bluuebunny/crossref_metadata_2025 huggingface dataset:
WCDMA multi‐service uplink capacity of highways cross‐shaped microcells
Authors: Ahmed Bazil Taha
Published: June 2008

The multi‐service uplink capacity and the interference (intracellular and intercellular) statistics (mean and variance) of the sectors of the cross‐shaped wide‐band code‐division multiple access (WCDMA) microcell are studied using a model of nine highway microcells in rural zone. The two‐slope propagation loss model with lognormal shadowing is used in the analysis. The capacity and the interference statistics of the microcell are studied for different sector range, antenna side lobe levels and different standard deviation of the power control (PC) error. It is shown that, reducing the antenna side lobe level increases the sector capacity. Also, it is shown that the sector range to get the quasi‐maximum sector capacity is on the order of 600–1200 m. Copyright © 2008 John Wiley & Sons, Ltd.
Time Dependent Ground Loosening Effect on Polilith Rock Mass Conditions in Shallow Tunnels
Authors: Kocak Bülent , Vardar Mahir
Published: June 2008

The time dependent rock mass behaviour, known as the stressdisplacement‐ time relationship, and tunnel stability depend fairly on the technical conditions of the rock mass which are taken into consideration as continuum, discontinuum or quasi‐continuum surroundings. Accurate definition of rock mass and understanding of rock mass behaviour are the fundament of engineering design. However, it is a fact that an exact simulation of system seniority is almost impossible especially in polilith rock mass conditions. In this paper, the application of ground loosening effect into numerical analysis has been studied. The core support method, the lining reduction method and the stress reduction method have been applied on a shallow urban tunnel. As an alternative, Vardar time dependent in‐situ rock mass method is applied to the case study, as well. The results have been compared with measured in‐situ tunnel displacements. It has been seen that, Vardar method is an effective method to define the polilith rock mass in discontinuum mechanics.
Comparing smooth transition and Markov switching autoregressive models of US unemployment
Authors: Deschamps Philippe J.
Published: June 2008

Logistic smooth transition and Markov switching autoregressive models of a logistic transform of the monthly US unemployment rate are estimated by Markov chain Monte Carlo methods. The Markov switching model is identified by constraining the first autoregression coefficient to differ across regimes. The transition variable in the LSTAR model is the lagged seasonal difference of the unemployment rate. Out‐of‐sample forecasts are obtained from Bayesian predictive densities. Although both models provide very similar descriptions, Bayes factors and predictive efficiency tests (both Bayesian and classical) favor the smooth transition model. Copyright © 2008 John Wiley & Sons, Ltd.
Insulin‐like growth factor‐I of pejerrey, Odontesthes bonariensis: cDNA characterization, tissue distribution and expression profiles after growth hormone administration
Authors: Sciara Andrés A. , Somoza Gustavo. M. , Arranz Silvia. E.
Published: June 2008

The liver production of the insulin‐like growth factor‐I (IGF‐I) is a key factor in the endocrine control of body growth by a growth hormone. As pejerrey Odontesthes bonariensis has been reported as a fish with low growth rates in captivity, basic research on this respect is needed in order to understand it. In this context, the pejerrey IGF‐I cDNA was cloned and its hepatic expression was examined in fish after recombinant pejerrey growth hormone (pjGHr) administration. The full length of IGF‐I transcript showed a high sequence similarity to other teleost sequences. The tissue distribution analysis by reverse transcriptase polymerase chain reaction in adult fish revealed that IGF‐I expressed ubiquitously with the highest mRNA levels in the liver, posterior intestine and brain. No alternative IGF‐I mRNA was found in the liver, as it was reported for other teleosts. IGF‐I transcript was measured in the liver after pjGHr in vivo stimulation by means of quantitative real‐time polymerase chain reaction assays. A dose‐dependent response of IGF‐I mRNA was observed after pjGHr administration, and reached a six‐fold IGF‐I maximum increase over control group when 2.5 µg pjGH/g‐body weight (bw) was injected. Temporal analysis of hepatic IGF‐I mRNA level showed that administration of a single dose of pjGHr into juvenile pejerrey resulted in a significant increase (P<0.02) 9 hours post‐injection (hpi). These results add novel information on the nucleotide sequence of IGF‐I in Atheriniformes and demonstrate that pjGHr could promote a dramatic response in liver, increasing the IGF‐I mRNA level. J. Exp. Zool. 309A:407–418, 2008. © 2008 Wiley‐Liss, Inc.
Effects of phenolic acids and transglutaminase on soft wheat flour dough and baked products
Authors: Koh Bong‐Kyung , Ng Perry KW
Published: June 2008

BACKGROUND:The effects of phenolic acids on the physical properties of soft wheat flour dough and baked soft wheat flour products were investigated. Transglutaminase (TG) was added to observe the effects of non‐disulfide crosslinks on phenolic acid treated dough. Ferulic acid,p‐coumaric acid or fumaric acid was blended with pastry flour at a level of 250, 500 or 1000 ppm of flour dry weight, respectively.

RESULTS:The addition of phenolic acids, TG or a mixture of phenolic acids and TG to flour had no effect on the mixing properties of the doughs but significantly affected 90 min rested dough. The addition of phenolic acids decreased the maximum resistance and increased the extensibility of 90 min rested dough, and TG reversed the effects of phenolic acids on the rested dough. The physical characteristics of cookies blended with each phenolic acid plus TG were not significantly different (P> 0.01) from those of the control cookies. However, TG with and without phenolic acids had significant effects on the moisture content, weight and volume of crackers.

