bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing the Human and Fish Genomes
Authors: Nakatani Yoichiro , Morishita Shinichi
Published: October 2009

How have the genomes of vertebrates evolved over the last 600 million years? In 1970, based on limited observations, Ohno postulated that whole genome duplication events took place in early vertebrates and were essential to increasing complexity of vertebrates. This issue, however, remains a biological quandary. Recent rapid progress in sequencing the genomes of many vertebrates has revealed fundamental insights into the evolutionary process, and the comparative genomics of the fish and human genomes is indispensable for providing conclusive support to Ohno's hypothesis.
Evolutionarily Conserved Intronic Splicing Regulatory Elements in the Human Genome
Authors: Van Nostrand Eric L , Yeo Gene W
Published: October 2009

Splicing is the process by which introns are removed from premature messenger
ribonucleic acid
(pre‐mRNA), and exons are ligated to form mature mRNA before translation into protein products. Aside from the consensus splice signals such as the branch point, acceptor and donor splice sites, additional
cis
‐regulatory elements embedded within the exons and introns control the recognition of exonic (approximately 150 bases) from intronic sequence (approximately 100–100 000 bases). Intronic splicing elements that are evolutionarily conserved across multiple species play important roles in the regulation of constitutive splicing, where a single mRNA is produced, and alternative splicing, where multiple mRNA isoforms are generated.
Evolution of Imprinting: Imprinted Gene Function in Human Disease
Authors: Dickins Benjamin JA , Kelsey Gavin
Published: October 2009

A subset of genes in mammals, known as imprinted genes, show a conditional expression strategy in which transcription depends on an allele's parental origin. Several explanations have been advanced to explain this phenomenon and these, with varying levels of success, predict the functions of imprinted genes. After outlining these explanations, we summarize what is known about human genetic disorders involving abnormal expression of imprinted genes and ask what this can tell us about the evolution of imprinting.
Fatty Acid Synthesis in Protozoan Parasites
Authors: Allary Marina , Prigge Sean T
Published: October 2009

Three metabolic pathways can be used by protozoan parasites for the

de novo

synthesis of fatty acids. Parasites employ diverse strategies involving these three pathways, as well as scavenging from the host, to obtain fatty acids required for growth.
Gene Inactivation and Tissue‐specific Metabolism
Authors: Flowers Matthew T , Ntambi James M
Published: October 2009

The application of gene inactivation strategies targeting genes with various metabolic functions has greatly advanced our understanding of metabolism at both the cellular and physiological level. Whole‐body genomic ablation of a gene of interest may be achieved using transgenic methods to introduce a null allele. Alternatively, the Cre‐loxP recombinase system allows for the generation of animals harbouring a tissue‐specific gene inactivation. Another approach is to alter the messenger
ribonucleic acid
(mRNA) abundance of the target gene using RNA interference (RNAi) or antisense oligonucleotide (ASO) methods. Together, these strategies help elucidate gene function through association of metabolic phenotypes with gene inactivation at a defined genetic locus.
Membrane Rafts and Caveolae
Authors: Thomas Candice M , Smart Eric J
Published: October 2009

The plasma membrane does more than serve as a barrier between the contents of the cell and the extracellular space. It is a highly organized structure which contains fatty acids, cholesterol and a variety of proteins and is functionally important in trafficking cellular signals. The concept of organized structures or domains within the plasma membrane has proven invaluable to understanding how the plasma membrane interacts with the surrounding environment. One class of these domains is lipid rafts which have been shown to organize and regulate signalling platforms. Caveolae are a subset of lipid rafts which contain specific proteins and lipids that aid in the regulation of signalling processes differently from other domains. Purification techniques have made it possible to study the biochemistry of lipid rafts and caveolae and to gain a better understanding of their roles in signal transduction.
Prokaryote Nomenclature
Authors: Oren Aharon
Published: October 2009

Nomenclature of prokaryotes is regulated by the provisions of the International Code of Nomenclature of Prokaryotes. To obtain standing in the nomenclature, names of new taxa must be validly published according to the rules of that Code.
Ficolins
Authors: Takahashi Kazue
Published: October 2009

Ficolins are soluble pattern‐recognition molecules of the innate immunity. Ficolins consist of a collagen‐like domain, a neck region and a fibrinogen‐like domain that binds specific molecular structures of pathogens and the body's own damaged cells by preferably recognizing acetylated compounds. Humans have three homologous proteins,
H‐ficolin
(or
ficolin‐3
),
L‐ficolin
(or
ficolin‐2
) and
M‐ficolin
(or
ficolin‐1
). The first two ficolins are circulating in blood whereas ficolin‐1 is locally secreted. Ficolins activates the lectin complement pathway, which results in neutralization of pathogens, thus ficolins play important roles in innate immunity, both to protect from infection as well as to maintain tissue health.
Ghini, Luca
Authors: Dröscher Ariane
Published: October 2009

Luca Ghini (1490 to
c
. 1556), an Italian scholar who was one of the founders of modern botany, of the first public botanical garden and probably of the first modern herbarium.
Cesalpino, Andrea
Authors: Dröscher Ariane
Published: October 2009

Andrea Cesalpino (1519/24–1603), a philosopher, anatomist and botanist, was the first to develop a model of blood circulation (of the inner circle) and a classification of plants and minerals.
Molecular Genetics of Polygenic Hypertension
Authors: Deng Alan Y
Published: October 2009

