bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic biomarkers for overall and progression‐free survival in ovarian cancer patients
Authors: Høgdall Estrid , Fung Eric T. , Christensen Ib Jarle , Yip Christine , Nedergaard Lotte , Engelholm Svend Aage , Risum Signe , Petri Anette Lykke , Lundvall Lene , Lomas Lee , Høgdall Claus
Published: October 2010

Purpose:To determine if the level of apolipoprotein A1, hepcidin, transferrin, inter‐α trypsin IV internal fragment, transthyretin (TT), connective‐tissue activating protein 3 (CTAP3), serum amyloid A1, β‐2 microglobulin (B2M) might have impact on overall and progression‐free survival for ovarian cancer (OC) patients.

Experimental design:Serum from 150 OC patients was tested using SELDI‐TOF‐MS.

Results:A proteomic prognostic index (xb‐pro) was constructed using the regression coefficients based on inter‐α trypsin IV internal fragment, B2M and TT. A multivariable Cox survival analysis including the xb‐pro index showed that xb‐pro (p<0.0001, HR=2.50, 95% CI: 1.65–3.79), residual tumor after primary surgery (p=0.0005), age (p=0.01) and chemotherapy (p=0.0002) are of independent prognostic value for overall survival. International Federation of Gynecology and Obstetrics stage, performance status, histological type of tumor and serum CA125 were found of no independent value. A proteomic index (xb‐pfs) based on B2M and CTAP3 was found to predict progression‐free survival (xb‐pfs:p=0.008, HR=1.77, 95% CI: 1.17–2.70 together with type of surgery, age and chemotherapy.

Conclusions and clinical relevance:We found an index with three proteomic biomarkers (xb‐pro) to be of independent prognostic value for overall survival and an index with two proteomic biomarkers (xb‐pfs) with evidence of independent prognostic value for progression‐free survival.
Human anelloviruses and the central nervous system
Authors: Maggi Fabrizio , Bendinelli Mauro
Published: October 2010

Torque teno virus and related anelloviruses are a recent addition to the list of agents that cause chronic productive infections and high levels of plasma viraemia in humans. Many aspects of the natural history and pathogenesis of these under many respects surprising viruses are still poorly understood. In this review, we briefly outline the general properties of anelloviruses, examine what is currently known about the interactions they establish with the central nervous system (CNS), and discuss the possible pathological consequences. Copyright © 2010 John Wiley & Sons, Ltd.
EnPassant: anonymous routing for disruption‐tolerant networks with applications in assistive environments
Authors: Vakde Gauri , Bibikar Radhika , Le Zhengyi , Wright Matthew
Published: October 2010

Disruption‐tolerant networking holds a great deal of potential for making communications easier and more flexible in pervasive assistive environments. However, security and privacy must be addressed to make these communications acceptable with respect to protecting patient privacy. We propose EnPassant, a system for using disruption‐tolerant networking in privacy‐preserving way. EnPassant uses concepts from anonymous communications, re‐routing messages through groups of peer nodes to hide the relation between the sources and destinations. We describe a set of protocols that explore a practical range of tradeoffs between privacy and communication costs by modifying how closely the protocol adheres to the optimal predicted path. We also describe the cryptographic tools needed to facilitate changes in‐group membership. Finally, we present the results of extensive trace‐based simulation experiments that allow us to both compare between our proposed protocols and observe the costs of increasing the number of groups and intermediate nodes in a path. Copyright © 2010 John Wiley & Sons, Ltd.
On Random Betweenness Constraints
Authors: GOERDT ANDREAS
Published: October 2010

Ordering constraints are formally analogous to instances of the satisfiability problem in conjunctive normal form, but instead of a boolean assignment we consider a linear ordering of the variables in question. A clause becomes true given a linear ordering if and only if the relative ordering of its variables obeys the constraint considered.

The naturally arising satisfiability problems are NP-complete for many types of constraints. We look at random ordering constraints. Previous work of the author shows that there is a sharp unsatisfiability threshold for certain types of constraints. The value of the threshold, however, is essentially undetermined. We pursue the problem of approximating the precise value of the threshold. We show that random instances of the betweenness constraint are satisfiable with high probability if the number of randomly picked clauses is ≤0.92n, where n is the number of variables considered. This improves the previous bound, which is <0.82n random clauses. The proof is based on a binary relaxation of the betweenness constraint and involves some ideas not used before in the area of random ordering constraints.
The impact of training for day-care educators on childhood anaemia in nurseries: an institutional randomised clinical trial
Authors: Konstantyner Tulio , Taddei José Augusto AC , Oliveira Mariana de Novaes , Palma Domingos , Colugnati Fernando AB
Published: October 2010

Objective

To test the impact of training for educators on the health of children enrolled in public and philanthropic day-care nurseries.

Design

A randomised, institutional, non-blind clinical trial was conducted. An educational intervention was performed in four day-care centres and the control group consisted of four other day-care centres. Interviews with the mothers, collection of blood from the children by digital puncture and anthropometry were performed. The chosen indicator for the improvement of health was anaemia (Hb <11 g/dl). An unconditional logistic regression model was set for the risk factors for anaemia, considering associations with P ≤ 0·05 as statistically significant.

Setting

Eight day-care centres in the city of Sao Paulo, Brazil.

Subjects

Two hundred and fifty-two children from day-care nurseries.

