bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Genome Analysis of “CandidatusPhytoplasma australiense” (Subgrouptuf-Australia I;rp-A) and “Ca. Phytoplasma asteris” Strains OY-M and AY-WB
Authors: Tran-Nguyen L. T. T. , Kube M. , Schneider B. , Reinhardt R. , Gibb K. S.
Published: March 2008

The chromosome sequence of “CandidatusPhytoplasma australiense” (subgrouptuf-Australia I;rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of “Ca.Phytoplasma australiense” with “Ca.Phytoplasma asteris” strains OY-M and AY-WB showed that the gene order was more conserved between the closely related “Ca.Phytoplasma asteris” strains than to “Ca. Phytoplasma australiense.” Differences observed between “Ca.Phytoplasma australiense” and “Ca.Phytoplasma asteris” strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function.
Cooperative Binding of Phosphorylated DevR to Upstream Sites Is Necessary and Sufficient for Activation of the Rv3134c-
devRS
Operon in
Mycobacterium tuberculosis
: Implication in the Induction of DevR Target Genes
Authors: Chauhan Santosh , Tyagi Jaya Sivaswami
Published: March 2008

The DevR-DevS two-component system of
Mycobacterium tuberculosis
mediates bacterial adaptation to hypoxia, a condition believed to be associated with the initiation and maintenance of dormant bacilli during latent tuberculosis. The activity of the Rv3134c-
devRS
operon was studied in
M. tuberculosis
using several transcriptional fusions comprised of promoter regions and the
gfp
reporter gene under inducing and aerobic conditions. Aerobic transcription was DevR independent, while hypoxic induction was completely DevR dependent. The hypoxia transcriptional start point, T
H
, was mapped at −40 bp upstream of Rv3134c. In contrast, the divergently transcribed Rv3135 gene was not induced under hypoxic conditions. DNase I footprinting and mutational analyses demonstrated that induction required the interaction of DevR∼P with binding sites centered at bp −42.5 and −63.5 relative to T
H
. Binding to the distal site (D) was necessary to recruit another molecule of DevR∼P to the proximal site (P), and interaction with both sequences was essential for promoter activation. These sites did not bind to either unphosphorylated or phosphorylation-defective DevR protein, which was consistent with an essential role for DevR∼P in activation. Phosphorylated DevR also bound to three copies of the motif at the
hspX
promoter. The Rv3134c and
hspX
promoters have a similar architecture, wherein the proximal DevR∼P binding site overlaps with the promoter −35 element. A model for the likely mode of action of DevR at these promoters is discussed.
Multiple Genes Repress Motility in Uropathogenic
Escherichia coli
Constitutively Expressing Type 1 Fimbriae
Authors: Simms Amy N. , Mobley Harry L. T.
Published: March 2008

Two surface organelles of uropathogenic
Escherichia coli
(UPEC), flagella and type 1 fimbriae, are critical for colonization of the urinary tract but mediate opposite actions. Flagella propel bacteria through urine and along mucus layers, while type 1 fimbriae allow bacteria to adhere to specific receptors present on uroepithelial cells. Constitutive expression of type 1 fimbriae leads to repression of motility and chemotaxis in UPEC strain CFT073, suggesting that UPEC may coordinately regulate motility and adherence. To identify genes involved in this regulation of motility by type 1 fimbriae, transposon mutagenesis was performed on a phase-locked type 1 fimbrial ON variant of strain CFT073 (CFT073
fim
L-ON), followed by a screen for restoration of motility in soft agar. Functions of the genes identified included attachment, metabolism, transport, DNA mismatch repair, and transcriptional regulation, and a number of genes had hypothetical function. Isogenic deletion mutants of these genes were also constructed in CFT073
fim
L-ON. Motility was partially restored in six of these mutants, including complementable mutations in four genes encoding known transcriptional regulators,
lrhA, lrp, slyA
, and
papX
; a mismatch repair gene,
mutS
; and one hypothetical gene,
ydiV
. Type 1 fimbrial expression in these mutants was unaltered, and the majority of these mutants expressed larger amounts of flagellin than the
fim
L-ON parental strain. Our results indicate that repression of motility in CFT073
fim
L-ON is not solely due to the constitutive expression of type 1 fimbriae on the surfaces of the bacteria and that multiple genes may contribute to this repression.
Roles of
pgaABCD
Genes in Synthesis, Modification, and Export of the
Escherichia coli
Biofilm Adhesin Poly-β-1,6-
N
-Acetyl-
d
-Glucosamine
Authors: Itoh Yoshikane , Rice John D. , Goller Carlos , Pannuri Archana , Taylor Jeannette , Meisner Jeffrey , Beveridge Terry J. , Preston James F. , Romeo Tony
Published: March 2008