Contrasting to rare monogenic forms of hypertension, essential hypertension is the most clinically diagnosed ailment leading to high morbidity and mortality; however, its underlying mechanisms continue to be undeciphered. To assist this endeavor, investigations utilizing rodent models have revealed multiplex genetic architecture for quantitative trait loci (QTLs), for blood pressure (BP), elaborate QTL–QTL interactions and efficacious genome regulations of QTL functions. Although BP is a quantitatively measured trait manifesting in a continuous variation, each QTL governing it appears to behave as an independent and ‘monogenic’ Mendelian determinant. Some QTLs are functionally modularized by epistasis that implies a common pathway or cascade; whereas others belong to parallel epistatic modules. These insights suggest that similar genetic mechanisms probably shepherd the genetic architecture for essential hypertension. Translation of gene discovery to therapeutic targets and diagnostic tools will require a consolidation of functional validation of genes in animal models with association studies in targeted human populations.

Key Concepts

The quantitative governance of blood pressure variations is realized by several genes or quantitative trait loci (QTLs). Each QTL can operate autonomously and comports in a ‘monogenic’ pattern. Those QTLs that occur to mutually conceal their BP effects can be epistatically modularized, consequently, solving the conundrum of overabundant QTLs in the genome. Despite the puissance of QTLs, potent genome regulations can disallow QTLs to influence blood pressure (BP). In both human and animal association/linkage studies, population‐dependence and the influence of genome heterogeneity on exhibiting the amplitude of BP effect are frequently observed occurrences.
Work‐related carpal tunnel syndrome in Washington State workers' compensation: Utilization of surgery and the duration of lost work
Authors: Daniell William E. , Fulton‐Kehoe Deborah , Franklin Gary M.
Published: October 2009

Background

Work‐related carpal tunnel syndrome (CTS) is a leading cause of lengthy disability.

Methods

This population‐based retrospective cohort study used Washington State workers' compensation claims for CTS to characterize associations between utilization of CTS surgery and duration of lost work. The sample included all claims (n = 8,224) filed during 1990–1994 (followed through 2000) and receiving lost‐work compensation.

Results

Sixty‐four percent of studied workers had CTS surgery. Among workers with >1 month of lost work, the total duration was much shorter when workers had surgery, versus those who did not (median 4.3 and 6.2 months, respectively; P < 0.001); there was no difference when disability extended >6 months. When workers had surgery, disability was less likely to end before 6 months if non‐CTS conditions were present, surgery occurred >3 months after claim filing, or employment was in an industry with high incidence of CTS; disability was more likely to end if the diagnosing provider and operating surgeon had higher CTS claims volume. Physical and rehabilitation medicine services were associated with lower probability of returning to work, with or without surgery.

Conclusions

There is a need to scrutinize the role of surgery and physical‐rehabilitation medicine modalities in the management of CTS covered by workers' compensation. The findings suggest disability can be minimized by establishing the CTS diagnosis as early as possible and, if surgery is appropriate, conducting surgery without substantial delay and maximizing post‐operative efforts to facilitate return to work. Use of surgery >6 months after filing should be considered with great caution. Am. J. Ind. Med. 52:931–942, 2009. © 2009 Wiley‐Liss, Inc.
Incidence of tuberculosis and HIV and progression of silicosis and lung function impairment among former basotho gold miners
Authors: Park Harriet H. , Girdler‐Brown Brendan V. , Churchyard Gavin J. , White Neil W. , Ehrlich Rodney I.
Published: October 2009

Background

Pulmonary tuberculosis and HIV incidence, mortality, and the progression of silicosis and lung function impairment are described over a 1‐year period in migrant ex‐gold miners from Lesotho.

Methods

Seven hundred seventy‐nine Basotho miners were followed for 1 year starting 18 months after lay‐off from a South African gold mine in 1998. At baseline and follow‐up, they underwent a respiratory symptom interview, physical examination, HIV test, chest radiograph, and spirometry.

Results

Five hundred thirteen of 779 (65.9%) participants attended both baseline and follow‐up visits. HIV incidence was 5.4/100 person‐years (95% CI: 3.4–8.2). Prevalence of silicosis (ILO score ≥1/1) was 26.6% at baseline and 27.0% at follow‐up. Active tuberculosis diagnosed at baseline was a strong predictor of radiological progression of silicosis. Lung function as measured by FEV1 declined an average of 91 ml between visits (95% CI: 67–116 ml). Calculated minimum incidence of tuberculosis was 3,085/100,000/years (95% CI: 1,797–4,940) at follow‐up. Of those seen at baseline, 18 died before their scheduled follow‐up visit (mean age: 51 years).

Conclusions

High rates of mortality and of HIV infection and pulmonary tuberculosis were found in this cohort after leaving the South African goldmines. Continuing lung function loss was also apparent. A partnership between the South African mining industry and governments in labor‐sending areas of Southern Africa is needed to provide continuity of care and access to HIV and tuberculosis treatment and prevention services. Active silicosis surveillance and an improved statutory compensation system are also needed. These findings can serve as a baseline against which the impact of such interventions can be assessed. Am. J. Ind. Med. 52:901–908, 2009. © 2009 Wiley‐Liss, Inc.
Free vibration of symmetric planar frames via the force method and canonical forms
Authors: Kaveh A. , Aalizadeh Arvanaq R.
Published: October 2009