Results

The children from the day-care centres that were not subject to intervention presented a 2·11 times greater risk (95% CI 1·04, 4·30; P = 0·40) of having anaemia at the end of the study independent of the control variables (sex, age, time in the day-care centre, anaemia at the beginning of the study, maternal age, use of oral iron supplements, number of siblings, per capita family income, use of antibiotics and the necessity of avoidable hospitalisations) used in the construction of the final logistical model.

Conclusions

The assessed educational intervention promoted significant changes in the health status of the children, reinforcing the importance of training for professionals who care for young children in day-care centres in developing countries in order to promote child health.
Low prevalence of iron-deficiency anaemia among Inuit preschool children: Nunavut Inuit Child Health Survey, 2007–2008
Authors: Pacey Angela , Weiler Hope , Egeland Grace M
Published: October 2010

Objective

To report the prevalence rates and correlates for anaemia, iron deficiency (ID) and iron-deficiency anaemia (IDA) among Inuit preschool-aged children.

Design

A cross-sectional study assessed iron intake, demographic information, medical history, anthropometrics, Hb, ferritin, C-reactive protein and antibodies toHelicobacter pylori.

Setting

Sixteen selected Inuit communities in Nunavut Territory, Canada.

Subjects

Inuit (n388) aged 3–5 years randomly recruited from communities.

Results

Anaemia (3–4 years: Hb < 110 g/l; 5 years: Hb < 115 g/l) was prevalent in 16·8 % of children. The prevalence of ID (ferritin < 12 μg/l) was 18·0 % and that of IDA was 5·4 %. When ID was defined as ferritin <10 μg/l, 10·8 % of children were iron deficient and 3·3 % had IDA. In multiple logistic regression, boys were more likely to be iron deficient (OR = 2·28, 95 % CI 1·17, 8·25), but no other risk factor emerged for ID. Three- to 4-year-olds were less likely than 5-year-olds to have anaemia from causes other than ID (OR = 0·11, 95 % CI 0·08, 0·58). Anaemia from other causes was more common among children residing in crowded homes (OR = 2·30, 95 % CI 1·37, 12·31) and those treated for past-year ear infection (OR = 1·35, 95 % CI 1·05, 7·21).

Conclusions

The low prevalence of ID and IDA is encouraging, but efforts are still needed to reduce rates as they continue to be higher than general population rates. Household crowding and infections may contribute to anaemia and warrant further research.
Sugar-sweetened beverage intake and overweight in children from a Mediterranean country
Authors: Valente Hugo , Teixeira Vitor , Padrão Patricia , Bessa Mariana , Cordeiro Tânia , Moreira André , Mitchell Vanessa , Lopes Carla , Mota Jorge , Moreira Pedro
Published: October 2010

Objective

To assess the association between sugar-sweetened beverage (SSB) consumption and overweight in children from a Mediterranean country.

Design

The children’s dietary intake was measured using a semi-quantitative FFQ completed by the parents. Overall, 2512 questionnaires were returned and 837 children were removed, leaving a final sample of 1675 children, aged between 5 and 10 years. Height and weight were measured according to international standards, and BMI was calculated. The definition of overweight and obesity was based on average centiles according to the International Obesity Task Force cut-offs. To determine the magnitude of the association between SSB consumption and overweight, OR estimates, including CI, were computed using unconditional logistic regression, adjusting for confounders.

Setting

Elementary schools throughout the city of Porto, Portugal.

Subjects

We invited 5867 children, randomly selected, and their parents to participate in the study. Of those schools that agreed to take part, 3391 parents signed and returned the fully filled out consent form.

Results

The prevalence of overweight (including obesity) was 36·6 % for girls and 38·8 % for boys. With regard to SSB consumption (serving/d), no differences between with overweight and non-overweight children were found even after adjustment for confounders (1–2 servings/d: OR = 1·67, 95 % CI 0·76, 3·66, in girls; OR = 1·63, 95 % CI 0·76, 3·47, in boys; and >2 servings/d: OR = 0·63, 95 % CI 0·33, 1·22, in girls; OR = 0·64, 95 % CI 0·33, 1·52, in boys).

Conclusions

The intake of SSB was not associated with increased risk of overweight in Portuguese schoolchildren.
Waist circumference percentiles for Kuwaiti children and adolescents
Authors: Jackson Robert T , Al Hamad Nawal , Prakash Prassana , Al Somaie Mona
Published: October 2010

Objective

Abdominal obesity is a major risk factor for chronic diseases. Yet there are no waist circumference (WC) cut-offs for children in the Arabian Gulf. We developed smoothed WC percentiles for 5–19-year-old Kuwaiti children and adolescents, which could be used in clinical and public health practice. We also examined the percentages of children who had WC ≥ 90th percentile, a value commonly associated with an elevated risk of CVD.

Design

This is a cross-sectional study that was conducted by the Kuwait National Nutrition Surveillance System.

Setting

Data were collected from representative primary-, intermediate- and secondary-school children as part of the yearly nutrition and health monitoring. Least mean square regression was used to develop smoothed WC curves.

Subjects

A total of 9593 healthy 5·0–18·9-year-old children of both sexes were studied from all areas of Kuwait. Age, gender, residency, education level, weight, height and WC were collected for all participants.