The linear homopolymer poly-β-1,6-
N
-acetyl-
d
-glucosamine (β-1,6-GlcNAc; PGA) serves as an adhesin for the maintenance of biofilm structural stability in diverse eubacteria. Its function in
Escherichia coli
K-12 requires the gene products of the
pgaABCD
operon, all of which are necessary for biofilm formation. PgaC is an apparent glycosyltransferase that is required for PGA synthesis. Using a monoclonal antibody directed against
E. coli
PGA, we now demonstrate that PgaD is also needed for PGA formation. The deletion of genes for the predicted outer membrane proteins PgaA and PgaB did not prevent PGA synthesis but did block its export, as shown by the results of immunoelectron microscopy (IEM) and antibody adsorption assays. IEM also revealed a conditional localization of PGA at the cell poles, the initial attachment site for biofilm formation. PgaA contains a predicted β-barrel porin and a superhelical domain containing tetratricopeptide repeats, which may mediate protein-protein interactions, implying that it forms the outer membrane secretin for PGA. PgaB contains predicted carbohydrate binding and polysaccharide
N
-deacetylase domains. The overexpression of
pgaB
increased the primary amine content (glucosamine) of PGA. Site-directed mutations targeting the
N
-deacetylase catalytic activity of PgaB blocked PGA export and biofilm formation, implying that
N
-deacetylation promotes PGA export through the PgaA porin. The results of previous studies indicated that
N
-deacetylation of β-1,6-GlcNAc in
Staphylococcus epidermidis
by the PgaB homolog, IcaB, anchors it to the cell surface. The deletion of
icaB
resulted in release of β-1,6-GlcNAc into the growth medium. Thus, covalent modification of β-1,6-GlcNAc by
N
-deacetylation serves distinct biological functions in gram-negative and gram-positive species, dictated by cell envelope differences.
Genome-Wide Transcriptional Responses ofEscherichia coliK-12 to Continuous Osmotic and Heat Stresses
Authors: Gunasekera Thusitha S. , Csonka Laszlo N. , Paliy Oleg
Published: March 2008

Osmotic stress is known to increase the thermotolerance and oxidative-stress resistance of bacteria by a mechanism that is not adequately understood. We probed the cross-regulation of continuous osmotic and heat stress responses by characterizing the effects of external osmolarity (0.3 M versus 0.0 M NaCl) and temperature (43°C versus 30°C) on the transcriptome ofEscherichia coliK-12. Our most important discovery was that a number of genes in the SoxRS and OxyR oxidative-stress regulons were up-regulated by high osmolarity, high temperature, or a combination of both stresses. This result can explain the previously noted cross-protection of osmotic stress against oxidative and heat stresses. Most of the genes shown in previous studies to be induced during the early phase of adaptation to hyperosmotic shock were found to be also overexpressed under continuous osmotic stress. However, there was a poorer overlap between the heat shock genes that are induced transiently after high temperature shifts and the genes that we found to be chronically up-regulated at 43°C. Supplementation of the high-osmolarity medium with the osmoprotectant glycine betaine, which reduces the cytoplasmic K+pool, did not lead to a universal reduction in the expression of osmotically induced genes. This finding does not support the hypothesis that K+is the central osmoregulatory signal inEnterobacteriaceae.
Expression and Porin Activity of P28 and OMP-1F during Intracellular
Ehrlichia chaffeensis
Development
Authors: Kumagai Yumi , Huang Haibin , Rikihisa Yasuko
Published: March 2008

Ehrlichia chaffeensis
, an obligatory intracellular gram-negative bacterium, must take up various nutrients and metabolic compounds because it lacks many genes involved in metabolism. Nutrient uptake by a gram-negative bacterium occurs primarily through pores or channels in the bacterial outer membrane. Here we demonstrate that isolated
E. chaffeensis
outer membranes have porin activities, as determined by a proteoliposome swelling assay. The activity was partially blocked by an antibody that recognizes the two most abundant outer membrane proteins, P28/OMP-19 and OMP-1F/OMP-18. Both proteins were predicted to have structural features characteristic of porins, including 12 transmembrane segments comprised of amphipathic and antiparallel β-strands. The sodium dodecyl sulfate stability of the two proteins was consistent with a β-barrel structure. Isolated native P28 and OMP-1F exhibited porin activities, with pore sizes similar to and larger than, respectively, that of OprF, which is the porin with the largest pore size known to date.
E. chaffeensis
experiences temperature changes during transmission by ticks. During the intracellular development of
E. chaffeensis
, both P28 and OMP-1F were expressed mostly in the mid-exponential growth phase at 37°C and the late-exponential growth phase at 28°C. The porin activity of proteoliposomes reconstituted with proteins from the outer membrane fractions derived from bacteria in the mid- and late-exponential growth phases at 28°C and 37°C correlated with the expression levels of P28 and OMP-1F. These results imply that P28 and OMP-1F function as porins with large pore sizes, suggesting that the differential expression of these two proteins might regulate nutrient uptake during intracellular
E. chaffeensis
development at both temperatures.
GENETIC PROGRAMMING BASED APPROACH FOR MODELING TIME SERIES DATA OF REAL SYSTEMS
Authors: AHALPARA DILIP P. , PARIKH JITENDRA C.
Published: March 2008

Analytic models of a computer generated time series (logistic map) and three real time series (ion saturation current in Aditya Tokamak plasma, NASDAQ composite index and Nifty index) are constructed using Genetic Programming (GP) framework. In each case, the optimal map that results from fitting part of the data set also provides a very good description of the rest of the data. Predictions made using the map iteratively are very good for computer generated time series but not for the data of real systems. For such cases, an extended GP model is proposed and illustrated. A comparison of these results with those obtained using Artificial Neural Network (ANN) is also carried out.
QUANTITATIVE LINK BETWEEN BIOLOGICAL EVOLUTION AND STATISTICAL MECHANICS
Authors: RAY TANE S.
Published: March 2008