In this paper, the method recently developed for the free vibration of symmetric frames using canonical forms of stiffness matrices is extended to the flexibility matrices. Weighted graphs are associated with the flexibility and mass matrices of the frame structures. Using graph symmetry, the models are decomposed into submodels and a healing process is employed, such that the union of the eigenvalue of the matrices corresponding to the healed submodels contains the eigenvalues of the entire model. This two‐step process is termed as the factorization of a weighted graph. The presented method is illustrated through simple examples having different symmetries. Copyright © 2009 John Wiley & Sons, Ltd.
Solvothermal Synthesis and Characterization of Chalcopyrite CuInSe2 Nanoparticles
Authors: Chen Huiyu , Yu Seong-Man , Shin Dong-Wook , Yoo Ji-Beom
Published: October 2009

The ternary I-III-VI2 semiconductor of CuInSe2 nanoparticles with controllable size was synthesized via a simple solvothermal method by the reaction of elemental selenium powder and CuCl as well as InCl3 directly in the presence of anhydrous ethylenediamine as solvent. X-ray diffraction patterns and scanning electron microscopy characterization confirmed that CuInSe2 nanoparticles with high purity were obtained at different temperatures by varying solvothermal time, and the optimal temperature for preparing CuInSe2 nanoparticles was found to be between 180 and 220 °C. Indium selenide was detected as the intermediate state at the initial stage during the formation of pure ternary compound, and the formation of copper-related binary phase was completely deterred in that the more stable complex [Cu(C2H8N2)2]+ was produced by the strong N-chelation of ethylenediamine with Cu+. These CuInSe2 nanoparticles possess a band gap of 1.05 eV calculated from UV–vis spectrum, and maybe can be applicable to the solar cell devices.
Synovial cyst of the fifth digit in a cat
Authors: Hittmair Katharina M. , Maedl Irene , Reifinger Martin , Mayrhofer Elisabeth
Published: October 2009

A synovial cyst of the fifth digit of the left forelimb in a 15-year-old cat was diagnosed. Radiographs showed severe osteoarthritis of the interphalangeal and metacarpophalangeal joints with soft tissue swelling. An ultrasound examination of the digit revealed a cystic structure. Following amputation of the digit, the cyst recurred 3 months later palmar to the carpus and metacarpus. The aetiology of synovial cysts is discussed.
A Lab of Their Own: Genomic sovereignty as postcolonial science policy
Authors: Benjamin Ruha
Published: October 2009

This paper analyzes the emergence of ‘genomic sovereignty’ policies as a newly popular way for postcolonial countries to frame their investment in genomics. It identifies three strands in the genealogy of this policy arena—the International Haplotype Mapping Project as a model and foil for postcolonial genomics; an emerging public health genomics field which stands in contrast to Western pursuits of personalized medicine; and North American drug companies increased focus on ethnic drug markets. I conceptualize postcolonial genomics as a nationalist project with contradictory tendencies—unifying and differentiating a diverse body politic, cultivating national scientific and commercial autonomy and dependence upon global knowledge networks and foreign capital. It argues that the ‘strategic calibration’ of socio-political versus biological taxonomies in postcolonial genomics creates two primary challenges for this arena, which I refer to heuristically as dilemmas of mapping and marketing.
Interwar fascism and the post-1989 radical right: Ideology, opportunism and historical legacy in Bulgaria and Romania
Authors: Frusetta James , Glont Anca
Published: October 2009

Do contemporary Bulgarian and Romanian radical right movements represent a legacy of interwar fascism? We argue that the key element is not that interwar movements provided legacies (of structures, ideologies, or organizations) but rather a symbolic “heritage” that contemporary movements can draw upon. The crucial legacy is, rather, the Socialist era, which in asserting its own definitions of interwar fascism created a “useable past” for populist movements. The Peoples’ Republics created a flawed historical consciousness whereby demonized interwar rightist movements could be mobilized after 1989 as historical expressions of “anti-Communist” — and, ergo, positive symbols among those of anti-Communist sentiment. Although radical right parties in both countries may cast themselves as “heirs” to interwar fascism, they share little in common in terms of ideology. Their claims to a fascist legacy is, rather, a factor of how their respective Socialist states characterized the past.
History education and historical remembrance in contemporary Russia: Sources of political attitudes of pro-Kremlin youth
Authors: Levintova Ekaterina , Butterfield Jim
Published: October 2009

Why during the last decade have many young Russians become politically active well beyond simply voting? Particularly striking among youth activists is their enthusiastic support for Putinism and a resounding rejection of the policies, symbols and political figures of the era of President Boris Yeltsin (1992–2000). The vast majority of youth activists are of college age (18–24), which means they were far too young to be aware of what was happening in the country in the 1990s, the period that while democratic and pro-Western, also represents a failure of the Russian state in their imagery. To what degree do the opinions and worldviews of politically active pro-Kremlin youth reflect the recently emerged, nearly ubiquitous interpretation of recent history as presented in the high school curriculum? To that end, we undertake a content analysis of 47 high school textbooks in Russian history, followed by open-ended interviews with 37 activists from the three most visible youth organizations, all of whom are pro-Kremlin in their orientation. Although demonstrating a causal relationship is methodologically unfeasible, we find a marked correlation between the views of both the Yeltsin and Putin eras presented in those textbooks and in the political beliefs of the youth groups.
Hepatocyte Growth Factor Suppresses Transforming Growth Factor‐Beta‐1 and Type III Collagen in Human Primary Renal Fibroblasts
Authors: Mou Shan , Wang Qin , Shi Beili , Gu Leyi , Ni Zhaohui
Published: October 2009