CONCLUSION:These results suggest that the addition of phenolic acids and TG in the absence of a fermentation process do not affect the physical properties of soft wheat flour products. The fermentation process allows the chemical reaction of the phenolic acids and TG to occur before the soft wheat flour products are baked. Copyright © 2008 Society of Chemical Industry
Unravelling the complexity of health effects of trans fatty acids: Insight from the TRANSFACT study
Authors: Destaillats Frédéric , Chardigny Jean‐Michel , Malpuech‐Brugère Corinne , Sébédio Jean‐Louis , Bezelgues Jean‐Baptiste , Dionisi Fabiola , Bauman Dale E.
Published: June 2008

The TRANSFACT study, a worldwide research initiative, revealed that the effects of trans fatty acids (TFA) found in ‘natural’ ruminant fat (R‐TFA) and industrially produced (IP‐TFA) sources on cardiovascular disease risk (CVD) factors are different. Moreover, it was observed for both dietary sources of TFA that women and men react differently to TFA consumption, the women being more sensitive than men. The TRANSFACT study demonstrates that the consumption of R‐TFA at the current level consumption does not impact significantly on CVD risk factors. Moreover, the TRANSFACT study confirmed that the complexity related to the consumption of TFA was oversimplified as recently suggested in an epidemiological study.
Fatty acid composition of post trans margarines and their health implications
Authors: Pedersen Jan I. , Kirkhus Bente
Published: June 2008

We have analysed the fatty acid composition of 45 different vegetable oil margarines collected in different European countries during 2004–2005 and estimated their effect on blood cholesterol. Trans fatty acids in amounts 4–6% of total fatty acids were detected in 3 margarines, otherwise only trace amounts (<1%) were detected. Of the 45 margarines 10 were found to have a neutral or a slight cholesterol decreasing effect. The others were found to be cholesterol increasing with substantial variation in effect, although less hypercholesterolemic than butter. Palmitic acid contributed most to the estimated cholesterol increasing effect and the correlation coefficient between the amount of palmitic acid and the change in cholesterol was 0.82. Myristic acid also contributed to a certain extent while lauric acid contributed little. The content of stearic acid was >10% in 6 samples but otherwise present in low amounts. It thus appears that palmitic acid, presumably from palm oil, to a large extent has replaced trans fatty acids in margarines. A better alternative might be to use fat blends with higher contents of the cholesterol neutral stearic acid, such as fully hydrogenated and interesterified fat.
Bulk and epitaxial growth of micropipe‐free silicon carbide on basal and rhombohedral plane seeds
Authors: Epelbaum B. M. , Filip O. , Winnacker A.
Published: June 2008

In this paper the criteria for reasonable choice of alternative to (0001) seed orientation are discussed. Growth conditions necessary to produce bulk 6H‐ and 4H‐SiC crystals on rhombohedral (01‐1n) plane seeds in PVT process are presented. Specific defect structures in such crystals are described in relation to growth conditions. In the second part of the paper, liquid phase epitaxial (LPE) growth using high‐temperature silicon based flux and rhombohedral plane seeds is compared to the LPE on basal plane seeds. In both bulk and epitaxial growth processes the employment of rhombohedral plane seed offers important advantages. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Managing parent involvement during crisis
Authors: Merriman Lynette S.
Published: June 2008

Parents define student crises every day. Communicating with parents during a crisis and responding to their concerns are critical skills when managing their involvement.
Modeling and performance analysis of multi‐service wireless CDMA cellular networks using smart antennas
Authors: Hartmann Christian , Nasser Nidal
Published: June 2008

In this paper, we present an analytical model to assess the blocking capacity of multi‐service code division multiple access (CDMA) systems. We include smart antenna systems in our model and show how the capacity of CDMA systems can be improved if smart antennas are employed at the base stations. Applying smart antennas can actually transform CDMA systems from being interference limited to being channel/code limited. To investigate this effect, we extend our model to include the limitation of channelization codes in CDMA‐based universal mobile telecommunication system (UMTS) systems. From the point of view of the call admission control (CAC) in a smart antenna CDMA system, we can either accept the capacity loss due to code limitation, or we can additionally apply space division multiple access (SDMA) techniques to re‐use channelization codes and thus re‐approach the capacity which is obtained if no code limitation is considered. Copyright © 2008 John Wiley & Sons, Ltd.
Synthesis and Surface Properties of Dicephalic Surfactants with a 1,3‐Dioxane Ring
Authors: Karczewski Sławomir , Piasecki Andrzej , Maliszewska Irena
Published: June 2008

A new group of surface active dicephalic derivatives of 1,3‐dioxane, i.e., 2‐alkyl‐5,5‐bis{[3‐(N,N‐dimethylamino)propyl]amido}‐1,3‐dioxane‐di‐N‐oxides, were synthesized with high yields by the reaction of an appropriate 2‐alkyl‐5,5‐bis‐(carboxyethyl)‐1,3‐dioxane with an excess of N,N‐dimethyl‐1,3‐propanediamine followed by oxidation with an aqueous solution of hydrogen peroxide. Structures and purity of all intermediates and final di‐N‐oxides were confirmed by means of 1H‐NMR and ESI‐MS spectroscopy. Synthesized compounds showed high surface activity with low values of critical micelle concentration and high effectiveness of surface tension reduction (γCMC). However, only derivative with the longest 2‐alkyl substituent showed good foaming and moderate emulsifying properties.
Fatty Acid Profile of Sunshine Bass: I. Profile Change is Affected by Initial Composition and Differs Among Tissues
Authors: Trushenski Jesse T. , Lewis Heidi A. , Kohler Christopher C.
Published: June 2008

