bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of Pulsed-Field Gel Electrophoresis and
spa
Typing for Long-Term, Nationwide Epidemiological Surveillance Studies of
Staphylococcus aureus
Infections
Authors: Hallin M. , Deplano A. , Denis O. , De Mendonça R. , De Ryck R. , Struelens M. J.
Published: November 2006

Pulsed-field gel electrophoresis (PFGE) of genomic macrorestriction fragments has been used by the Belgian Reference Laboratory for Staphylococci for national hospital surveys of methicillin-resistant
Staphylococcus aureus
since 1992. The sequencing of the polymorphic X region of the protein A gene (
spa
typing) offers significant advantages over PFGE in terms of speed, ease of interpretation, and exportability. To validate its potential use for national surveillance, we evaluated the robustness of
spa
typing compared with that of PFGE based on a collection of 217
S. aureus
strains representative of the Belgian
S. aureus
epidemiology during the last 13 years.
spa
typing and PFGE both showed high discriminatory power (discriminatory indexes of 0.98 and 0.96, respectively) and achieved high concordance (95.9%) in type classification. Both methods also showed good concordance with multilocus sequence typing (MLST) (95.5%). However, we observed occasional “violations” of MLST clonal complex assignment by
spa
typing. Our results suggest that both PFGE and
spa
typing are reliable methods for long-term, nationwide epidemiological surveillance studies. We suggest that
spa
typing, which is a single-locus-based method, should preferably be used in combination with additional markers, such as staphylococcal cassette chromosome
mec
typing or resistance or virulence gene detection.
Mutational Analysis of Aminopeptidase N, a Receptor for Several Group 1 Coronaviruses, Identifies Key Determinants of Viral Host Range
Authors: Tusell Sonia M. , Schittone Stephanie A. , Holmes Kathryn V.
Published: November 2006

Feline coronavirus (FCoV), porcine transmissible gastroenteritis coronavirus (TGEV), canine coronavirus (CCoV), and human coronavirus HCoV-229E, which belong to the group 1 coronavirus, use aminopeptidase N (APN) of their natural host and feline APN (fAPN) as receptors. Using mouse-feline APN chimeras, we identified three small, discontinuous regions, amino acids (aa) 288 to 290, aa 732 to 746 (called R1), and aa 764 to 788 (called R2) in fAPN that determined the host ranges of these coronaviruses. Blockade of infection with anti-fAPN monoclonal antibody RG4 suggested that these three regions lie close together on the fAPN surface. Different residues in fAPN were required for infection with each coronavirus. HCoV-229E infection was blocked by an N-glycosylation sequon present between aa 288 to 290 in murine APN. TGEV required R1 of fAPN, while FCoV and CCoV required both R1 and R2 for entry. N740 and T742 in fAPN and the homologous R741 in human APN (hAPN) were key determinants of host range for FCoV, TGEV, and CCoV. Residue N740 in fAPN was essential only for CCoV receptor activity. A conservative T742V substitution or a T742R substitution in fAPN destroyed receptor activity for the pig, dog, and cat coronaviruses, while a T742S substitution retained these receptor activities. Thus, the hydroxyl on T742 is required for the coronavirus receptor activity of fAPN. In hAPN an R741T substitution caused a gain of receptor activity for TGEV but not for FCoV or CCoV. Therefore, entry and host range of these group 1 coronaviruses depend on the ability of the viral spike glycoproteins to recognize small, species-specific amino acid differences in the APN proteins of different species.
GB Virus B Disrupts RIG-I Signaling by NS3/4A-Mediated Cleavage of the Adaptor Protein MAVS
Authors: Chen Zihong , Benureau Yann , Rijnbrand Rene , Yi Jianzhong , Wang Ting , Warter Lucile , Lanford Robert E. , Weinman Steven A. , Lemon Stanley M. , Martin Annette , Li Kui
Published: November 2006

