bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of microwave‐assisted protein digestion based on trypsin‐immobilized magnetic microspheres for highly efficient proteolysis followed by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry analysis
Authors: Lin Shuang , Lin Zhenxin , Yao Guoping , Deng Chunhui , Yang Pengyuan , Zhang Xiangmin
Published: November 2007

In this study, very easily prepared trypsin‐immobilized magnetic microspheres were applied in microwave‐assisted protein digestion and firstly applied for proteome analysis by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS). Magnetic microspheres with small size were synthesized and modified by 3‐glycidoxypropyltrimethoxysilane (GLYMO). Trypsin was immobilized onto magnetic microspheres through only a one‐step reaction of its amine group with GLYMO. When these easily prepared trypsin‐immobilized magnetic microspheres were applied in microwave‐assisted protein digestion, the magnetic microspheres not only functionalized as substrate for trypsin immobilization, but also as an excellent microwave absorber and thus improved the efficiency of microwave‐assisted digestion greatly. Cytochrome c was used as a model protein to verify its digestion efficiency. Without any additives such as organic solvents or urea, peptide fragments produced in 15 s could be confidently identified by MALDI‐TOF‐MS and better digestion efficiency was obtained comparing to conventional in‐solution digestion (12 h). Besides, with an external magnet, trypsin could be used repeatedly and at the same time no contaminants were introduced into the sample solution. It was verified that the enzyme maintained high activity after seven runs. Furthermore, reversed‐phase liquid chromatography (RPLC) fractions of rat liver extract were also successfully processed using this novel method. These results indicated that this fast and efficient digestion method, which combined the advantages of immobilized trypsin and microwave‐assisted protein digestion, will greatly hasten the application of top‐down proteomic techniques for large‐scale analysis in biological and clinical research. Copyright © 2007 John Wiley & Sons, Ltd.
A semi‐Markov model for multistate and interval‐censored data with multiple terminal events. Application in renal transplantation
Authors: Foucher Yohann , Giral Magali , Soulillou Jean‐Paul , Daures Jean‐Pierre
Published: November 2007

The semi‐Markov assumption emphasizes the importance of time spent in a state. In order to compute this type of multistate model, most transition times are always considered to be exactly identified or right censored. However, in the longitudinal analysis of chronic diseases, investigators are often confronted with interval‐censored data (transition times are known to have occurred in some interval). Thus, the two key issues are the modeling of the duration dependence and the interval censoring. In this article, we define a semi‐Markov model, allowing for interval censoring, for parametric hazard functions with a ∪‐ or ∩‐shape and for determination of initial states according to covariates. Our modeling approach is specific to each transition, so as to obtain a more coherent model. Parallel to competing risks models, the multistate model takes into account several final events. We consider an example of kidney transplant recipient follow‐up to illustrate the utility of the method. Copyright © 2007 John Wiley & Sons, Ltd.
Mobility protocols and RSVP performance in wireless IPv6 networks: shortcomings and solutions
Authors: Belhoul Ahmad , Şekercioğlu Y. Ahmet , Mani Nallasamy
Published: November 2007

Resource reservation protocol (RSVP) is a network‐control protocol used to guarantee Quality‐of‐Service (QoS) requirements for real‐time applications such as Voice‐over‐IP (VoIP) or Video‐over‐IP (VIP). However, RSVP was designed for end‐systems whose IP addresses do not change. Once mobility of an end‐system is allowed, the dynamically changing mobile IP address inevitably impacts on RSVP performance. Our study aims to first quantify the significance of this impact, and then propose a modified RSVP mechanism that provides improved performance during handoffs. Our simulations reveal that the deployment of standard RSVP over Mobile IPv6 (MIPv6) does not yield a satisfactory result, particularly in the case of VIP traffic. Fast Handovers for Mobile IPv6 (FMIPv6) was found to be providing the best performance in all tested scenarios, followed by Hierarchical Mobile IPv6 (HMIPv6) with a single exception: during low handoff rates with VoIP traffic, MIPv6 outperformed HMIPv6. We then designed a new RSVP mechanism, and tested it against standard RSVP. We found that the proposed approach provides a significant improvement of 54.1% in the Total Interruption in QoS (TIQoS) when deployed over a MIPv6 wireless network. For HMIPv6, performance depended primarily on the number of hierarchical levels in the network, with no improvement in TIQoS for single‐level hierarchy and up to 37% for a 5‐level hierarchy. FMIPv6 on the other hand, provided no room for improvement due to pre‐handoff signaling and the tunneling mechanism used to ensure a mobile node (MN)'s connectivity during a handoff, regardless of the RSVP mechanism used. Copyright © 2007 John Wiley & Sons, Ltd.
God's purpose as irrelevant to life's meaning: reply to Affolter
Authors: METZ THADDEUS
Published: November 2007

Elsewhere I have contended that if a God-centred account of meaning in life were true, it would not be because meaning comes from fulfilling God's purpose for us. Specifically, I have argued that this ‘purpose theory’ of life's meaning cannot be the correct God-based view since God would have to be atemporal, immutable, and simple for meaning to logically depend on His existence, and since such a being lacking extension could not be purposive. Jacob Affolter has developed a fresh account of the kind of purpose that is necessary for meaning in life, has argued that a God without extension could ground it, and has also provided some tentative reason to believe that only such a God could do so. I respond in three ways: by questioning whether the sort of purpose Affolter thinks is necessary for meaning in fact is; by arguing that an extensionless God could not ground it; and by indicating the way that a purely physical world could.
Reasons for worship: a response to Bayne and Nagasawa
Authors: CROWE BENJAMIN D.
Published: November 2007

