bluuebunny/crossref_metadata_2025 huggingface dataset:
NSF independent fusion of Salmonella‐containing late phagosomes with early endosomes
Authors: Parashuraman Seetharaman , Madan Richa , Mukhopadhyay Amitabha
Published: February 2010

Initial characterizations of live‐Salmonella‐containing early (LSEP) and late phagosomes (LSLP) in macrophages show that both phagosomes retain Rab5 and EEA1. In addition, LSEP specifically contain transferrin receptor whereas LSLP possess relatively more rabaptin‐5. In contrast to LSLP, late‐Salmonella‐containing vacuoles in epithelial cells show significantly reduced levels of Rab5 and EEA1. Subsequent results demonstrate that both phagosomes efficiently fuse with early endosomes (EE). In contrast to LSEP, fusion between LSLP and EE is insensitive to ATPγS treatment. Furthermore, LSLP fuses with EE in absence of NEM‐sensitive fusion factor (NSF) as well as in the presence of NSF:D1EQ mutant demonstrating that LSLP fusion with EE is NSF independent.
The antiviral protein viperin is a radical SAM enzyme
Authors: Duschene Kaitlin S. , Broderick Joan B.
Published: February 2010

Viperin, an interferon‐inducible antiviral protein, is shown to bind an iron‐sulfur cluster, based on iron analysis as well as UV–Vis and electron paramagnetic resonance spectroscopic data. The reduced protein contains a [4Fe‐4S]1+ cluster whose g‐values are altered upon addition of S‐adenosylmethionine (SAM), consistent with SAM coordination to the cluster. Incubation of reduced viperin with SAM results in reductive cleavage of SAM to produce 5′‐deoxyadenosine (5′‐dAdo), a reaction characteristic of the radical SAM superfamily. The 5′‐dAdo cleavage product was identified by a combination of HPLC and mass spectrometry analysis.
Dimerisation and structural integrity of Heparin Binding Hemagglutinin A from Mycobacterium tuberculosis: Implications for bacterial agglutination
Authors: Esposito Carla , Carullo Paola , Pedone Emilia , Graziano Giuseppe , Vecchio Pompea Del , Berisio Rita
Published: February 2010

MINT‐
7709940
, MINT‐
7709948
: HBHA (uniprotkb:A5TZK3) and HBHA (uniprotkb:A5TZK3) bind (MI:
0407) by circular dichroism (MI:
0016)MINT‐
7709966: HBHA (uniprotkb:A5TZK3) and HBHA (uniprotkb:A5TZK3) bind (MI:
0407) by biophysical (MI:
0013)MINT‐
7709955: HBHA (uniprotkb:A5TZK3) and HBHA (uniprotkb:A5TZK3) bind (MI:
0407) by dynamic light scattering (MI:
0038)
Mitochondrial ion channels as therapeutic targets
Authors: Peixoto Pablo M. , Ryu Shin-Young , Kinnally Kathleen W.
Published: February 2010

The study of mitochondrial ion channels changed our perception of these double‐wrapped organelles from being just the power house of a cell to the guardian of a cell's fate. Mitochondria communicate with the cell through these special channels. Most of the time, the message is encoded by ion flow across the mitochondrial outer and inner membranes. Potassium, sodium, calcium, protons, nucleotides, and proteins traverse the mitochondrial membranes in an exquisitely regulated manner to control a myriad of processes, from respiration and mitochondrial morphology to cell proliferation and cell death. This review is an update on both well established and putative mitochondrial channels regarding their composition, function, regulation, and therapeutic potential.
Hierarchical organization of the plasma membrane: Investigations by single‐molecule tracking vs. fluorescence correlation spectroscopy
Authors: Kusumi Akihiro , Shirai Yuki M. , Koyama-Honda Ikuko , Suzuki Kenichi G.N. , Fujiwara Takahiro K.
Published: February 2010

Single‐molecule tracking and fluorescence correlation spectroscopy (FCS) applied to the plasma membrane in living cells have allowed a number of unprecedented observations, thus fostering a new basic understanding of molecular diffusion, interaction, and signal transduction in the plasma membrane. It is becoming clear that the plasma membrane is a heterogeneous entity, containing diverse structures on nano‐meso‐scales (2–200 nm) with a variety of lifetimes, where certain membrane molecules stay together for limited durations. Molecular interactions occur in the time‐dependent inhomogeneous two‐dimensional liquid of the plasma membrane, which might be a key for plasma membrane functions.
Pharmacology of mitochondrial potassium channels: dark side of the field
Authors: Szewczyk Adam , Kajma Anna , Malinska Dominika , Wrzosek Antoni , Bednarczyk Piotr , Zabłocka Barbara , Dołowy Krzysztof
Published: February 2010

Mitochondrial potassium channels play an important role in cytoprotection. Potassium channels in the inner mitochondrial membrane are modulated by inhibitors and activators (potassium channel openers) previously described for plasma membrane potassium channels. The majority of mitochondrial potassium channel modulators exhibit a broad spectrum of off‐target effects. These include uncoupling properties, inhibition of the respiratory chain and effects on cellular calcium homeostasis. Therefore, the rational application of channel inhibitors or activators is crucial to understanding the cellular consequences of mitochondrial channel inhibition or activation. Moreover, understanding their side‐effects should facilitate the design of a specific mitochondrial channel opener with cytoprotective properties. In this review, we discuss the complex interactions of potassium channel inhibitors and activators with cellular structures.
The role of PI3P phosphatases in the regulation of autophagy
Authors: Vergne Isabelle , Deretic Vojo
Published: February 2010