Understanding the mechanisms of hepatitis C virus (HCV) pathogenesis and persistence has been hampered by the lack of small, convenient animal models. GB virus B (GBV-B) is phylogenetically the closest related virus to HCV. It causes generally acute and occasionally chronic hepatitis in small primates and is used as a surrogate model for HCV. It is not known, however, whether GBV-B has evolved strategies to circumvent host innate defenses similar to those of HCV, a property that may contribute to HCV persistence in vivo. We show here in cultured tamarin hepatocytes that GBV-B NS3/4A protease, but not a related catalytically inactive mutant, effectively blocks innate intracellular antiviral responses signaled through the RNA helicase, retinoic acid-inducible gene I (RIG-I), an essential sensor molecule that initiates host defenses against many RNA viruses, including HCV. GBV-B NS3/4A protease specifically cleaves mitochondrial antiviral signaling protein (MAVS; also known as IPS-1/Cardif/VISA) and dislodges it from mitochondria, thereby disrupting its function as a RIG-I adaptor and blocking downstream activation of both interferon regulatory factor 3 and nuclear factor kappa B. MAVS cleavage and abrogation of virus-induced interferon responses were also observed in Huh7 cells supporting autonomous replication of subgenomic GBV-B RNAs. Our data indicate that, as in the case of HCV, GBV-B has evolved to utilize its major protease to disrupt RIG-I signaling and impede innate antiviral defenses. These data provide further support for the use of GBV-B infection in small primates as an accurate surrogate model for deciphering virus-host interactions in hepacivirus pathogenesis.
Biochemical and Genetic Analysis of the Vaccinia Virus D5 Protein: Multimerization-Dependent ATPase Activity Is Required To Support Viral DNA Replication
Authors: Boyle Kathleen A. , Arps Lisa , Traktman Paula
Published: November 2006

The vaccinia virus-encoded D5 protein is an essential ATPase involved in viral DNA replication. We have expanded the genotypic and phenotypic analysis of six temperature-sensitive (
ts
) D5 mutants (C
ts
17, C
ts
24, E
ts
69, D
ts
6389 [also referred to as D
ts
38], D
ts
12, and D
ts
56) and shown that at nonpermissive temperature all of the
ts
D5 viruses exhibit a dramatic reduction in DNA synthesis and virus production. For C
ts
17 and C
ts
24, this restriction reflects the thermolability of the D5 proteins. The D
ts
6389, D
ts
12, and D
ts
56 D5 proteins become insoluble at 39.7°C, while the E
ts
69 D5 protein remains stable and soluble and retains the ability to oligomerize and hydrolyze ATP when synthesized at 39.7°C. To investigate which structural features of D5 are important for its biological and biochemical activities, we generated targeted mutations in invariant residues positioned within conserved domains found within D5. Using a transient complementation assay that assessed the ability of D5 variants to sustain ongoing DNA synthesis during nonpermissive C
ts
24 infections, only a
wt
D5 allele supported DNA synthesis. Alleles of D5 containing targeted mutations within the Walker A or B domains, the superfamily III helicase motif C, or the AAA+ motif lacked biological competency. Furthermore, purified preparations of these variant proteins revealed that they all were defective in ATP hydrolysis. Multimerization of D5 appeared to be a prerequisite for enzymatic activity and required the Walker B domain, the AAA+ motif, and a region located upstream of the catalytic core. Finally, although multimerization and enzymatic activity are necessary for the biological competence of D5, they are not sufficient.
Cytostatic and Antiviral 6-Arylpurine Ribonucleosides VIII. Synthesis and Evaluation of 6-Substituted Purine 3'-Deoxyribonucleosides
Authors: Hocek Michal , Šilhár Peter , Pohl Radek
Published: November 2006

A series of purine 3'-deoxyribonucleosides bearing diverse C-substituents (alkyl, aryl, hetaryl or hydroxymethyl) in the position 6 was prepared by Pd-catalyzed cross-coupling reactions of 6-iodo-9-[2,5-bis-O-(tert-butyldimethylsilyl)-3-deoxy-β-D-ribofuranosyl]purine with the corresponding organometallics followed by deprotection by (HF)3·Et3N. None of the title 3'-deoxyribonucleoside showed any cytostatic activity or anti-HCV effect in replicon assay.
A cosmology with variable c
Authors: Shojaie H , Farhoudi M
Published: November 2006

A new varying-c cosmological model, constructed using two additional assumptions, which was introduced in our previous work, is briefly reviewed and the dynamic equation of the model is derived distinctly from a semi-Newtonian approach. The results of this model, using a [Formula: see text] term and an extra energy-momentum tensor, are considered separately. It is shown that the Universe began from a hot Big Bang and expands forever with a constant deceleration parameter regardless of its curvature. Finally, the age, the radius, and the energy content of the Universe are estimated and some discussion about the type of the geometry of the Universe is provided.