Fatty acid (FA) composition of fillet tissue can be tailored by transitioning fish from alternative lipid‐based, low long‐chain polyunsaturated fatty acid (LC‐PUFA) grow‐out feeds to high LC‐PUFA “finishing” feeds. To address whether grow‐out feed composition influences the responsiveness of fillet tissue to finishing, sunshine bass (SB, Morone chrysops × M. saxatilis) were reared to a submarketable size on grow‐out feeds containing fish oil (FO) or a 50:50 blend of FO and coconut (CO), grapeseed (GO), linseed (LO), or poultry (PO) oil. For the final 8 weeks of the trial, fish were either maintained on assigned grow‐out feeds or finished with the 100% FO feed. Production performance was unaffected by dietary lipid source, but fillet FA profile generally conformed to nutritional history. Regardless of grow‐out regimen, finishing had a significant restorative effect on fillet FA composition; however, complete restoration of control levels of 20:5n‐3, 22:6n‐3, total LC‐PUFA and n‐3:n‐6 FA ratio was achieved only among fish fed the CO‐based grow‐out feed. Saturated fatty acids (SFA) appear to be preferential catabolic substrates, whereas medium‐chain and long‐chain PUFA are selectively deposited in tissues. Provision of SFA in grow‐out feeds appears to optimize selective FA metabolism and restoration of beneficial fillet FA profile during finishing.
On the subjectivity of human-authored summaries
Authors: KOLLURU BALAKRISHNA , GOTOH YOSHIHIKO
Published: June 2008

Human-generated summaries are a blend of content and style, bound by the task restrictions, but are ‘subject to subjectiveness’ of the individuals summarising the documents. We study the impact of various facets that cause subjectivity such as brevity, information content and information coverage on human-authored summaries. The scale of subjectivity is quantitatively measured among various summaries using a question–answer-based cross-comprehension test. The test evaluates summaries for meaning rather than exact words based on questions, framed by the summary authors, derived from the summary. The number of questions that cannot be answered after reading the candidate summary reflects its subjectivity. The qualitative analysis of the outcome of the cross-comprehension test shows the relationship between the length of a summary, information content and nature of questions framed by the summary author.
Analysis of the mechanism by which melatonin inhibits human eosinophil peroxidase
Authors: Lu T , Galijasevic S , Abdulhamid I , Abu‐Soud H M
Published: June 2008

Background and purpose:

Eosinophil peroxidase (EPO) catalyses the formation of oxidants implicated in the pathogenesis of various respiratory diseases including allergy and asthma. Mechanisms for inhibiting EPO, once released, are poorly understood. The aim of this work is to determine the mechanisms by which melatonin, a hormone produced in the brain by the pineal gland, inhibits the catalytic activity of EPO.

Experimental approach:

We utilized H2O2‐selective electrode and direct rapid kinetic measurements to determine the pathways by which melatonin inhibits human EPO.

Key results:

In the presence of plasma levels of bromide (Br−), melatonin inactivates EPO at two different points in the classic peroxidase cycle. First, it binds to EPO and forms an inactive complex, melatonin‐EPO‐Br, which restricts access of H2O2 to the catalytic site of the oxidation enzyme. Second, melatonin competes with Br− and switches the reaction from a two electron (2e−) to a one electron (1e−) pathway allowing the enzyme to function with catalase‐like activity. Melatonin is a bulky molecule and binds to the entrance of the EPO haem pocket (regulatory sites). Furthermore, Br− seems to enhance the affinity of this binding. In the absence of Br−, melatonin accelerated formation of EPO Compound II and its decay by serving as a 1e− substrate for EPO Compounds I and II.

Conclusions and implications:

The interplay between EPO and melatonin may have a broader implication in the function of several biological systems. This dual regulation by melatonin is unique and represents a new mechanism for melatonin to control EPO and its downstream inflammatory pathways.

British Journal of Pharmacology (2008) 154, 1308–1317; doi:10.1038/bjp.2008.173; published online 2 June 2008
Regulation of two‐pore‐domain (K2P) potassium leak channels by the tyrosine kinase inhibitor genistein
Authors: Gierten J , Ficker E , Bloehs R , Schlömer K , Kathöfer S , Scholz E , Zitron E , Kiesecker C , Bauer A , Becker R , Katus H A , Karle C A , Thomas D
Published: June 2008

Background and purpose:

Two‐pore‐domain potassium (K2P) channels mediate potassium background (or ‘leak’) currents, controlling excitability by stabilizing membrane potential below firing threshold and expediting repolarization. Inhibition of K2Pcurrents permits membrane potential depolarization and excitation. As expected for key regulators of excitability, leak channels are under tight control from a plethora of stimuli. Recently, signalling via protein tyrosine kinases (TKs) has been implicated in ion channel modulation. The objective of this study was to investigate TK regulation of K2Pchannels.

Experimental approach:

The two‐electrode voltage clamp technique was used to record K2Pcurrents inXenopusoocytes. In addition, K2Pchannels were studied in Chinese hamster ovary (CHO) cells using the whole‐cell patch clamp technique.