Autophagy initiation is strictly dependent on phosphatidylinositol 3‐phosphate (PI3P) synthesis. PI3P production is under tight control of PI3Kinase, hVps34, in complex with Beclin‐1. Mammalian cells express several PI3P phosphatases that belong to the myotubularin family. Even though some of them have been linked to serious human diseases, their cellular function is largely unknown. Two recent studies indicate that PI3P metabolism involved in autophagy initiation is further regulated by the PI3P phosphatases Jumpy and MTMR3. Additional pools of PI3P, upstream of mTOR and on the endocytic pathway, may modulate autophagy indirectly, suggesting that other PI3P phosphatases might be involved in this process. This review sums up our knowledge on PI3P phosphatases and discusses the recent progress on their role in autophagy.
Mapping of the basic amino‐acid residues responsible for tubulation and cellular protrusion by the EFC/F‐BAR domain of pacsin2/Syndapin II
Authors: Shimada Atsushi , Takano Kazunori , Shirouzu Mikako , Hanawa-Suetsugu Kyoko , Terada Takaho , Toyooka Kiminori , Umehara Takashi , Yamamoto Masaki , Yokoyama Shigeyuki , Suetsugu Shiro
Published: February 2010

MINT‐7710892: EFCS pacsin2 (uniprotkb:Q9UNF0) and EFCS pacsin2 (uniprotkb:Q9UNF0) bind (MI:0407) by X‐ray crystallography (MI:0114)
Peripartum hysterectomy: An evolving picture
Authors: Turner Michael J.
Published: February 2010

Peripartum hysterectomy (PH) is one of the obstetric catastrophes. Evidence is emerging that the role of PH in modern obstetrics is evolving. Improving management of postpartum hemorrhage and newer surgical techniques should decrease PH for uterine atony. Rising levels of repeat elective cesarean deliveries should decrease PH following uterine scar rupture in labor. Increasing cesarean rates, however, have led to an increase in the number of PHs for morbidly adherent placenta. In the case of uterine atony or rupture where PH is required, a subtotal PH is often sufficient. In the case of pathological placental localization involving the cervix, however, a total hysterectomy is required. Furthermore, the involvement of other pelvic structures may prospectively make the diagnosis difficult and the surgery challenging. If resources permit, PH for pathological placental localization merits a multidisciplinary approach. Despite advances in clinical practice, it is likely that peripartum hysterectomy will be more challenging for obstetricians in the future.
Kant's Political Religion: The Transparency of Perpetual Peace and the Highest Good
Authors: Taylor Robert S.
Published: February 2010

Scholars have long debated the relationship between Kant's doctrine of right and his doctrine of virtue (including his moral religion or ethico-theology), which are the two branches of his moral philosophy. This article will examine the intimate connection in his practical philosophy between perpetual peace and the highest good, between political and ethico-religious communities, and between the types of transparency peculiar to each. It will show how domestic and international right provides a framework for the development of ethical communities, including a kingdom of ends and even the noumenal ethical community of an afterlife, and how the transparency and trust achieved in these communities are anticipated in rightful political society by publicity and the mutual confidence among citizens that it engenders. Finally, it will explore the implications of this synthesis of Kant's political and religious philosophies for contemporary Kantian political theories, especially those of Jürgen Habermas and John Rawls.
“Bare Life” and Politics in Agamben's Reading of Aristotle
Authors: Finlayson James Gordon
Published: February 2010

Giorgio Agamben's critique of Western politics inHomo Sacerand three related books has been highly influential in the humanities and social sciences. The critical social theory set out in these works depends essentially on his reading of Aristotle'sPolitics. His diagnosis of what ails Western politics and his suggested remedy advert to a “biopolitical paradigm,” at the center of which stand a notion of “bare life” and a purported opposition betweenbiosandzoē. Agamben claims that this distinction is found in Aristotle's text, in ancient Greek, and in a tradition of political theory and political society stemming from fourth-century Athens to the present. However, a close reading of Aristotle refutes this assertion. There is no such distinction. I show that he bases this view on claims about Aristotle by Arendt and Foucault, which are also unfounded.
Constitutions, EU Law and Judicial Strategies in the Czech Republic, Hungary and Poland
Authors: MATCZAK MARCIN , BENCZE MATYAS , KÜHN ZDENEK
Published: February 2010

Given far-reaching changes in the legal systems of East Central Europe since the mid-1990s, one might expect administrative court judges to have modified the way in which they decide cases, in particular by embracing less formalistic adjudication strategies. Relying on an original dataset of over one thousand business-related cases from the Czech Republic, Hungary and Poland, this article shows that – despite some variation across countries and time – judges have largely failed to respond to the incentives contained in the new constitutional frameworks. They continue to adopt the most-locally-applicable-rule approach and are reluctant to apply general principles of law or to rely on Dworkinian ‘policies’ in deciding hard cases. The analysis links these weak institutional effects to the role of constitutional courts, case overload and educational legacies.
Etoposide-related cardiotoxicity in a child with haemophagocytic lymphohistiocytosis
Authors: Escoto Heather , Ringewald Jeremy , Kalpatthi Ram
Published: February 2010

We report a male child with haemophagocytic lymphohistiocytosis who developed myocardial infarction after receiving etoposide. He recovered well with supportive measures and after discontinuation of etoposide. We discuss the possible mechanisms and differential diagnoses of myocardial infarction in our patient.
Effective communication and information provision in radiotherapy—the role of radiation therapists
Authors: Halkett Georgia K.B. , Merchant Susan , Jiwa Moyez , Short Michala , Arnet Hayley , Richardson Sharon , Kearvell Rachel , Carson Sharron , Spry Nigel , Taylor Mandy , Kristjanson Linda
Published: February 2010

Introduction:Health professionals have a duty of care to radiotherapy patients in providing them with adequate information before treatment. There is a lack of research that describes the roles of radiation therapists and radiation oncology nurses in providing information to patients. This study aimed to: (1) explore how radiation therapists communicate with breast cancer patients during a radiotherapy planning appointment; (2) determine what information is provided during this appointment and (3) explore radiation therapists’ perspectives on their role in providing patient information and support.