Results

We developed the first smoothed WC curves for Kuwaiti children. Male children had higher WC than female children. WC increased with age in both genders, but larger percentages of male children had WC ≥ 90th percentile. Male children aged >10 years have higher WC percentiles than do female children at the 50th, 75th, 90th and 97th percentiles.

Conclusions

Male children (especially those aged >10 years) are at higher risk than female children. Few health-care professionals routinely measure WC. WC measurement should be promoted as an important tool in paediatric primary care practice. The use of these age- and gender-specific percentiles can impact public health recommendations for Kuwaiti and other Arab children from the Gulf.
Multivariate multiparameter extreme value models and return periods: A copula approach
Authors: Salvadori G. , De Michele C.
Published: October 2010

Multivariate extreme value models are a fundamental tool in order to assess potentially dangerous events. The target of this paper is two‐fold. On the one hand we outline how, exploiting recent theoretical developments in the theory of copulas, new multivariate extreme value distributions can be easily constructed; in particular, we show how a suitable number of parameters can be introduced, a feature not shared by traditional extreme value models. On the other hand, we introduce a proper new definition of multivariate return period and show the differences with (and the advantages over) the definition presently used in literature. An illustration involving flood data is presented and discussed, and a generalization of the well‐known multivariate logistic Gumbel model is also given.
Numerical investigations of apatite 4He/3He thermochronometry
Authors: Farley K. A. , Shuster D. L. , Watson E. B. , Wanser K. H. , Balco G.
Published: October 2010

Apatite 4He/3He thermochronometry has the potential to constrain cooling histories for individual samples provided that several presently untested assumptions are valid. Here we simulate the sensitivity of 4He/3He spectra to assumptions regarding geometric model, crystallographic anisotropy, broken grain terminations, parent nuclide zonation, and the accuracy of results obtained from analyses of aggregates of multiple crystals. We find that 4He/3He spectra obtained from a cylinder with isotropic diffusion are almost indistinguishable from those obtained from an equivalent sphere with an equivalent initial 4He distribution. Under similar conditions anisotropic diffusion from the cylinder can greatly bias 4He/3He spectra, but only if diffusion is >10 times faster in the axial than the radial direction. Existing data argue against anisotropy of this magnitude. We find that analysis of apatites with broken terminations will also bias 4He/3He spectra, but not greatly so. In contrast, we find that zonation of a factor of 3 in parent nuclide concentration produces 4He/3He spectra that deviate substantially from the homogeneous model. When parent nuclides are highly concentrated near the grain rim and/or cooling is fast, the resulting 4He/3He spectra will be readily identified as aberrant. However, more subtle zonation, higher concentrations in the grain interior, or samples that have cooled slowly regardless of zonation style can yield 4He/3He spectra that look acceptable but will lead to inaccurate thermochronometric interpretation if parent homogeneity is assumed. Finally, we find that analysis of an aggregate of crystals with identical 4He distributions can yield 4He/3He spectra (and diffusion Arrhenius arrays) that are very different from those that would be obtained on the individual crystals if even small variations in He diffusion exist among the grains. Overall, our observations suggest that modeling tools that assume spherical geometry and isotropic diffusion are appropriate for interpreting apatite 4He/3He spectra. However, it is essential to analyze only individual crystals and to assess the degree of parent nuclide zonation in those crystals.
On the generation of large wave parallel electric fields responsible for electron heating in the high‐latitude E region
Authors: Bahcivan Hasan , Cosgrove Russell
Published: October 2010

The sources of parallel electric fields (E∥) to explain E region electron heating measurements made by incoherent scatter radars have not been resolved. This paper considers the effect of electron density gradients parallel to the geomagnetic field (∇∥n) on the Farley‐Buneman instability and the resulting change in wave δE∥. The dispersion relation including the ∇∥n effect is derived and solved for a set of wave vectors at marginal stability. It is shown that ∇∥n with scales of several kilometers enable propagation of 50 m or longer wavelength waves at large angles (up to 5°) from perpendicularity to the geomagnetic field. The fact that kilometric scales of ∇∥n were previously shown to occur during strong electrojet and that they coincide statistically well with the altitudes of strongest electron heating support the role of these long‐wavelength waves in electron heating. Furthermore, unlike the gradient‐drift instability, the ∇∥n effect contributes to the growth of the waves with the proper k∥ sign regardless of the direction of the convection electric field Ec; this makes the ∇∥n effect eligible as a source of electron heating, resulting in the consistent increase of electron temperature with the magnitude of Ec. Moreover, it is shown that the inclusion of the ∇∥n effect reduces the discrepancy between the theoretically required perpendicular electric field turbulence (to raise the electron temperature to the measured values) and the in situ rocket measurements.
Heterogeneous expression of toll‐like receptors in lymphatic endothelial cells derived from different tissues
Authors: Garrafa Emirena , Imberti Luisa , Tiberio Guido , Prandini Alberto , Giulini Stefano Maria , Caimi Luigi
Published: October 2010