Tubulointerstitial changes in the diabetic kidney correlate closely with renal fibrosis, and transforming growth factor‐beta‐1 (TGF‐β1) is thought to play a key role in this process. In contrast, hepatocyte growth factor (HGF) has shown therapeutic effects on injured renal tubules in animal models. This study was undertaken to test the hypothesis that the preventive effects of HGF may result from interventions in TGF‐β1‐mediated signaling and collagen III secretion. We examined the expression of HGF/HGF receptor (c‐Met) and TGF‐β1 in renal fibroblasts at multiple time points. The effects of recombinant human HGF on TGF‐β1 expression were studied by RT‐PCR and Western blotting, and the levels of collagen III were measured by ELISA. In the high‐glucose condition, the expression of HGF and c‐Met in renal fibroblasts was detected as early as 6 hours following cell culture while the level of TGF‐β1 peaked at 96 hours. The addition of recombinant human HGF to the culture media dose‐dependently inhibited TGF‐β1 mRNA expression and reduced collagen III secretion by 34%. These results indicate that, during hyperglycemia, HGF inhibits TGF‐β1 signaling and type III collagen activation in interstitial fibroblasts. Furthermore, we should recognize that changes in the balance between HGF and TGF‐β1 might be decisive in the pathogenesis of chronic renal fibrosis. Therefore, administration of HGF to restore this balance may offer a novel therapeutic intervention in managing renal fibrogenesis in diabetic nephropathy.
Follow‐Up Study of Behavioral Development and Parenting Stress Profiles in Children with Congenital Hypothyroidism
Authors: Chao Mei‐Chyn , Yang Pinchen , Hsu Hsiu‐Yi , Jong Yuh‐Jyh
Published: October 2009

Recent longitudinal experiences have emphasized that the follow‐up of children with treated congenital hypothyroidism (CHT) should not be limited to the cognitive domain. This study attempted to evaluate the emotional–behavioral profiles in children with CHT together with maternal parenting stress profiles. Data for child and family characteristics were collected from 47 families with a 3–12‐year‐old CHT child diagnosed and treated since the newborn period. Cognitive assessments were performed. The main caregiver completed the following questionnaires: (1) Strengths and Difficulties Questionnaire, which rated behavioral symptoms in children; (2) Parenting Stress Index, which determined the quality and magnitude of parenting stress experienced by the caregiver; and (3) Symptom Checklist‐90‐R, which evaluated the psychopathological symptoms of the caregiver. In addition, 31 unaffected siblings were recruited as a comparative control group. The results revealed that children with treated CHT had normal intelligence quotients (mean, 93.6 ± 16.2) at the time of the study. However, CHT children had more problems in emotional–behavioral domains than sibling controls (p = 0.01). Overall, 29.8% (14/47) of the CHT children had emotional–behavioral problems above the clinical cutoff. In addition, 13% of the caregivers of CHT children had parenting stress above the clinical cutoff. Therefore, professional intervention is warranted in these subgroups of CHT children and parents.
Intraobserver and Interobserver Variability of Fuhrman and Modified Fuhrman Grading Systems for Conventional Renal Cell Carcinoma
Authors: Bektas Sibel , Bahadir Burak , Kandemir Nilufer Onak , Barut Figen , Gul Aylin Ege , Ozdamar Sukru Oguz
Published: October 2009

The Fuhrman nuclear grade is the most widely used grading system for renal cell carcinoma. The aim of this study was to evaluate the intraobserver and interobserver variability of the Fuhrman and modified Fuhrman grading systems for conventional renal cell carcinoma. In this study, five pathologists independently classified 110 cases of conventional renal cell carcinoma according to the Fuhrman and modified (three‐ and two‐tiered) Fuhrman grading systems. The intraobserver and interobserver variability of these systems were assessed using κ statistics. The associations between the Fuhrman and modified Fuhrman grades, pathologic stage and tumor size were determined by correlation analysis. The intraobserver and interobserver combined mean κ values for four‐tiered Fuhrman grading were 0.48 and 0.41, respectively. The highest agreement was detected in two‐tiered modification (including grades 1 + 2 and 3 + 4); the intraobserver and inter‐observer combined mean κ values were 0.67 and 0.62, respectively. Correlations between pathologic stage and tumor size with two‐tiered modification (including grades 1 + 2 and 3 + 4) were greater than those in three‐ and four‐tiered Fuhrman grading. Collapsing the Fuhrman grading into a two‐tiered scheme improved the intraobserver and interobserver reproducibility.
Simultaneous 99mTC and 123I Dual‐Isotope Brain Striatal Phantom Single Photon Emission Computed Tomography: Validation of 99mTC‐Trodat‐1 and 123I‐IBZM Simultaneous Dopamine System Brain Imaging
Authors: Kao Pan‐Fu , Wey Shiaw‐Pyng , Yang An‐Shoei
Published: October 2009