Methods:The following methodologies were used: self-report questionnaires; simulated radiotherapy planning sessions and joint interpretive forums. Statistical analysis was used to analyse the questionnaires and the simulated planning sessions and forums were analysed qualitatively.

Results:A total of 110 radiation therapists participated in the survey. We simulated two radiotherapy planning appointments and held two forums. Four themes emerged: role definitions, reducing patient anxiety and distress, barriers and strategies for effective communication and confidence in patient communication.

Conclusion:Radiation therapists play an important role in communicating with patients and providing information, particularly if patients exhibit anxiety and distress. Further research is required to determine whether patients’ information needs can be met with additional information provided by radiation therapists.
Comparing plaque brachytherapy and proton therapy for choroidal melanoma: a review of the literature
Authors: Appleton Jeremy P. , Bridge Peter
Published: February 2010

The aims of conservative treatment in patients with ocular melanoma are globe retention, good visual acuity (VA) and local control. Two well-established radiation conservative treatment options are proton beam radiotherapy and episcleral plaque brachytherapy (EPB). Patients who receive treatment with either of these options will experience some degree of radiation-related ocular complications and poor VA. The purpose of this review of the literature is to establish whether there is a significant clinical difference in normal tissue morbidity and local tumour control between proton therapy and EPB, and whether this difference can justify the purchase and implementation of additional proton therapy facilities. Based on this review, evidence suggested that both treatment options are comparable, and that neither proton therapy nor EPB is clinically superior than the other regarding normal tissue morbidity and local tumour control. This review highlighted the need for further research on a larger scale in order to bridge the gap that is apparent within the literature.
Postoperative radiotherapy for head and neck cancer with single positive node
Authors: Ampil Federico L. , Caldito Gloria , Nathan Cherie-Ann , Ghali Ghali , Baluna Roxana , Jones Stephen
Published: February 2010

The essential need for postoperative irradiation in people with carcinoma of the upper aerodigestive tract and limited metastatic nodal spread is controversial. An experience with postoperative radiotherapy in head and neck cancer (HNC) patients with one histologically positive cervical node is presented. Between 1976 and 2000, 37 individuals with confirmed metastatic disease in a single neck node underwent postoperative radiotherapy. The median follow-up period was 24 months. Among the 35 evaluable patients, the observed failure rates at the primary site, neck and distant location were 11%, 15% and 6%, respectively. The overall 5-year relapse-free survival rate was 60%. The relapse-free survival rate at 5 years was 86% in individuals who did not have additional histopathological risk factors and 55% in those patients who did (p = 0.46). The precise role of postoperative radiotherapy in people with HNC and documented metastasis in a single cervical lymph node remains to be defined including the identification of select individuals who may truly benefit from the combined therapy program.
Polytool: Polynomial interpretations as a basis for termination analysis of logic programs
Authors: NGUYEN MANH THANG , DE SCHREYE DANNY , GIESL JÜRGEN , SCHNEIDER-KAMP PETER
Published: February 2010

Our goal is to study the feasibility of porting termination analysis techniques developed for one programming paradigm to another paradigm. In this paper, we show how to adapt termination analysis techniques based on polynomial interpretations—very well known in the context of term rewrite systems—to obtain new (nontransformational) termination analysis techniques for definite logic programs (LPs). This leads to an approach that can be seen as a direct generalization of the traditional techniques in termination analysis of LPs, where linear norms and level mappings are used. Our extension generalizes these to arbitrary polynomials. We extend a number of standard concepts and results on termination analysis to the context of polynomial interpretations. We also propose a constraint-based approach for automatically generating polynomial interpretations that satisfy the termination conditions. Based on this approach, we implemented a new tool, called Polytool, for automatic termination analysis of LPs.
Oil in the age of steam
Authors: Madureira Nuno Luís
Published: February 2010

This article explains how oil as an energy carrier evolved alongside the technology of the steam engine. In practical terms, fuel oil was adapted to machines that were originally devised to be coal-fuelled and this led to the flexible switchover between energy carriers. The article links the micro account of technological developments with the macro records of energy consumption, to reveal how steam technology set the stage for the commoditization of oil, the customary fuel of the internal combustion engine. The analysis of the oil–steam combine embraces its diffusion across leading producing nations such as Russia and the United States, the diffusion in industrial and transport activities in South America, and the diffusion throughout European navies. What was at stake was the transformation of oil into a geostrategic good and the triggering of an international race for the seizure of fossil fuels.
Rayleigh‐Taylor type instability in auroral patches
Authors: Shiokawa K. , Nakajima A. , Ieda A. , Sakaguchi K. , Nomura R. , Aslaksen T. , Greffen M. , Donovan E.
Published: February 2010