As lymphatic endothelial cells (LECs) express different lymphatic and vascular markers depending on the organ they are derived from, we analysed whether they also show a heterogeneity of response against pathogens. To this end we analysed, for the presence of mRNA encoding for all human toll‐like receptor (TLR), LECs isolated from lymph nodes and thymuses. RNA for TLR1–6 and 9 was identified in thymus‐derived cells, whereas cells derived from lymph nodes contained mRNA for TLR1–4, 6 and 9, but failed to express mRNA specific for TLR5. The differential expression of TLRs was confirmed by the phosphorylation of nuclear factor‐κB p65 only when the two types of LECs were incubated with the appropriate TLR agonists. The stimulation with specific agonists gives rise to a heterogeneous pattern of cytokine and chemokine secretion: thymus‐derived LECs produced preferentially interleukin‐6, interferon‐inducible protein (IP)‐10 and tumour necrosis factor‐α, whereas cells prepared from lymph nodes mainly released interleukin‐8, monocyte chemotactic protein‐1, RANTES and (IP)‐10. Finally, cells purified from lymph nodes expressed a higher level of intercellular adhesion molecule‐1 than did cells prepared from the thymus when stimulated with several TLR agonists. The expression of a large set of TLRs and the responsiveness to specific agonists suggest that LECs are able to respond to pathogens, and the observed differences reflect specialized functions, redundancy and/or roles of LECs of different origin.
B cells do not take up bacterial DNA: an essential role for antigen in exposure of DNA to toll‐like receptor‐9
Authors: Roberts Tara L , Turner Marian L , Dunn Jasmyn A , Lenert Petar , Ross Ian L , Sweet Matthew J , Stacey Katryn J
Published: October 2010

Murine dendritic cells (DC) and macrophages respond to bacterial CpG DNA through toll‐like receptor 9 (TLR9). Although it is frequently assumed that bacterial DNA is a direct stimulus for B cells, published work does not reliably show responses of purified B cells. Here we show that purified splenic B cells did not respond to Escherichia coli DNA with induction of CD86, despite readily responding to single‐stranded (ss) phosphodiester CpG oligodeoxynucleotides (ODN). This was due to a combination of weak responses to both long and double‐stranded (ds) DNA. B‐cell DNA uptake was greatly reduced with increasing DNA length. This contrasts with macrophages where DNA uptake and subsequent responses were enhanced with increasing DNA length. However, when DNA was physically linked to hen egg lysozyme (HEL), HEL‐specific B cells showed efficient uptake of DNA, and limited proliferation in response to the HEL–DNA complex. We propose that, in the absence of other signals, B cells have poor uptake and responses to long dsDNA to prevent polyclonal activation. Conversely, when DNA is physically linked to a B‐cell receptor (BCR) ligand, its uptake is increased, allowing TLR9‐dependent B‐cell activation in an antigen‐specific manner. We could not generate fragments of E. coli DNA by limited DNaseI digestion that could mimic the stimulatory effect of ss CpG ODN on naïve B cells. We suggest that the frequently studied polyclonal B‐cell responses to CpG ODN are relevant to therapeutic applications of phosphorothioate‐modified CpG‐containing ODN, but not to natural responses to foreign or host dsDNA.
The Discovery of TRPV1 Antagonists: Turning up the Heat
Authors: Norman Mark H.
Published: October 2010

The Transient Receptor Potential Vanilloid 1 (TRPV1) ion channel was first cloned and characterized in late 1997 by Michael Caterina, David Julius and colleagues. In the decade that followed an explosion of research from pharmaceutical and biotech companies ensued and an elegant series of experiments, both genetic and pharmacological, positioned TRPV1 as a key target for developing novel pain therapeutics. As a result of these efforts, TRPV1 as a potential therapeutic target, as well as the progress made towards identifying selective antagonists of TRPV1, has been extensively reviewed. This chapter will not attempt to provide a comprehensive view of the TRPV1 research area, and therefore the reader is referred to a number of the excellent reviews on the subject. Rather this chapter will outline the case study of one TRPV1 antagonist program conducted at Amgen, Inc., which started from an initial high throughput screening hit and culminated in the identification of two clinical candidates, AMG 517 and AMG 628. Methods used to identify the initial hit, strategies to generate the proof-of-concept compound, and key structure-activity relationships (SAR) studies leading to AMG 517 and AMG 628 will be outlined. In addition, the preclinical and clinical profiles of AMG 517 will also be described. Finally, two subsequent approaches to eliminate or minimize the on-target hyperthermic effect observed in the clinical studies will be summarized.
Identification of α7 Nicotinic Acetylcholine Receptor Agonists for their Assessment in Improving Cognition in Schizophrenia
Authors: Rogers Bruce N. , Jon Jacobsen E. , O’Donnell Christopher J. , Shaffer Christopher L. , Walker Daniel P. , Wishka Donn G.
Published: October 2010

The α7 nicotinic acetylcholine receptor (nAChR) has been a target of interest to the neuroscience area for the treatment of cognitive deficits in schizophrenia for some time. The pentameric α7 nAChR is the most abundant nAChR in the brain and consist of five α7 subunits, each with an orthosteric low affinity binding site for the endogenous agonist, acetylcholine. This account describes the discovery efforts undertaken at Pharmacia and Pfizer to identify novel agonists of the α7 nAChR. It establishes the importance of a robust High Throughput Screen (HTS) to identify high quality chemical matter, and the critical nature of lead optimization strategies to deliver a series of compounds to enter the clinical setting. In addition to the medicinal chemistry efforts, the full screening strategy and path to the clinic are described for compounds emerging from the synergies of merging two independent programs into one. This target remains a challenge within the pharmaceutical industry, which is charged with delivering innovative medicines to patients with schizophrenia.
Transmission grating based extreme ultraviolet imaging spectrometer for time and space resolved impurity measurements
Authors: Kumar Deepak , Stutman Dan , Tritz Kevin , Finkenthal Michael , Tarrio Charles , Grantham Steven
Published: October 2010