Key results:

Here, we report inhibition of human K2P3.1 (TASK‐1) currents by the TK antagonist, genistein, inXenopusoocytes (IC50=10.7 μM) and in CHO cells (IC50=12.3 μM). The underlying molecular mechanism was studied in detail. hK2P3.1 was not affected by genistin, an inactive analogue of genistein. Perorthovanadate, an inhibitor of tyrosine phosphatase activity, reduced the inhibitory effect of genistein. Current reduction was voltage independent and did not require channel protonation at position H98 or phosphorylation at the single TK phosphorylation site, Y323. Among functional hK2Pfamily members, genistein also reduced K2P6.1 (TWIK‐2), K2P9.1 (TASK‐3) and K2P13.1 (THIK‐1) currents, respectively.

Conclusions and implications:

Modulation of K2Pchannels by the TK inhibitor, genistein, represents a novel molecular mechanism to alter background K+currents.

British Journal of Pharmacology(2008)154, 1680–1690; doi:10.1038/bjp.2008.213; published online 2 June 2008
Potential role of 2,2'-biphenylquinones in the carcinogenic/anti-cancer activity of dioxins
Authors: Rayne Sierra
Published: May 2008

Modes of carcinogenicity for the well-known environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) have been investigated over the past several decades. However, the mechanisms underlying TCDD carcinogenicity are still unclear. Recent work also suggests TCDD may have anti-cancer activity. Based on established photochemical generation of reactive 2,2'-biphenylquinone intermediates from dioxins, a novel toxicological mechanism for TCDD that may be operative is proposed. 2,2'-Biphenylquinones may be obtained via biochemical activation of dioxins such as TCDD, and these intermediates may play a role in expressing both the carcinogenic and anti-cancer activities of this important contaminant class. The broader research community is encouraged to consider this potential new mechanism for dioxin toxicology in the design of future studies, the positive or negative findings from which will supplement the datasets developed by previous and current research groups.
Multidimensional nonlinear dust acoustic shock waves in nonuniform magnetized dusty plasmas with nonadiabatic dust charge fluctuation
Authors: Zhang Li-Ping , Xue Ju-Kui
Published: June 2008

The propagation of multidimensional nonlinear dust acoustic shock waves in inhomogeneous dusty plasmas due to spatial gradients of dust charge and plasma densities is investigated. A modified variable coefficients Korteweg–de Vries Burgers equation is derived with the nonadiabatic dust charge fluctuation, the nonthermally distributed ions, dust-neutral collision, and the external magnetic field. The numerical results show that the inhomogeneity, the nonthermal ions and the nonadiabatic dust charge fluctuation have strong influence on the nonlinear properties of dust acoustic shock waves.
Real-time studies of gallium adsorption and desorption kinetics on sapphire (0001) by grazing incidence small-angle x-ray scattering and x-ray fluorescence
Authors: Wang Yiyi , Özcan Ahmet S. , Ludwig Karl F. , Bhattacharyya Anirban
Published: June 2008

Gallium adsorption and desorption on c-plane sapphire has been studied by real-time grazing incidence small-angle x-ray scattering and x-ray fluorescence as a function of substrate temperature (680–740°C) and Ga flux. The x-ray techniques monitor the surface morphology evolution and amount of Ga on the surface. During deposition, nanodroplets of liquid Ga are observed to form on the surface and coarsen. The growth of droplet size during continuous deposition follows dynamical scaling, in agreement with expectations from theory and simulations which include deposition-induced droplet coalescence. However, observation of continued droplet distance scale coarsening during desorption points to the necessity of including further physical processes in the modeling. The desorption rate at different substrate temperatures gives the activation energy of Ga desorption as 2.7eV, comparable to measured activation energies for desorption from Ga droplets on other substrates and to the Ga heat of vaporization.
Effects of oxygen gas pressure on structural, electrical, and thermoelectric properties of (ZnO)3In2O3 thin films deposited by rf magnetron sputtering
Authors: Orikasa Yuki , Hayashi Naoaki , Muranaka Shigetoshi
Published: June 2008

Zinc indium oxide films were deposited by the rf magnetron sputtering method using a (ZnO)3In2O3 target. The films were prepared at 573 K in various Ar/O2 sputtering gases (O2 content: 0%–25%). The effect of the oxygen gas content in the sputtering gas on the structural, optical, electrical, and thermoelectric properties of the films was investigated. The films had a c-axis oriented layer structure. The films deposited at 0%–3% oxygen gas contents exhibited a high electrical conductivity with a high carrier concentration, n≈1020 cm−3, while the conductivity of the films significantly decreased above the 3% oxygen gas content, having a carrier concentration below 1018 cm−3. From the optical transmission measurement, the band gap of the films was estimated to be 3.01 eV. The films deposited at 3%–8% oxygen gas contents showed a high Seebeck coefficient, −300 μV/K, while the maximum power factor, 4.78×10−5 W/m K2, was obtained at the 2% oxygen gas content. The Seebeck coefficient and the power factor were calculated on the basis of degenerate semiconductors. These results suggest that zinc indium oxide films have the possibility of being high performance thermoelectric materials.
A nonneural epithelial domain of embryonic cranial neural folds gives rise to ectomesenchyme
Authors: Breau Marie Anne , Pietri Thomas , Stemmler Marc P. , Thiery Jean Paul , Weston James A.
Published: May 2008

