bluuebunny/crossref_metadata_2025 huggingface dataset:
Altered signalling and gene expression associated with the immune system and the inflammatory response in obesity
Authors: Gil Angel , María Aguilera Concepción , Gil-Campos Mercedes , Cañete Ramón
Published: October 2007

White adipose tissue functions not only as an energy store but also as an important endocrine organ and is involved in the regulation of many pathological processes. The obese state is characterised by a low-grade systemic inflammation, mainly a result of increased adipocyte as well as fat resident- and recruited-macrophage activity. In the past few years, various products of adipose tissue including adipokines and cytokines have been characterised and a number of pathways linking adipose tissue metabolism with the immune system have been identified. In obesity, the pro- and anti-inflammatory effects of adipokines and cytokines through intracellular signalling pathways mainly involve the nuclear factor kappa B (NF-κB) and the Jun N-terminal kinase (JNK) systems as well as the I kappa B kinase beta (IKK-β). Mitogen-activated protein kinase (MAPK) and extracellular-signal-regulated kinase (ERK) pathways, which lead to signal transducer and activator of transcription 3 (STAT3) activation, are also important in the production of pro-inflammatory cytokines. Obesity increases the expression of leptin and other cytokines, as well as some macrophage and inflammatory markers, and decreases adiponectin expression in adipose tissue. A number of cytokines, e.g. tumour necrosis factor alpha (TNF-α) and monocyte chemotactic protein 1 (MCP-1), and some pro-inflammatory interleukins, leuckocyte antigens, chemochines, surface adhesion molecules and metalloproteases are up-regulated whereas other factors are down-regulated. The present paper will focus on the molecular mechanisms linking obesity and inflammation with emphasis on the alteration of signalling and gene expression in adipose cell components.
Bovine whey protein concentrate supplementation modulates maturation of immune system in suckling rats
Authors: Pérez-Cano Francisco J. , Marín-Gallén Silvia , Castell Margarida , Rodríguez-Palmero María , Rivero Montserrat , Franch Àngels , Castellote Cristina
Published: October 2007

During neonatal life, challenges from breast milk and microbial flora promote immune system maturation. Immunonutrition in these stages may become an important way to increase natural defence systems. The aim of this study was to determine the effect of a daily bovine milk whey protein concentrate (WPC) supplement on the intestinal and systemic immune systems in suckling rats. The composition of intraepithelial and lamina propria lymphocytes (IEL and LPL) was analysed by flow cytometry. Systemic and intestinal humoral immune responses were determined by sera Ig levels and Ig-secreting cell quantification by ELISA and ELISPOT, respectively. From birth, suckling Wistar rats were supplemented with WPC or standard infant formula (SIF). The WPC group showed the same proportion of most of the main mucosal cell subsets as the reference animals. However, in the first days of life WPC enhanced the innate immunity by increasing the NK cell proportion in both epithelial and lamina propria (LP) compartments. A rise in intestinal CD8αα+ IEL was also induced by WPC supplementation. A time-course of sera Ig levels and spontaneous IgA, IgM and IgG production by LPL and mononuclear cells from blood and spleen, in the WPC group, exhibited a similar pattern to those pups fed only by dam's milk. In summary, the present results show the effects of WPC on enhancing mucosal innate immunity during early life.
Lifestyle-related determinants of inflammation in adolescence
Authors: Wärnberg Julia , Nova Esther , Romeo Javier , Moreno Luís A. , Sjöström Michael , Marcos Ascensión
Published: October 2007

Inflammatory processes are involved in the pathogenesis of the most common chronic non-communicable diseases and may also play an important initiating role in their development. Only recently have inflammatory markers been included in epidemiological studies focusing on nutritional status, body composition and physical activity. We are just starting to understand how different lifestyles can determine basal levels of inflammatory biomarkers in early ages. This review aims to summarise what is known about the relationships between lifestyle-related determinants (focusing on overweight, physical activity and dietary habits) and inflammatory markers in apparently healthy young populations. Obesity is the most widely studied determinant. Several large-scale studies have now demonstrated that healthy young subjects with more body fat or higher BMI have moderately higher concentrations of inflammatory markers than their leaner peers, supporting the idea that obesity should be considered as a state of chronic low-grade inflammation. Less data is available to allow us to elucidate how physical activity/fitness or dietary patterns may have a direct effect on inflammation in apparently healthy, disease-free young populations.
Supplementary feeding at milking and minimum milking interval effects on cow traffic and milking performance in a pasture-based automatic milking system
Authors: Jago Jenny G , Davis Kendra L , Copeman Peter J , Ohnstad Ian , Woolford Murray M
Published: October 2007