A free standing transmission grating based imaging spectrometer in the extreme ultraviolet range has been developed for the National Spherical Torus Experiment (NSTX). The spectrometer operates in a survey mode covering the approximate spectral range from 30 to 700 Å and has a resolving capability of δλ/λ on the order of 3%. Initial results from space resolved impurity measurements from NSTX are described in this paper.
Phase diagram of magnetization switching in a nanostructured magnetic thin film
Authors: Lee Jong Min , Lim S. H.
Published: October 2010

The magnetization switching behavior in a nanostructured magnetic thin film, under combined in-plane fields along the longitudinal and the transverse directions, is investigated both analytically and numerically. Two critical curves under a static and a dynamic condition are calculated analytically by using an equation for the total energy. The analytically calculated critical curves are compared with the micromagnetic simulation results for the switching phase diagrams of nonswitching, incoherent switching, and coherent switching. The comparison indicates that the dynamic critical curve is the boundary separating the nonswitching from the incoherent switching, while the static critical curve acts as the boundary between the incoherent switching and the coherent switching. The present results indicate that the switching phase diagram can be constructed analytically with the use of a total energy equation. The analytically calculated critical curves are less accurate in the presence of the simplifying assumptions of a single and in-plane domain state for a small angle between the applied magnetic field and the easy axis. In this case, an accurate value of the anisotropy energy, an input to the total energy equation, must be accurately estimated by micromagnetic simulation.
GaN photovoltaic leakage current and correlation to grain size
Authors: Matthews K. D. , Chen X. , Hao D. , Schaff W. J. , Eastman L. F.
Published: October 2010

GaN p-i-n solar PV structures grown by rf plasma assisted molecular beam epitaxy (MBE) produce high performance IV characteristics with a leakage current density of less than 1×10−4 mA cm−2 at 0.1 V forward bias and an on-resistance of 0.039 Ω cm2. Leakage current measurements taken for different size diodes processed on the same sample containing the solar cells reveal that current density increases with diode area, indicating that leakage is not a large function of surface leakage along the mesa. Nonannealed Pt/Au Ohmic p-contacts produce a contact resistivity of 4.91×10−4 Ω cm−2 for thin Mg doped contact layers with sheet resistivity of 62196 Ω/◻. Under concentrated sunlight the cells produce an open-circuit voltage of 2.5 V and short circuit currents as high as 30 mA cm−2. Multiple growths comprised the study and on each wafer the IV curves representing several diodes showed considerable variation in parasitic leakage current density at low voltages on some wafers and practically no variation on others. It appears that a smaller grain size within the GaN thin film accounts for higher levels of dark current.
The fabrication of GaN-based nanopillar light-emitting diodes
Authors: Zhu Jihong , Wang Liangji , Zhang Shuming , Wang Hui , Zhao Degang , Zhu Jianjun , Liu Zongshun , Jiang Desheng , Yang Hui
Published: October 2010

InGaN/GaN multiple quantum well-based light-emitting diode (LED) nanopillar arrays were fabricated using Ni self-assembled nanodots as etching mask. The Ni nanodots were fabricated with a density of 6×108–1.5×109 cm−2 and a dimension of 100–250 nm with varying Ni thickness and annealing duration time. Then LED nanopillar arrays with diameter of approximately 250 nm and height of 700 nm were fabricated by inductively coupled plasma etching. In comparison to the as-grown LED sample an enhancement by a factor of four of photoluminescence (PL) intensity is achieved for the nanopillars and a blueshift as well as a decrease in full width at half maximum of the PL peak are also observed. The method of additional chemical etching was used to remove the etching-induced damage. Then nano-LED devices were further completed using a planarization approach to deposit p-type electrode on the tips of nanopillars. The current-voltage curves of both nanopillars and planar LED devices are measured for comparison.
Holonomy of a principal composite bundle connection, non-Abelian geometric phases, and gauge theory of gravity
Authors: Viennot David
Published: October 2010

We show that the holonomy of a connection defined on a principal composite bundle is related by a non-Abelian Stokes theorem to the composition of the holonomies associated with the connections of the component bundles of the composite. We apply this formalism to describe the non-Abelian geometric phase (when the geometric phase generator does not commute with the dynamical phase generator). We find then an assumption to obtain a new kind of separation between the dynamical and the geometric phases. We also apply this formalism to the gauge theory of gravity in the presence of a Dirac spinor field in order to decompose the holonomy of the Lorentz connection into holonomies of the linear connection and of the Cartan connection.
A TiAl2O5 nanocrystal charge trap memory device
Authors: Zhou Yue , Yin Jiang , Xu Hanni , Xia Yidong , Liu Zhiguo , Li Aidong , Gong Youpin , Pu Lin , Yan Feng , Shi Yi
Published: October 2010