Based on observations by a high‐resolution narrow field‐of‐view CCD camera, we found small‐scale (5–25 km) finger‐like structures at the western boundary of auroral patches in images obtained at Gillam (geomagnetic latitude: 65.5°N), Canada, in January 2008. Since shear motion was not observed along the boundary of the patches, we suggest that these structures are formed by macroscopic Rayleigh‐Taylor type plasma instability arising in the magnetospheric equatorial plane from the force balancing of the (eastward) magnetic tension force and the (westward) pressure gradient force.
Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary
Authors: Cottrell Matthew T , Ras Josephine , Kirchman David L
Published: February 2010

Photoheterotrophic microbes use organic substrates and light energy to satisfy their demand for carbon and energy and seem to be well adapted to eutrophic estuarine and oligotrophic oceanic environments. One type of photoheterotroph, aerobic anoxygenic phototrophic (AAP) bacteria, is especially abundant in particle-rich, turbid estuaries. To explore questions regarding the controls of these photoheterotrophic bacteria, we examined their abundance by epifluorescence microscopy, concentrations of the light-harvesting pigment, bacteriochlorophyll a (BChl a) and the diversity of pufM and 16S ribosomal RNA (rRNA) genes in the Chesapeake Bay. Concentrations of BChl a varied substantially, much more so than AAP bacterial abundance, along the estuarine salinity gradient. The BChl a concentration was correlated with turbidity only when oceanic and estuarine waters were considered together. Concentrations of BChl a and BChl a quotas were higher in particle-associated than in free-living AAP bacterial communities and appear to reflect physiological adaptation, not different AAP bacterial communities; pufM genes did not differ between particle-associated and free-living communities. In contrast, particle-associated and free-living bacterial communities were significantly different, on the basis of the analysis of 16S rRNA genes. The BChl a quota of AAP bacteria was not correlated with turbidity, suggesting that pigment synthesis varies in direct response to particles, not light attenuation. The AAP bacteria seem to synthesize more BChl a when dissolved and particulate substrates are available than when only dissolved materials are accessible, which has implications for understanding the impact of substrates on the level of photoheterotrophy compared with heterotrophy in AAP bacteria.
β‐Cell Function Improvement After Biliopancreatic Diversion in Subjects With Type 2 Diabetes and Morbid Obesity
Authors: Briatore Lucia , Salani Barbara , Andraghetti Gabriella , Maggi Davide , Adami Gian Franco , Scopinaro Nicola , Cordera Renzo
Published: February 2010

In subjects with obesity and type 2 diabetes mellitus (T2DM), biliopancreatic diversion (BPD) improves glucose stimulated insulin secretion, whereas the effects on other secretion mechanisms are still unknown. Our objective was to evaluate the early effects of BPD on nonglucose‐stimulated insulin secretion. In 16 morbid obese subjects (9 with T2DM and 7 with normal fasting glucose (NFG)), we measured insulin secretion after glucose‐dependent arginine stimulation test and after intravenous glucose tolerance test (IVGTT) before and 1 month after BPD. After surgery the mean weight lost was 13% in both groups. The acute insulin response during IVGTT was improved in T2DM after BDP (from 55 ± 10 to 277 ± 91 pmol/l, P = 0.03). A reduction of insulin response to arginine was observed in NFG, whereas opposite was found in T2DM. In particular, acute insulin response to arginine at basal glucose concentrations (AIRbasal) was reduced but insulin response at 14 mmol/l of plasma glucose (AIR14) was increased. Therefore, after BPD any statistical difference in AIR14 between NFG and T2DM disappeared (1,032 ± 123 for NFG and 665 ± 236 pmol/l for T2DM, P = ns). The same was observed for SlopeAIR, a measure of glucose potentiation, reduced in T2DM before BPD but increased after surgery, when no statistically significant difference resulted compared with NFG (SlopeAIR after BPD: 78 ± 11 in NFG and 56 ± 18 pmol/l in T2DM, P = ns). In conclusion, in obese T2DM subjects 1 month after BPD we observed a great improvement of both glucose‐ and nonglucose‐stimulated insulin secretions. The mechanisms by which BDP improve insulin secretion are still unknown.
Glutamate–haem ester bond formation is disfavoured in flavocytochrome P450 BM3: characterization of glutamate substitution mutants at the haem site of P450 BM3
Authors: Girvan Hazel M. , Levy Colin W. , Williams Paul , Fisher Karl , Cheesman Myles R. , Rigby Stephen E. J. , Leys David , Munro Andrew W.
Published: February 2010

Bacillus megaterium flavocytochrome P450 BM3 (CYP102A1) is a biotechnologically important cytochrome P450/P450 reductase fusion enzyme. Mutants I401E, F261E and L86E were engineered near the haem 5-methyl group, to explore the ability of the glutamate carboxylates to form ester linkages with the methyl group, as observed for eukaryotic CYP4 relatives. Although no covalent linkage was detected, mutants displayed marked alterations in substrate/inhibitor affinity, with L86E and I401E mutants having lower Kd values for arachidonic acid and dodecanoic (lauric) acid than WT (wild-type) BM3. All mutations induced positive shifts in haem Fe(III)/Fe(II) potential, with substrate-free I401E (−219 mV) being >170 mV more positive than WT BM3. The elevated potential stimulated FMN-to-haem electron transfer ~2-fold (to 473 s−1) in I401E, and resulted in stabilization of Fe(II)O2 complexes in the I401E and L86E P450s. EPR demonstrated some iron co-ordination by glutamate carboxylate in L86E and F261E mutants, indicating structural plasticity in the haem domains. The Fe(II)O2 complex is EPR-silent, probably resulting from antiferromagnetic coupling between Fe(III) and bound superoxide in a ferric superoxo species. Structural analysis of mutant haem domains revealed modest rearrangements, including altered haem propionate interactions that may underlie the thermodynamic perturbations observed. The mutant flavocytochromes demonstrated WT-like hydroxylation of dodecanoic acid, but regioselectivity was skewed towards ω−3 hydroxydodecanoate formation in F261E and towards ω−1 hydroxydodecanoate production in I401E. Our data point strongly to a likelihood that glutamate–haem linkages are disfavoured in this most catalytically efficient P450, possibly due to the absence of a methylene radical species during catalysis.
CFTR is required for cellular entry and internalization of Chlamydia trachomatis
Authors: Ajonuma Chukwuemeka Louis , Fok Lam Kin , Ho Sze Lok , Chan Sheung Kay Paul , Chow Pak H. , Tsang Ling Lai , Wong Yan Hau Connie , Chen Jie , Li Shen , Rowlands Kenneth Dewi , Chung Wa Yiu , Chan Chang Hsiao
Published: February 2010