In extensive pastoral dairy farming systems herds graze 12 months of the year with the majority fed a near-100% pasture or conserved pasture diet. The viability of automatic milking in these systems will depend partly upon the amount of supplementary feed necessary to encourage cows to walk from the pasture to the milking unit but also on the efficient use of the automatic milking system (AMS). This paper describes a study to determine the importance of offering concentrate in the milking unit and the effect of minimum milking interval on cow movement and milking performance in a pasture-based AMS. The effects of feeding rate (FR0=0 kg or FR1=1 kg crushed barley/d) and minimum milking interval (MM6=6 h or MM12=12 h) on cow movement and behaviour during milking were studied in a multi-factorial cross-over (feeding level only, 4 weeks per treatment) experiment involving 27 mixed-breed cows milked through a single AMS. Feeding 1 kg barley in the milking unit resulted in a higher visiting frequency to the pre-selection unit (FR0=4·6 visits/d, FR1=5·4 visits/d,sed=0·35,P<0·05) and a higher yield (FR0=22·5 kg/d, FR1=23·6 kg/d,sed=0·385,P<0·01) but had no effect on milking frequency (FR0=1·6 milkings/d, FR1=1·7 milkings/d,sed=0·04, NS). Minimum milking interval was the major factor influencing milking frequency (MM6=1·9, MM12=1·4 milkings/d,sed=0·15,P<0·01). The absence of feeding in the milking unit had no negative effect on behaviour during milking or the number of cows that had to be manually driven from the paddock. The results show that automatic milking can be combined with a near-100% pasture diet and that milking interval is an important determinant for maximizing milk harvested per AMS.
PROGRAM FOR A NEW CATHOLIC WISSENSCHAFT: DEVOTIONAL ACTIVISM AND CATHOLIC MODERNITY IN THE NINETEENTH CENTURY
Authors: SCHAEFER RICHARD
Published: October 2007

This article seeks to establish a new perspective for understanding Catholic intellectual history in the German territories during the mid-nineteenth century. By analyzing scholars' efforts to revamp “Catholic Wissenschaft” in the context of a broader revival movement, it reveals how both “liberals” and “ultramontanes” engaged in a form of devotional activism which made Catholicism the measure of social action and scholarly practice alike. Important differences notwithstanding, scholars of all stripes saw their task as transforming Catholicism into a relevant tool for meeting the needs of the age. Rooting their efforts in the broader Catholic revival movement in this way, the article proposes “Catholic modernity” as a salient category for interpreting the significance of their work, and for better integrating it into the broader framework of German history.
“WHAT IS THE HISTORY OF BOOKS?” REVISITED
Authors: DARNTON ROBERT
Published: October 2007

Having accepted the invitation to revisit my essay of 1982, “What Is the History of Books?”, I find that I can do it only in the first person singular and therefore must ask to be excused for indulging in some autobiographical detail. I would also like to make a disclaimer: in proposing a model for studying the history of books twenty-four years ago, I did not mean to tell book historians how they ought to do their jobs. I hoped that the model might be useful in a heuristic way and never thought of it as comparable to the models favored by economists, the kind in which you insert data, work it over, and arrive at a bottom line. (I do not believe that bottom lines exist in history.) It seemed to me in 1982 that the history of books was suffering from fissiparousness: experts were pursuing such specialized studies that they were losing contact with one another. The esoteric elements of book history needed to be integrated into an overview that would show how the parts could connect to form a whole—or what I characterized as a communications circuit. The tendency toward fragmentation and specialization still exists.
INCITING READINGS AND READING CITES: VISITS TO MARX'S THE EIGHTEENTH BRUMAIRE OF LOUIS BONAPARTE
Authors: REID DONALD
Published: October 2007

Karl Marx's The Eighteenth Brumaire of Louis Bonaparte can be read as a guidebook, but it is also a site of pilgrimage for those seeking to come to terms with the Marxist legacy, from within and from without. This essay examines the reading and citing of The Eighteenth Brumaire by Marxist and non-Marxist political analysts, historians of the Second Republic, and cultural theorists. Invoking this text and claiming to rescue it from the distorted glosses others have given it, readers both confront and evade their own political and intellectual anxieties.
The Use of Solubility, Dialyzability, and Caco-2 Cell Methods to Predict Iron Bioavailability
Authors: Fairweather-Tait  , Phillips  , Wortley  , Harvey  , Glahn
Published: October 2007

An update on in vitro methods employed to assess iron bioavailability is presented. Solubility and dialyzability are not useful predictors of iron absorption, whereas Caco-2 cell models provide useful comparisons on the availability of iron from different sources. Strengths and weaknesses of in vitro approaches are briefly described, including the need to characterize Caco-2 cells in order to interpret results correctly. Further developments are required to refine Caco-2 model systems, including optimization and standardization of methods.
Iron Absorption: Comparison of Prediction Equations and Reality. Results from a Feeding Trial in the Philippines
Authors: Beard  , Murray-Kolb  , Haas  , Lawrence
Published: October 2007