A model of evolution called the modified Wright–Fisher model (MWF) is introduced. It is shown to exhibit a second order phase transition, and a quantitative mapping is established between the mean field Ising model and itself. An equation of state and scaling function are derived for the MWF from the steady state solution of the governing quasispecies equations. The critical exponents are identical to those of the mean-field Ising model. Simulation data for the MWF on a two-dimensional square lattice show good evidence for a critical point. The susceptibility exponent is estimated and is found, within the uncertainty of the simulation data, to be equal to that of the two-dimensional Ising model, suggesting that the two models are in the same universality class.
ON THE STUDY OF DELAY FEEDBACK CONTROL AND ADAPTIVE SYNCHRONIZATION NEAR SUB-CRITICAL HOPF BIFURCATION
Authors: GHOSH DIBAKAR , SAHA PAPRI , CHOWDHURY A. ROY
Published: March 2008

The effect of delay feedback control and adaptive synchronization is studied near sub-critical Hopf bifurcation of a nonlinear dynamical system. Previously, these methods targeted the nonlinear systems near their chaotic regime but it is shown here that they are equally applicable near the branch of unstable solutions. The system is first analyzed from the view point of bifurcation, and the existence of Hopf bifurcation is established through normal form analysis. Hopf bifurcation can be either sub-critical or super-critical, and in the former case, unstable periodic orbits are formed. Our aim is to control them through a delay feedback approach so that the system stabilizes to its nearest stable periodic orbit. At the vicinity of the sub-critical Hopf point, adaptive synchronization is studied and the effect of the coupling parameter and the speed factor is analyzed in detail. Adaptive synchronization is also studied when the system is in the chaotic regime.
LEARNING AND EVALUATING BAYESIAN NETWORK EQUIVALENCE CLASSES FROM INCOMPLETE DATA
Authors: BORCHANI HANEN , AMOR NAHLA BEN , KHALFALLAH FÉDIA
Published: March 2008

In this paper, we propose a new method, named Greedy Equivalence Search-Expectation Maximization (GES-EM), for learning Bayesian networks from incomplete data. Our method extends the recently proposed Greedy Equivalence Search (GES) algorithm10 to deal with incomplete data. For the quality evaluation of learned networks, we make use of the expected Bayesian Information Criterion (BIC) scoring function. In addition, we propose a new structural evaluation criterion. This so-called SEC criterion is more suitable than existing structural evaluation criteria, since it is based on the comparison of learned networks to the generating ones through Completed Partially Directed Acyclic Graphs (CPDAGs). Experimental results show that GES-EM algorithm yields more accurate structures than the standard Alternating Model Selection-Expectation Maximization (AMS-EM) algorithm.15.
RECOVERY OF NONRIGID STRUCTURES FROM 2D OBSERVATIONS
Authors: ZHOU HUIYU , LI XUELONG , LIU TANGWEI , LIN FAQUAN , PANG YUSHENG , WU JI , DONG JUNYU , WU JIAHUA
Published: March 2008

We present a new method for simultaneously determining three-dimensional (3D) motion and structure of a nonrigid object from its uncalibrated two-dimensional (2D) data with Gaussian or non-Gaussian distributions. A nonrigid motion can be treated as a combination of a rigid component and a nonrigid deformation. To reduce the high dimensionality of the deformable structure or shape, we estimate the probability distribution function (PDF) of the structure through random sampling, integrating an established probabilistic model. The fitting between the observations and the estimated 3D structure will be evaluated using the pooled variance estimator. The recovered structure is only available when the 2D feature points have been properly corresponded over two image frames. Applications of the proposed method to both synthetic and real image sequences are demonstrated with promising results.
ON DETERMINING SUITABLE SUBSETS OF DECISION RULES USING CHOQUET INTEGRAL
Authors: RENDEK JAN , WENDLING LAURENT
Published: March 2008

We present an approach to automatically extract a pertinent subset of soft output classifiers, and to aggregate them into a global decision rule using the Choquet integral. This approach relies on two key points. The first is a learning algorithm that uses a measure of the confusion between the categories to be recognized. The second is a selection scheme that discards weak or redundant decision rules, keeping only the most relevant subset. An experimental study, based on real world data, is then described. It analyzes the improvements achieved by these points first when used independently, then when combined together.
ATTRACTOR GALLERY FROM A NEW HIGHER DIMENSIONAL CHAOTIC CIRCUIT
Authors: KILIÇ RECAI
Published: March 2008

In this paper, a chaotic attractor gallery obtained from a new higher dimensional chaotic circuit combining LMT (Lindberg–Murali and Tamasevicious) circuit and Chua's circuit is presented. This circuit is capable of exhibiting a rich variety of chaotic attractors including temporary multiscroll attractors.
CHAOTIC CRYPTOGRAPHIC SCHEME BASED ON COMPOSITION MAPS
Authors: BEHNIA SOHRAB , AKHSHANI AFSHIN , MAHMODI HADI , AKHAVAN AMIR
Published: March 2008

In recent years, a growing number of cryptosystems based on chaos have been proposed. But most of them have encountered many problems such as small key space and weak security. In the present paper, a new kind of chaotic cryptosystem based on Composition of Trigonometric Chaotic Maps is proposed. These maps which are defined as ratios of polynomials of degree N, have interesting properties such as invariant measure, ergodicity, variable chaotic region with respect to the control parameters and ability to construct composition form of maps. We have used a composition of chaotic map to shuffle the position of image pixels. Another composition of chaotic map is used in diffusion process. According to the performed analysis, the introduced algorithm can satisfy the required performances such as high level security, large key space and the acceptable encryption speed.
INNOVATIVE CAPABILITY, INNOVATION STRATEGY AND MARKET ORIENTATION: AN EMPIRICAL ANALYSIS IN TURKISH SOFTWARE INDUSTRY
Authors: AKMAN GÜLŞEN , YILMAZ CENGIZ
Published: March 2008