The neural crest is generally believed to be the embryonic source of skeletogenic mesenchyme (ectomesenchyme) in the vertebrate head and other derivatives, including pigment cells and neurons and glia of the peripheral nervous system. Although classical transplantation experiments leading to this conclusion assumed that embryonic neural folds were homogeneous epithelia, we reported that embryonic cranial neural folds contain spatially and phenotypically distinct domains, including a lateral nonneural domain with cells that coexpress E-cadherin and PDGFRα and a thickened mediodorsal neuroepithelial domain where these proteins are reduced or absent. We now show that Wnt1-Cre is expressed in the lateral nonneural epithelium of rostral neural folds and that cells coexpressing Cre-recombinase and PDGFRα delaminate precociously from some of this nonneural epithelium. We also show that ectomesenchymal cells exhibit β-galactosidase activity in embryos heterozygous for an Ecad-
lacZ
reporter knock- in allele. We conclude that a lateral nonneural domain of the neural fold epithelium, which we call “metablast,” is a source of ectomesenchyme distinct from the neural crest. We suggest that closer analysis of the origin of ectomesenchyme might help to understand (
i
) the molecular-genetic regulation of development of both neural crest and ectomesenchyme lineages; (
ii
) the early developmental origin of skeletogenic and connective tissue mesenchyme in the vertebrate head; and (
iii
) the presumed origin of head and branchial arch skeletal and connective tissue structures during vertebrate evolution.
Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus
Authors: Jäälinoja Harri T. , Roine Elina , Laurinmäki Pasi , Kivelä Hanna M. , Bamford Dennis H. , Butcher Sarah J.
Published: May 2008

The Archaea, and the viruses that infect them, are the least well understood of all of the three domains of life. They often grow in extreme conditions such as hypersaline lakes and sulfuric hot springs. Only rare glimpses have been gained into the structures of archaeal viruses. Here, we report the subnanometer resolution structure of a recently isolated, hypersalinic, membrane-containing, euryarchaeal virus, SH1, in which different viral proteins can be localized. The results indicate that SH1 has a complex capsid formed from single β-barrels, an important missing link in hypotheses on viral capsid protein evolution. Unusual, symmetry-mismatched spikes seem to play a role in host adsorption. They are connected to highly organized membrane proteins providing a platform for capsid assembly and potential machinery for host infection.
Population structure of the genes encoding the polymorphic
Plasmodium falciparum
apical membrane antigen 1: Implications for vaccine design
Authors: Duan Junhui , Mu Jianbing , Thera Mahamadou Ali , Joy Deirdre , Kosakovsky Pond Sergei L. , Diemert David , Long Carole , Zhou Hong , Miura Kazutoyo , Ouattara Amed , Dolo Amagana , Doumbo Ogobara , Su Xin-zhuan , Miller Louis
Published: May 2008

Immunization with the highly polymorphic
Plasmodium falciparum
apical membrane antigen 1 (
Pf
AMA1) induces protection in animals but primarily against parasites that express the same or similar alleles. One strategy to overcome the obstacle of polymorphism is to combine
Pf
AMA1 proteins representing major haplotypes into one vaccine. To determine the minimum number of haplotypes that would confer broad protection, we sequenced the coding region of
PfAMA1
from 97 clones from around the world and 61 isolates from Mali, identifying 150 haplotypes for domains 1 to 3 that included previous sequences. A clustering algorithm grouped the 150 haplotypes into six populations that were independent of geographic location. Each of the six populations contained haplotypes predominantly of that population (predominant haplotypes) and haplotypes that were a mixture of haplotypes represented in other populations (admixed haplotypes). To determine the biological relevance of the populations identified through the clustering algorithm, antibodies induced against one predominant haplotype of population 1 (3D7) and one admixed haplotype of population 5 (FVO) were tested for their ability to block parasite invasion of erythrocytes. Parasites expressing
Pf
AMA1s belonging to population 1 were efficiently inhibited by 3D7-specific antibodies, whereas parasites expressing
Pf
AMA1s belonging to other populations were not. For FVO-specific antibodies, we observed growth inhibition against itself as well as isolates belonging to populations 3 and 6. Our data suggests that the inclusion of
Pf
AMA1 sequences from each of the six populations may result in a vaccine that induces protective immunity against a broad range of malaria parasites.
Functional significance of axonal Kv7 channels in hippocampal pyramidal neurons
Authors: Shah Mala M. , Migliore Michele , Valencia Ignacio , Cooper Edward C. , Brown David A.
Published: May 2008

Members of the Kv7 family (Kv7.2–Kv7.5) generate a subthreshold K+current, the M− current. This regulates the excitability of many peripheral and central neurons. Recent evidence shows that Kv7.2 and Kv7.3 subunits are targeted to the axon initial segment of hippocampal neurons by association with ankyrin G. Further, spontaneous mutations in these subunits that impair axonal targeting cause human neonatal epilepsy. However, the precise functional significance of their axonal location is unknown. Using electrophysiological techniques together with a peptide that selectively disrupts axonal Kv7 targeting (ankyrin G-binding peptide, or ABP) and other pharmacological tools, we show that axonal Kv7 channels are critically and uniquely required for determining the inherent spontaneous firing of hippocampal CA1 pyramids, independently of alterations in synaptic activity. This action was primarily because of modulation of action potential threshold and resting membrane potential (RMP), amplified by control of intrinsic axosomatic membrane properties. Computer simulations verified these data when the axonal Kv7 density was three to five times that at the soma. The increased firing caused by axosomatic Kv7 channel block backpropagated into distal dendrites affecting their activity, despite these structures having fewer functional Kv7 channels. These results indicate that axonal Kv7 channels, by controlling axonal RMP and action potential threshold, are fundamental for regulating the inherent firing properties of CA1 hippocampal neurons.
Interleukin-18, together with interleukin-12, induces severe acute pancreatitis in obese but not in nonobese leptin-deficient mice
Authors: Sennello Joseph A. , Fayad Raja , Pini Maria , Gove Melissa E. , Ponemone Venkatesh , Cabay Robert J. , Siegmund Britta , Dinarello Charles A. , Fantuzzi Giamila
Published: May 2008