[2[[2‐[[[3‐(4‐chlorophenyl)‐8‐methyl‐8‐azabicyclo[3,2,1]‐oct‐2‐yl]‐methyl](2‐mercaptoethyl)amino]ethyl]amino]ethanethiolato(3‐)‐N2,N2′,S2,S2]oxo‐[1R‐exo‐exo)])‐[99mTc]‐technetium (99mTc‐TRODAT‐1) and 123I‐iodobenzamide (123I‐IBZM) are radiotracers for brain dopamine preand postsynaptic neuron imaging. The purpose of this study was to evaluate imaging parameters and crossed energy interference using simultaneous single photon emission computed tomography (SPECT) 99mTc and 123I data acquisition. A five‐compartment brain striatal phantom was filled with 99mTc and/or 123I radioactive solutions with different striatal‐to‐background ratios, ranging from 3:1 to 9:1. SPECT data were acquired with energy window settings of 15% for the centered window at 140 keV for 99mTc and a 10% asymmetric window at 159 keV for 123I. The experiments were carried out using either individual (99mTc or 123I only) or both radionuclides. The striatal‐to‐background ratios and energy crossed interference between 99mTc and 123I were calculated. The phantom SPECT images demonstrated that the energy crossed interferences from 123I to 99mTc, and vice versa, were 22 ± 12.4% and 0.4 ± 1.0%, respectively. A net interference of 7.1 ± 4.0% for the counts in the 15% centered 99mTc window can be expected from 123I and a net interference of 1.6 ± 3.3% for the counts in the 10% asymmetric 123I window was derived from 99mTc. The correlation of striatal‐to‐background ratios between single isotope and simultaneous dual‐isotope was excellent (R2 = 0.99). The imaging parameters used in this simultaneous dual‐isotope SPECT imaging could be used in future clinical practice for imaging patients with movement disorders by using 99mTc‐TRODAT‐1 and 123I‐IBZM. The striatal‐to‐background ratios were not affected by the crossed interference between 99mTc and 123I.
Female Epispadias: A Case Report and Review of the Literature
Authors: Atilgan Dogan , Uluocak Nihat , Erdemir Fikret , Parlaktas Bekir S.
Published: October 2009

Isolated female epispadias without exstrophy is an extremely rare syndrome. The symptoms of female epispadias are primary urinary incontinence and abnormal anatomical features. A 12‐year‐old girl presented with primary urinary incontinence. On physical examination, bifid clitoris and labia minora were seen. The vagina and hymen were normal. Voiding cystourethrogram showed no reflux. With the diagnosis of isolated female epispadias, one‐stage reconstruction of the urethra, bladder neck and labia minora and clitoris was performed.
Intravitreal Ranibizumab for the Treatment of Choroidal Neovascularization Secondary to Endogenous Endophthalmitis
Authors: Sheu Shwu‐Jiuan
Published: October 2009

Choroidal neovascularization is a major cause of visual loss in age‐related macular degeneration. It is also a potential vision‐threatening complication of pathologic myopia, uveitis, traumatic choroidal rupture and, rarely, endophthalmitis. Here, we report a 36‐year‐old woman with acute lymphocytic leukemia and fungal pneumonia after chemotherapy who developed endogenous endophthalmitis in both eyes. The infection was controlled by systemic antibiotic and antifungal agents. Unfortunately, choroidal neovascularization developed in the right macula 1 month later. One dose of intravitreal injection of ranibizumab (0.5 mg/0.05 mL) was given, and the macular exudates resolved rapidly. There was no recurrence or complications during the 10‐month follow‐up.
Transient ion ejection during nanocomposite thermite reactions
Authors: Zhou Lei , Piekiel Nicholas , Chowdhury Snehaunshu , Lee Donggeun , Zachariah Michael R.
Published: October 2009

We observe an intense ion pulse from nanocomposite thermite reactions, which we temporally probe using a recently developed temperature jump/time of flight mass spectrometer. These ion pulses are observed to be much shorter in duration than the overall thermite reaction time. Ion ejection appears in stages as positive ions are ejected prior to nanocomposite thermite ignition, and ignition of the thermite mixtures leads to a second ionization step which is primarily dominated by negative species. The positive species are identified from mass spectrometric measurements and the results show that the positive ion species are comprised of Na ions with minor species of Al and K ions. This observation can be explained by a diffusion based ion-current mechanism, in which strong Al ion diffusion flux formed through the oxide shell, and the surface Na and K ions from salt contaminations are ejected by the strong electrostatic repulsion. The fact that the negative ionization step occurs during the ignition event suggests a strong relation between the nanocomposite thermite reaction and the negative ionization process.
Resonant excitation of shear Alfvén perturbations by trapped energetic ions in a tokamak
Authors: Abel I. G. , Breizman B. N. , Sharapov S. E. ,   JET-EFDA Contributors
Published: October 2009

A new analytic expression is derived for the resonant drive of high n Alfvénic modes by particles accelerated to high energy by ion cyclotron resonance heating. This derivation includes finite orbit effects, and the formalism is completely nonperturbative. The high-n limit is used to calculate the complex particle response integrals along the orbits explicitly. This new theory is applied to downward sweeping Alfvén cascade quasimodes completing the theory of these modes and making testable predictions. These predictions are found to be consistent with experiments carried out on the Joint European Torus [P. H. Rebut and B. E. Keen, Fusion Technol. 11, 13 (1987)].
Local behavior of the first-order gradient correction to the Thomas–Fermi kinetic energy functional
Authors: García-Aldea David , Martín-Blas T. , Alvarellos J. E.
Published: October 2009

The first-order gradient correction to the Thomas–Fermi functional proposed by Haq et al. [Chem. Phys. Lett. 111, 79 (1984)] has been tested by evaluating both the total kinetic energy and the local kinetic energy density. For the kinetic energy density, we have evaluated its deviation from the exact orbital-based result through a quality factor that reflects the quality of the functionals in a better way than their relative errors. The study is performed on two different systems: Light atoms (up to Z=18) and a noninteracting model of fermions confined in a Coulombic-type potential, a system that provides useful insights about the performance of the functionals when the ground state is degenerate. It is found that this approximation gives very low relative errors and a better local behavior than any other kinetic energy density functional.
A pathway to p-type wide-band-gap semiconductors
Authors: Janotti Anderson , Snow Eric , Van de Walle Chris G.
Published: October 2009