Background: A number of algorithms have been developed that seek to predict the bioavailability of iron from mixed meals and diets, but their direct validity in predicting change in iron status remains questionable. Throughout the course of conducting a large feeding trial in convents in Manila, we collected weighed food-intake data and have the opportunity to directly compare the performance of these prediction equations. Aims: The specific aims of this particular analysis are as follows: (a) to determine habitual intakes of macro- and micronutrients in religious sisters in Manila, (b) to determine the predicted efficiency of iron absorption from each of the published bioavailability algorithms (Monsen, Hallberg, Reddy, Tseng, Barghava, and Du), and (c) to determine which of these equations best predicts the actual "gain" in iron in religious sisters over the duration of the trial. Design: The efficacy of consuming high-iron rice was tested during a nine-month feeding trial with a double-blinded dietary intervention; these results have been published [7]. Religious sisters living in 10 convents around metropolitan Manila, the Philippines were randomly assigned to consume either high-iron rice (3.21 mg/kg Fe) or a local variety of control rice (0.57 mg/kg Fe) within each convent. Results: Religious sisters in convents consumed a diet that appeared to be typical of habitual intakes of macro- and micronutrients in this part of the Philippines. The analysis of the six equations revealed highly significant differences in predicted efficiency of iron absorption. The Hallberg, Monsen, and Reddy equations all predicted similar median efficiency (6.88, 7.92, and 6.42%). In contrast, Bhargava (4.68%), Tseng (3.23%), and Du (2.92%) were significantly lower. The correlation (r = 0.98) of Monsen to Hallberg was highly significant and the slope was not different than unity. The median efficiency of absorption based on the gain in body iron in 114 subjects over nine months, combined with an estimate of daily iron requirements, was 17.2%. Thus, none of these equations approximated the computed iron absorption based on improvement in serum ferritin and suggests alternative approaches to predicting iron accumulation from diet need to be formulated. Conclusions: Inhibitory factors in the prediction equations either had little effect or had too large of an effect on apparent bioavailability as compared to median absorption over a nine-month period. The causes of the lack of agreement between computed iron gain and predicted absorption are open to discussion and will need to be resolved.
Interactions of Vitamin A and Iodine Deficiencies: Effects on the Pituitary-Thyroid Axis
Authors: Zimmermann
Published: October 2007

Vitamin A (VA) deficiency (VAD) and the iodine deficiency disorders (IDD) affect > 30% of the global population and these deficiencies often coexist in vulnerable groups. VAD has multiple effects on the pituitary-thyroid axis; VA status modulates thyroid gland metabolism, peripheral metabolism of thyroid hormone, and production of thyrotropin (TSH) by the pituitary. Findings from Africa children indicate that VAD in severely-IDD-affected children increases TSH stimulation and thyroid size, and reduces risk for hypothyroidism. In children with VAD, the higher TSH concentrations in the face of higher circulating total thyroxine suggest central resistance to normal TSH suppression by thyroid hormone. In IDD- and VAD-affected children receiving iodized salt, concurrent VA supplementation improves iodine efficacy. Recent VA and iodine depletion studies in rats indicate moderate VAD alone has no measurable effect on the pituitary-thyroid axis; however, concurrent iodine deficiency (ID) and VAD produce more severe primary hypothyroidism than ID alone. Repletion studies in VA- and iodine-deficient animals suggest: 1) primary hypothyroidism in animals with concurrent moderate VAD and ID does not reduce the efficacy of high doses of oral VA; 2) VAD does not reduce the efficacy of dietary iodine to correct pituitary-thyroid axis dysfunction due to iodine deficiency; and 3) given alone, without iodine repletion, high-dose VA supplementation in combined VAD and ID may reduce thyroid hyperstimulation and reduce risk for goiter.
Wind velocity profiles with a blowing sand boundary layer: Theoretical simulation and experimental validation
Authors: Dong Zhibao , Mu Qingsong , Wang Hongtao
Published: October 2007

Describing wind velocity profiles modified by the movement of blown sand is of continuing significance because they are thought to bear rich information about wind‐sand interaction in a blowing sand cloud. This paper treats the saltating cloud as a fluidized particle flow and develops a mathematical model of the wind‐sand interactions. The force exerted on the air by saltating particles is characterized by introducing a drag coefficient of the fluidized aeolian particle flow that is modified after the drag coefficients proposed for liquid fluidized particle flow. The resulting model was then used to simulate wind velocity profiles in the presence of a saltation cloud on the basis of the mean particle velocity and particle concentration profiles of the fluidized particle flow obtained from wind tunnel tests. The simulated velocity profiles agree well with those directly measured in the wind tunnel. The blowing sand boundary layer is divided into a saltation subboundary layer, in which saltating particles participate in momentum exchange with the wind, and an outer subboundary layer above the saltation subboundary layer. The wind velocity profiles within the saltation subboundary layer are characterized by convex‐upward curves in a log (height)‐linear (wind velocity) plot rather than the straight lines in the velocity profiles of clean wind. The upward convexity of the velocity profiles increases as wind velocity increases, suggesting that more wind momentum is absorbed by the saltating particles as the sand transport rate increases. The wind velocity profiles in the outer subboundary layer approach the Prandtl logarithmic law with the saltation subboundary layer providing increased aerodynamic roughness. Our results suggest that the wind shear velocity in the presence of a saltation cloud is a physical dimension that can reflect the effect of saltation.
Multiyear satellite observations of the atmospheric response to Atlantic tropical instability waves
Authors: Wu Qiaoyan , Bowman Kenneth P.
Published: October 2007