Obesity is associated with increased severity of acute pancreatitis (AP). The cytokines IL-18 and IL-12 are elevated in patients with AP, and IL-18 levels are high in obesity. We aimed to develop a pathologically relevant model to study obesity-associated severe AP. Lean WT and obese leptin-deficient
ob/ob
mice received two injections of IL-12 plus IL-18. Survival, pancreatic inflammation, and biochemical markers of AP were measured. Dosing with IL-12 plus IL-18 induced 100% lethality in
ob/ob
mice; no lethality was observed in WT mice. Disruption of pancreatic exocrine tissue and acinar cell death as well as serum amylase and lipase levels were significantly higher in
ob/ob
than in WT mice. Edematous AP developed in WT mice, whereas obese
ob/ob
mice developed necrotizing AP. Adipose tissue necrosis and saponification were present in cytokine-injected
ob/ob
but not in WT mice. Severe hypocalcemia and elevated acute-phase response developed in
ob/ob
mice. The cytokine combination induced high levels of regenerating protein 1 and pancreatitis-associated protein expression in the pancreas of WT but not of
ob/ob
mice. To differentiate the contribution of obesity to that of leptin deficiency, mice received short- and long-term leptin replacement therapy. Short-term leptin reconstitution in the absence of major weight loss did not protect
ob/ob
mice, whereas leptin deficiency in the absence of obesity resulted in a significant reduction in the severity of the pancreatitis. In conclusion, we developed a pathologically relevant model of AP in which obesity
per se
is associated with increased severity.
Effect of Telephoned Notification of PositiveClostridium difficileTest Results on the Time to the Ordering of Antimicrobial Therapy
Authors: Verdoorn Brandon P. , Orenstein Robert , Wilson John W. , Estes Lynn L. , Wendt Randy F. , Schleck Cathy D. , Harmsen William S. , Nyre Lisa M. , Patel Robin
Published: June 2008

The time between electronic-medical-record reporting of a positive result of a test forClostridium difficiletoxin in stool and the ordering of antimicrobial therapy was compared during consecutive periods when results were not telephoned (n= 274) and when results were telephoned (n= 90) to the clinical service. The mean times to the ordering of antimicrobial therapy were 11.9 and 3.6 hours, respectively (P< .001).
Web-based design and evaluation of T-cell vaccine candidates
Authors: Thurmond James , Yoon Hyejin , Kuiken Carla , Yusim Karina , Perkins Simon , Theiler James , Bhattacharya Tanmoy , Korber Bette , Fischer Will
Published: May 2008

Summary: We present a suite of on-line tools to design candidate vaccine proteins, and to assess antigen potential, using coverage of k-mers (as proxies for potential T-cell epitopes) as a metric. The vaccine design tool uses the recently published ‘mosaic’ method to generate protein sequences optimized for coverage of high-frequency k-mers; the coverage-assessment tools facilitate coverage comparisons for any potential antigens. To demonstrate these tools, we designed mosaic protein sets for B-clade HIV-1 Gag, Pol and Nef, and compared them to antigens used in a recent human vaccine trial.

Availability:  http://hiv.lanl.gov/content/sequence/MOSAIC/

Contact:  wfischer@lanl.gov

Supplementary information: Supplementary data are available at ftp://ftp-t10.lanl.gov/pub/btk/WebToolsData
Sparse kernel methods for high-dimensional survival data
Authors: Evers Ludger , Messow Claudia-Martina
Published: May 2008

Sparse kernel methods like support vector machines (SVM) have been applied with great success to classification and (standard) regression settings. Existing support vector classification and regression techniques however are not suitable for partly censored survival data, which are typically analysed using Cox's proportional hazards model. As the partial likelihood of the proportional hazards model only depends on the covariates through inner products, it can be ‘kernelized’. The kernelized proportional hazards model however yields a solution that is dense, i.e. the solution depends on all observations. One of the key features of an SVM is that it yields a sparse solution, depending only on a small fraction of the training data. We propose two methods. One is based on a geometric idea, where—akin to support vector classification—the margin between the failed observation and the observations currently at risk is maximised. The other approach is based on obtaining a sparse model by adding observations one after another akin to the Import Vector Machine (IVM). Data examples studied suggest that both methods can outperform competing approaches.

Availability: Software is available under the GNU Public License as an R package and can be obtained from the first author's website http://www.maths.bris.ac.uk/~maxle/software.html

Contact:  l.evers@bris.ac.uk
The Future of Alfred Chandler
Authors: Lipartito Kenneth J.
Published: May 2008

One could make a career of throwing darts at the work of Alfred Chandler. I don't mean just criticizing him. You could take the pages of Chandler's books, paste them up on a wall, and start throwing. Almost everywhere a point struck would be a little gem of business history to draw your interest.
Phenotypic Analysis of Arabidopsis Mutants: Auxin Hormone Response
Authors: Estelle Mark
Published: June 2008

INTRODUCTION

The hormone auxin is transported directionally through the plant body to effect a variety of morphological processes. In the embryo, auxin is required in the early stages of development to establish the bilateral axis of the developing embryo. Later, it participates in vascular element patterning and differentiation, lateral organ outgrowth in the root and shoot, and local growth responses to external stimuli such as light and gravity. A convenient way to measure auxin response, described in this protocol, is to monitor the effects of auxins or of auxin transport inhibitors on root growth.
Selectable Tolerance to Herbicides by Mutated Acetolactate Synthase Genes Integrated into the Chloroplast Genome of Tobacco
Authors: Shimizu Masanori , Goto Maki , Hanai Moeko , Shimizu Tsutomu , Izawa Norihiko , Kanamoto Hirosuke , Tomizawa Ken-Ichi , Yokota Akiho , Kobayashi Hirokazu
Published: May 2008