A charge trapping memory device using Ti0.2Al0.8Ox film as charge trapping layer and amorphous Al2O3 as the tunneling and blocking layers was fabricated for nonvolatile memory application. TiAl2O5 nanocrystals are precipitated from the phase separation of Ti0.2Al0.8Ox film annealed at 900 °C. A memory window of 2.3 V and a stored electron density of 1×1013/cm2 were obtained. Good retention characteristics of the memory device at 80 °C were observed due to the deep charge trapping level as identified by the valence band offsets and electron energy loss spectrum measurements.
Operation stability enhancement in organic photovoltaic device by a metal doped organic exciton blocking layer
Authors: Lo M. F. , Ng T. W. , Lai S. L. , Wong F. L. , Fung M. K. , Lee S. T. , Lee C. S.
Published: October 2010

While metal diffusion in organic layers have been considered as causes for performance degradation in organic light-emitting devices, we show that suitable metal doping can instead improve physical stability of organic films. By using a metal doped organic exciton blocking layer (EBL), enhanced stability is demonstrated in unpackaged CuPc/C60 organic photovoltaic devices (OPV). While devices with a pure organic EBL of bathocuproine and tris(8-hydroxyquinolinato)aluminum (Alq3) show over ∼20% decreases in efficiency for first 150 min of operation, the device with magnesium-doped Alq3 EBL shows less than ∼5% variation in efficiency during the same period.
Erbium diffusion in silicon dioxide
Authors: Lu Ying-Wei , Julsgaard B. , Petersen M. Christian , Jensen R. V. Skougaard , Pedersen T. Garm , Pedersen K. , Larsen A. Nylandsted
Published: October 2010

Erbium diffusion in silicon dioxide layers prepared by magnetron sputtering, chemical vapor deposition, and thermal growth has been investigated by secondary ion mass spectrometry, and diffusion coefficients have been extracted from simulations based on Fick’s second law of diffusion. Erbium diffusion in magnetron sputtered silicon dioxide from buried erbium distributions has in particular been studied, and in this case a simple Arrhenius law can describe the diffusivity with an activation energy of 5.3±0.1 eV. Within a factor of two, the erbium diffusion coefficients at a given temperature are identical for all investigated matrices.
The effects of energetic disorder and polydispersity in conjugation length on the efficiency of polymer-based light-emitting diodes
Authors: Konezny S. J. , Rothberg L. J. , Galvin M. E. , Smith D. L.
Published: October 2010

Energetic disorder plays a critical role in governing the performance of organic light-emitting diodes (OLEDs). This is particularly true for polymer-based OLEDs in which disorder can be controlled but not eliminated. Contrary to the common assumption that energetic disorder has only a negative effect on performance, we provide experimental evidence of improved efficiency when the energetic disorder is increased upon deliberate addition of traps via an increase in polymer chain length distribution. We use numerical calculations to extract the mechanisms responsible for the observed improvements and discuss the general conditions under which traps can be introduced to increase device efficiency.
Dependence of domain wall stability on vortex chirality in asymmetric nanoring
Authors: Wang X. H. , Goolaup S. , Lew W. S.
Published: October 2010

We report on the direct observation of notch-free domain wall (DW) trapping and field history effect on the DW behavior in Ni80Fe20 asymmetric ring. We found that a 360° DW is trapped at the narrow arm while the ring adopts a vortex configuration. The stability of DW is dependent on the chirality of the vortex state and the external field direction. A 360° DW trapped in a clockwise vortex configuration is highly resistant to annihilation upon the application of +x field; the 360° DW trapped in an anticlockwise vortex breaks apart with a small +x field.
Formation of iridium nanocrystals with highly thermal stability for the applications of nonvolatile memory device with excellent trapping ability
Authors: Wang Terry Tai-Jui , Chu Chang-Lung , Hsieh Ing-Jar , Tseng Wen-Shou
Published: October 2010

This paper presents the formation of iridium nanocrystals (Ir-NCs) embedded in SiO2 matrix and it can be used for potential applications of nonvolatile memory devices. The NC formation is investigated by varying Ir film thickness; and the thermal agglomeration is also studied by applying various annealing temperatures and process time. The results of systematic characterization including capacitance-voltage, transmission electron microscopy, and x-ray photoelectron spectroscopy show that the high work-function (5.27 eV) metallic-NCs have a highly thermal stability (up to 900 °C) and the resulted Al/SiO2/Ir-NCs/SiO2/Si/Al stack can have a good retention ability and significant hysteresis window of 17.4 V.
Structures of aminoacylase 3 in complex with acetylated substrates
Authors: Hsieh Jennifer M. , Tsirulnikov Kirill , Sawaya Michael R. , Magilnick Nathaniel , Abuladze Natalia , Kurtz Ira , Abramson Jeff , Pushkin Alexander
Published: October 2010

Trichloroethylene (TCE) is one of the most widespread environmental contaminants, which is metabolized toN-acetyl-S-1,2-dichlorovinyl-l-cysteine (NA-DCVC) before being excreted in the urine. Alternatively, NA-DCVC can be deacetylated by aminoacylase 3 (AA3), an enzyme that is highly expressed in the kidney, liver, and brain. NA-DCVC deacetylation initiates the transformation into toxic products that ultimately causes acute renal failure. AA3 inhibition is therefore a target of interest to prevent TCE induced nephrotoxicity. Here we report the crystal structure of recombinant mouse AA3 (mAA3) in the presence of its acetate byproduct and two substrates:Nα-acetyl-l-tyrosine and NA-DCVC. These structures, in conjunction with biochemical data, indicated that AA3 mediates substrate specificity through van der Waals interactions providing a dynamic interaction interface, which facilitates a diverse range of substrates.
Recruitment of genes and enzymes conferring resistance to the nonnatural toxin bromoacetate
Authors: Desai Kevin K. , Miller Brian G.
Published: October 2010