Chlamydia trachomatis is an obligate intracellular Gram‐negative pathogen affecting over 600 million people worldwide with 92 million new cases occurring globally each year. C. trachomatis enter the cells and replicate to infect different tissues/organs, giving rise to a spectrum of pathological conditions; however, the exact mechanism or receptor(s) for their entry is not well understood. Here we report that CFTR (cystic fibrosis transmembrane conductance regulator), an apical epithelial anion channel, is required for cellular entry and internalization of C. trachomatis. Human epithelial cell lines expressing functional CFTR internalized more C. trachomatis than the cells expressing mutant Δ508 CFTR. The in vitro cellular uptake of C. trachomatis can be blocked by CFTR inhibitors or antibody, and the in vivo cellular uptake of C. trachomatis in CFTR mutant (CFTR−/−) mice was significantly less compared with that in the wild‐type. Direct interaction between CFTR and C. trachomatis LPS (lipopolysaccharide) is demonstrated by their immune‐co‐localization and co‐immunoprecipitation. Despite an increase in CFTR expression observed upon C. trachomatis LPS challenge, a reduction in its ion channel activity is observed, consistent with the notion that CFTR functions as a receptor for cellular entry and internationization of C. trachomatis, with compromised ion‐channel function. These findings, for the first time, demonstrate that CFTR functions as a cell‐surface receptor for epithelial cell entry, and internalization of C. trachomatis and these findings may lead to the development of new treatment strategies to curtail the spread of chlamydial infections.
Spatially correlated erbium and Si nanocrystals in coimplanted SiO2 after a single high temperature anneal
Authors: Crowe Iain F. , Kashtiban Reza J. , Sherliker Ben , Bangert Ursel , Halsall Matthew P. , Knights Andrew P. , Gwilliam Russell M.
Published: February 2010

We present a study of silicon (Si) and erbium (Er) coimplanted silica (SiO2) in which we observe, by combining high resolution scanning transmission electron microscopy and selective electron energy loss spectroscopy (EELS), a high spatial correlation between silicon nanocrystals (Si-NCs), Er, and oxygen (O) after a single high temperature (1100 °C) anneal. The observation of a spatial overlap of the EELS chemical maps of dark field (DF) images at the Er N4,5, Si L2,3, and O K edges is concomitant with an intense room temperature infrared luminescence around 1534 nm. We suggest that these observations correspond to Er–O complexes within an amorphous silicon (a-Si) shell at the Si-NC/SiO2 interface. The presence of a crystalline phase at the Si-NC center, verified by high resolution electron micrographs and DF diffraction contrast images and the low solubility of Er in crystalline Si (c-Si) would tend to suggest a preferential Er agglomeration toward the Si-NC/SiO2 interface during formation, particularly when high concentrations of both Si and Er are obtained in a narrow region of the SiO2 after coimplantation. The absence of narrow Stark related features in the Er emission spectrum at low temperature and an inhomogeneous broadening with increasing temperature, which are characteristic of Er confined by an amorphous, rather than a crystalline host further support these hypotheses. After comparing the luminescence to that from a SiO2:Er control sample prepared in exactly the same manner but without Si-NCs, we find that, despite the observed spatial correlation, only a small fraction (∼7%) of the Er are sensitized by the Si-NCs. We ascribe this low fraction to a combination of low sensitizer (Si-NC) density and Auger-type losses arising principally from Er ion-ion interactions.
Theoretical study of the factor of merit of porous silicon based optical biosensors
Authors: Charrier J. , Dribek M.
Published: February 2010

Porous silicon is an attractive material for label-free optical biosensors because of its biocompatibility, its large internal surface area, its open pore network, and its widely tunable refractive index. Many structures using this material and exploring reflectometry can be used for biosensing. The sensor performances and sensitivity depends on the parameters of the porous silicon layers and its thermal treatment such as porosity, pore size, oxidation degree, and used wavelength. A theoretical framework to model the reflectance spectra of three optical nanostructures (monolayer, Bragg mirror, and microcavity based on porous silicon layers) before and after the functionalization step is used to study the merit parameters for each device. Based on this theoretical work, optimized conditions to fabricate glucagon biosensors are proposed. A microcavity formed by a period constituted of two porous layers of porosities equal to 95% and 65% with a pore size of 60 and 51 nm, respectively, and with 40% oxidation degree allows a significant redshift to be obtained. The value of minimum detectable coating thickness for a detection system capable of resolving a wavelength shift of 0.1 nm is about 5×10−3 nm.
Measurement of ion cascade energies through resolution degradation of alpha particle microcalorimeters
Authors: Horansky Robert D. , Stiehl Gregory M. , Beall James A. , Irwin Kent D. , Plionis Alexander A. , Rabin Michael W. , Ullom Joel N.
Published: February 2010