High‐resolution satellite measurements from the Tropical Rainfall Measuring Mission (TRMM), Quick Scatterometer (QuikSCAT), and Special Sensor Microwave Imager (SSM/I) are used to study the variability of sea surface temperature (SST), surface wind velocity, water vapor, cloud liquid water, and precipitation associated with westward moving tropical instability waves (TIWs) in the Atlantic Ocean from 1998 to 2005. Coherent ocean‐atmosphere patterns are shown during these 8 years. Southeasterly trades strengthen and water vapor increases over warm SST anomalies associated with TIWs. The opposite is true over cold TIW SST anomalies. The cloud liquid water and rain response to the SSTs follows a similar pattern, appearing generally downstream of SST anomalies in the central tropical Atlantic. The atmospheric response to the TIW SST anomalies extends north of the TIW active region, suggesting a remote response to the TIWs. The atmospheric response to the Atlantic TIWs also exhibits interannual variations. In 1999, owing to the southward movement of the Atlantic Intertropical Convergence Zone (ITCZ), the rainfall response to the TIW SST anomalies is much larger than in other years. When the Atlantic ITCZ moves south, it is more susceptible to TIW influence.
Modeled contributions of three types of diazotrophs to nitrogen fixation at Station ALOHA
Authors: Goebel Nicole L , Edwards Christopher A , Church Matthew J , Zehr Jonathan P
Published: October 2007

A diagnostic model based on biomass and growth was used to assess the relative contributions of filamentous nonheterocystous Trichodesmium and unicellular cyanobacteria, termed Groups A and B, to nitrogen fixation at the North Pacific Station ALOHA over a 2-year period. Average (and 95% confidence interval, CI) annual rates of modeled monthly values for Trichodesmium, Group B and Group A were 92 (52), 14 (4) and 12 (8) mmol N per m2 per year, respectively. The fractional contribution to modeled instantaneous nitrogen fixation by each diazotroph fluctuated on interannual, seasonal and shorter time scales. Trichodesmium fixed substantially more nitrogen in year 1 (162) than year 2 (12). Group B fixed almost two times more nitrogen in year 1 (17) than year 2 (9). In contrast, Group A fixed two times more nitrogen in year 2 (16) than year 1 (8). When including uncertainties in our estimates using the bootstrap approach, the range of unicellular nitrogen fixation extended from 10% to 68% of the total annual rate of nitrogen fixation for all three diazotrophs. Furthermore, on a seasonal basis, the model demonstrated that unicellular diazotrophs fixed the majority (51%–97%) of nitrogen during winter and spring, whereas Trichodesmium dominated nitrogen fixation during summer and autumn (60%–96%). Sensitivity of the modeled rates to some parameters suggests that this unique attempt to quantify relative rates of nitrogen fixation by different diazotrophs may need to be reevaluated as additional information on cell size, variability in biomass and C:N, and growth characteristics of the different cyanobacterial diazotrophs become available.
The Immune Response in Patients with SARS: differential gene expression profiling.
Authors: Pushparaj Peter Natesan , Manikandan Jayapal , Melendez Alirio Jose
Published: October 2007

Severe acute respiratory syndrome (SARS) emerged in 2003, as a new epidemic form of life-threatening infection. As of 26th September 2003, there were 8422 cases of SARS from 29 countries with 908 deaths (WHO). However, the pathogenesis of SARS is poorly understood. To understand the host response to this pathogen, we profiled the gene expression patterns of peripheral blood mononuclear cells (PBMC) from SARS patients compared to healthy controls using one of the latest techniques, high density oligonucleotide expression probe array (HG-Focus array, Gene Chip, Affymetrix, Santa Clara, CA). High-density oligonucleotide microarray is a promising approach for high throughput analysis. It has been extensivelyused in many areas of biomedical research for different purposes. Thus we could compare the expression levels of thousands of genes which are differentially expressed in SARS patients over healthy controls. Among the most prominent findings, we observed 2 to 200-fold increased expression of transcripts of various genes. This enabled us to classify and cluster genes by functional families as well as to understand known genes in signalingpathways.
Differential Gene Expression of Human Mast cell Activation Reveals Gene profiles of Innate and Adaptive Immunity.
Authors: Manikandan Jayapal , Renji Reghunathan , Pushparaj Peter Natesan , Melendez Alirio Jose
Published: October 2007

High-density oligonucleotide microarray is a promising approach for high throughput analysis. It has been extensively used in many areas of biomedical research. Immunoglobulin E (IgE) mediated allergic response (type-1 hypersensitivity) is one of the most powerful reactions of the immune system. Tissue Mast Cells (MCs) and circulating basophils are the major effector cells in these reactions. By dissecting the regulatory circuitry of mast cells by analyzing the genome wide effects of antigen stimulation triggered by FcεRI, offers a potential for finding novel genes as ‘targets’ for therapeutic intervention. In this work, we tried to study the gene expression pattern in IgE sensitized and FcεRI cross linked cord blood derived MCs using one of the latest techniques, high density oligonucleotide expression probe array (HG-Focus array, Gene Chip, Affymetrix, Santa Clara, CA). Microarray hybridization of RNA from cord blood derived MCs revealed coordinated changes in gene expression in response to IgE stimulation and receptor cross linking at different time points. Among the most prominent findings, we observed 2 to 32-fold increased expression of different transcripts. Real-time PCR confirmed reliability of microarray data. This enabled us to classify and cluster genes by functional families as well as to understand known genes in signaling pathways. These results defined a list of primary candidates for finding novel genes as ‘targets’ for therapeutic intervention.
Genome activity profiling of monomeric-IgE and Fc-epsilon-RI-aggregation on human mast cells reveals a complex network of genes involved in inflammatory responses.
Authors: Manikandan Jayapal , Melendez Alirio Jose , Pushparaj Peter Natesan
Published: October 2007