Based on first-principles calculations we devise an alternative approach to p-type doping in AlN, ZnO, and ZnMgO. Instead of searching for acceptors on the left of the host atoms in the Periodic Table, we propose to search on the far right. We find that F placed at interstitial sites in AlN, ZnO, and ZnMgO acts as a shallow acceptor, leaving a hole in an effective-mass state near the valence-band maximum. We investigate the stability of F impurities and propose a procedure to selectively introduce F in the interstitial lattice sites of the above wide-band-gap semiconductors.
Single fiber Bragg grating sensor with two sections of different diameters for longitudinal strain and temperature discrimination with enhanced strain sensitivity
Authors: Mondal Samir K. , Tiwari Umesh , Poddar Gopal C. , Mishra Vandana , Singh Nahar , Jain Subhash C. , Sarkar S. N. , Chattoypadhya K. D. , Kapur Pawan
Published: October 2009

A single fiber Bragg grating (FBG) sensor with two sections of different diameters is proposed and experimentally demonstrated for discrimination and measurement of strain and temperature. A section of single FBG is etched in hydrofluoric acid solution to reduce diameter of the fiber by factor of <1/2 to increase its strain sensitivity. Different shifts of the Bragg wavelengths of chemically etched and nonetched gratings caused by different strain sensitivities are used to discriminate and measure strain and temperature. Maximum errors of ±13με (microstrain) and ±1 °C are reported over 1700με and 60 °C measurement ranges, respectively. Depending upon the diameter of the etched fiber grating, the design can also discriminate nanostrain from temperature.
Solid-solid phase transition in hard ellipsoids
Authors: Radu M. , Pfleiderer P. , Schilling T.
Published: October 2009

We present a computer simulation study of the crystalline phases of hard ellipsoids of revolution. A previous study [P. Pfleiderer and T. Schilling, Phys. Rev. E 75, 020402 (2007)]. showed that for aspect ratios a/b≥3 the previously suggested stretched-fcc phase [D. Frenkel and B. Mulder, Mol. Phys. 55, 1171 (1985)] is unstable with respect to a simple monoclinic phase with two ellipsoids of different orientations per unit cell (SM2). In order to study the stability of these crystalline phases at different aspect ratios and as a function of density we have calculated their free energies by thermodynamic integration. The integration path was sampled by an expanded ensemble method in which the weights were adjusted by the Wang–Landau algorithm. We show that for aspect ratios a/b≥2.0 the SM2 structure is more stable than the stretched-fcc structure for all densities above solid-nematic coexistence. Between a/b=1.55 and a/b=2.0 our calculations reveal a solid-solid phase transition.
Complete list of Darboux integrable chains of the form t1x=tx+d(t,t1)
Authors: Habibullin Ismagil , Zheltukhina Natalya , Pekcan Aslı
Published: October 2009

We study differential-difference equation (d/dx)t(n+1,x)=f(t(n,x),t(n+1,x),(d/dx)t(n,x)) with unknown t(n,x) depending on continuous and discrete variables x and n. Equation of such kind is called Darboux integrable, if there exist two functions F and I of a finite number of arguments x, {t(n+k,x)}k=−∞∞, {(dk/dxk)t(n,x)}k=1∞, such that DxF=0 and DI=I, where Dx is the operator of total differentiation with respect to x and D is the shift operator: Dp(n)=p(n+1). Reformulation of Darboux integrability in terms of finiteness of two characteristic Lie algebras gives an effective tool for classification of integrable equations. The complete list of Darboux integrable equations is given in the case when the function f is of the special form f(u,v,w)=w+g(u,v).
Extension of the electron dissipation region in collisionless Hall magnetohydrodynamics reconnection
Authors: Sullivan Brian P. , Bhattacharjee A. , Huang Yi-Min
Published: October 2009

This paper presents Sweet–Parker type scaling arguments in the context of hyper-resistive Hall magnetohydrodynamics. Numerical experiments suggest that both cusplike and modestly more extended geometries are realizable. However, the length of the electron dissipation region, which is taken as a parameter by several recent studies, is found to depend explicitly on the level of hyper-resistivity. Furthermore, although hyper-resistivity can produce more extended electron dissipation regions, the length of the region remains smaller than one ion skin depth for the largest values of hyper-resistivity considered here, significantly shorter than current sheets seen in many recent kinetic studies. The length of the electron dissipation region is found to depend on electron inertia as well, scaling like (me/mi)3/8. However, the thickness of the region appears to scale similarly, so that the aspect ratio is at most very weakly dependent on (me/mi).
Photodissociation of phosgene: Theoretical evidence for the ultrafast and synchronous concerted three-body process
Authors: Fang Qiu , Zhang Feng , Shen Lin , Fang Wei-Hai , Luo Yi
Published: October 2009