Atomic cascades caused by ions impinging on bulk materials have remained of interest to the scientific community since their discovery by Goldstein in 1902. While considerable effort has been spent describing and, more recently, simulating these cascades, tools that can study individual events are lacking and several aspects of cascade behavior remain poorly known. These aspects include the material energies that determine cascade magnitude and the variation between cascades produced by monoenergetic ions. We have recently developed an alpha particle detector with a thermodynamic resolution near 100 eV full-width-at-half-maximum (FWHM) and an achieved resolution of 1.06 keV FWHM for 5.3 MeV particles. The detector relies on the absorption of particles by a bulk material and a thermal change in a superconducting thermometer. The achieved resolution of this detector provides the highest resolving power of any energy dispersive technique and a factor of 8 improvement over semiconductor detectors. The exquisite resolution can be directly applied to improved measurements of fundamental nuclear decays and nuclear forensics. In addition, we propose that the discrepancy between the thermodynamic and achieved resolution is due to fluctuations in lattice damage caused by ion-induced cascades in the absorber. Hence, this new detector is capable of measuring the kinetic energy converted to lattice damage in individual atomic cascades. This capability allows new measurements of cascade dynamics; for example, we find that the ubiquitous modeling program, SRIM, significantly underestimates the lattice damage caused in bulk tin by 5.3 MeV alpha particles.
Theoretical study of the stabilization mechanisms of the different stable oxygen incorporated (101¯) surface of III-nitrides
Authors: Ye Honggang , Chen Guangde , Wu Yelong , Zhu Youzhang
Published: February 2010

By using the first-principles calculation methods, the stable structures of oxygen incorporated (101¯0) surface of AlN and InN are explored in comparison with that of GaN. The one for AlN is found to be VAl−(ON)3, a complex of Al vacancy and three substitutional O in N sites, while the one for InN is consistent with that of GaN, which is comprised by two monolayers of O replacing the N atoms, denoted by 2(ON). The stabilization mechanisms of the two surface structures and the origin of the discrepancy between AlN and GaN are further given by analyzing their electronic structures.
Highly nonlinear tellurite microstructured fibers for broadband wavelength conversion and flattened supercontinuum generation
Authors: Qin Guanshi , Yan Xin , Kito Chihiro , Liao Meisong , Suzuki Takenobu , Mori Atsushi , Ohishi Yasutake
Published: February 2010

We demonstrate four-wave mixing-based broadband (>68 nm) wavelength conversion and flattened supercontinuum generation spanning from 900 to 2800 nm in a 36-cm-long tellurite microstructured fiber which has a high nonlinearity. By reducing the size of air holes of the tellurite microstructured fibers, single mode propagation and small dispersion slope are obtained without the propagation loss enhancement. Our results show that chromatic-dispersion controlled tellurite microstructured fibers are promising candidates for nonlinear applications.
Generation of zonal flows by electrostatic drift waves in electron-positron-ion plasmas
Authors: Kaladze T. D. , Shad M. , Tsamalashvili L. V.
Published: February 2010

Generation of large-scale zonal flows by comparatively small-scale electrostatic drift waves in electron-positron-ion plasmas is considered. The generation mechanism is based on the parametric excitation of convective cells by finite amplitude drift waves having arbitrary wavelengths (as compared with the ion Larmor radius of plasma ions at the plasma electron temperature). Temperature inhomogeneity of electrons and positrons is taken into account assuming ions to be cold. To describe the generation of zonal flow generalized Hasegawa–Mima equation containing both vector and two scalar (of different nature) nonlinearities is used. A set of coupled equations describing the nonlinear interaction of drift waves and zonal flows is deduced. Explicit expressions for the maximum growth rate as well as for the optimal spatial dimensions of the zonal flows are obtained. Enriched possibilities of zonal flow generation with different growth rates are revealed. The present theory can be used for interpretations of drift wave observations in laboratory and astrophysical plasmas.
Direct numerical simulation of hypersonic boundary layer transition over a blunt cone with a small angle of attack
Authors: Li Xinliang , Fu Dexun , Ma Yanwen
Published: February 2010

The direct numerical simulation of boundary layer transition over a 5° half-cone-angle blunt cone is performed. The free-stream Mach number is 6 and the angle of attack is 1°. Random wall blow-and-suction perturbations are used to trigger the transition. Different from the authors’ previous work [Li et al., AIAA J. 46, 2899 (2008)], the whole boundary layer flow over the cone is simulated (while in the author’s previous work, only two 45° regions around the leeward and the windward sections are simulated). The transition location on the cone surface is determined through the rapid increase in skin fraction coefficient (Cf). The transition line on the cone surface shows a nonmonotonic curve and the transition is delayed in the range of 20°≤θ≤30° (θ=0° is the leeward section). The mechanism of the delayed transition is studied by using joint frequency spectrum analysis and linear stability theory (LST). It is shown that the growth rates of unstable waves of the second mode are suppressed in the range of 20°≤θ≤30°, which leads to the delayed transition location. Very low frequency waves (VLFWs) are found in the time series recorded just before the transition location, and the periodic times of VLFWs are about one order larger than those of ordinary Mack second mode waves. Band-pass filter is used to analyze the low frequency waves, and they are deemed as the effect of large scale nonlinear perturbations triggered by LST waves when they are strong enough.
Convergence of adiabatic family of anti-self-dual connections on products of Riemann surfaces
Authors: Nishinou Takeo
Published: February 2010

