it bears on political behaviour. The opening section is intended to orient these international policy debates in wider traditions of political theory, particularly as they bear on the nature of sovereignty and the state. On this basis, the two prominent, recent instances of controversial recourse to war (Kosovo and Iraq) are considered from the perspective of legality and legitimacy, first as a matter of juridical evaluation and then from the perspective of international reputation. The focus throughout reflects a concern with the qualities of American global leadership since September 11th, and how this leadership should or should not be guided by canons of legality.
The age of liberal wars
Authors: FREEDMAN LAWRENCE
Published: March 2006

Three different types of arguments were used to justify the 2003 Iraq War. The first was based on the requirements of national security. Iraq was believed to be developing deadly weapons which it might use against neighbouring states or hand over to terrorist groups such as al-Qaeda. A second argument was based on international security. Iraq was supposed to comply with a series of UN Security Council Resolutions and was failing to do so, thereby undermining the credibility of the leading international institutions. The third argument was based on human security. The Iraqi people had suffered too long under a tyrannical regime and this was an opportunity to overthrow it and replace it with something much better.
War and international relations: a military-historical perspective on force and legitimacy
Authors: BLACK JEREMY
Published: March 2006

Writing on international relations frequently makes reference to the use of force, but rarely integrates changes in its nature into a central role in the explanatory model. In particular, force, in the shape of military capability, is often seen as the ‘servant’ of ideas about its appropriate use, and thus of the norms of the international system, rather than as an independent element, let alone playing a central role in affecting the latter. This article addresses the issue with particular reference to relations between the West and the ‘non-West’, arguing that the contested relationship between the different narratives of military history impinge directly on the character of international relations.
Veränderung des Schmerzerlebens bei Alzheimer-Patienten
Authors: Kunz Miriam , Lautenbacher Stefan
Published: March 2006

Zusammenfassung: Klinische Studien, die nahe legen, dass Alzheimer-Patienten im Vergleich zur Altersgruppe deutlich seltener über Schmerzen berichten und deutlich weniger Analgetika verschrieben bekommen, haben die Frage aufgeworfen, inwieweit die Alzheimer-Erkrankung zu Veränderungen im Schmerzerleben führt. Um diese Frage zu beantworten, sind experimentelle Studien unabdingbar, da nur sie erlauben, Veränderungen des Schmerzsystems selbst zu erfassen. Die bisherigen experimentellen Befunde weisen darauf hin, dass die Schmerztoleranzschwelle deutlich erhöht und die vegetative Schmerzreaktion teilweise erheblich vermindert ist. Die Schmerzschwelle und schmerzkorrelierten Hirnpotenziale zeigten sich hingegen weitestgehend unverändert. Dies spräche eher für eine Abschwächung der Schmerzreagibilität bei Alzheimer-Demenz. Als mögliche Erklärungen hierfür diskutieren wir altersbedingte Veränderungen des Schmerzerlebens und neuroanatomische Veränderungen im Rahmen der Alzheimer-Erkrankung. Erste Ergebnisse einer eigenen Studie mit alternativer Methodik (mimische Schmerzreaktion, nozifensiver RIII-Reflex, u. a.) lassen im Gegensatz zu früheren Annahmen auch an die Möglichkeit einer erhöhten Schmerzreagibilität denken. Auch die beeinträchtigte Fähigkeit der Demenzpatienten zur verbalen Schmerzkommunikation und die Notwendigkeit alternativer, nonverbaler Messmethoden sind Thema der vorliegenden Übersichtsarbeit
“Abnormal Response to Negative Feedback”
Authors: Scheurich A. , Fellgiebel A. , Müller M.J. , Singer P. , Hautzinger M.
Published: March 2006

Zusammenfassung: Es wurden alkoholabhängige Patienten unter Stressbedingungen neuropsychologisch untersucht. Fragestellung: Zeigt sich wie bei depressiven Patienten eine abnorme Reaktion auf negative Rückmeldung oder gar eine generelle Stressanfälligkeit? Die alkoholabhängigen Patienten wurden in der Testbatterie zur Aufmerksamkeitsprüfung (TAP) nach negativer Rückmeldung tendenziell langsamer und die Kontrollpersonen tendenziell schneller. Insgesamt ergab sich ein signifikanter Unterschied in Visuellem Scanning und Reaktionswechsel. Damit ist die “abnormal response to negative feedback” nicht spezifisch für depressive Patienten. Unter 90 dBA Lärm als Stressor zeigten sich dagegen keine Effekte auf die Leistungsfähigkeit oder die Stressverarbeitung. Eine Leistungsminderung durch generelle Stressanfälligkeit konnte somit nicht beobachtet werden. Kontinuierliches Stressmonitoring zeigte, dass sich die alkoholabhängigen Patienten wie testängstliche Probanden verhalten und nach negativer Rückmeldung leistungsminderndes Bedrohungs- und Verlusterleben vorherrscht, während gesunde Probanden auch nach negativer Rückmeldung an der Einschätzung als Herausforderung festhalten und sich steigern.
Einsatz der Symptom-Checkliste (SCL-90-R) bei Patienten mit Hirnschädigung
Authors: Harth Sandy
Published: March 2006