The potential energy surfaces for Cl2CO dissociation into CO+Cl+Cl in the lowest two electronic singlet states (S0 and S1) have been determined by the complete active space self-consistent field, coupled-cluster method with single and double excitations (CCSD), and equation-of-motion CCSD calculations, which are followed by direct ab initio molecular dynamics simulations to explore its photodissociation dynamics at 230 nm. It is found that the C–O stretching mode is initially excited upon irradiation and the excess internal energies are transferred to the C–Cl symmetric stretching mode within 200 fs. On average, the first and the second C–Cl bonds break completely within subsequent 60 and 100 fs, respectively. Electronic structure and dynamics calculations have thus provided a strong evidence that the photoinitiated dissociation of Cl2CO at 230 nm or shorter wavelengths is an ultrafast, adiabatic, and concerted three-body process. Since the two C–Cl bonds begin to break at the same time and the time interval between the two C–Cl bond broken fully is very short (∼40 fs), the photoinitiated dissociation of Cl2CO to CO+2Cl can be considered as the synchronous concerted process.
Quantum effects on the dispersion of ion acoustic waves
Authors: Mushtaq A. , Melrose D. B.
Published: October 2009

The longitudinal response function for an isotropic, nonrelativistic, thermal plasma with the quantum recoil included exactly is used to generalize the dispersion relation for ion acoustic waves and the absorption coefficient for Landau damping to include the quantum recoil. The results are compared to recent treatment of the dispersion relation derived using a fluid theory with the quantum effects included through the Bohm potential.
Correction to the Clausius–Mosotti equation: The dielectric constant of nonpolar fluids from Monte Carlo simulations
Authors: Valiskó Mónika , Boda Dezső
Published: October 2009

We examine the dielectric constant of nonpolar fluids by direct Monte Carlo simulations on the basis of the polarizable hard sphere (PHS) model, where the spheres carry molecular polarizabilities. Point dipoles are induced in the spheres partly by an external electric field and partly by other molecules. It has been known that the Clausius–Mosotti equation needs a correction due to mutual polarization between molecules. We reproduce the qualitative behavior found in experiments: the correction increases with increasing density, reaches a maximum, and decreases at high densities. We show that the classic theory of Kirkwood and Yvon is quantitatively correct for the PHS model.
Transition state analysis of solid-solid transformations in nanocrystals
Authors: Grünwald Michael , Dellago Christoph
Published: October 2009

A systematic simulation methodology is introduced for the accurate determination of experimentally measurable quantities characterizing solid-solid phase transformations under pressure. The atomistic mechanisms of nucleation and growth in a structural transformation of pressurized CdSe nanocrystals are identified using transition path sampling computer simulation. A committor-based transition state analysis is applied to extract activation enthalpies and activation volumes from transformation pathways at experimental conditions. The qualitative dependence of activation enthalpies on nanocrystal size is in good agreement with experimental data and supports the observed nucleation mechanism, which is characterized by a critical nucleus of elongated shape located on the crystal surface. Based on committor distributions along typical transformation pathways, the coordination number is identified as a suitable reaction coordinate for the process.
State-resolved manipulations of optical gain in semiconductor quantum dots: Size universality, gain tailoring, and surface effects
Authors: Cooney Ryan R. , Sewall Samuel L. , Sagar D. M. , Kambhampati Patanjali
Published: October 2009

Optical gain in strongly confined colloidal semiconductor quantum dots is measured using state resolved pump/probe spectroscopy. Though size tunable optical amplification has been previously reported for these materials, the influence of confinement enhanced multiexcitonic interactions has limited prior demonstrations to specific particle sizes or host media. Here we show that the influence of the interfering multiexcitonic interactions, and hence the development of optical gain, is dependent on the identity of the initially prescribed excitonic state. By maintaining a constant excitonic state in the size tunable electronic structure of these materials, we recover the predicted universal development of optical gain, reflected by size-independent occupation thresholds, and differential gains. In addition, we explicitly compare the influence of surface passivation on the development and lifetime of the optical gain. Furthermore, we introduce a general, state-resolved pumping scheme which enables control over the optical gain spectrum. The capacity to manipulate the optical gain spectra of these spherically confined systems is evident in both the measured stimulated emission and amplified spontaneous emission. We anticipate that state-resolved optical excitation will be a useful method of enabling the development and manipulation of optical gain in any quantized nanostructure.
Thermal crosslinking of organic semiconducting polythiophene improves transverse hole conductivity
Authors: Gearba Ioana R. , Nam Chang-Yong , Pindak Ron , Black C. T.
Published: October 2009

Thermal crosslinking using a suitable radical initiator simultaneously improves electrical conductivity in the semiconducting polymer poly(3-hexylthiophene) and makes the material insoluble. Crosslinked polythiophene shows as much as a fivefold increase in hole conductivity across the film thickness without any shift in spectral light absorption. Grazing incidence x-ray diffraction reveals more in-plane polymer lamellae stacking with only a small decrease in film crystallinity. Improved transverse conductivity increases the performance of model planar solar cells by threefold, from 0.07% to 0.2%. The ability to render polythiophene insoluble without disrupting film structural order enables fabrication pathways to more complex device architectures.
Low ionization potentials of binuclear superalkali B2Li11
Authors: Tong Jing , Li Ying , Wu Di , Li Zhi-Ru , Huang Xu-Ri
Published: October 2009