Mast cell activation, mediates type-1 allergic responses, one of the most powerful reactions of the immune system. However, mast cells activation is becoming increasingly linked to inflammatory, autoimmunity, and to adaptive immunity by regulating T-cell activation.Here we analyzed the gene expression pattern in IgE-sensitized and FcεRI aggregation on human mast cells. Our data revealed coordinated changes in gene expression. We observed increased expression of gene-transcripts involved in allergic, innate and adaptiveimmune responses. Among the most prominent findings is the increased expression of transcripts encoding for MIP3a, SPARCL1, AREG, IL18, CCL1, TNFRSF9, IL1b, CX3CR1, PTGER3, MIF, MMP12, ADORA3, IL8RB, and other genes involved in innate and cellmediatedimmunity. These results represent a substantial advance in our understanding of the genome-wide effects triggered by “passive sensitization” or active stimulation of human mast cells, and how this relate to mast cells involvement not only in allergicresponses but also in innate and adaptive immunity.
Tumor necrosis factor and caspase in response to soluble or microparticle-incorporated drugs in Mycobacterium tuberculosis infection
Authors: Yadav Awadh Bihari , Misra Amit
Published: September 2007

We compared the effects of microparticles (MP) containig anti-tubercular drugs and those of the drugs themselves on the host macrophage (MΦ) response to infection with Mycobacterium tuberculosis H37Ra (Mtb). Mice infected intravenously with M. tb. were either administered rifampicin and isoniazid by oral gavage or through inhalation of biodegradable MP containing the two anti-tubercular drugs. Bronchoalveolar lavage (BAL) was perfomed to recover lung MΦ, which were cultured and the supernatant analysed for TNFα by ELISA. The murine MΦ cell line J774 or the human monocyte line THP-1 differentiated with phorbol myristate were infected in vitro and treated with MP or soluble drugs. The kinetics of secretion of TNFα were determined. Caspase-3 activity after infection and treatment was assesed using a substrate cleavage detection kit.MP, but not soluble drugs, strongly induced TNFα in infected cells. Uninfected cells also responded to MP, although less strongly. Caspase-3 was observed to be upregulatedWe conclude that MP treatment induces infected MΦ to upregulate the Th1 cytokine TNFα and Caspase-3, creating conditions for induction of apoptosis in these cells as a strategy to overcome infection.
The Bovine Cervix During the Oestrous Cycle: Regional Differences in Morphology and Density of Steroid Hormone Receptors
Authors: Breeveld‐Dwarkasing VNA , Van Der Weijden GC , Taverne MAM , Van Dissel‐Emiliani FMF
Published: October 2007

Contents

During oestrus collagen breakdown in the bovine cervix is significantly higher in the superficial stromal layer than in the deep stromal layer. Steroid hormones are known to play a role in the regulation of cervical softening. Therefore an immunohistochemical study on the expression of oestrogen and progesterone receptors was performed to investigate a possible relationship between steroid hormone receptor density and collagen breakdown in different regions of the cervix in cyclic cows with no functional corpus luteum. The density of oestrogen and progesterone receptors along the cross‐sectional axis shows an increasing gradient from the epithelium towards the deep stromal layer of the cervix. It is not yet clear how this is related to softening of the bovine cervix during the oestrous phase.
Supersymmetric biorthogonal quantum systems
Authors: Curtright Thomas , Mezincescu Luca , Schuster David
Published: September 2007

We discuss supersymmetric biorthogonal systems, with emphasis given to the periodic solutions that occur at spectral singularities of PT symmetric models. For these periodic solutions, the dual functions are associated polynomials that obey inhomogeneous equations. We construct in detail some explicit examples for the supersymmetric pairs of potentials V±(z)=−U(z)2±z(d∕dz)U(z) where U(z)≡∑k>0υkzk. In particular, we consider the cases generated by U(z)=z and z∕(1−z). We also briefly consider the effects of magnetic vector potentials on the partition functions of these systems.
Homoclinic snaking: Structure and stability
Authors: Burke John , Knobloch Edgar
Published: September 2007

The bistable Swift-Hohenberg equation exhibits multiple stable and unstable spatially localized states of arbitrary length in the vicinity of the Maxwell point between spatially homogeneous and periodic states. These states are organized in a characteristic snakes-and-ladders structure. The origin of this structure in one spatial dimension is reviewed, and the stability properties of the resulting states with respect to perturbations in both one and two dimensions are described. The relevance of the results to several different physical systems is discussed.
Interaction of dissipative Bragg solitons in active nonlinear fibers
Authors: Rosanov N. N. , Tran Tr. X.
Published: September 2007