Innovation could be recognised as a key success factor in an increasingly competitive, global economy. The purpose of this paper is to examine the relations among market orientation, innovation strategy, innovative capability and innovation success in small and medium-sized business in developing countries. This study builds a model related to the most important factors that influence mostly innovative capability of firms, such as market orientation, technological orientation and innovation strategy. Then it examines the relationships between these factors and the innovative capability. A practical research was carried out in the Turkish software industry. Analysis, futurity and proactiveness dimensions of innovation strategy influence the innovative capability of software firms. Also, only customer orientation component of market orientation influences the innovative capability of the firms. Effects of other factors are not significant. Results of this study could lead to effective management of innovation for the software firms and benefits for the firms' managers.
Myocardial susceptibility to ischemic-reperfusion injury in a prediabetic model of dietary-induced obesity
Authors: du Toit Eugene F. , Smith Wayne , Muller Christo , Strijdom Hans , Stouthammer Bernadette , Woodiwiss Angela J. , Norton Gavin R. , Lochner Amanda
Published: March 2008

We assessed the myocardial susceptibility to ischemic-reperfusion injury in obese rat hearts in the absence and the presence of predicted circulating concentrations of insulin and fatty acids. Feeding rats a high-calorie diet resulted in increases in body weight, visceral fat content, cardiac hypertrophy, plasma insulin, nonesterified free fatty acid, and triglyceride concentrations. In the absence of both insulin and fatty acids in the coronary perfusate, the hearts of obese rats developed an increased infarct size (41.9 ± 1.9% for obese vs. 22.9 ± 2.3% for control, P < 0.05) and a reduced percent recovery of aortic output (4.2 ± 4.2% for obese vs. 27.7 ± 3.4% for controls, P < 0.05) after coronary artery occlusion and reperfusion. In the presence of insulin in the coronary perfusate, a cardioprotective effect was noted in both groups, an action that was greater in hearts from obese compared with control rats and which abolished the obesity-induced changes in infarct size (13.8 ± 1.2% for controls vs. 21.0 ± 1.6% for obese), and percent recovery of aortic output (60.2 ± 4.7% for controls vs. 45.7 ± 9.4% for obese). Fatty acids (0.7 mM, control; and 1.5 mM, obese) added to the coronary perfusate with in vivo concentrations of insulin dramatically increased infarct size (48.2 ± 3.1% for obese, and 37.5 ± 2.7% for control; P < 0.05 vs. without fatty acids) and decreased percent aortic output recovery (control, 10.4 ± 5.2%, and obese 7.8 ± 3.5%; P < 0.05 vs. without fatty acids) in both groups to similar values. In conclusion, in obesity, the impact of an increased susceptibility of the myocardium to ischemic-reperfusion injury on myocardial injury is likely to be overshadowed by the comparatively greater roles played by predicted increases in circulating insulin and fatty acids found in vivo. These data support the notion that adiposity per se is unlikely to be a valuable predictor of outcomes in ischemic-reperfusion injury.
Lovastatin interferes with the infarct size-limiting effect of ischemic preconditioning and postconditioning in rat hearts
Authors: Kocsis Gabriella F. , Pipis Judit , Fekete Veronika , Kovács-Simon Andrea , Odendaal Louise , Molnár Éva , Giricz Zoltán , Janáky Tamás , van Rooyen Jacques , Csont Tamás , Ferdinandy Péter
Published: March 2008

Statins have been shown to be cardioprotective; however, their interaction with endogenous cardioprotection by ischemic preconditioning and postconditioning is not known. In the present study, we examined if acute and chronic administration of the 3-hydroxy-3-methylglutaryl CoA reductase inhibitor lovastatin affected the infarct size-limiting effect of ischemic preconditioning and postconditioning in rat hearts. Wistar rats were randomly assigned to the following three groups: 1) vehicle (1% methylcellulose per os for 12 days), 2) chronic lovastatin (15 mg·kg−1·day−1 per os for 12 days), and 3) acute lovastatin (1% methylcellulose per os for 12 days and 50 μmol/l lovastatin in the perfusate). Hearts isolated from the three groups were either subjected to a nonconditioning (aerobic perfusion followed by 30-min coronary occlusion and 120-min reperfusion, i.e., test ischemia-reperfusion), preconditioning (three intermittent periods of 5-min ischemia-reperfusion cycles before test ischemia-reperfusion), or postconditioning (six cycles of 10-s ischemia-reperfusion after test ischemia) perfusion protocol. Preconditioning and postconditioning significantly decreased infarct size in vehicle-treated hearts. However, preconditioning failed to decrease infarct size in acute lovastatin-treated hearts, but the effect of postconditioning remained unchanged. Chronic lovastatin treatment abolished postconditioning but not preconditioning; however, it decreased infarct size in the nonconditioned group. Myocardial levels of coenzyme Q9 were decreased in both acute and chronic lovastatin-treated rats. Western blot analysis revealed that both acute and chronic lovastatin treatment attenuated the phoshorylation of Akt; however, acute but not chronic lovastatin treatment increased the phosphorylation of p42 MAPK/ERK. We conclude that, although lovastatin may lead to cardioprotection, it interferes with the mechanisms of cardiac adaptation to ischemic stress.
Effect of obesity on pulmonary inflammation induced by acute ozone exposure: role of interleukin-6
Authors: Lang Jason E. , Williams Erin S. , Mizgerd Joseph P. , Shore Stephanie A.
Published: March 2008