Zusammenfassung: Die Symptom-Checkliste (SCL-90-R) ist ein im klinisch-psychologischen Bereich weit verbreitetes Verfahren und wird zunehmend auch im neuropsychologischen Kontext eingesetzt. Die vorliegende Testbeschreibung fokussiert auf den Einsatz der Checkliste bei Patienten mit Erkrankungen des zentralen Nervensystems (ZNS), insbesondere mit Schädelhirntrauma. Dabei werden Daten aus einer eigenen Befragung Hirngeschädigter mit der SCL-90-R diskutiert. Die Checkliste ist leicht anzuwenden, ökonomisch und erlaubt einen raschen Überblick vorhandener subjektiver Beschwerden auf Seiten des Patienten. Da für den Bereich der psychischen und physischen Beschwerden von Patienten nach einer Hirnschädigung bislang nur wenig passende Instrumente verfügbar sind, ist der Einsatz der SCL-90-R eine sinnvolle Ergänzung. Die Ergebnisse bei Patienten nach Hirnschädigung sollten jedoch vorsichtig interpretiert werden, da einige Items nicht nur die psychische Belastung widerspiegeln, sondern ebenso neuropsychologisch bzw. neurologisch bedingte Defizite aufzeigen.
Seasonal variation of diurnal perturbations in mesopause region temperature, zonal, and meridional winds above Fort Collins, Colorado (40.6°N, 105°W)
Authors: Yuan Tao , She C. Y. , Hagan Maura E. , Williams B. P. , Li Tao , Arnold Kam , Kawahara Takuya D. , Acott P. E. , Vance J. D. , Krueger David , Roble Raymond G.
Published: March 2006

On the basis of lidar observations from May 2002 through April 2003, covering both day and night, we performed a harmonic analysis to extract the diurnal perturbations in mesopause region temperature, zonal and meridional winds over Fort Collins, Colorado (40.6°N, 105°W), binned every 2 months. The results were compared to predictions of the 2000 and 2002 versions of Global‐Scale Wave Model (GSWM00 and GSWM02). The diurnal tidal period oscillations showed a mixture of propagating and evanescent (trapped) modes, but the propagating modes dominated for most of the year. The agreement in temperature diurnal phases between observation and GSWM prediction is marginal. On the other hand, other than July‐August meridional winds, the observed diurnal phases in both wind components are in good agreement with GSWM predictions for most of the altitude range reported. The diurnal amplitude predictions of GSWM00 were reasonably close to lidar observations, while other than January‐February, the GSWM02 amplitude prediction overestimated the observations, typically by a factor of two. We also conducted comparisons on tidal perturbations in zonal wind between radar campaigns and our lidar observations. The lidar data agreed reasonably well with the MF radar data from 2000 to 2001 at nearby Platteville, Colorado (40.2°N, 104.7°W), but showed considerable differences with the data from other midlatitude stations from 1992 to 1993. The dominance of the evanescent mode in the temperature diurnal tidal oscillation during the early winter (November and December), which reached a peak value at midnight, was interesting and anomalous. By invoking the more recent data (November and December in 2003), as well as the diurnal temperature observations from December 1998, we report that the evanescent (trapped) diurnal tidal perturbations were robust and persisted from one year to the next.
Coda wave interferometric detection of seismic velocity changes associated with the 1999 M = 3.6 event at Mt. Vesuvius
Authors: Pandolfi D. , Bean C. J. , Saccorotti G.
Published: March 2006

We detect seismic wave velocity changes at Mt. Vesuvius, using doublets and the Coda Wave Interferometry method. The high sensitivity of multiply scattered coda waves to temporal changes in the medium allows us to detect velocity variation smaller than 0.4%. We use 17 doublets, some of them grouped in families of multiplets, spanning January 1996 to December 1999. Data show a systematic increase in velocity from 1996 to end‐September 1999, followed by a rapid drop in velocity. This drop immediately precedes a sustained swarm of VT‐type earthquakes, including the 9th October 1999 M = 3.6 event, the largest in the region since at least 1972. We propose a long term fluid pressurization followed by influx as a possible causative mechanism.
Parameter identification using the level set method
Authors: Lu Zhiming , Robinson Bruce A.
Published: March 2006