Strategies employed for the production of genetically modified (GM) crops are premised on (1) the avoidance of gene transfer in the field; (2) the use of genes derived from edible organisms such as plants; (3) preventing the appearance of herbicide-resistant weeds; and (4) maintaining transgenes without obstructing plant cell propagation. To this end, we developed a novel vector system for chloroplast transformation with acetolactate synthase (ALS). ALS catalyzes the first step in the biosynthesis of the branched amino acids, and its enzymatic activity is inhibited by certain classes of herbicides. We generated a series of Arabidopsis (Arabidopsis thaliana) mutated ALS (mALS) genes and introduced constructs with mALS and the aminoglycoside 3′-adenyltransferase gene (aadA) into the tobacco (Nicotiana tabacum) chloroplast genome by particle bombardment. Transplastomic plants were selected using their resistance to spectinomycin. The effects of herbicides on transplastomic mALS activity were examined by a colorimetric assay using the leaves of transplastomic plants. We found that transplastomic G121A, A122V, and P197S plants were specifically tolerant to pyrimidinylcarboxylate, imidazolinon, and sulfonylurea/pyrimidinylcarboxylate herbicides, respectively. Transplastomic plants possessing mALSs were able to grow in the presence of various herbicides, thus affirming the relationship between mALSs and the associated resistance to herbicides. Our results show that mALS genes integrated into the chloroplast genome are useful sustainable markers that function to exclude plants other than those that are GM while maintaining transplastomic crops. This investigation suggests that the resistance management of weeds in the field amid growing GM crops is possible using (1) a series of mALSs that confer specific resistance to herbicides and (2) a strategy that employs herbicide rotation.
The Arabidopsis Phosphatidylinositol 3-Kinase Is Important for Pollen Development
Authors: Lee Yuree , Kim Eun-Sook , Choi Yunjung , Hwang Inwhan , Staiger Christopher J. , Chung Yong-Yoon , Lee Youngsook
Published: May 2008

Phosphatidylinositol 3-kinase has been reported to be important for normal plant growth. To characterize the role of the enzyme further, we attempted to isolate Arabidopsis (Arabidopsis thaliana) plants that do not express the gene, but we could not recover homozygous mutant plants. The progeny of VPS34/vps34 heterozygous plants, harboring a T-DNA insertion, showed a segregation ratio of 1:1:0 for wild-type, heterozygous, and homozygous mutant plants, indicating a gametophytic defect. Genetic transmission analysis showed that the abnormal segregation ratio was due to failure to transmit the mutant allele through the male gametophyte. Microscopic observation revealed that 2-fold higher proportions of pollen grains in heterozygous plants than wild-type plants were dead or showed reduced numbers of nuclei. Many mature pollen grains from the heterozygous plants contained large vacuoles even until the mature pollen stage, whereas pollen from wild-type plants contained many small vacuoles beginning from the vacuolated pollen stage, which indicated that vacuoles in many of the heterozygous mutant pollen did not undergo normal fission after the first mitotic division. Taken together, our results suggest that phosphatidylinositol 3-kinase is essential for vacuole reorganization and nuclear division during pollen development.
Comparative Analysis of Divergent and Convergent Gene Pairs and Their Expression Patterns in Rice, Arabidopsis, andPopulus
Authors: Krom Nicholas , Ramakrishna Wusirika
Published: May 2008

Comparative analysis of the organization and expression patterns of divergent and convergent gene pairs in multiple plant genomes can identify patterns that are shared by more than one species or are unique to a particular species. Here, we study the coexpression and interspecies conservation of divergent and convergent gene pairs in three plant species: rice (Oryza sativa), Arabidopsis (Arabidopsis thaliana), and black cottonwood (Populus trichocarpa). Strongly correlated expression levels between divergent and convergent genes were found to be quite common in all three species, and the frequency of strong correlation appears to be independent of intergenic distance. Conservation of divergent or convergent arrangement among these species appears to be quite rare. However, conserved arrangement is significantly more frequent when the genes display strongly correlated expression levels or have one or more Gene Ontology (GO) classes in common. A correlation between intergenic distance in divergent and convergent gene pairs and shared GO classes was observed, in varying degrees, in rice and Populus but not in Arabidopsis. Furthermore, multiple GO classes were either overrepresented or underrepresented in Arabidopsis and Populus gene pairs, while only two GO classes were underrepresented in rice divergent gene pairs. Three cis-regulatory elements common to both Arabidopsis and rice were overrepresented in the intergenic regions of strongly correlated divergent gene pairs compared to those of noncorrelated pairs. Our results suggest that shared as well as unique mechanisms operate in shaping the organization and function of divergent and convergent gene pairs in different plant species.
MAPK Signaling Regulates Nitric Oxide and NADPH Oxidase-Dependent Oxidative Bursts inNicotiana benthamiana
Authors: Asai Shuta , Ohta Kohji , Yoshioka Hirofumi
Published: May 2008