To determine the role of interleukin (IL)-6 in the increased ozone (O3)-induced inflammation and injury observed in obese vs. lean mice, lean wild-type and leptin-deficient obese ( ob/ob) mice were injected with anti-IL-6 antibody (Ab) or isotype control Ab 24 h before exposure to either O3 (2 ppm for 3 h) or room air. Four or 24 h after O3 exposure, bronchoalveolar lavage (BAL) was performed, and the lungs were harvested for Western blotting. Anti-IL-6 Ab caused substantial reductions in O3-induced increases in BAL IL-6 in mice of both genotypes. Four hours following O3, ob/ob mice had increased BAL neutrophils compared with controls, and anti-IL-6-Ab virtually abolished this difference. At 24 h, O3-induced increases in BAL protein and BAL serum albumin were augmented in ob/ob vs. wild-type mice, and anti-IL-6 Ab ablated these obesity-related differences in epithelial barrier injury. O3 increased tyrosine phosphorylation of STAT-3 and STAT-1. There was no effect of obesity on STAT-3 phosphorylation, whereas obesity decreased STAT-1 expression, resulting in reduced STAT-1 phosphorylation. IL-6 neutralization did not alter STAT-3 or STAT-1 phosphorylation in ob/ob or wild-type mice. O3 increased BAL leukemia inhibitory factor (LIF) to a greater extent in obese than in lean mice, and LIF may account for effects on STAT phosphorylation. Our results suggest that IL-6 plays a complex role in pulmonary responses to O3, a role that differs between wild-type and ob/ob mice. Moreover, obesity-related differences in activation of STAT proteins may contribute to some of the differences in the response of obese vs. lean mice.
Intratracheal perfluorocarbons diminish LPS-induced increase in systemic TNF-α
Authors: Burkhardt Wolfram , Koehne Petra , Wissel Heide , Graf Susanne , Proquitté Hans , Wauer Roland R. , Rüdiger Mario
Published: March 2008

Perfluorocarbons (PFC) reduce the production of various inflammatory cytokines, including TNF-α. The anti-inflammatory effect is not entirely understood. If anti-inflammatory properties are caused by a mechanical barrier, PFC in the alveoli should have no effect on the inflammatory response to intravenous LPS administration. To test that hypothesis, rats ( n = 31) were administered LPS intravenously and were either spontaneously breathing (Spont), conventionally ventilated (CMV), or receiving partial liquid ventilation (PLV). Serum concentration of TNF-α was measured. The pulmonary expressions of TNF-α and TNF-α receptor 1 protein and of TNF-α and ICAM-1 mRNA were determined. LPS caused a significant ( P < 0.001) increase in serum TNF-α. Serum TNF-α concentration was similar in LPS/Spont (525 ± 180 pg/ml) and LPS/CMV (504 ± 154 pg/ml) but was significantly ( P < 0.001) lower in animals of the LPS/PLV group (274 ± 101 pg/ml). Immunohistochemical data on TNF-α protein expression showed a LPS-induced increase in TNF-α and TNF-α receptor 1 expression that was diminished by partial liquid ventilation. PCR measurements revealed a lower expression of TNF-α and ICAM-1 mRNA in LPS/PLV than in LPS/CMV or LPS/Spont animals. Semiquantitative histological evaluation revealed only minor alveolar inflammation with no significant differences between the groups. Low serum TNF-α concentration in PFC-treated animals is most likely explained by a decreased production of TNF-α in the lung.
Effects of chronic l-NAME treatment lung tissue mechanics, eosinophilic and extracellular matrix responses induced by chronic pulmonary inflammation
Authors: Angeli Patrícia , Prado Carla M. , Xisto Débora G. , Silva Pedro L. , Pássaro Caroline P. , Nakazato Hugo D. , Leick-Maldonado Edna A. , Martins Milton A. , Rocco Patricia R. M. , Tibério Iolanda F. L. C.
Published: March 2008

The importance of lung tissue in asthma pathophysiology has been recently recognized. Although nitric oxide mediates smooth muscle tonus control in airways, its effects on lung tissue responsiveness have not been investigated previously. We hypothesized that chronic nitric oxide synthase (NOS) inhibition by Nω-nitro-l-arginine methyl ester (l-NAME) may modulate lung tissue mechanics and eosinophil and extracellular matrix remodeling in guinea pigs with chronic pulmonary inflammation. Animals were submitted to seven saline or ovalbumin exposures with increasing doses (1∼5 mg/ml for 4 wk) and treated or not with l-NAME in drinking water. After the seventh inhalation (72 h), animals were anesthetized and exsanguinated, and oscillatory mechanics of lung tissue strips were performed in baseline condition and after ovalbumin challenge (0.1%). Using morphometry, we assessed the density of eosinophils, neuronal NOS (nNOS)- and inducible NOS (iNOS)-positive distal lung cells, smooth muscle cells, as well as collagen and elastic fibers in lung tissue. Ovalbumin-exposed animals had an increase in baseline and maximal tissue resistance and elastance, eosinophil density, nNOS- and iNOS-positive cells, the amount of collagen and elastic fibers, and isoprostane-8-PGF2α expression in the alveolar septa compared with controls ( P < 0.05). l-NAME treatment in ovalbumin-exposed animals attenuated lung tissue mechanical responses ( P < 0.01), nNOS- and iNOS-positive cells, elastic fiber content ( P < 0.001), and isoprostane-8-PGF2α in the alveolar septa ( P < 0.001). However, this treatment did not affect the total number of eosinophils and collagen deposition. These data suggest that NO contributes to distal lung parenchyma constriction and to elastic fiber deposition in this model. One possibility may be related to the effects of NO activating the oxidative stress pathway.
Indicator dilution measurements of extravascular lung water: basic assumptions and observations
Authors: Effros Richard M. , Pornsuriyasak Prapaporn , Porszasz Janos , Casaburi Richard
Published: March 2008