Worship is a topic that is rarely considered by philosophers of religion. In a recent paper, Tim Bayne and Yujin Nagasawa challenge this trend by offering an analysis of worship and by considering some difficulties attendant on the claim that worship is obligatory. I argue that their case for there being these difficulties is insufficiently supported. I offer two reasons that a theist might provide for the claim that worship is obligatory: (1) a divine command, and (2) the demands of justice with respect to God's redemption of humanity. I also challenge the soundness of some of the analogies they employ in their argument.
Prävalenz von Über- und Untergewicht in einer Mittelschulpopulation
Authors: Thaler  , Vetter  , Suter
Published: November 2007

Die Häufigkeit von Übergewicht und Adipositas bei Kindern, Jugendlichen und Erwachsenen ist zunehmend. Dieser Umstand wird vor allem auf Umwelteinflüsse zurückgeführt. Auch der Körperfettanteil wird wesentlich von Lebensstilfaktoren beeinflusst. 409 Schüler im Alter von 15–22 Jahren der Aargauischen Kantonsschule Wohlen wurden erfasst. Die Prävalenz des Übergewichtes nach den internationalen Definitionskriterien von Cole et al. [1] betrug bei den Gymnasiastinnen 6.13%, bei den Gymnasiasten 5.95%. 9.52% der Schüler und 16.51% der Schülerinnen hatten einen BMI < 18.5 kg/m². 16.98% der Schülerinnen hatten einen Fettanteil > 30%. 2.98% der Schüler hatten einen Fettanteil > 20%. Die Schüler mit Körperfettanteil > 15% schätzten ihre körperliche Aktivität (Mittelwert ± SEM) signifikant geringer ein als Schüler mit Körperfettanteil < 15% (4.49 ± 2.08 vs. 6.00 ± 2.08, p = 0.03). Die entsprechenden Daten der Schülerinnen mit Körperfettanteil > 30% gegenüber Schülerinnen mit Fettanteil < 30% waren signifikant (4.84 ± 1.74 vs. 5.68 ± 1.82, p = 0.04). Unsere Studie zeigt, dass Übergewicht und Adipositas, aber auch Untergewicht bei Gymnasiasten keine Seltenheit ist.
Reply to Comment on “Emergence of complex societies after sea level stabilized”
Authors: Day John W. , Gunn Joel D. , Folan William J. , Yáñez‐Arancibia, Alejandro , Horton Benjamin P.
Published: November 2007

Washington [this issue] raised a number of interesting points that serve to clarify the origins of civilizations on continental margins. We linked the initial development of civilizations to coastal margin productivity [Day et al., 2007]. Washington argues that a number of early civilizations were not related to marine productivity, but rather were centered around the exploitation and cultivation of riparian grains. However, we defined coastal margins to include upwellings, estuaries, and lower floodplains affected by coastal water levels. Thus, the Nile, Mesopotamia, Indus, Mississippi, and Yellow societies were influenced by coastal margin productivity.
Accuracy assessment of LiDAR‐derived DEMs of bedrock river channels: Holtwood Gorge, Susquehanna River
Authors: Reusser Lucas , Bierman Paul
Published: November 2007

We evaluate the accuracy of 1 m, LiDAR‐derived DEMs of an exposed bedrock channel, and use these high‐resolution terrain models to calculate erosional fluxes between four levels of strath terraces dated previously with 10Be. Recent investigations into the timing, rates, and processes by which rivers incise their bedrock channels have greatly enhanced our understanding of landscape evolution. However, measuring channel geometries in 3 dimensions is difficult; thus, volumes of bedrock eroded during incision events are rarely considered. Although our analysis successfully demonstrates the proportionality between incision rates and erosional fluxes for terraces high above the channel floor in this gorge, unusually high river flows on the date of acquisition inundated lower bedrock surfaces, preventing accurate volume estimates. To ensure optimal low‐flow LiDAR coverage for fluvial environments, we discuss methods to improve the scheduling of data acquisition by using archived discharge records and predictive models based on real‐time data.
Magnesium and calcium sulfate stabilities and the water budget of Mars
Authors: Chou I‐Ming , Seal Robert R.
Published: November 2007

Magnesium sulfate probably plays a dominant role in the water cycle of Mars away from the polar ice caps through hydration and dehydration reactions. This prominence is due to its abundance, its occurrence in numerous hydration states, and its ability to hydrate and dehydrate rapidly. New experimental studies on the metastable reaction between hexahydrite (MgSO4·6H2O) and starkeyite (MgSO4·4H2O) as a function of temperature and relative humidity, supplemented by recent investigations of the stable reaction between epsomite (MgSO4·7H2O) and hexahydrite and by phase equilibrium calculations, suggest that the most important magnesium sulfate phases involved in the Martian water cycle are MgSO4·11H2O, epsomite, starkeyite, and possibly kieserite (MgSO4·H2O). Hexahydrite is not predicted to be stable on the surface of Mars. During diurnal variations in temperature and relative humidity, 1 kg of MgSO4 can release or remove from the atmosphere 1.5 kg of H2O by cycling between kieserite and MgSO4·11H2O. Despite subequal abundances of calcium sulfate, calcium sulfates are not likely to be important in the water cycle of the planet because of sluggish rates of hydration and dehydration and a more limited range of H2O concentrations per kilogram of CaSO4 (0.00 to 0.26 kg kg−1). Modern or recent erosion on Mars attributed to liquid water may be due to the dehydration of MgSO4·11H2O because of the inferred abundance and likelihood of occurrence of this phase and its limited stability relative to known variations in temperature and relative humidity.
Adenosine transport in peripheral blood lymphocytes from Lesch-Nyhan patients
Authors: TORRES Rosa J. , DeANTONIO Isabel , PRIOR Carmen , PUIG Juan G.
Published: November 2007