This study describes an inverse approach for efficiently identifying the spatial shapes of zones of low (or high) permeability using the level set method, given a set of spatially distributed head measurements. By this method, the boundaries of zones are characterized by a level set function. From an initial setting, the unknown regions of zones are determined by evolving the boundaries in artificial time using a pseudo velocity field that is related to the sensitivity of head to permeability and the residual between the measured head and modeled head at the current time. A synthetic example presented to illustrate the method.
Amazon rainforests green‐up with sunlight in dry season
Authors: Huete Alfredo R. , Didan Kamel , Shimabukuro Yosio E. , Ratana Piyachat , Saleska Scott R. , Hutyra Lucy R. , Yang Wenze , Nemani Ramakrishna R. , Myneni Ranga
Published: March 2006

Metabolism and phenology of Amazon rainforests significantly influence global dynamics of climate, carbon and water, but remain poorly understood. We analyzed Amazon vegetation phenology at multiple scales with Moderate Resolution Imaging Spectroradiometer (MODIS) satellite measurements from 2000 to 2005. MODIS Enhanced Vegetation Index (EVI, an index of canopy photosynthetic capacity) increased by 25% with sunlight during the dry season across Amazon forests, opposite to ecosystem model predictions that water limitation should cause dry season declines in forest canopy photosynthesis. In contrast to intact forests, areas converted to pasture showed dry‐season declines in EVI‐derived photosynthetic capacity, presumably because removal of deep‐rooted forest trees reduced access to deep soil water. Local canopy photosynthesis measured from eddy flux towers in both a rainforest and forest conversion site confirm our interpretation of satellite data, and suggest that basin‐wide carbon fluxes can be constrained by integrating remote sensing and local flux measurements.
Whistler propagation in inhomogeneous plasma
Authors: Streltsov A. V. , Lampe M. , Manheimer W. , Ganguli G. , Joyce G.
Published: March 2006

We present a numerical study of the propagation of VLF whistler waves in the magnetospheric plasma. In this study the plasma is considered to be homogeneous in the direction along the ambient magnetic field and strongly inhomogeneous across it. The goal of this investigation is to understand whistler propagation in magnetic‐field‐aligned channels (also called ducts) with either enhanced or depleted plasma density. In particular, the paper is focused on situations where the transverse scale size of the duct is comparable to or smaller than the perpendicular wavelength of the whistler. In this case, classical analysis of the whistler dynamics based on the geometrical optic approximation becomes invalid, and numerical solutions of the full wave equations should be performed. Our simulations extend the earlier analysis based on the ray‐tracing technique and analytical studies of the very low frequency wave equations. We show that high‐density ducts are inherently leaky and this leakage depends on the perpendicular wavelength of the wave inside the duct. We also show that whistler trapping occurs not only at density maxima and minima but also at critical points along a density gradient. This effect can explain whistler guiding along strong transverse plasma density gradients at the plasmapause.
Development of quantitative PCR methods to analyse neural progenitor cell culture state
Authors: Abranches Elsa , O'Neill Analeah , Robertson Matthew J. , Schaffer David V. , Cabral Joaquim M. S.
Published: March 2006

Stem cells have significant potential for tissue engineering and regeneration, and neural stem and progenitor cells have proven promising for neuroregeneration in numerous animal disease and injury models. However, improved approaches must be developed to culture, expand and control the cells. Therefore the development of enhanced methods to quantify cell differentiation would significantly aid both in the basic investigation of cell‐fate control mechanisms and in the optimization and validation of cell culture and expansion conditions. Quantitative reverse transcription–PCR methods were developed to quantify cell differentiation state by monitoring the expression of several cell‐lineage‐specific markers. These methods provide more rapid and readily quantitative results when compared with immunostaining. These methods were also applied in a preliminary investigation of cell‐culture conditions, and it was found that regular feeding of cells with fresh medium is necessary to maintain them in an undifferentiated and highly proliferative state. The present study may aid both basic efforts to study the control of neural stem and progenitor differentiation as well as endeavours to optimize cell culture and expansion conditions for biomedical applications.
Cell‐cycle‐dependent cortical localization of pEg3 protein kinase in Xenopus and human cells
Authors: Chartrain Isabelle , Couturier Anne , Tassan Jean‐Pierre
Published: March 2006

Background information. Protein kinase pEg3 belongs to the evolutionarily conserved KIN1/PAR‐1/MARK family, whose members are involved in a variety of functions, including cell polarity, microtubule stability, intracellular signalling and the cell cycle. Activity and phosphorylation of pEg3 are cell‐cycle dependent and rise to maximum levels during mitosis. pEg3 was shown to interact with and phosphorylate phosphatase CDC25B, and to potentially control cell‐cycle progression. Subcellular localization of pEg3 was investigated in Xenopus and human cultured cells.