A new type of binuclear superalkali B2Li11 and its corresponding cation B2Li11+ were theoretically predicted based on the density functional theory calculations. B2Li11 was found to have six minimum energy structures corresponding to five cation states exhibiting superalkali nature. The global minima of B2Li11 and B2Li11+ are similar to each other in structure, where two central boron atoms directly link each other and the whole geometry resembles a capsule with an additional Li atom localized on its side. The vertical electron affinities for the B2Li11+ cations at the OVGF/6-311+G(3df) level are in the range of 3.40–3.73 eV, which are lower than the ionization potential (IP) of Cs atom, and even lower than the IP=3.75 eV of the mononuclear superalkali BLi6. Hence, the studied B2Li11+ species should be classified as superalkali cations, and the B2Li11 species can be regarded as superalkalies. Such binuclear superalkalies added candidates to the research on superatoms and offered potential building blocks for the assembly of new materials in which strong electron donors are involved. Note that the electronic shell structure of B2Li11 is not consistent with the prediction of the cluster electronic shell model. It demonstrates that the doped nonmetal atoms make the molecular orbital-level distribution of heteronuclear species much more complex than that of homonuclear metal clusters.
Reduction of NOx in the exhaust gas of DI- diesel engine fueled with mahua methyl ester along with exhaust gas recirculation
Authors: Prasad V. J. J. , Babu N. Hari , Rao B. V. Appa
Published: October 2009

Biodiesels are alternative fuels for petroleum-based diesel without major modifications of engine. In the environmental aspect, also biodiesel gives fewer pollutants than petroleum diesel. However, the NOx level is slightly higher. To reduce NOx, some of the methods are being used, which include direct injection, turbocharging, air-to-air intercooling, combustion optimization with and without swirl support, multivalve cylinder head, advanced high pressure injection system, i.e., split injection or rate shaping, and electronic management system. However, technologies such as exhaust gas recirculation (EGR), soot traps, and exhaust gas after treatment are gaining emphasis to cater to the challenges posed by increasingly stringent environmental emission legislations. In this work, experimentation was conducted on a single cylinder diesel engine with mahua methyl ester (MME) in the neat form along with the cooled EGR and performance, combustion pressure, and emission parameters are collected by using suitable instrumentation. Same experimentation was repeated for the petroleum diesel and a comparison was made to evaluate the applicability of MME along with EGR without major modifications. After the analysis of results, it was found that 5% EGR is recommendable with neat biodiesel (MME) run, and in most of the situations, it proved its merit over neat diesel run.
Growth of high-density vertically aligned arrays of carbon nanotubes by plasma-assisted catalyst pretreatment
Authors: Esconjauregui S. , Bayer B. C. , Fouquet M. , Wirth C. T. , Ducati C. , Hofmann S. , Robertson J.
Published: October 2009

A plasma-assisted thermal pretreatment of catalyst films (Ni, Co, or Fe) greatly facilitates the direct growth of high-density vertically aligned arrays of small diameter carbon nanotubes (CNTs) on conductive TiN by purely thermal chemical vapor deposition. Purely thermal catalyst pretreatment gives limited or no growth. The plasma-assisted pretreatment promotes a stronger catalyst-support interaction, which reduces catalyst mobility and hence stabilizes smaller catalyst particles with a higher number density.
The van der Waals coefficients between carbon nanostructures and small molecules: A time-dependent density functional theory study
Authors: Kamal C. , Ghanty T. K. , Banerjee Arup , Chakrabarti Aparna
Published: October 2009

We employ all-electron ab initio time-dependent density functional theory based method to calculate the long-range dipole-dipole dispersion coefficient, namely, the van der Waals (vdW) coefficient (C6) between fullerenes and finite-length carbon nanotubes as well as between these structures and different small molecules. Our aim is to accurately estimate the strength of the long-range vdW interaction in terms of the C6 coefficients between these systems and also compare these values as a function of shape and size. The dispersion coefficients are obtained via Casimir–Polder relation. The calculations are carried out with the asymptotically correct exchange-correlation potential—the statistical average of orbital potential. It is observed from our calculations that the C6 coefficients of the carbon nanotubes increase nonlinearly with length, which implies a much stronger vdW interaction between the longer carbon nanostructures compared with the shorter ones. Additionally, it is found that the values of C6 and polarizability are about 40%–50% lower for the carbon cages when compared with the results corresponding to the quasi-one-dimensional nanotubes with equivalent number of atoms. From our calculations of the vdW coefficients between the small molecules and the carbon nanostructures, it is observed that for H2, the C6 value is much larger compared with that of He. It is found that the rare gas atoms have very low values of vdW coefficient with the carbon nanostructures. In contrast, it is found that other gas molecules, including the ones that are environmentally important, possess much higher C6 values. Carbon tetrachloride as well as chlorine molecule show very high C6 values with themselves as well as with the carbon nanostructures. This is due to the presence of the weakly bound seven electrons in the valence state for the halogen atoms, which makes these compounds much more polarizable compared with the others.
Electrostatic drift modes in quantum dusty plasmas with Jeans terms
Authors: Ren Haijun , Wu Zhengwei , Cao Jintao , Chu Paul K.
Published: October 2009

Electrostatic drift waves (EDWs) are investigated in nonuniform quantum magnetized dusty plasmas by taking into account dust gravitational effects with the help of the quantum hydrodynamic model. Ions and electrons are viewed as low-temperature Fermi gases, whereas quantum effects are neglected for the dust grains. The analytical dispersion relationship of the quantum EDWs is derived. Quantum effects are shown to affect the dispersion of EDW significantly. The Jeans terms induce a driftlike instability, which does not exist with the absence of gravitational effects. The criteria and growth rate of the kind of instability are presented. Our results are relevant to dense astrophysical objects such as the interiors of astrophysical compact objects (e.g., white dwarfs and neutron stars).