We postulated that adenosine function could be related to some of the neurological features of Lesch–Nyhan syndrome and therefore characterized adenosine transport in PBLs (peripheral blood lymphocytes) obtained from Lesch–Nyhan patients (PBLLN) and from controls (PBLC). Adenosine transport was significantly lower in PBLLN when compared with that in PBLC and a significantly lower number of high affinity sites for [3H]nitrobenzylthioinosine binding were quantified per cell (Bmax) in PBLLN when compared with that in PBLC. After incubation with 25 µM hypoxanthine, adenosine transport was significantly decreased in PBLLN with respect to PBLC. Hypoxanthine incubation lowers [3H]nitrobenzylthioinosine binding in PBLC, with respect to basal conditions, but does not affect it in PBLLN. This indicates that hypoxanthine affects adenosine transport in control and hypoxanthine–guanine phosphoribosyltransferase-deficient cells by different mechanisms.
Characterization of a novel, cytokine-inducible carboxypeptidase D isoform in haematopoietic tumour cells
Authors: O'Malley Padraic G. P. , Sangster Shirley M. , Abdelmagid Salma A. , Bearne Stephen L. , Too Catherine K. L.
Published: November 2007

CPD-N is a cytokine-inducible CPD (carboxypeptidase-D) isoform identified in rat Nb2 T-lymphoma cells. The prototypic CPD (180 kDa) has three CP domains, whereas CPD-N (160 kDa) has an incomplete N-terminal domain I but intact domains II and III. CPD processes polypeptides in the TGN (trans-Golgi network) but the Nb2 CPD-N is nuclear. The present study identified a cryptic exon 1′, downstream of exon 1 of the rat CPD gene, as an alternative transcription start site that encodes the N-terminus of CPD-N. Western-blot analysis showed exclusive synthesis of the 160 kDa CPD-N in rat Nb2 and Nb2-Sp lymphoma cells. Several haematopoietic cell lines including human K562 myeloma, Jurkat T-lymphoma and murine CTLL-2 cytotoxic T-cells express a 160 kDa CPD-immunoreactive protein, whereas mEL4 T-lymphoma cells express the 180 kDa CPD. The CPD-immunoreactive protein in hK562 cells is also nuclear and cytokine-inducible. In contrast, MCF-7 breast cancer cells express only the 180 kDa CPD, which is mainly in the TGN. CPD/CPD-N assays using substrate dansyl-L-alanyl-L-arginine show approx. 98% of CPD-N activity in the Nb2 nucleus, whereas MCF-7 CPD activity is enriched in the post-nuclear 10000 g pellet. The Km for CPD-N and CPD are 132±30 and 63±9 μM respectively. Specific activity/Km ratios show that dansyl-L-alanyl-L-arginine is a better substrate for CPD-N than for CPD. CPD-N has an optimal pH of 5.6 (due to domain II), whereas CPD has activity peaks at pH 5.6 (domain II) and pH 6.5–7.0 (domain I). CPD and CPD-N are inhibited non-competitively by zinc chelator 1,10-phenanthroline and competitively by peptidomimetic inhibitor DL-2-mercaptomethyl-3-guanidinoethylthiopropanoic acid. The Nb2 CPD-N co-immunoprecipitated with phosphatase PP2A (protein phosphatase 2A) and α4 phosphoprotein. In summary, a cytokine-inducible CPD-N is selectively expressed in several haematopoietic tumour cells. Nuclear CPD-N is enzymatically active and interacts with known partners of CPD.
Site-directed modifications indicate differences in axial haem c iron ligation between the related NrfH and NapC families of multihaem c-type cytochromes
Authors: Gross Roland , Eichler Robert , Simon Jörg
Published: November 2007

During the last decade, a number of related bacterial membrane-bound multihaem c-type cytochromes, collectively referred to as the NapC/NirT family, were identified. These proteins are generally thought to catalyse electron transport between the quinone/quinol pool and periplasmic oxidoreductases. The best-characterized members, the tetrahaem c-type cytochromes NrfH and NapC, mediate electron transport to NrfA and NapA respectively. Amino acid sequence alignments suggest that the nature and position of distal haem c iron ligands differs in NrfH and NapC proteins. Site-directed modification of potential haem c iron-ligating histidine, lysine and methionine residues in Wolinella succinogenes NrfH was performed to determine the implication in electron transport from formate to nitrite. Two histidine, one lysine and one methionine residues were found to be essential, whereas the replacement of three other conserved histidine residues, one methionine and two lysines did not prevent growth by nitrite respiration. The results contrast those previously obtained for Paracoccus pantotrophus NapC, in which four essential histidine residues have been identified that are highly likely to serve as distal haem c iron ligands. The combined experimental evidence suggests different haem ligation patterns within NapC and NrfH proteins, which might reflect their different functions in the bacterial electron transfer.
Polyphosphate blocks tumour metastasis via anti-angiogenic activity
Authors: Han Kyu Yeon , Hong Bok Sil , Yoon Yae Jin , Yoon Chang Min , Kim Yoon-Keun , Kwon Young-Guen , Gho Yong Song
Published: November 2007