Results. By expression of GFP (green fluorescent protein)‐tagged pEg3 and indirect immunofluorescence with specific antibodies, pEg3 was found to be localized in the cytoplasm and the nucleus in interphase cells. During mitosis pEg3 was also found in the cytoplasm. From anaphase to telophase, a proportion of the protein was detected at the cell cortex. The cortical distribution in mitotic cells was dependent on F‐actin, because the actin‐depolymerization‐inducing drugs cytochalasin D or latrunculin A prevented pEg3 cortical localization. The protein lacking the conserved C‐terminal domain was not detected at the cell cortex, whereas the C‐terminal domain was targeted to the cell periphery. In contrast with full‐length pEg3, the cortical localization of the C‐terminal domain and construct lacking the N‐terminal domain was cell‐cycle independent, and these constructs were found at the cell periphery in interphase cells.

Conclusions. pEg3 is localized at the cell periphery specifically during mitosis. The C‐terminal domain is the only pEg3 domain found to be necessary and sufficient for cortical targeting. Cortical distribution of pEg3 also requires the F‐actin cytoskeleton. The cell‐cycle‐independent cortical localization of the pEg3 C‐terminal domain and a construct lacking the N‐terminal domain indicates that a negative control mechanism involving the pEg3 catalytic N‐terminal domain probably acts to prevent pEg3 cortical distribution during interphase. These results suggest that pEg3 might play a role at the cell cortex during mitosis.
Ion-beam lithography by use of highly charged Ar-ion beam
Authors: Momota Sadao , Iwamitsu Shingo , Goto Shougo , Nojiri Yoichi , Taniguchi Jun , Miyamoto Iwao , Ohno Hirohisa , Morita Noboru , Kawasegi Noritaka
Published: March 2006

In order to fabricate a nanoscale three-dimensional (3D) structure by using the ion-beam lithography (IBL), we tried to control the etching rate and the etching depth by means of the charge state, the beam energy, and the fluence of the ion beam. Ar-ion beams with E=90keV and 80–400keV were irradiated onto spin on glass (SOG) and Si, respectively. The Ar ions were prepared by a facility built at the Kochi University of Technology, which included an electron cyclotron resonance ion source (NANOGAN, 10GHz). It was found that the irradiation of highly charged ions (HCIs) enhanced the etching rate of SOG. The etching rate and etching depth of Si were controlled by the beam energy and the fluence of Ar4+ ions. The present results show the effectiveness of IBL with HCIs to fabricate a nanoscale 3D structure.
Electrostatic plasma lens for accelerator injection application
Authors: Chekh Yu. M. , Goncharov A. A. , Protsenko I. M. , Dobrovolsky A. M. , Brown I. G.
Published: March 2006

We describe the results of investigations of the suitability of the electrostatic plasma lens as a focusing element in the low-energy injection beam lines of particle accelerators. We have explored the focusing of high-current, wide-aperture, heavy-ion beams by a plasma lens. The results indicate that for optimal focusing conditions the lens does not increase the beam emittance nor the beam noise. The ion current density was increased by a factor of 30, up to 250mA∕cm2 in the work described here. We project that with an optimized ion extraction system, the plasma lens can provide an ion-beam current density of up to 400mA∕cm2 or more.
New method of high brightness ion extraction based on bias electrode
Authors: Kim Y. J. , Park D. H. , Jeong H. S. , Hwang Y. S.
Published: March 2006

It is well known that beam brightness can be enhanced with smaller extraction aperture in plasma ion sources. Reducing aperture size to micrometer scale, however, decreases beam currents significantly since the extraction field cannot be penetrated into the plasma source. In this article, a novel extraction method based on bias electrode is proposed and demonstrated by observing the existence of high current mode with 100μm aperture diameter. Ion current with a positively biased electrode is increased by an order of magnitude from that of the nonbiased case. Locally converging electrons near positively biased electrode are thought to be the main cause of the high current mode.
How strong is the interaction between a noble gas atom and a noble metal atom in the insertion compounds MNgF (M=Cu and Ag, and Ng=Ar, Kr, and Xe)?
Authors: Ghanty Tapan K.
Published: March 2006