We prove a convergence theorem for a sequence of anti-self-dual connections on a family of products of two Riemann surfaces, where the metric of one factor shrinks, establishing the conjecture of Bershadsky et al. [Topological reduction of 4D SYM to 2D sigma-models,” Nucl. Phys. B 448, 166 (1995)].
Thermal capillary waves relaxing on atomically thin liquid films
Authors: Willis A. M. , Freund J. B.
Published: February 2010

Atomistic simulations are used to investigate the relaxation dynamics of thermal capillary waves on thin flat liquid films. Short Lennard-Jones polymers (n=2, 4, and 8) model the liquid in films of thickness 6σ to 96σ, where σ is the Lennard-Jones atomic length-scale parameter. Assuming no-slip boundary conditions on the solid wall and constant surface tension and viscosity, the standard continuum model predicts that capillary waves decay with rates ω that scale with wavenumber q as ω∼q4 for long wavelengths and ω∼q for short wavelengths. The atomistic simulations do indeed show these scalings for ranges of q, and, of course, this model must fail for large q as wavelengths approach atomic scales. However, before a complete breakdown of the continuum description, an unexpected intermediate regime is found. Here the decay rates follow an apparent ω∼q2 power law. The behavior in this range collapses for all the cases simulated when q is scaled with the radius of gyration of the polymers, indicating that a molecular-scale effect underlies the relaxation mechanics of these short waves.
Forward tunneling current in GaN-based blue light-emitting diodes
Authors: Yan Dawei , Lu Hai , Chen Dunjun , Zhang Rong , Zheng Youdou
Published: February 2010

Forward tunneling current in InGaN/GaN multiquantum-well blue light-emitting diodes grown on sapphire substrate was studied by temperature-variable current-voltage (I-V) measurement. All semilog I-V curves obtained in the temperature range from 100 to 300 K exhibit two successive linearly dependent regions at low forward bias. The corresponding slopes appear to be insensitive to temperature, which indicates a dominant defect-assisted tunneling process. It is found that the tunneling current varies approximately as a function of ∼exp(−βEg+λeV), where β and λ are constants independent of temperature and voltage. The temperature- and voltage-dependence of forward tunneling current are explained by thermally induced band gap shrinkage and bias-induced route change of diagonal tunneling, respectively. The likely tunneling entities involved in the forward tunneling process are also discussed.
Spreading of colloid clusters in a quasi-one-dimensional channel
Authors: Xu Xinliang , Lin Binhua , Cui Bianxiao , Dinner Aaron R. , Rice Stuart A.
Published: February 2010

The effect of hydrodynamic interactions on the spreading of clusters of colloid particles in a quasi-one-dimensional channel is analyzed both experimentally and theoretically. An n-particle cluster spreading diffusion coefficient is defined, in terms of the displacement Δx(t) in time t, by Dn≡⟨[∑i=1nΔxi(t)]2⟩/2nt, where the average is taken over all groups of n adjacent particles. Our study focuses on the n-dependence of Dn with some attention to the dependence of Dn on colloid packing fraction. We find that the ratio of Dn to the infinite dilution self-diffusion coefficient DS0 increases as n increases, eventually saturating for large n. The observed dependence of Dn on n is in satisfactory agreement with the predictions obtained from both Stokesian dynamics simulations and hydrodynamic calculations using the method of reflections.
Kelvin probe force microscopy study on nanotriboelectrification
Authors: Sun Hao , Chu Haibin , Wang Jinyong , Ding Lei , Li Yan
Published: February 2010

Nanotriboelectrification is studied by a Kelvin probe force microscopy (KFM)-based method. The electrostatic potentials produced by the friction between the atomic force microscope tips and the substrates are recorded with KFM and the electric quantity is calculated. Charge sign reversal is found when different loaded forces are applied between tips and substrates of similar properties. A model is built to explain this phenomenon. The factors which can affect the properties of surface charges, such as loaded force, friction speed, friction time, and relative humidity are discussed in detail.
Plasma density measurements by phase resolved cutoff
Authors: Kwon J. H. , You S. J. , Kim J. H. , Shin Y. H.
Published: February 2010

A method for precise measurement of absolute electron density in the plasma using plasma frequency is proposed. The phase difference between two antennas (radiating and detecting antennas) and its slow time modulation was used, instead of the transmittance used in previous cutoff probe, and a remarkable result is observed. This method can determine the absolute electron density precisely: It is not only in a good agreement with the previous method very closely but also is able to find the cutoff point clearly even in difficult conditions where there are ambiguities to determine the cutoff point with previous method.
Bismuth doping of graphene
Authors: Aktürk Olcay Üzengi , Tomak Mehmet
Published: February 2010

In this work, we have studied bismuth as a dopant in graphene using density functional theory (DFT). We find that bismuth is weakly physisorbed within DFT. On the other hand, we show that bismuth n-dopes graphene when it is substitutional. We observe that local density approximation results give higher substitutional energy than that of generalized gradient approximation. The electronic structure of graphene is changed when Bi is substitutional.
Electrical transport and low-temperature scanning tunneling microscopy of microsoldered graphene
Authors: Geringer V. , Subramaniam D. , Michel A. K. , Szafranek B. , Schall D. , Georgi A. , Mashoff T. , Neumaier D. , Liebmann M. , Morgenstern M.
Published: February 2010