PolyP (inorganic polyphosphate) is a linear polymer of many tens or hundreds of orthophosphate residues found in a wide range of organisms, including bacteria, fungi, insects, plants and vertebrates. Despite its wide distribution in mammalian tissues and plasma, the biological functions of polyP on tumour metastasis and angiogenesis have not been previously examined. In the present study, we have shown that polyP effectively blocked in vivo pulmonary metastasis of B16BL6 cells by suppression of neovascularization, whereas it did not affect proliferation or adhesion to extracellular matrix proteins. PolyP not only inhibited bFGF (basic fibroblast growth factor)-induced proliferation and ERK (extracellular-signal-regulated kinase)/p38 MAPK (mitogen-activated protein kinase) activation of human endothelial cells, but also blocked the binding of bFGF to its cognate cell-surface receptor. Furthermore, polyP inhibited bFGF-induced in vitro and in vivo angiogenesis, suggesting that polyP possesses an anti-angiogenic activity. Since neovascularization is essential for tumour metastasis, our present findings clearly indicate that polyP has an in vivo anti-metastatic activity via its anti-angiogenic activity. Taken together with the fact that angiogenesis occurs under various normal and pathological conditions, our observations suggest that endogenous polyP may play a critical role during embryonic development, wound healing and inflammation, as well as in the progress of pathological diseases such as rheumatoid arthritis and cancer.
NOX4 activity is determined by mRNA levels and reveals a unique pattern of ROS generation
Authors: Serrander Lena , Cartier Laetitia , Bedard Karen , Banfi Botond , Lardy Bernard , Plastre Olivier , Sienkiewicz Andrzej , Fórró Lászlo , Schlegel Werner , Krause Karl-Heinz
Published: November 2007

NOX4 is an enigmatic member of the NOX (NADPH oxidase) family of ROS (reactive oxygen species)-generating NADPH oxidases. NOX4 has a wide tissue distribution, but the physiological function and activation mechanisms are largely unknown, and its pharmacology is poorly understood. We have generated cell lines expressing NOX4 upon tetracycline induction. Tetracycline induced a rapid increase in NOX4 mRNA (1 h) followed closely (2 h) by a release of ROS. Upon tetracycline withdrawal, NOX4 mRNA levels and ROS release decreased rapidly (<24 h). In membrane preparations, NOX4 activity was selective for NADPH over NADH and did not require the addition of cytosol. The pharmacological profile of NOX4 was distinct from other NOX isoforms: DPI (diphenyleneiodonium chloride) and thioridazine inhibited the enzyme efficiently, whereas apocynin and gliotoxin did not (IC50>100 μM). The pattern of NOX4-dependent ROS generation was unique: (i) ROS release upon NOX4 induction was spontaneous without need for a stimulus, and (ii) the type of ROS released from NOX4-expressing cells was H2O2, whereas superoxide (O2−) was almost undetectable. Probes that allow detection of intracellular O2− generation yielded differential results: DHE (dihydroethidium) fluorescence and ACP (1-acetoxy-3-carboxy-2,2,5,5-tetramethylpyrrolidine) ESR measurements did not detect any NOX4 signal, whereas a robust signal was observed with NBT. Thus NOX4 probably generates O2− within an intracellular compartment that is accessible to NBT (Nitro Blue Tetrazolium), but not to DHE or ACP. In conclusion, NOX4 has a distinct pharmacology and pattern of ROS generation. The close correlation between NOX4 mRNA and ROS generation might hint towards a function as an inducible NOX isoform.
Endothelin-1 (ET-1) promotes MMP-2 and MMP-9 induction involving the transcription factor NF-κB in human osteosarcoma
Authors: Felx Mélanie , Guyot Marie-Claude , Isler Marc , Turcotte Robert E. , Doyon Josée , Khatib Abdel-Majid , Leclerc Séverine , Moreau Alain , Moldovan Florina
Published: November 2007

In the present study, we have investigated the effect of (i) ET-1 (endothelin-1) and its precursor, big ET-1, on MMP (matrix metalloproteinase)-2 and MMP-9 synthesis and activity in osteosarcoma tissue, and (ii) ET-1 receptor antagonists on cell invasion. Using Western blotting, zymography, RT-PCR (reverse transcription–PCR), immunohistochemistry, immunofluorescence and Northern blotting, we have shown that ET-1 and ET-1 receptors (ETA and ETB) were expressed in these cells. Additionally, we have demonstrated that ET-1 markedly induced the synthesis and activity of MMP-2, which was significantly increased when compared with MMP-9. Furthermore, inhibition of NF-κB (nuclear factor κB) activation blocked MMP-2 production and activity, indicating the involvement of NF-κB, a ubiquitous transcription factor playing a central role in the differentiation, proliferation and malignant transformation. Since ET-1 acts as an autocrine mediator through gelatinase induction and because inhibition of ETA receptor is beneficial for reducing both basal and ET-1-induced osteosarcoma cell invasion, targeting this receptor could be an attractive therapeutic alternative for the successful treatment of osteosarcoma.
Lessons on autoimmune diabetes from animal models
Authors: Yang Yang , Santamaria Pere
Published: November 2007