Ab initio molecular orbital calculations have been carried out to investigate the structure and the stability of noble gas insertion compounds of the type MNgF (M=Cu and Ag, and Ng=Ar, Kr, and Xe) through second order Møller-Plesset perturbation method. All the species are found to have a linear structure with a noble gas–noble metal bond, the distance of which is closer to the respective covalent bond length in comparison with the relevant van der Waals limit. The dissociation energies corresponding to the lowest energy fragmentation products, MF+Ng, have been found to be in the range of −231 to −398kJ∕mol. The respective barrier heights pertinent to the bent transition states (M–Ng–F bending mode) are quite high for the CuXeF and AgXeF species, although for the Ar and Kr containing species the same are rather low. Nevertheless the M–Ng bond length in MNgF compounds reported here is the smallest M–Ng bond ever predicted through any experimental or theoretical investigation, indicating strongest M–Ng interaction. All these species (except AgArF) are found to be metastable in their respective potential energy surface, and the dissociation energies corresponding to the M+Ng+F fragments have been calculated to be 30.1–155.3kJ∕mol. Indeed, in the present work we have demonstrated that the noble metal–noble gas interaction strength in MNgF species (with M=Cu and Ag, and Ng=Kr and Xe) is much stronger than that in NgMF systems. Bader’s [Atoms in molecules-A Quantum Theory (Oxford University Press, Oxford, 1990)] topological theory of atoms in molecules (AIM) has been employed to explore the nature of interactions involved in these systems. Geometric as well as energetic considerations along with AIM results suggest a partial covalent nature of M–Ng bonds in these systems. The present results strengthen our earlier work and further support the proposition on the possibility of experimental identification of this new class of insertion compounds of noble gas atoms containing noble gas–noble metal bond.
Impulsive solvent heating probed by picosecond x-ray diffraction
Authors: Cammarata M. , Lorenc M. , Kim T. K. , Lee J. H. , Kong Q. Y. , Pontecorvo E. , Lo Russo M. , Schiró G. , Cupane A. , Wulff M. , Ihee H.
Published: March 2006

The time-resolved diffraction signal from a laser-excited solution has three principal components: the solute-only term, the solute-solvent cross term, and the solvent-only term. The last term is very sensitive to the thermodynamic state of the bulk solvent, which may change during a chemical reaction due to energy transfer from light-absorbing solute molecules to the surrounding solvent molecules and the following relaxation to equilibrium with the environment around the scattering volume. The volume expansion coefficient α for a liquid is typically ∼1×10−3K−1, which is about 1000 times greater than for a solid. Hence solvent scattering is a very sensitive on-line thermometer. The decomposition of the scattered x-ray signal has so far been aided by molecular dynamics (MD) simulations, a method capable of simulating the solvent response as well as the solute term and solute/solvent cross terms for the data analysis. Here we present an experimental procedure, applicable to most hydrogen containing solvents, that directly measures the solvent response to a transient temperature rise. The overtone modes of OH stretching and CH3 asymmetric stretching in liquid methanol were excited by near-infrared femtosecond laser pulses at 1.5 and 1.7μm and the ensuing hydrodynamics, induced by the transfer of heat from a subset of excited CH3OH* to the bulk and the subsequent thermal expansion, were probed by 100ps x-ray pulses from a synchrotron. The time-resolved data allowed us to extract two key differentials: the change in the solvent diffraction from a temperature change at constant density, seen at a very short time delay ∼100ps, and a term from a change in density at constant temperature. The latter term becomes relevant at later times ∼1μs when the bulk of liquid expands to accommodate its new temperature at ambient pressure. These two terms are the principal building blocks in the hydrodynamic equation of state, and they are needed in a self-consistent reconstruction of the solvent response during a chemical reaction. We compare the experimental solvent terms with those from MD simulations. The use of experimentally determined solvent differentials greatly improved the quality of global fits when applied to the time-resolved data for C2H4I2 dissolved in methanol.
Analytical electrostatics for biomolecules: Beyond the generalized  Born approximation
Authors: Sigalov Grigori , Fenley Andrew , Onufriev Alexey
Published: March 2006

The modeling and simulation of macromolecules in solution often benefits from fast analytical approximations for the electrostatic interactions. In our previous work [G. Sigalov et al., J. Chem. Phys. 122, 094511 (2005)], we proposed a method based on an approximate analytical solution of the linearized Poisson-Boltzmann equation for a sphere. In the current work, we extend the method to biomolecules of arbitrary shape and provide computationally efficient algorithms for estimation of the parameters of the model. This approach, which we tentatively call ALPB here, is tested against the standard numerical Poisson-Boltzmann (NPB) treatment on a set of 579 representative proteins, nucleic acids, and small peptides. The tests are performed across a wide range of solvent/solute dielectrics and at biologically relevant salt concentrations. Over the range of the solvent and solute parameters tested, the systematic deviation (from the NPB reference) of solvation energies computed by ALPB is 0.5–3.5kcal∕mol, which is 5–50 times smaller than that of the conventional generalized Born approximation widely used in this context. At the same time, ALPB is equally computationally efficient. The new model is incorporated into the AMBER molecular modeling package and tested on small proteins.
Mean-field kinetic nucleation theory
Authors: Kalikmanov V. I.
Published: March 2006