Nitric oxide (NO) and reactive oxygen species (ROS) act as signals in innate immunity in plants. The radical burst is induced by INF1 elicitin, produced by the oomycete pathogen Phytophthora infestans. NO ASSOCIATED1 (NOA1) and NADPH oxidase participate in the radical burst. Here, we show that mitogen-activated protein kinase (MAPK) cascades MEK2-SIPK/NTF4 and MEK1-NTF6 participate in the regulation of the radical burst. NO generation was induced by conditional activation of SIPK/NTF4, but not by NTF6, in Nicotiana benthamiana leaves. INF1- and SIPK/NTF4-mediated NO bursts were compromised by the knockdown of NOA1. However, ROS generation was induced by either SIPK/NTF4 or NTF6. INF1- and MAPK-mediated ROS generation was eliminated by silencing Respiratory Burst Oxidase Homolog B (RBOHB), an inducible form of the NADPH oxidase. INF1-induced expression of RBOHB was compromised in SIPK/NTF4/NTF6-silenced leaves. These results indicated that INF1 regulates NOA1-mediated NO and RBOHB-dependent ROS generation through MAPK cascades. NOA1 silencing induced high susceptibility to Colletotrichum orbiculare but not to P. infestans; conversely, RBOHB silencing decreased resistance to P. infestans but not to C. orbiculare. These results indicate that the effects of the radical burst on the defense response appear to be diverse in plant–pathogen interactions.
XAP5 CIRCADIAN TIMEKEEPERCoordinates Light Signals for Proper Timing of Photomorphogenesis and the Circadian Clock inArabidopsis
Authors: Martin-Tryon Ellen L. , Harmer Stacey L.
Published: May 2008

Numerous, varied, and widespread taxa have an internal circadian clock that allows anticipation of rhythmic changes in the environment. We have identified XAP5 CIRCADIAN TIMEKEEPER (XCT), an Arabidopsis thaliana gene important for light regulation of the circadian clock and photomorphogenesis. XCT is essential for proper clock function: xct mutants display a shortened circadian period in all conditions tested. Interestingly, XCT plays opposite roles in plant responses to light depending both on trait and wavelength. The clock in xct plants is hypersensitive to red but shows normal responses to blue light. By contrast, inhibition of hypocotyl elongation in xct is hyposensitive to red light but hypersensitive to blue light. Finally, XCT is important for ribulose-1,5-bisphosphate carboxylase/oxygenase production and plant greening in response to light. This novel combination of phenotypes suggests XCT may play a global role in coordinating growth in response to the light environment. XCT contains a XAP5 domain and is well conserved across diverse taxa, suggesting it has a common function in higher eukaryotes. Downregulation of the XCT ortholog in Caenorhabditis elegans is lethal, suggesting that studies in Arabidopsis may be instrumental to understanding the biochemical activity of XCT.
Biochemical Networks and Epistasis Shape theArabidopsis thalianaMetabolome
Authors: Rowe Heather C. , Hansen Bjarne Gram , Halkier Barbara Ann , Kliebenstein Daniel J.
Published: May 2008

Genomic approaches have accelerated the study of the quantitative genetics that underlie phenotypic variation. These approaches associate genome-scale analyses such as transcript profiling with targeted phenotypes such as measurements of specific metabolites. Additionally, these approaches can help identify uncharacterized networks or pathways. However, little is known about the genomic architecture underlying data sets such as metabolomics or the potential of such data sets to reveal networks. To describe the genetic regulation of variation in the Arabidopsis thaliana metabolome and test our ability to integrate unknown metabolites into biochemical networks, we conducted a replicated metabolomic analysis on 210 lines of an Arabidopsis population that was previously used for targeted metabolite quantitative trait locus (QTL) and global expression QTL analysis. Metabolic traits were less heritable than the average transcript trait, suggesting that there are differences in the power to detect QTLs between transcript and metabolite traits. We used statistical analysis to identify a large number of metabolite QTLs with moderate phenotypic effects and found frequent epistatic interactions controlling a majority of the variation. The distribution of metabolite QTLs across the genome included 11 QTL clusters; 8 of these clusters were associated in an epistatic network that regulated plant central metabolism. We also generated two de novo biochemical network models from the available data, one of unknown function and the other associated with central plant metabolism.
Prepenetration Apparatus Assembly Precedes and Predicts the Colonization Patterns of Arbuscular Mycorrhizal Fungi within the Root Cortex of BothMedicago truncatulaandDaucus carota
Authors: Genre Andrea , Chabaud Mireille , Faccio Antonella , Barker David G. , Bonfante Paola
Published: May 2008

Arbuscular mycorrhizas (AM) are widespread, ancient endosymbiotic associations that contribute significantly to soil nutrient uptake in plants. We have previously shown that initial fungal penetration of the host root is mediated via a specialized cytoplasmic assembly called the prepenetration apparatus (PPA), which directs AM hyphae through the epidermis (Genre et al., 2005). In vivo confocal microscopy studies performed on Medicago truncatula and Daucus carota, host plants with different patterns of AM colonization, now reveal that subsequent intracellular growth across the root outer cortex is also PPA dependent. On the other hand, inner root cortical colonization leading to arbuscule development involves more varied and complex PPA-related mechanisms. In particular, a striking alignment of polarized PPAs can be observed in adjacent inner cortical cells of D. carota, correlating with the intracellular root colonization strategy of this plant. Ultrastructural analysis of these PPA-containing cells reveals intense membrane trafficking coupled with nuclear enlargement and remodeling, typical features of arbusculated cells. Taken together, these findings imply that prepenetration responses are both conserved and modulated throughout the AM symbiosis as a function of the different stages of fungal accommodation and the host-specific pattern of root colonization. We propose a model for intracellular AM fungal accommodation integrating peri-arbuscular interface formation and the regulation of functional arbuscule development.