T1DM (Type I diabetes mellitus) results from selective destruction of the insulin-producing β-cells of the pancreas by the immune system, and is characterized by hyperglycaemia and vascular complications arising from suboptimal control of blood glucose levels. The discovery of animal models of T1DM in the late 1970s and early 1980s, particularly the NOD (non-obese diabetic) mouse and the BB (BioBreeding) diabetes-prone rat, had a fundamental impact on our ability to understand the genetics, aetiology and pathogenesis of this disease. NOD and BB diabetes-prone rats spontaneously develop a form of diabetes that closely resembles the human counterpart. Early studies of these animals quickly led to the realization that T1DM is caused by autoreactive T-lymphocytes and revealed that the development of T1DM is controlled by numerous polymorphic genetic elements that are scattered throughout the genome. The development of transgenic and gene-targeting technologies during the 1980s allowed the generation of models of T1DM of reduced genetic and pathogenic complexity, and a more detailed understanding of the immunogenetics of T1DM. In this review, we summarize the contribution of studies in animal models of T1DM to our current understanding of four fundamental aspects of T1DM: (i) the nature of genetic elements affording T1DM susceptibility or resistance; (ii) the mechanisms underlying the development and recruitment of pathogenic autoreactive T-cells; (iii) the identity of islet antigens that contribute to the initiation and/or progression of islet inflammation and β-cell destruction; and (iv) the design of avenues for therapeutic intervention that are rooted in the knowledge gained from studies of animal models. Development of new animal models will ensure continued progress in these four areas.
Numerical investigation of ion energy distribution and ion angle distribution in a dual-frequency capacitively coupled plasma with a hybrid model
Authors: Wang Shuai , Xu Xiang , Wang You-Nian
Published: November 2007

A one-dimensional hybrid model is developed to study the characteristics of energy and angular distributions of the ions and fast neutrals impinging on the rf-biased electrode in a dual-frequency capacitively coupled Ar discharge. The hybrid model consists of a fluid model that determines the spatiotemporal evolution of the discharge, and a Monte-Carlo model that, including the electron-neutral, ion-neutral, and fast neutral-neutral collisions, predicts the energy and angular distributions of the ions and fast neutrals on the rf-biased electrode. The influence of pressure, voltage amplitude, and frequencies of the two rf sources on the energy and angular distributions is discussed. The ion energy distributions (IEDs) appear to have multiple peaks in the dual-frequency capacitively coupled rf discharge rather than bimodal shape in a conventional single-frequency rf discharge. The ion angle distributions (IADs) have a significant peak at a small angle, and most ions strike to the process surface with the angle less than 4°. With the increase of the pressure, the maximum energy of IEDs and the peaks of IADs decrease. The structures of IEDs are controlled mainly by the voltage and frequency applied to the two rf sources. By decreasing the frequency or adding the voltage applied to the low-frequency (LF) source, the width of IEDs and the maximum energy increase. More ions strike to the electrode with a small angle by increasing either the voltage of LF source or the frequency of high-frequency source. The energy and angular distributions of the fast neutrals are correlative with those of the ions. Compared with the ions, the fast neutrals have a much lower energy and the scattering effect becomes more prominent.
Saffman-Taylor instability of shear thinning fluids
Authors: Tordjeman Ph.
Published: November 2007

A theoretical study of the Saffman-Taylor instability criterion in a Hele-Shaw cell when an inviscid fluid pushes a shear thinning fluid, is presented. The shear thinning fluid model consists of three independent fluids, two of which are Newtonian while the viscosity of the third is linearly dependent of the shear rate. The corresponding Darcy’s law is computed, and then the dispersion relation is obtained in a linear perturbative analysis. We show how the dispersion relation characteristic of the Saffman-Taylor instability is controlled by a “shear thinning characteristic number” that takes into account the rheological behavior of the shear thinning fluid in the Hele-Shaw cell. The model is discussed compared with the experimental pattern formation.
Conditions for subeutectic growth of Ge nanowires by the vapor-liquid-solid mechanism
Authors: Adhikari Hemant , McIntyre Paul C. , Marshall Ann F. , Chidsey Christopher E. D.
Published: November 2007

The requirement of the presence of a liquid for the widely accepted vapor-liquid-solid (VLS) mechanism suggests that nanowire growth should be carried out at temperatures above the catalyst-nanowire eutectic melting point. In this paper, we examine the nanowire growth at the deep subeutectic temperatures often employed for germanium nanowire growth with Au catalyst nanoparticles. The effects of germane partial pressure on the low temperature limit for Au-catalyzed Ge nanowire growth by chemical vapor deposition from GeH4(g) were studied thoroughly, both with and without initial heating above the bulk eutectic temperature. A model to explain the temperature and pressure limits of subeutectic VLS nanowire growth was developed. The interdependence of the pressure and temperature required for good quality germanium nanowire growth may also apply in other cases of nanowire growth, beyond the Au–Ge system.
Simulated performance of an ultracold ion source
Authors: van der Geer S. B. , Reijnders M. P. , de Loos M. J. , Vredenbregt E. J. D. , Mutsaers P. H. A. , Luiten O. J.
Published: November 2007