A new semiphenomenological model of homogeneous vapor-liquid nucleation is proposed in which the cluster kinetics follows the “kinetic approach to nucleation” and the thermodynamic part is based on the revised Fisher droplet model with the mean-field argument for the cluster configuration integral. The theory is nonperturbative in a cluster size and as such is valid for all clusters down to monomers. It contains two surface tensions: macroscopic (planar) and microscopic. The latter is a temperature dependent quantity related to the vapor compressibility factor at saturation. For Lennard-Jones fluids the microscopic surface tension possesses a universal behavior with the parameters found from the mean-field density functional calculations. The theory is verified against nucleation experiments for argon, nitrogen, water, and mercury, demonstrating very good agreement with experimental data. Classical nucleation theory fails to predict experimental results when a critical cluster becomes small.
Electron density fitting for the Coulomb problem in relativistic density-functional theory
Authors: Belpassi Leonardo , Tarantelli Francesco , Sgamellotti Antonio , Quiney Harry M.
Published: March 2006

A density fitting approach for the Coulomb matrix representation within the four-component formulation of relativistic density-functional theory is presented. Our implementation, which uses G-spinor basis sets, shares all the advantages of those found in nonrelativistic quantum chemistry. We show that very accurate Coulomb energies may be obtained using a modest number of scalar auxiliary basis functions for molecules containing heavy atoms. The efficiency of this new implementation is demonstrated in a detailed study of the spectroscopic properties of the gold dimer, and its scaling behavior has been tested by calculations of some closed-shell gold clusters (Au2,Au3+,Au4,Au5+). The algorithm is found to scale as O(N3), just as it does in the nonrelativistic case, and represents a dramatic improvement in efficiency over the conventional approach in the calculation of the Coulomb matrix, with computation times that are reduced to less than 3% for Au2 and up to 1% in the case of Au5+.
Theoretical investigation of two-photon absorption allowed excited states in symmetrically substituted diacetylenes by ab initio molecular-orbital method
Authors: Ohta Koji , Kamada Kenji
Published: March 2006

Symmetrically substituted diacetylene compounds, which shows large two-photon absorption (TPA) cross sections, have been theoretically investigated by the ab initio molecular-orbital method employing several theoretical models including the configuration interaction with single excitation (CIS), random phase approximation (RPA), and time-dependent density-functional theory (TDDFT) methods. The calculated excited energies are overestimated by CIS or RPA, whereas underestimated by TDDFT with the B3LYP parametrization for both one-photon absorption (OPA) and TPA allowed states. The lowest OPA state is well described by the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) transition. On the other hand, lower TPA allowed states can be represented as the superposition of the HOMO-LUMO+1 and HOMO−1-LUMO transitions, giving rise to two TPA allowed states. The absorption intensity for the lower TPA state of the diacetylenes molecules is discussed in terms of the alternancy symmetry and its breaking. The symmetry property is differently manifested for neutral and dicationic diacetylenes. Introduction of charges breaks the alternancy symmetry, which gives rise to an increase in the TPA cross sections at the lower frequency. The upper TPA state is calculated to show huge TPA cross sections, which reproduces the enhancement of the TPA cross section experimentally observed for one of the diacetylenes at the higher-frequency region. The enhancement is discussed employing an index defined as the ratio of the transition polarizability and its static limit, which represents the degree of influence of one-photon resonance on the TPA intensity. The huge TPA cross sections are found to be due to a near-resonance effect. The present theoretical calculation approves the previously proposed assumption based on the four-state (dual three-state) model, which consists of the ground, one OPA allowed, and two TPA allowed states.
High-repetition-rate (6kHz) and long-pulse-duration (50ns) ArF excimer laser for sub-65nm lithography
Authors: Kakizaki Koji , Sasaki Yoichi , Inoue Toyoharu , Sakai Yosuke
Published: March 2006