Since they were introduced more than five decades ago, a variety of single-pass indicator, thermal, and osmotic dilution approaches have been developed for detecting and measuring excess fluid in the lungs. This brief review discusses why studies of the extravascular lung water (EVLW) continue to intrigue physiologists and clinicians and the likelihood that they will become sufficiently reliable for more widespread use. Emphasis is placed on the basic assumptions that underlie these measurements and limitations imposed by the nature of the data that are collected. A distinction is made between approaches that are based on compartmental models of solute and water exchange and those that represent extensions of more conventional washout procedures, which have been utilized extensively for measurements of gas volumes in the lungs. Although the compartmental approach has been used to simplify indicator dilution studies by eliminating the need for a vascular indicator, it is based on assumptions that may not be realistic. Early recirculation inevitably limits the period in which observations can be made and impairs detection of those portions of the lungs with decreased perfusion. These general principles are also used to develop a new method of analyzing osmotic transient studies. A short account is given of EVLW observations that have been made in animals and humans. Both the sensitivity and specificity of EVLW measurements in humans are uncertain, and the normal clinical range of EVLW remains in doubt.
Lagrangian Diagnostics of Tropical Deep Convection and Its Effect upon Upper-Tropospheric Humidity
Authors: Horváth Ákos , Soden Brian J.
Published: March 2008

This study combines geostationary water vapor imagery with optical cloud property retrievals and microwave sea surface observations in order to investigate, in a Lagrangian framework, (i) the importance of cirrus anvil sublimation on tropical upper-tropospheric humidity and (ii) the sea surface temperature dependence of deep convective development. Although an Eulerian analysis shows a strong spatial correlation of ∼0.8 between monthly mean cirrus ice water path and upper-tropospheric humidity, the Lagrangian analysis indicates no causal link between these quantities. The maximum upper-tropospheric humidity occurs ∼5 h after peak convection, closely synchronized with the maximum cirrus ice water path, and lagging behind it by no more than 1.0 h. Considering that the characteristic e-folding decay time of cirrus ice water is determined to be ∼4 h, this short time lag does not allow for significant sublimative moistening. Furthermore, a tendency analysis reveals that cirrus decay and growth, in terms of both cloud cover and integrated ice content, is accompanied by the drying and moistening of the upper troposphere, respectively, a result opposite that expected if cirrus ice were a primary water vapor source. In addition, it is found that an ∼2°C rise in sea surface temperature results in a measurable increase in the frequency, spatial extent, and water content of deep convective cores. The larger storms over warmer oceans are also associated with slightly larger anvils than their counterparts over colder oceans; however, anvil area per unit cumulus area, that is, cirrus detrainment efficiency, decreases as SST increases.
The Impacts of Convective Parameterization and Moisture Triggering on AGCM-Simulated Convectively Coupled Equatorial Waves
Authors: Lin Jia-Lin , Lee Myong-In , Kim Daehyun , Kang In-Sik , Frierson Dargan M. W.
Published: March 2008

This study examines the impacts of convective parameterization and moisture convective trigger on convectively coupled equatorial waves simulated by the Seoul National University (SNU) atmospheric general circulation model (AGCM). Three different convection schemes are used, including the simplified Arakawa–Schubert (SAS) scheme, the Kuo (1974) scheme, and the moist convective adjustment (MCA) scheme, and a moisture convective trigger with variable strength is added to each scheme. The authors also conduct a “no convection” experiment with deep convection schemes turned off. Space–time spectral analysis is used to obtain the variance and phase speed of dominant convectively coupled equatorial waves, including the Madden–Julian oscillation (MJO), Kelvin, equatorial Rossby (ER), mixed Rossby–gravity (MRG), and eastward inertio-gravity (EIG) and westward inertio-gravity (WIG) waves.

The results show that both convective parameterization and the moisture convective trigger have significant impacts on AGCM-simulated, convectively coupled equatorial waves. The MCA scheme generally produces larger variances of convectively coupled equatorial waves including the MJO, more coherent eastward propagation of the MJO, and a more prominent MJO spectral peak than the Kuo and SAS schemes. Increasing the strength of the moisture trigger significantly enhances the variances and slows down the phase speeds of all wave modes except the MJO, and usually improves the eastward propagation of the MJO for the Kuo and SAS schemes, but the effect for the MCA scheme is small. The no convection experiment always produces one of the best signals of convectively coupled equatorial waves and the MJO.
Observed Inconsistencies between Snow Extent and Snow Depth Variability at Regional/Continental Scales
Authors: Ge Yan , Gong Gavin
Published: March 2008

Snow extent and snow depth are two related characteristics of a snowpack, but they do not need to be mutually consistent. Differences between these two variables at local scales are readily apparent. However, at larger scales, which interact with atmospheric circulation and climate, snow extent is the primary variable considered, owing largely to the scarcity of snow depth data. In this study, three regional-/continental-scale gridded snow depth/snow water equivalent (SWE) datasets, derived from station observations or passive microwave satellite sensors, are utilized to quantitatively evaluate the relationship between snow extent and snow depth/SWE over North America. Various statistical methods are used to ensure the robustness of the results, including correlations, composites, and singular value decomposition analyses.