Using the recently developed technique of microsoldering, we perform systematic transport studies of the influence of polymethylmethacrylate on graphene revealing a doping effect with a n-type dopant density Δn of up to Δn=3.8×1012 cm−2 but negligible influence on mobility and hysteresis. Moreover, we show that microsoldered graphene is free of contamination and exhibits very similar intrinsic rippling as found for lithographically contacted flakes. Characterizing the microsoldered sample by scanning tunneling spectroscopy, we demonstrate a current induced closing of the phonon gap and a B-field induced double peak attributed to the 0 Landau level.
Novel Acentric Organic Solids with Non-linear Optical and Ferroelectric Properties
Authors: Wang Yong-Tao , Tang Gui-Mei , Li Tian-Duo , Yu Jian-Chao , Wei Yong-Qin , Ling Ji-Bei , Long Xi-Fa
Published: February 2010

A series of compounds obtained through one-pot three-component reaction, present non-centrosymmetric polar packing arrangement, resulting in strong second harmonic generation responses and ferroelectric behaviours.
Convergent Solution Phase Synthesis of Chimeric Oligonucleotides by a 2+2 and 3+3 Phosphoramidite Strategy
Authors: Chen Chih-Hau , Chen Wei-Yu , Chen Yu-Chie , Lee Ming-Juan , Huang Chyuan-Der , Chanda Kaushik , Sun Chung-Ming
Published: February 2010

A chimeric oligonucleotide tetramer and hexamer were synthesized by the phosphoramidite approach using a 2+2 and 3+3 strategy, respectively. The concept of convergent synthesis provides an efficient route toward the synthesis of longer chimeric oligonucleotides, such as small interfering RNA oligonucleotides without the pollution of n – 1 or shorter failures. This methodology offers an efficient and economical way to scale-up the synthesis of high purity oligonucleotides for clinical trials and commercial uses.
Ligand Exchange Processes on the Solvated Zinc Cation II. [Zn(H2O)4L]2+·2H2O with L = NH3, NH2(CH3), NH(CH3)2, and N(CH3)3
Authors: Alzoubi Basam M. , Puchta Ralph , van Eldik Rudi
Published: February 2010

Water-exchange mechanisms for the complexes [Zn(H2O)4L]2+·2H2O, L = NH3, NH2CH3, NH(CH3)2, and N(CH3)3, have been studied by density functional theory calculations (B3LYP/6–311+G**). The water-exchange reactions follow an associative (A) pathway involving formation of a six-coordinate intermediate [Zn(H2O)5L]2+·H2O. Electronic and steric effects of the amine ligands influence the activation barrier and the stability of the six-coordinate intermediate.
A diver survey method to quantify the clustering of sedentary invertebrates by the scale of spatial autocorrelation
Authors: McGarvey Richard , Feenstra John E. , Mayfield Stephen , Sautter Erin V.
Published: February 2010

Sedentary benthic invertebrates exhibit clustering at a range of spatial scales. Animal clustering reduces the precision of diver surveys and can accelerate overexploitation in dive fisheries. Dive harvesters target the densest aggregations of males and females that produce the highest rates of egg fertilisation during mass spawning events. By quantifying these effects of harvesting on fertilisation success, measuring animal clustering can inform stock management for reproductive sustainability. We present a method to measure the spatial extent of density aggregations down to 1 m, extending a previously described leaded-line survey design. Applying this method to abalone, research divers counted individuals in successive 1 × 2 m2 quadrats lying along adjoining pairs of 1 × 100 m2 transects. Clusters were observed as neighbouring quadrats of high animal density. Spatial autocorrelations at inter-quadrat distances of 1 to 100 m were calculated for four surveys, with eight pairs of transects swum in each survey. For all four surveys, inside two survey regions, spatial autocorrelation declined to non-significant levels at a distance of ~20 m. Quantified by the distance within which density counts are correlated, this quadrat-within-transect method provides a diver survey measure of the scale of spatial aggregation for sedentary invertebrates such as abalone, sea cucumbers and urchins.
Spatial variability of cadmium, copper, manganese, nickel and zinc in the Port Curtis Estuary, Queensland, Australia
Authors: Angel Brad M. , Hales Leigh T. , Simpson Stuart L. , Apte Simon C. , Chariton Anthony A. , Shearer Damon A. , Jolley Dianne F.
Published: February 2010

Port Curtis is a rapidly growing industrialised and urbanised harbour in Central Queensland, Australia. The spatial variability of trace metals in waters and suspended particulates was determined along axial transects within the harbour and in oceanic waters adjacent to Port Curtis. Dissolved metal concentrations were significantly elevated in Port Curtis compared with the concentrations measured in the adjacent coastal waters. Dissolved copper and zinc concentrations ranged from <19 to 800 and <31 to 580 ng L–1, respectively, and maxima were observed in inner harbour waters adjacent to the southern entrance to the Narrows and in close proximity to anthropogenic sources. Dissolved nickel concentrations were measured in the range of 110 to 900 ng L–1, and exhibited a maximum concentration in the central to northern Narrows, in an area that was not adjacent to anthropogenic sources. Dissolved manganese concentration maxima were measured in close proximity to the dissolved nickel maxima. It appears likely that the elevated dissolved metal concentrations in Port Curtis and the Narrows were not caused by a single point source, and are the result of several factors, including industrial activity around the foreshore, fluxes from sediment-porewater, low flushing durations, lower water pH and possibly episodic inputs from adjacent rivers.