Development of high-repetition-rate ArF excimer lasers is vital requirement for achieving high throughput and high energy-dose stability in a scanner system. ArF excimer laser, with increasing light pulse duration, can reduce the peak power without the energy-dose change. Then, the spectral bandwidth ΔλFWHM becomes narrower by increasing the number of light round trips in a cavity, and optical damage is reduced from high-peak power. Laser operation exceeding 4kHz is needed for next-generation technologies that can enable high numerical aperture and development of high-throughput scanners. In the present work, we examined the possibilities of achieving a repetition rate to 6kHz from 4kHz in the ArF laser the authors developed, taking the following innovations. The spatial width of discharge region was reduced by about 30%. The uniform gas flow condition between the electrodes was obtained by improving gas flow guides. As a result, we have obtained an average power of 42W, a standard deviation for pulse-to-pulse energy of 3.5%, and an integral-square pulse width Tis of 44ns at 6kHz for ΔλFWHM<0.40pm. Finally, it was concluded that developing a 6kHz ArF excimer laser for the next-generation sub-65nm lithography is feasible.
Versatile wide angle diffraction setup for simultaneous wide and small angle x-ray scattering measurements with synchrotron radiation
Authors: Rueda D. R. , García-Gutiérrez M. C. , Nogales A. , Capitán M. J. , Ezquerra T. A. , Labrador A. , Fraga E. , Beltrán D. , Juanhuix J. , Herranz J. F. , Bordas J.
Published: March 2006

Here we present a novel, simple, and versatile experimental setup aimed to perform wide angle x-ray scattering (WAXS) measurements alone or in simultaneous combination with small angle x-ray scattering measurements. The design of the WAXS goniometer allows one to obtain high resolution diffraction patterns in a broad angular range. The setup can incorporate a hot stage in order to evaluate temperature resolved experiments. The performance of the equipment has been verified in the BM16 beam line of the European Synchrotron Radiation Facility with different well known samples such as alumina, isotropic film of high density polyethylene (HDPE), and oriented HPDE fiber.
Ultrafast progressive breakdown associated with metal-like filament formation of a breakdown path in a HfO2∕TaN∕TiN transistor
Authors: Ranjan R. , Pey K. L. , Tung C. H. , Ang D. S. , Tang L. J. , Kauerauf T. , Degraeve R. , Groeseneken G. , De Gendt S. , Bera L. K.
Published: March 2006

Ultrafast progressive breakdown has been observed in a TaN∕TiN metal gate metal-oxide-semiconductor field effect transistor (MOSFET) compared to a polycrystalline silicon gate MOSFET. Physical analysis by transmission electron microscopy and electrical characterization shows that the ultrafast progressive breakdown is likely to be associated with a metal-like filament formation of the breakdown path. It has been observed that the metal-like filament of the breakdown path is detrimental to the metal gate MOSFET progressive breakdown lifetime.
Self-assembled three-dimensional structures of single-crystalline ZnS submicrotubes formed by coalescence of ZnS nanowires
Authors: Shen Guozhen , Bando Yoshio , Golberg Dmitri
Published: March 2006

Self-assembled three-dimensional (3D) dandelionlike ZnS structures have been successfully synthesized by a simple thermochemical process using ZnS and Ge powders as the source material. The as-synthesized dandelionlike structures consist of radially aligned ZnS submicrotubes with well-faceted hexagonal cross sections, which are formed by the coalescence of neighboring ZnS nanowires. A two-step self-assembly process was proposed to explain the formation mechanism. The as-synthesized 3D dandelionlike ZnS structures show strong green emission centered at about 550nm as well as a weak emission at 720nm.
Quantum confinement effect in crystalline silicon quantum dots in silicon nitride grown using SiH4 and NH3
Authors: Kim Tae-Wook , Cho Chang-Hee , Kim Baek-Hyun , Park Seong-Ju
Published: March 2006

Crystalline silicon quantum dots (Si QDs) were spontaneously grown in the silicon nitride films by plasma-enhanced chemical vapor deposition using SiH4 and NH3 as precursors. When the size of the Si QDs was reduced from 4.9 to 2.9nm, the photoluminescence peak energy was shifted from 1.73 to 2.77eV. The photoluminescence peak energy was fitted to the relationship, E(eV)=1.13+13.9∕d2, where d is the diameter of the Si QD in nanometers. The measured band-gap energies of the Si QDs were in good agreement with the quantum confinement model for crystalline Si QDs. These results suggest that the hydrogen dissociated from NH3 plays an important role in improving the crystallinity and surface passivation of Si QDs.
Characteristics of HfxSiyO films grown on Si0.8Ge0.2 layer by electron-beam evaporation
Authors: Cheng Xinhong , Song Zhaorui , Yu Yuehui , Yang Wenwei , Shen DaShen
Published: March 2006

Hf x Si y O gate dielectric films on strained Si0.8Ge0.2 layer were prepared by electron-beam evaporation. Their structural and electrical characteristics along with interface properties have been investigated by high-resolution transmission electron microscopy, energy dispersive x-ray spectroscopy, x-ray photoelectron spectroscopy, and electrical measurements of metal-insulator-semiconductor capacitors. The dielectric film remained amorphous after annealing at 800°C. The dielectric constant is 9, a breakdown electrical field is higher than 8MV∕cm, and the leakage current is 0.1μA∕cm2 at the gate bias of 2V. Postdeposition anneal resulted in the formation of suboxidized states of Si and Ge at interface, which were responsible for the fixed oxide charges density of −5×1012cm2. No Ge-rich region was found.
TEX14 is essential for intercellular bridges and fertility in male mice
Authors: Greenbaum Michael P. , Yan Wei , Wu Meng-Hsieh , Lin Yi-Nan , Agno Julio E. , Sharma Manju , Braun Robert E. , Rajkovic Aleksandar , Matzuk Martin M.
Published: March 2006