We investigate numerically and analytically interaction of dissipative optical solitons in active nonlinear fibers with Bragg grating. In the framework of the coupled mode theory, we analyze the effect of initial separation and phase difference between the pulses on the final solitons’ characteristics. Beyond the framework of this approach, a number of new phenomena are studied, including location of centers of motionless solitons near the maxima of refractive index grating, the discreteness of moving solitons velocity and the existence of a motionless weakly coupled two-soliton structure.
Spatiotemporal optical solitons in nonlinear dissipative media: From stationary light bullets to pulsating complexes
Authors: Akhmediev Nail , Soto-Crespo J. M. , Grelu Philippe
Published: September 2007

Nonlinear dissipative systems display the full (3+1)D spatiotemporal dynamics of stable optical solitons. We review recent results that were obtained within the complex cubic-quintic Ginzburg-Landau equation model. Numerical simulations reveal the existence of stationary bell-shaped (3+1)D solitons for both anomalous and normal chromatic dispersion regimes, as well as the formation of double soliton complexes. We provide additional insight concerning the possible dynamics of these soliton complexes, consider collision cases between two solitons, and discuss the ways nonstationary evolution can lead to optical pattern formation.
Optical solitons as quantum objects
Authors: Pomeau Yves , Le Berre Martine
Published: September 2007

The intensity of classical bright solitons propagating in linearly coupled identical fibers can be distributed either in a stable symmetric state at strong coupling or in a stable asymmetric state if the coupling is small enough. In the first case, if the initial state is not the equilibrium state, the intensity may switch periodically from fiber to fiber, while in the second case the asymmetrical state remains forever, with most of its energy in either fiber. The latter situation makes a state of propagation with two exactly reciprocal realizations. In the quantum case, such a situation does not exist as an eigenstate because of the quantum tunneling between the two fibers. Such a tunneling is a purely quantum phenomenon without counterpart in the classical theory. We estimate the rate of tunneling by quantizing a simplified dynamics derived from the original Lagrangian equations with test functions. This tunneling could be within reach of the experiments, particularly if the quantum coherence of the soliton can be maintained over a sufficient amount of time.
Stability of asymmetric spike solutions to the Gierer-Meinhardt system
Authors: Iron D. , Rumsey J.
Published: September 2007

In this paper, we study the spectra of asymmetric spike solutions to the Gierer-Meinhardt system. It has previously been shown that the spectra of such solutions may be determined by finding the generalized eigenvalues of matrices, which are determined by the positions of the spikes and various parameters from the system. We will examine the spectra of asymmetric solutions near the point at which they bifurcate off of a symmetric branch. We will confirm that all such solutions are unstable in a neighborhood of the bifurcation point and we derive an explicit expression for the leading order terms of the critical eigenvalues.
Localized patterns in reaction-diffusion systems
Authors: Vanag Vladimir K. , Epstein Irving R.
Published: September 2007

We discuss a variety of experimental and theoretical studies of localized stationary spots, oscillons, and localized oscillatory clusters, moving and breathing spots, and localized waves in reaction-diffusion systems. We also suggest some promising directions for future research in this area.
Nonvariational real Swift-Hohenberg equation for biological, chemical, and optical systems
Authors: Kozyreff G. , Tlidi M.
Published: September 2007

We derive asymptotically an order parameter equation in the limit where nascent bistability and long-wavelength modulation instabilities coalesce. This equation is a variant of the Swift-Hohenberg equation that generally contains nonvariational terms of the form ψ∇2ψ and ∣∇ψ∣2. We briefly review some of the properties already derived for this equation and derive it on three examples taken from chemical, biological, and optical contexts. Finally, we derive the equation on a general class of partial differential systems.
Trotter derivation of algorithms for Brownian and dissipative particle dynamics
Authors: Thalmann Fabrice , Farago Jean
Published: September 2007

This paper focuses on the temporal discretization of the Langevin dynamics, and on different resulting numerical integration schemes. Using a method based on the exponentiation of time dependent operators, we carefully derive a numerical scheme for the Langevin dynamics, which we found equivalent to the proposal of Ermak and Buckholtz [J. Comput. Phys. 35, 169 (1980)] and not simply to the stochastic version of the velocity-Verlet algorithm. However, we checked on numerical simulations that both algorithms give similar results, and share the same “weak order two” accuracy. We then apply the same strategy to derive and test two numerical schemes for the dissipative particle dynamics. The first one of them was found to compare well, in terms of speed and accuracy, with the best currently available algorithms.
Classical solutions and pattern formation for a volume filling chemotaxis model
Authors: Wang Zhian , Hillen Thomas
Published: September 2007

We establish the global existence of classical solutions to a generalized chemotaxis model, which includes the volume filling effect expressed through a nonlinear squeezing probability. This novel choice of squeezing probability reflects the elastic properties of cells. Necessary and sufficient conditions for spatial pattern formation are given and the underlying bifurcations are analyzed. In numerical simulations, the complex dynamics of merging and emerging patterns are shown for zero cell kinetics and nonzero cell kinetics, respectively. We conclude that the emerging process of pattern formation is due to cell growth.
Localized structures in dryland vegetation: Forms and functions
Authors: Meron Ehud , Yizhaq Hezi , Gilad Erez
Published: September 2007