At present, the smallest spot size which can be achieved with state-of-the-art focused ion beam (FIB) technology is mainly limited by the chromatic aberrations associated with the 4.5 eV energy spread of the liquid-metal ion source. Here we numerically investigate the performance of an ultracold ion source which has the potential for generating ion beams which combine high brightness with small energy spread. The source is based on creating very cold ion beams by near-threshold photoionization of a laser-cooled and trapped atomic gas. We present ab initio numerical calculations of the generation of ultracold beams in a realistic acceleration field and including all Coulomb interactions, i.e., both space charge effects and statistical Coulomb effects. These simulations demonstrate that with existing technology reduced brightness values exceeding 105 A m−2 sr−1 V−1 are feasible at an energy spread as low as 0.1 eV. The estimated spot size of the ultracold ion source in a FIB instrument ranges from 10 nm at a current of 100 pA to 0.8 nm at 1 pA.
Effect of ammonia adsorption on the electrical characteristics of mesoporous silicon
Authors: Borini Stefano
Published: November 2007

A detailed study of the current-voltage curves of mesoporous silicon (mesoPS) has been carried out for various dosages of ammonia, employing two different measurement configurations. The gas adsorption strongly modifies the electrical characteristics of the material, both affecting their shape and varying the conductivity values. In particular, it is found that the conductivity gap, arising from a collective Coulomb blockade phenomenon, and the electrical anisotropy of mesoPS can be gradually cancelled by NH3 molecules. Moreover, a nonmonotonic behavior of the conductivity with respect to the gas pressure is observed, in analogy with previous infrared spectroscopy results. From the analysis of such experimental findings, we propose an interaction mechanism between the mesoPS surface and ammonia, involving the screening of trapped positive charges through the dipole moment of NH3 molecules.
Electrical characteristics of palladium Schottky contacts to hydrogen peroxide treated hydrothermally grown ZnO
Authors: Schifano R. , Monakhov E. V. , Grossner U. , Svensson B. G.
Published: November 2007

The formation of Schottky barrier contacts to hydrogen peroxide treated ZnO has been investigated. Low resistivity hydrothermally grown single crystal ZnO wafers of n-type were used. Pd contacts deposited on organic solvent cleaned O face (0001¯) showed Ohmic behavior, while on the H2O2 treated O face up to nine orders of magnitude in rectification of the current was obtained for biases of −2 and +2V. Concurrently, the surface roughness increases from 1.0±0.5 up to 2.0±0.5nm due to the H2O2 treatment. A majority of the contacs deposited were stable or improved their performance by annealing in air at 200°C for 30min. However, the contacts both before and after the annealing exhibited ideality factors of at least ∼1.8 at +0.5V suggesting that the current transport cannot be described as purely thermionic. Finally, results of capacitance versus voltage and capacitance versus temperature measurements are discussed and show a dominant electron state at ∼0.32eV below the conduction band edge.
Fabrication of L10-PdCoFe nanocrystalline particles with tilted magnetic easy axis
Authors: Kovács András , Hirotsu Yoshihiko
Published: November 2007

Tilted magnetic easy axis L10-PdCoFe nanoparticles were fabricated by sequential evaporation and postdeposition annealing. The MgO(110) substrate was used to prepare the faceted Pd seed crystals with {100} surfaces tilted by 45° from the surface normal. A bcc–Co–Fe layer formed on the seed Pd crystals. The L10-FeCoPd nanoparticles were formed immediately after the start of interdiffusion of Pd and Co, Fe atoms. Their tetragonal c axes were mutually tilted by 45°. The shape of the Pd seed nanocrystals and the top-down interdiffusion are the main factors influencing tilted easy axis L10 particle formation. Magnetic properties of L10-FeCoPd nanoparticles are also discussed.
Pattern identification using lattice spin systems: A thermodynamic formalism
Authors: Gupta Shalabh , Ray Asok
Published: November 2007

The paper addresses data-driven statistical pattern identification in complex dynamical systems, where the concept is built upon thermodynamic formalism of symbolic data sequences in the setting of lattice spin systems. The transfer matrix approach has been used for generation of pattern vectors from time series data of observed parameters. Efficacy of pattern identification is demonstrated for early detection of anomalies (i.e., deviations from the nominal pattern) on an experimental apparatus of nonlinear active electronic circuits.
A photosensory two-component system regulates bacterial cell attachment
Authors: Purcell Erin B. , Siegal-Gaskins Dan , Rawling David C. , Fiebig Aretha , Crosson Sean
Published: November 2007

Flavin-binding LOV domains are blue-light photosensory modules that are conserved in a number of developmental and circadian regulatory proteins in plants, algae, and fungi. LOV domains are also present in bacterial genomes, and are commonly located at the amino termini of sensor histidine kinases. Genes predicted to encode LOV-histidine kinases are conserved across a broad range of bacterial taxa, from aquatic oligotrophs to plant and mammalian pathogens. However, the function of these putative prokaryotic photoreceptors remains largely undefined. The differentiating bacterium,
Caulobacter crescentus
, contains an operon encoding a two-component signaling system consisting of a LOV-histidine kinase, LovK, and a single-domain response regulator, LovR. LovK binds a flavin cofactor, undergoes a reversible photocycle, and displays increased ATPase and autophosphorylation activity in response to visible light. Deletion of the response regulator gene,
lovR
, results in severe attenuation of cell attachment to a glass surface under laminar flow, whereas coordinate, low-level overexpression of
lovK
and
lovR
results in a light-independent increase in cell–cell attachment, a response that requires both the conserved histidine phosphorylation site in LovK and aspartate phosphorylation site in LovR. Growing
C. crescentus
in the presence of blue light dramatically enhances cell–cell attachment in the
lovK–lovR
overexpression background. A conserved cysteine residue in the LOV domain of LovK, which forms a covalent adduct with the flavin cofactor upon absorption of visible light, is necessary for the light-dependent regulation of LovK enzyme activity and is required for the light-dependent enhancement of intercellular attachment.
Two-dimensional Infrared Spectroscopy of a Model Peptide Homodimer
Authors: Wang Jian-ping
Published: November 2007