Cytokinesis in somatic cells concludes with the formation of a midbody, which is abscised to form individual daughter cells. In contrast, germ cell cytokinesis results in a permanent intercellular bridge connecting the daughter cells through a large cytoplasmic channel. During spermatogenesis, proposed roles for the intercellular bridge include germ cell communication, synchronization, and chromosome dosage compensation in haploid cells. Although several essential components of the midbody have recently been identified, essential components of the vertebrate germ cell intercellular bridge have until now not been described. Herein, we show that testis-expressed gene 14 (TEX14) is a novel protein that localizes to germ cell intercellular bridges. In the absence of TEX14, intercellular bridges are not observed by using electron microscopy and other markers. Spermatogenesis in
Tex14
−/−
mice progresses through the transit amplification of diploid spermatogonia and the expression of early meiotic markers but halts before the completion of the first meiotic division. Thus, TEX14 is required for intercellular bridges in vertebrate germ cells, and these studies provide evidence that the intercellular bridge is essential for spermatogenesis and fertility.
An intronic insertion in
KPL2
results in aberrant splicing and causes the immotile short-tail sperm defect in the pig
Authors: Sironen Anu , Thomsen Bo , Andersson Magnus , Ahola Virpi , Vilkki Johanna
Published: March 2006

The immotile short-tail sperm defect is an autosomal recessive disease within the Finnish Yorkshire pig population. This disease specifically affects the axoneme structure of sperm flagella, whereas cilia in other tissues appear unaffected. Recently, the disease locus was mapped to a 3-cM region on porcine chromosome 16. To facilitate identification of candidate genes, we constructed a porcine-human comparative map, which anchored the disease locus to a region on human chromosome 5p13.2 containing eight annotated genes. Sequence analysis of a candidate gene
KPL2
revealed the presence of an inserted retrotransposon within an intron. The insertion affects splicing of the
KPL2
transcript in two ways; it either causes skipping of the upstream exon, or causes the inclusion of an intronic sequence as well as part of the insertion in the transcript. Both changes alter the reading frame leading to premature termination of translation. Further work revealed that the aberrantly spliced exon is expressed predominantly in testicular tissue, which explains the tissue-specificity of the immotile short-tail sperm defect. These findings show that the
KPL2
gene is important for correct axoneme development and provide insight into abnormal sperm development and infertility disorders.
An evolutionarily mobile antigen receptor variable region gene: Doubly rearranging NAR-TcR genes in sharks
Authors: Criscitiello Michael F. , Saltis Mark , Flajnik Martin F.
Published: March 2006

Distinctive Ig and T cell receptor (TcR) chains define the two major lineages of vertebrate lymphocyte yet similarly recognize antigen with a single, membrane-distal variable (V) domain. Here we describe the first antigen receptor chain that employs two V domains, which are generated by separate VDJ gene rearrangement events. These molecules have specialized “supportive” TcRδV domains membrane-proximal to domains with most similarity to IgNAR V. The ancestral NAR V gene encoding this domain is hypothesized to have recombined with theTRDlocus in a cartilaginous fish ancestor >200 million years ago and encodes the first V domain shown to be used in both Igs and TcRs. Furthermore, these data support the view that γ/δ TcRs have for long used structural conformations recognizing free antigen.
Dynamic properties of orientation discrimination assessed by using classification images
Authors: Mareschal Isabelle , Dakin Steven C. , Bex Peter J.
Published: March 2006

Recent physiological studies indicate that the tuning properties of neurons under acute preparation in primary visual cortex can change over time. We used a psychophysical reverse correlation paradigm to examine the potential repercussions of this neuronal property for human observers' ability to discriminate the orientation of targets over time. Observers were required to identify the orientation of a Gabor target presented within dynamic white noise. Frames from the noise movies were pooled to compute dynamic classification images (CIs) associated with the observers' discrimination performance, which then were fit with a weighted difference-of-Gabor function. Best-fitting templates were temporally bandpass, tuned to more oblique orientations than the stimulus but, crucially, did not change over time. The results suggest that the template for orientation discrimination is selected within the first 50 ms of stimulus onset and that, unlike the response of single cells, there is no measurable dynamic component to either orientation or spatial frequency tuning of human orientation discrimination.