Vegetation patches in drylands are localized structures of biomass and water. We study these structures using a mathematical modeling approach that captures biomass-water feedbacks. Biomass-water structures are found to differ in their spatial forms and ecological functions, depending on species type, soil conditions, precipitation range, and other environmental factors. Asymptotic spot structures can destabilize to form ring structures, expanding in the radial direction, or crescent structures, migrating uphill. Stable spot structures can differ in their soil-water distributions, forming water-enriched patches or water-deprived patches. The various biomass-water structures are expected to function differently in the context of a plant community, forming landscapes of varying species diversity.
Dynamic and static position control of optical feedback solitons
Authors: Gütlich Björn , Zimmermann Holger , Cleff Carsten , Denz Cornelia
Published: September 2007

We report on the experimental implementation of an external control for optical feedback solitons using incoherent spatial intensity distributions in a liquid crystal light valve (LCLV) optical single feedback system. The external control provides excellent experimental possibilities for static and dynamic control of the lateral positions of the optical feedback solitons which will be demonstrated. Particularly, the influence of different gradients onto the drift motion of spatial solitons is experimentally investigated in detail. In agreement with theoretical predictions, the drift velocity of the soliton increases according to the steepness of the gradient. Additionally, a completely incoherent addressing scheme including creation and erasure of feedback solitons is demonstrated for the LCLV setup.
Field patterns in periodically modulated optical parametric amplifiers and oscillators
Authors: Brazhnyi V. A. , Konotop V. V. , Coulibaly S. , Taki M.
Published: September 2007

Spatially localized and periodic field patterns in periodically modulated optical parametric amplifiers and oscillators are studied. In the degenerate case (equal signal and idler beams) we elaborate on the systematic method of construction of the stationary localized modes in the amplifiers, and study their properties and stability. We describe a method of constructing periodic solutions in optical parametric oscillators, by adjusting the form of the external driven field to the given form of either signal or pump beams.
Stability of spikes in the shadow Gierer-Meinhardt system with Robin boundary conditions
Authors: Maini Philip K. , Wei Juncheng , Winter Matthias
Published: September 2007

We consider the shadow system of the Gierer-Meinhardt system in a smooth bounded domain Ω⊂RN,At=ϵ2ΔA−A+Apξq,x∊Ω,t>0, τ∣Ω∣ξt=−∣Ω∣ξ+1ξs∫ΩArdx,t>0 with the Robin boundary condition ϵ∂A∂ν+aAA=0, x∊∂Ω, where aA>0, the reaction rates (p,q,r,s) satisfy 1
0, r>0, s≥0, 1<qr(s+1)(p−1)<+∞, the diffusion constant is chosen such that ϵ≪1, and the time relaxation constant is such that τ≥0. We rigorously prove the following results on the stability of one-spike solutions: (i) If r=2 and 1
1 and τ sufficiently small the interior spike is stable. (ii) For N=1 if r=2 and 1
1 such that for a∊(a0,1) and μ=2q∕(s+1)(p−1)∊(1,μ0) the near-boundary spike solution is unstable. This instability is not present for the Neumann boundary condition but only arises for the Robin boundary condition. Furthermore, we show that the corresponding eigenvalue is of order O(1) as ϵ→0.
On homoclinic snaking in optical systems
Authors: Firth W. J. , Columbo L. , Maggipinto T.
Published: September 2007

The existence of localized structures, including so-called cavity solitons, in driven optical systems is discussed. In theory, they should exist only below the threshold of a subcritical modulational instability, but in experiment they often appear spontaneously on parameter variation. The addition of a nonlocal nonlinearity may resolve this discrepancy by tilting the “snaking” bifurcation diagram characteristic of such problems.
Dissipative structures in left-handed material cavity optics
Authors: Tassin Philippe , Gelens Lendert , Danckaert Jan , Veretennicoff Irina , Van der Sande Guy , Kockaert Pascal , Tlidi Mustapha
Published: September 2007

We study the spatiotemporal dynamics of spatially extended nonlinear cavities containing a left-handed material. Such materials, which have a negative index of refraction, have been experimentally demonstrated recently, and allow for novel electromagnetic behavior. We show that the insertion of a left-handed material in an optical resonator allows for controlling the value and the sign of the diffraction coefficient in dispersive Kerr resonators and degenerate optical parametric oscillators. We give an overview of our analytical and numerical studies on the stability and formation of dissipative structures in systems with negative diffraction.
Molecular structure and dynamics of off-center Cu2+ ions and strongly coupled Cu2+–Cu2+ pairs in BaF2 crystals: Electron paramagnetic resonance and electron spin relaxation studies
Authors: Hoffmann S. K. , Goslar J. , Lijewski S. , Ulanov V. A.
Published: September 2007