Results indicate that continental-scale snow depth variations are substantial in their own right and that depth and extent anomalies are largely unrelated over broad high-latitude regions north of the snow line. Snow extent and snow depth vary more consistently in the vicinity of the snow line, especially in autumn and spring, during which precipitation and ablation can affect both variables. It is also found that deeper (shallower) winter snow translates into larger (smaller) snow-covered areas in the following spring/summer season, and also a longer (shorter) snow season, but only in specific regions. These results suggest a possible influence of snow depth on spring and summer climate. Overall, the observed lack of mutual consistency between these two snowpack variables at continental/regional scales suggests that snow depth variations may be of sufficiently large magnitude, spatial scope, and temporal duration to interact with regional–hemispheric climate, in a manner unrelated to the more extensively studied snow extent variations.
Sensitivity of Thermal Infrared Radiation at the Top of the Atmosphere and the Surface to Ice Cloud Microphysics
Authors: Dubuisson Philippe , Giraud Vincent , Pelon Jacques , Cadet Bertrand , Yang Ping
Published: March 2008

This paper reports on the sensitivity of the brightness temperatures associated with radiances at the surface and the top of the atmosphere, simulated for the Imaging Infrared Radiometer (IIR) 8.7-, 10.6-, and 12-μm channels under ice cloudy conditions, to the optical and microphysical properties of ice clouds. The 10.6- and 12-μm channels allow simultaneous retrieval of ice cloud optical thickness and effective particle size (Deff) less than 100 μm. It is illustrated that the particle shape and size distributions of ice crystals have noticeable effects on the brightness temperatures. Using the split window technique based on the 10.6- and 12-μm channels in conjunction with cloud properties assumed a priori, the authors show that the influence of the cloud microphysical properties can lead to differences on the order of ±10% and ±25% in retrieved effective particle sizes for small (Deff < 20 μm) and large particles (Deff > 40 μm), respectively. The impact of cloud model on retrieved optical thickness is on the order of ±10%. Different particle habits may lead to ±25% differences in ice water path (IWP). Theoretically, the use of an additional channel (i.e., 8.7 μm) can give a stronger constraint on cloud model and improve the retrieval of Deff and IWP. The present simulations have confirmed that cloud microphysics has a significant impact on the 8.7-μm brightness temperatures mainly because of particle shape. This impact is larger than the errors of the IIR measurements for cloud optical thicknesses (at 12 μm) ranging from 0.3 to 8. Furthermore, it is shown that the characterization of optical and microphysical properties of ice clouds from ground-based measurements is quite challenging. Especially, water vapor in the atmosphere has an important impact on ground-based cloud retrievals. Observation stations at higher altitudes or airborne measurements would minimize the atmospheric effect.
Modeling the View Angle Dependence of Gap Fractions in Forest Canopies: Implications for Mapping Fractional Snow Cover Using Optical Remote Sensing
Authors: Liu Jicheng , Woodcock Curtis E. , Melloh Rae A. , Davis Robert E. , McKenzie Ceretha , Painter Thomas H.
Published: March 2008

Forest canopies influence the proportion of the land surface that is visible from above, or the viewable gap fraction (VGF). The VGF limits the amount of information available in satellite data about the land surface, such as snow cover in forests. Efforts to recover fractional snow cover from the spectral mixture analysis model Moderate Resolution Imaging Spectroradiometer (MODIS) snow-covered area and grain size (MODSCAG) indicate the importance of view angle effects in forested landscapes. The VGF can be estimated using both hemispherical photos and forest canopy models. For a set of stands in the Cold Land Field Processes Experiment (CLPX) sites in the Fraser Experimental Forest in Colorado, the convergence of both measurements and models of the VGF as a function of view angle supports the idea that VGF can be characterized as a function of forest properties. A simple geometric optical (GO) model that includes only between-crown gaps can capture the basic shape of the VGF as a function of view zenith angle. However, the GO model tends to underestimate the VGF compared with estimates derived from hemispherical photos, particularly at high view angles. The use of a more complicated geometric optical–radiative transfer (GORT) model generally improves estimates of the VGF by taking into account within-crown gaps. Small footprint airborne lidar data are useful for mapping forest cover and height, which makes the parameterization of the GORT model possible over a landscape. Better knowledge of the angular distribution of gaps in forest canopies holds promise for improving remote sensing of snow cover fraction.
NASA Cold Land Processes Experiment (CLPX 2002/03): Atmospheric Analyses Datasets
Authors: Liston Glen E. , Birkenheuer Daniel L. , Hiemstra Christopher A. , Cline Donald W. , Elder Kelly
Published: March 2008

This paper describes the Local Analysis and Prediction System (LAPS) and the 20-km horizontal grid version of the Rapid Update Cycle (RUC20) atmospheric analyses datasets, which are available as part of the Cold Land Processes Field Experiment (CLPX) data archive. The LAPS dataset contains spatially and temporally continuous atmospheric and surface variables over Colorado, Wyoming, and parts of the surrounding states. The analysis used a 10-km horizontal grid with 21 vertical levels and an hourly temporal resolution. The LAPS archive includes forty-six 1D surface fields and nine 3D upper-air fields, spanning the period 1 September 2001 through 31 August 2003. The RUC20 dataset includes hourly 3D atmospheric analyses over the contiguous United States and parts of southern Canada and northern Mexico, with 50 vertical levels. The RUC20 archive contains forty-six 1D surface fields and fourteen 3D upper-air fields, spanning the period 1 October 2002 through 31 September 2003. The datasets are archived at the National Snow and Ice Data Center (NSIDC) in Boulder, Colorado.
Intercomparison of Evapotranspiration Estimates at the Different Ecological Zones in Jordan
Authors: Suleiman Ayman , Al-Bakri Jawad , Duqqah Mohammad , Crago Rich
Published: March 2008