A pair of peptide groups in space, as modeled by formamide dimer, was used to evaluate vibrational coupling between the amide-I modes and the spatial behavior of the coupling using ab initio quantum chemical calculations. It was found that the coupling between two C=O groups, which is electrostatic in nature, is still quite significant as the intermolecular distance reaches 10 A. One- and two-dimensional infrared spectra of the dimer at several configurations were calculated using a vibrational exciton model that utilizes the ab initio computation-obtained parameters. The distance dependence of the coupling is dramatically shown in both the 1D and 2D infrared spectral features. The results suggest that the C=O stretching modes in polypeptide can be coupled and their states can be delocalized over quite a long distance in space.
Binding Properties of CO, NO, and O2 to P450 Heme: a Density Functional Study
Authors: Sun Xiao-min , Wang Huan-jie , Feng Da-cheng
Published: November 2007

The structural and binding properties of diatomic molecules CO, NO and O2 to P450 heme were investigated in two different models (labeled as M1 and M2) using density functional method at the B3LYP/6-31G(d) level. The effects of the serine residue near diatomic molecules XO were considered in the model M2. The results show that the serine residue near the heme enforced the binding of XO to heme. Frequency analysis indicates that the stretching vibrational frequency decreased as CO, NO, and O2 complex with heme.
Dynamic Theory of Die Swell for Entangled Polymeric Liquids in Tube Extrusions: New Set of Equations for the Growth and Ultimate Extrudate Swelling Ratios under the Free States
Authors: Zhu Chang-wei , Song Ming-shi , Hu Gui-xian , Wu Da-ming , Zhao Jing
Published: November 2007

A new dynamic theory of die swell for entangled polymeric liquids in a steady simple shear flow is proposed which can be used to predict the correlation of the time-dependent and time-independent extrudate swelling behaviors to the molecular parameters of polymers and the operational variables. The theory is based on the O-W-F constitutive equation and the free recovery from Poioeuille flow with different ratios. Experiments show that the magnitudes of the simple shear in the steady simple shear flow may be resolved into the free recoil resulting from the recoverable elastic strains and the viscous heating resulting from the unrecoverable viscoelastic strains. For distinguishing the recoil from the viscous heating, a partition function and two exponential fractions of conformation for the recoil and the viscous heating were defined. Thus the instantaneous, delayed and ultimate recoverable strain, and recoil in the free recovery were correlated to the partition function, the fraction of recoverable conformation, the molecular parameters, and the operational variables. Also the dynamics of the growth equation on the delayed viscoelastic strain and the delayed recoil in free state were deduced. After introducing the condition of uniform two dimensional extensions, the definition of swell ratio and the operational variables into the above correlation expressions and growth equations, then the correlations of the delayed extrudate swelling effect and the ultimate extrudate swelling effects to the molecular parameters and the operational variables were derived. Finally, two new sets of equations on the growth variables and ultimate extrudate swelling ratios under the dynamic and equilibrium states were also deduced from this dynamic theory of die swell. The first set of equations on the ultimate extrudate swelling ratio under the free and equilibrium states was verified by HDPE experimental data at two temperatures and different operational variables. The second set of equations on the growth extrudate swelling ratios under free and dynamic states was verified by PBD experimental data with different molecular weights and different operational variables. An excellent agreement is obtained, which shows that the two sets of equations for the growth and ultimate extrudate swelling ratios can be used directly to predict the correlation of extrudate swelling ratios to the molecular parameters and the operational variables.
Preparation of Manganese-doped ZnSe Precursor Nanoribbon Bundles and Investigation of its Magneto-optical Properties
Authors: Zhang Yuan-yuan , Chen Jia-fu , Zheng Xu-sheng , Dong Xue-hui
Published: November 2007

Mn2+-doped ZnSe ethylenediamine-intercalated precursor nanoribbon bundles (MnxZn1xSeen3, en=ethylenediamine) were prepared through an improved solvothermal route, which is time-saving and more efficient compared with the traditional route. XPS, TGA, and FESEM were used to characterize morphology and composites of the precursor and it was proved that the doping process was successful. Electron paramagnetic resonance and photoluminescence (PL) spectra were used in a detailed experiment to characterize and study the Mn2+ doping state and Mn2+-Mn2+ interaction in MnxZn1xSeen3. Six well-resolved hyperfine lines, which are attributed to the Mn2+ allowed transition imply that the Mn ions were embedded inside MnxZn1xSeen3 lattices and partly replaced Zn. As shown in PL spectrum; the introduction of Mn2+ strongly increases the intensity of the PL peak. The internal Mn transition (4T16A1), which strongly increases the peak intensity depends on the average number of Mn atoms in the nanoparticals. As the Mn-doped concentration increases, the PL peak intensity is enhanced. A series of samples with different Mn-doping concentrations were prepared and studied. Combining the EPR results with PL spectra of the samples prepared, it is believed that under conditions of heating 40 h at 180 C and controlling Mn2+ ion concentration percentage at 2%-3% (x=0.02-0.03) in the compounds, the best doping can be achieved.
Cross-generational fitness benefits of mating and male seminal fluid
Authors: Priest Nicholas K , Roach Deborah A , Galloway Laura F
Published: November 2007