X -band and Q-band electron paramagnetic resonance (EPR) spectra of Cu2+ in BaF2 crystal were recorded in the temperature range of 4.2–200K. Spin-Hamiltonian parameters of single Cu2+ complexes and of Cu2+–Cu2+ pairs were derived and discussed. A special attention was paid to the dimeric species. Their molecular ground state configuration was found as having antiferromagnetic intradimer coupling with the singlet-triplet splitting J=−35cm−1. The zero-field splitting being D=0.0365cm−1 at 4.2K increases with temperature as an effect of thermal population of excited dimer configurations. Electron spin echo (ESE) method was used for measurements of electron spin lattice and phase relaxation. The spin-lattice relaxation data show that except for coupling to the host lattice phonons the Cu2+ ions are involved in local mode motions with energy of 82cm−1. Phase relaxation (ESE dephasing) of single Cu2+ ions is due to spin diffusion at low temperatures. This relaxation is hampered for temperatures higher than 30K due to the triplet state population of neighboring Cu2+–Cu2+ dimers, which disturb dipolar coupling between Cu2+ ions. For higher temperatures the relaxation is dominated by Raman T1 processes. Fourier transform ESE spectrum displays dipolar Cu–F splitting which allowed determination of the off-center shift of Cu2+ as δs=0.132nm. The dynamical effects observed in EPR spectra and in electron spin relaxation both for single Cu2+ ions and Cu2+–Cu2+ pairs are discussed as due to jumps between six off-center positions in the crystal unit cell and jumps between various dimer configurations.
Kinetic Monte Carlo model of charge transport in hematite (α-Fe2O3)
Authors: Kerisit Sebastien , Rosso Kevin M.
Published: September 2007

The mobility of electrons injected into iron oxide minerals via abiotic and biotic electron transfer processes is one of the key factors that control the reductive dissolution of such minerals. Building upon our previous work on the computational modeling of elementary electron transfer reactions in iron oxide minerals using ab initio electronic structure calculations and parametrized molecular dynamics simulations, we have developed and implemented a kinetic Monte Carlo model of charge transport in hematite that integrates previous findings. The model aims to simulate the interplay between electron transfer processes for extended periods of time in lattices of increasing complexity. The electron transfer reactions considered here involve the II∕III valence interchange between nearest-neighbor iron atoms via a small polaron hopping mechanism. The temperature dependence and anisotropic behavior of the electrical conductivity as predicted by our model are in good agreement with experimental data on hematite single crystals. In addition, we characterize the effect of electron polaron concentration and that of a range of defects on the electron mobility. Interaction potentials between electron polarons and fixed defects (iron substitution by divalent, tetravalent, and isovalent ions and iron and oxygen vacancies) are determined from atomistic simulations, based on the same model used to derive the electron transfer parameters, and show little deviation from the Coulombic interaction energy. Integration of the interaction potentials in the kinetic Monte Carlo simulations allows the electron polaron diffusion coefficient and density and residence time around defect sites to be determined as a function of polaron concentration in the presence of repulsive and attractive defects. The decrease in diffusion coefficient with polaron concentration follows a logarithmic function up to the highest concentration considered, i.e., ∼2% of iron(III) sites, whereas the presence of repulsive defects has a linear effect on the electron polaron diffusion. Attractive defects are found to significantly affect electron polaron diffusion at low polaron to defect ratios due to trapping on nanosecond to microsecond time scales. This work indicates that electrons can diffuse away from the initial site of interfacial electron transfer at a rate that is consistent with measured electrical conductivities, but that the presence of certain kinds of defects will severely limit the mobility of donated electrons.
Behavior of density functionals with respect to basis set. VI. Truncation of the correlation consistent basis sets
Authors: Prascher Brian P. , Wilson Brent R. , Wilson Angela K.
Published: September 2007

Systematic truncation of the correlation consistent basis sets has been investigated in first and second row atoms and molecules to better understand basis set requirements for density functional theory, particularly the need for high angular momentum functions, as well as to understand possible computational cost savings that could be achieved by using reduced basis sets. The truncation scheme employed follows that recently introduced for ab initio methods [B. Mintz et al., J. Chem. Phys. 121, 5629 (2004)]. Properties examined in the current study include geometries, ionization potentials, electron affinities, and dissociation energies. In general, this investigation shows that a degree of truncation of higher angular momentum functions is possible with limited impact upon energetic properties, and does result in useful CPU time savings. However, not all properties investigated have the same level of dependence upon high angular momentum functions, and, thus, careful selection of truncated basis sets should be made.
Theoretical investigation of the dissociation dynamics of vibrationally excited vinyl bromide on an ab initio potential-energy surface obtained using modified novelty sampling and feedforward neural networks. II. Numerical application of the method
Authors: Malshe M. , Raff L. M. , Rockley M. G. , Hagan M. , Agrawal Paras M. , Komanduri R.
Published: October 2007

A previously reported method for conducting molecular dynamics simulations of gas-phase chemical dynamics on ab initio potential-energy surfaces using modified novelty sampling and feedforward neural networks is applied to the investigation of the unimolecular dissociation of vinyl bromide. The neural network is fitted to a database comprising the MP4(SDQ) energies computed for 71 969 nuclear configurations using an extended basis set. Dissociation rate coefficients and branching ratios at an internal excitation energy of 6.44eV for all six open reaction channels are reported. The distribution of vibrational energy in HBr formed in three-center dissociation is computed and found to be in excellent accord with experimental measurements. Computational requirements for the electronic structure calculations, neural network training, and trajectory calculations are given. The weight and bias matrices required for implementation of the neural network potential are made available through the Supplementary Material.