An estimate of evapotranspiration (ET) is needed for many applications in diverse disciplines such as agriculture, hydrology, and meteorology. The objective of this study was to compare two methods for estimating daily actual ET (ETa) from six sites located in four different ecological zones within Jordan. The first method used the analytical land–atmosphere radiometer model (ALARM) and the dimensionless temperature procedure, whereas the second method used ETa calculated from the FAO-56 reference evapotranspiration. ALARM converts general remotely sensed surface temperatures to aerodynamic temperature. Standard meteorological data from weather stations were used with both methods, and the Moderate Resolution Imaging Spectroradiometer (MODIS)–based leaf area index, surface temperature, and albedo were obtained to estimate ETa, using the former method. A validation study was conducted on an alfalfa field in Jordan Valley using ALARM and the American Society of Civil Engineers’ (ASCE) method, which is very similar to FAO-56 except it uses alfalfa as a reference crop. Because this alfalfa field was irrigated and because of warm air advection, ET rates based on measurements of soil moisture change ranged from about 6 to 10 mm day−1. For this range, the root-mean-square error (RMSE) for ALARM was 0.87 mm day−1 and the coefficient of determination r 2 was 0.36, whereas the RMSE for ASCE was 1.25 mm day−1 and r 2 = 0.06. There was good agreement between minimum, maximum, and average ETa for the two methods at all sites except for Irbid, for which the minimum and, consequently, the average were different. Much of the site-to-site and temporal variability was found to be statistically significant. Reasons for this variability include soil types, vegetation cover, irrigation, and warm advection.
NASA Cold Land Processes Experiment (CLPX 2002/03): Spaceborne Remote Sensing
Authors: Davis Robert E. , Painter Thomas H. , Forster Rick , Cline Don , Armstrong Richard , Haran Terry , McDonald Kyle , Elder Kelly
Published: March 2008

This paper describes satellite data collected as part of the 2002/03 Cold Land Processes Experiment (CLPX). These data include multispectral and hyperspectral optical imaging, and passive and active microwave observations of the test areas. The CLPX multispectral optical data include the Advanced Very High Resolution Radiometer (AVHRR), the Landsat Thematic Mapper/Enhanced Thematic Mapper Plus (TM/ETM+), the Moderate Resolution Imaging Spectroradiometer (MODIS), and the Multi-angle Imaging Spectroradiometer (MISR). The spaceborne hyperspectral optical data consist of measurements acquired with the NASA Earth Observing-1 (EO-1) Hyperion imaging spectrometer. The passive microwave data include observations from the Special Sensor Microwave Imager (SSM/I) and the Advanced Microwave Scanning Radiometer (AMSR) for Earth Observing System (EOS; AMSR-E). Observations from the Radarsat synthetic aperture radar and the SeaWinds scatterometer flown on QuikSCAT make up the active microwave data.
Dependent Correlations in Meta-Analysis
Authors: Shu Fai Cheung  , Chan Darius K.-S.
Published: March 2008

In meta-analysis, it is common to have dependent effect sizes, such as several effect sizes from the same sample but measured at different times. Cheung and Chan proposed the adjusted-individual and adjusted-weighted procedures to estimate the degree of dependence and incorporate this estimate in the meta-analysis. The present study extends the previous study by examining the case of heterogeneous degree of dependence. Simulation results reveal that these two procedures again generated less biased estimates of the degree of heterogeneity than the commonly used samplewise procedure and were statistically more powerful to detect true variations. In addition, the adjusted-weighted procedure generated slightly less biased estimates of the degree of heterogeneity than the adjusted-individual weighted procedure across conditions. Future directions to further refine these procedures are discussed.
The Empirical Verification of an Assignment of Items to Subtests
Authors: Stuive Ilse , Kiers Henk A. L. , Timmerman Marieke E. , ten Berge Jos M. F.
Published: March 2008

This study compares two confirmatory factor analysis methods on their ability to verify whether correct assignments of items to subtests are supported by the data. The confirmatory common factor (CCF) method is used most often and defines nonzero loadings so that they correspond to the assignment of items to subtests. Another method is the oblique multiple group (OMG) method, which defines subtests as unweighted sums of the scores on all items assigned to the subtest, and (corrected) correlations are used to verify the assignment. A simulation study compares both methods, accounting for the influence of model error and the amount of unique variance. The CCF and OMG methods show similar behavior with relatively small amounts of unique variance and low interfactor correlations. However, at high amounts of unique variance and high interfactor correlations, the CCF detected correct assignments more often, whereas the OMG was better at detecting incorrect assignments.
The Guidance of God
Authors: Thornton-Duesbery J.P.
Published: March 2008

'ALMOST in secret, a strange work has been going on for the last two or three years among the undergraduates of many universities, not only here in England, but all over the world. This work of which the general public knows nothing at all, and of which the religious authorities so far as I can gather have never heard, is the activity of a single person.'