Microbial niches contain toxic chemicals capable of forcing organisms into periods of intense natural selection to afford survival. Elucidating the mechanisms by which microbes evade environmental threats has direct relevance for understanding and combating the rise of antibiotic resistance. In this study we used a toxic small-molecule, bromoacetate, to model the selective pressures imposed by antibiotics and anthropogenic toxins. We report the results of genetic selection experiments that identify nine genes from
Escherichia coli
whose overexpression affords survival in the presence of a normally lethal concentration of bromoacetate. Eight of these genes encode putative transporters or transmembrane proteins, while one encodes the essential peptidoglycan biosynthetic enzyme, UDP-
N
-acetylglucosamine enolpyruvoyl transferase (MurA). Biochemical studies demonstrate that the primary physiological target of bromoacetate is MurA, which becomes irreversibly inactivated via alkylation of a critical active-site cysteine. We also screened a comprehensive library of
E. coli
single-gene deletion mutants and identified 63 strains displaying increased susceptibility to bromoacetate. One hypersensitive bacterium lacks
yliJ
, a gene encoding a predicted glutathione transferase. Herein, YliJ is shown to catalyze the glutathione-dependent dehalogenation of bromoacetate with a
k
cat
/
K

m

value of 5.4 × 10
3
 M
-1
 s
-1
. YliJ displays exceptional substrate specificity and produces a rate enhancement exceeding 5 orders of magnitude, remarkable characteristics for reactivity with a nonnatural molecule. This study illustrates the wealth of intrinsic survival mechanisms that can be exploited by bacteria when they are challenged with toxins.
Characterization ofGeminivirusResistance in an Accession ofCapsicum chinenseJacq.
Authors: García-Neria Marco A. , Rivera-Bustamante Rafael F.
Published: October 2010

Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV), members of the Geminiviridae family, are important pathogens of pepper (Capsicum annuum L.) and other solanaceous crops. Accession BG-3821 of C. chinense Jacq. was reported earlier as resistant to mixed infection with PepGMV and PHYVV. In this work, we characterized the Geminivirus resistance trait present in BG-3821. Segregation analysis suggested that resistance depends on two genes. Our data showed that PepGMV replication in protoplast of resistant plants is approximately 70% lower when compared with the levels observed in protoplasts from susceptible plants. Additionally, viral movement is less efficient in resistant plants. We also evaluated several characteristics commonly associated with systemic acquired resistance (SAR), which is a conserved defensive mechanism. The concentration of salicylic acid was higher in resistant plants inoculated with PepGMV than in susceptible plants. Marker genes for SAR were induced after inoculation with PepGMV in resistant leaves. Similarly, we found a higher accumulation of reactive oxygen species on resistant leaves compared with susceptible ones. A model for the mechanism acting in the Geminivirus resistance detected in BG-3821 is proposed. Finally, the importance of BG-3821 in Geminivirus resistance breeding programs is discussed.
Phenotypic Characterization of Potato Late Blight Resistance Mediated by the Broad-Spectrum Resistance Gene RB
Authors: Chen Yu , Halterman Dennis A.
Published: October 2010

The potato gene RB, cloned from the wild potato species Solanum bulbocastanum, confers partial resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. In order to better characterize this partial resistance phenotype, we have compared host resistance responses mediated by RB with those mediated by the S. demissum-derived R gene R9, which confers immunity to P. infestans carrying the corresponding avirulence gene avrR9. We found that both RB and R9 genes were capable of eliciting a hypersensitive cell death response (HR). However, in RB plants, the pathogen escaped HR lesions and continued to grow beyond the inoculation sites. We also found that callose deposition was negatively correlated with resistance levels in tested plants. Transcription patterns of pathogenesis-related (PR) genes PR-1 basic, PR-2 acidic, and PR-5 indicated that P. infestans inoculation induced transcription of these defense-related genes regardless of the host genotype; however, transcription was reduced in both the susceptible and partially resistant plants later in the infection process but remained elevated in the immune host. Most interestingly, transcription of the HR-associated gene Hin1 was suppressed in both Katahdin and RB-transgenic Katahdin but not in R9 4 days after inoculation. Together, this suggests that suppression of certain defense-related genes may allow P. infestans to spread beyond the site of infection in the partially resistant host despite elicitation of hypersensitive cell death.
Young proteins experience more variable selection pressures than old proteins
Authors: Vishnoi Anchal , Kryazhimskiy Sergey , Bazykin Georgii A. , Hannenhalli Sridhar , Plotkin Joshua B.
Published: October 2010