In many species, the physical act of mating and exposure to accessory gland proteins (Acps) in male seminal fluid reduces female survival and offspring production. It is not clear what males gain from harming their sexual partners or why females mate frequently despite being harmed. Using sterile strains of
Drosophila melanogaster
that differ in their production of Acps, we found that both the physical act of mating and exposure to male seminal fluid in mothers increase the fitness of daughters. We show that the changes in daughter fitness are mediated by parental effects, not by sexual selection involving good genes or owing to variation in maternal egg production. These results support the idea that male harm of females might partly evolve through cross-generational fitness benefits.
Mountaintop island age determines species richness of boreal mammals in the American Southwest
Authors: Frey Jennifer K. , Bogan Michael A. , Yates Terry L.
Published: November 2007

Models that describe the mechanisms responsible for insular patterns of species richness include the equilibrium theory of island biogeography and the nonequilibrium vicariance model. The relative importance of dispersal or vicariance in structuring insular distribution patterns can be inferred from these models. Predictions of the alternative models were tested for boreal mammals in the American Southwest. Age of mountaintop islands of boreal habitat was determined by constructing a geographic cladogram based on characteristics of intervening valley barriers. Other independent variables included area and isolation of mountaintop islands. Island age was the most important predictor of species richness. In contrast with previous studies of species richness patterns in this system, these results supported the nonequilibrium vicariance model, which indicates that vicariance has been the primary determinant of species distribution patterns in this system.
Local habitat patch pattern of the Siberian flying squirrel in a managed boreal forest landscape
Authors: Hurme Eija , Reunanen Pasi , Mönkkönen Mikko , Nikula Ari , Nivala Vesa , Oksanen Jari
Published: November 2007

We examined how the structure of a boreal forest landscape is related to the occurrence of the Siberian flying squirrelPteromys volansin northern Finland. The flying squirrel inhabits mature spruce‐dominated (Picea abies) mixed forests and is categorised as vulnerable species due to habitat loss and change. We classified a landscape of 374.5 km2into potential habitat patches, potential dispersal areas, and areas incapable of being inhabited using national forest inventory data, and surveyed all 136 potential habitat patches for the presence of the species. Different landscape variables were defined, and also connections by the shortest distances to neighbouring habitat patches along both straight lines and least‐cost distances based on specific movement costs were measured. Occupied patches were larger in size, contained more deciduous trees for food and nesting cavities, and were in closer proximity to the nearest occupied patches. Occupied patches were mainly located below 300 m a.s.l. The occurrence of flying squirrels was correctly predicted for 88% of the habitat patches using landscape variables. This modelling result proved to be rather general. In addition, the configuration of occupied patches was mainly clustered across the landscape, and distant occupied patches seemed to be linked to other patches via forested connections. We suggest that maintaining a clustered arrangement of good quality habitat patches and regenerating new potential habitat as well as dispersal areas between the habitat patches seem to be appropriate goals for long‐term forest management planning to sustain populations of the flying squirrel in the landscape.
Fine‐scale dynamics of rhizomes in a grassland community
Authors: Wildová Radka , Wild Jan , Herben Tomáš
Published: November 2007

Spatial dynamics in grassland communities are constrained by the belowground spatial distribution of roots and rhizomes. Their dynamics are difficult to measure as underground data collection tends to be destructive and cannot be repeated at the same plot over time. We investigated rhizome dynamics indirectly by examining rhizome spatial structure on long‐term grassland study plots where aboveground shoot counts have been recorded using a fine‐scale grid over nine years. Number of rhizome apical ends, basal ends and total rhizome length of both live and dead rhizomes were obtained from the data by scanning rhizomes and processing them by GIS vectorization. These rhizome variables were correlated with the above‐ground shoot counts in grid cells over varying temporal lags. There was a general decrease in the intensity of correlation between live rhizomes and shoot counts with increasing time lags. Correlation of dead rhizomes increased with increasing time lag, reaching a maximum after several years, and then declined. Species differed strongly in the change of rhizome‐shoot counts correlation over varying time lags. These differences were used to infer rhizome growth dynamics, namely rhizome growth rate and lifespan, and rhizome mean decomposition time. The species involved differed in all these traits. Mean rhizome growth rate ranged from 0.2 (Polygonum bistorta) to 3.3 cm ur−1 (Deschampsia flexuosa); mean rhizome lifespan ranged from 5 yr (Anthoxanthum alpinum) to over 8 yr (Nardus stricta) and mean decomposition time from one growing season (Anthoxanthum) to 7 yr (Polygonum). Presence of dead rhizomes below living rhizomes or aboveground shoots was taken as an indication of fine‐scale replacements between species. These were highly non‐random, with some species pairs replacing significantly more frequently. These differences in rhizome growth parameters underlie different strategies of horizontal growth and dieback between species. These can serve as one of the mechanisms of species replacements and contribute to the fine‐scale coexistence of species.