It is well known that young proteins tend to experience weaker purifying selection and evolve more quickly than old proteins. Here, we show that, in addition, young proteins tend to experience more variable selection pressures over time than old proteins. We demonstrate this pattern in three independent taxonomic groups: yeast, Drosophila, and mammals. The increased variability of selection pressures on young proteins is highly significant even after controlling for the fact that young proteins are typically shorter and experience weaker purifying selection than old proteins. The majority of our results are consistent with the hypothesis that the function of a young gene tends to change over time more readily than that of an old gene. At the same time, our results may be caused in part by young genes that serve constant functions over time, but nevertheless appear to evolve under changing selection pressures due to depletion of adaptive mutations. In either case, our results imply that the evolution of a protein-coding sequence is partly determined by its age and origin, and not only by the phenotypic properties of the encoded protein. We discuss, via specific examples, the consequences of these findings for understanding of the sources of evolutionary novelty.
Interleukin 1 receptor antagonist is associated with changes in body composition during physiological GH substitution in patients with adult‐onset growth hormone deficiency
Authors: Ueland Thor , Jørgensen Anders P. , Godang Kristin , Fougner Kristian J. , Aukrust Pål , Burman Pia , Bollerslev Jens
Published: October 2010

Objective  We examined the effect of GH substitution on adipose tissue–derived hormones and cytokines and sought to identify predictors for changes in body composition during therapy. Long‐standing adult‐onset GH deficiency (AO‐GHD) is associated with increased body fat mass (FM) which, through production of hormones and inflammatory cytokines from adipose tissue, may contribute to different manifestations of the metabolic syndrome.

Design, Patients and Measurements  Fifty‐five patients with AO‐GHD (24 women, 31 men, mean age 49 years) were enrolled in a placebo‐controlled, double‐blind crossover study. GH therapy was individually dosed to obtain an IGF‐I concentration within the normal range for age and sex. GH and placebo were administered for 9 months each, separated by a 4‐month washout period. Adipose tissue–derived cytokines were measured by enzyme immunoassay.

Results  GH treatment was associated with a significant decrease in IL‐1 receptor antagonist (IL‐1Ra) compared to placebo, which correlated with declining body FM (truncal and total) after GH substitution. The change in IL‐1Ra was the strongest predictor of the variation in BFM in regression models. No changes were observed for leptin, adiponectin, soluble TNF receptor 1 or interleukin (IL)‐8.

Conclusion  The data indicate a possible unrecognized association between IL‐1Ra and changes in body composition during GH substitution and suggest further research on the interaction between the GH‐IGF axis and the IL‐1 system.
Demographic characteristics of southern flounder, Paralichthys lethostigma, harvested by an estuarine gillnet fishery
Authors: SMITH W. E. , SCHARF F. S.
Published: October 2010

Abstract  The North Carolina (NC) southern flounder, Paralichthys lethostigma (Jordan and Gilbert), stock has experienced heavy exploitation during the past two decades. Recently, several management changes were initiated to lower harvest rates and restore stock biomass. Here, the age, growth and maturity of southern flounder harvested by a southeast NC estuarine gillnet fishery are characterised and compared with observations from previous studies and with statewide data on the stock to evaluate any regulatory effects and assess the potential for selective removal by the fishery. Despite regulatory changes, the estuarine gillnet fishery still harvested mainly age‐0 and age‐1 individuals that were mostly immature, meaning that the current fishing practices likely only allow a small portion of the harvestable stock the opportunity to reproduce. Relative to length‐at‐age patterns observed within the stock from statewide collections, fish captured by the gillnet fishery were above average length at each age; the legal size and the gear appeared to cause selective harvest of the fastest growers within each cohort. If the demographic characteristics of the catch observed in this study are broadly representative of gillnet fisheries in other estuarine nursery habitats throughout NC, the harvesting tactics in this sector of the fishery have the potential to cause population‐level effects and negatively affect long‐term fishery yield.
When and why do smallmouth bass abandon their broods? The effects of brood and parental characteristics
Authors: STEINHART G. B. , LUNN B. D.
Published: October 2010

Abstract  Variation in brood abandonment was explored by conducting partial brood removals from smallmouth bass, Micropterus dolomieu Lacepède, nests in two north temperate lakes. In both lakes, percent of the brood removed had no effect on nest failure rates. Nest failure prior to offspring swim‐up was more common, but unrelated to brood size after removal, in the lake with higher post‐spawning mortality and lower growth and fecundity. Brood size after removal was negatively related to nest failure in the lake with high survival, growth and fecundity. Nests guarded by young males failed more frequently than those of old males, and young broods failed more frequently than old broods. Dynamic programming and logistic regression models developed to predict nest fate worked better for the lake with selective pressures that theoretically favoured abandonment (e.g. high post‐spawning mortality). Both models identified male age and brood age as important factors in predicting nest fates. Because nest success is related to the age of the parent, this could have consequences for overall nest success for populations with different demographics.
Role of origin and release location in pre‐spawning distribution and movements of anadromous alewife
Authors: FRANK H. J. , MATHER M. E. , SMITH J. M. , MUTH R. M. , FINN J. T.
Published: October 2010

Abstract  Capturing adult anadromous fish that are ready to spawn from a self sustaining population and transferring them into a depleted system is a common fisheries enhancement tool. The behaviour of these transplanted fish, however, has not been fully evaluated. The movements of stocked and native anadromous alewife, Alosa pseudoharengus (Wilson), were monitored in the Ipswich River, Massachusetts, USA, to provide a scientific basis for this management tool. Radiotelemetry was used to examine the effect of origin (native or stocked) and release location (upstream or downstream) on distribution and movement during the spawning migration. Native fish remained in the river longer than stocked fish regardless of release location. Release location and origin influenced where fish spent time and how they moved. The spatial mosaic of available habitats and the entire trajectory of freshwater movements should be considered to restore effectively spawners that traverse tens of kilometres within coastal rivers.