PACS Nos.: 98.80.Bp, 98.80.Jk
Growth and development of ponderosa pine on sites of contrasting productivities: relative importance of stand density and shrub competition effects
Authors: Zhang Jianwei , Oliver William W , Busse Matt D
Published: November 2006

Effects of stand density and shrub competition on growth and development were compared across a gradient of study sites. Challenge, the most productive site, is located in the foothills of the Sierra Nevada, northern California. Pringle Falls is of intermediate productivity in the rain shadow of the central Oregon Cascades. Trough Springs Ridge is the poorest site with minimally developed soils in California's North Coast Range. Treatments included a minimum of four stand densities, from 150 to 2700 trees·ha–1, in combination with at least no or full shrub removal. Challenge produced almost twice as much tree volume as Pringle Falls, and about three times the volume of Trough Springs Ridge. Regardless of site quality, growth was significantly greater in full shrub removal plots for stand densities <2000 trees·ha–1. After 26–36 years, stand volumes were 25–67 m3·ha–1 (11%–38%) greater at Challenge, 30–33 m3·ha–1 (25%–52%) greater at Pringle Falls, and 27–41 m3·ha–1 (115%–326%) greater at Trough Springs Ridge when shrubs were removed. Periodic volume growth declined substantially during the last 10 years at Challenge and Pringle Falls, regardless of treatment, because of confounding effects of mortality, drought, inter-tree competition, and insect defoliation. Further, the importance of shrub control on growth increment was not evident during the last 10 years at both sites, as tree–shrub competition likely switched to tree–tree competition. On the low quality site, shrub control is critical for stand development.
Taking charge in forest vegetation management
Authors: Newton Michael
Published: November 2006

Management of forest vegetation is the determinant of goal achievement in forestry enterprises. Cultural patterns with a limited long-term outlook have led to large-scale deforestation in many parts of the world, but have left many examples of what is possible with forest management in many of those places, as well as in developed countries. Some of these examples indicate that managed forests, especially plantations, may eventually produce a surplus of wood for world markets. This is of central importance in view of the withdrawal of many productive regions from timber harvest to meet noncommodity demands. Development of intensive vegetation management to meet specific objectives on fewer hectares will require research in both basic processes and applications of technology specifically adapted for management professionals. Because of their tendency to seek predominantly basic research funding, public research organizations often lack focus on managed ecosystems, hence findings are difficult to apply or to use for education of both lay and professional audiences. While modern forest vegetation management methods have led to achievement of many yield and habitat goals, less certain is acceptance of modern ecosystem management methodology by general publics. Cultural challenges must be met in primary and secondary schools and graduate and undergraduate university programs. Interaction with the media is also of fundamental importance for ensuring a level of public understanding compatible with long-term advancements in forest ecosystem management.
How to shift unproductive Kalmia angustifolia – Rhododendron groenlandicum heath to productive conifer plantation
Authors: Thiffault Nelson , Jobidon Robert
Published: November 2006

Conifer-regeneration failure is often observed on sites invaded by ericaceous shrubs. In northeastern Quebec, Canada, these sites are frequently characterized by dense Kalmia angustifolia L. – Rhododendron groenlandicum (Oeder) K.A. Kron & Judd cover. Such failures are potential consequences of nutrient limitation, allelopathy, or low soil temperatures. Conversion of productive forests into heaths poses a threat to the maintenance of forest productivity and biodiversity. We evaluated scarification, spot fertilization, and increased seedling foliar N concentration as treatments to promote planted black spruce (Picea mariana (Mill.) BSP) seedling survival and growth. We measured seedling, vegetation, and soil responses to the treatments for 5 years following planting. Scarification had positive impacts on seedling growth: the differences between scarified and unscarified plots increased over time, and double-pass scarification proved slightly more effective than a single-pass treatment. Responses to scarification were enhanced when seedlings were fertilized. A slow-release fertilizer with micronutrients proved slightly more effective than the 26N–12P–6K formulation; the latter also induced higher mortality than the former or no fertilizer. Gains due to increased N concentrations based on nursery practices were significant but short-lived. Our results demonstrate how silviculture and nursery practices can be used for resetting the secondary succession where ecosystem retrogression is observed following K. angustifolia – R. groenlandicum invasion.
Effects of mulching and insecticides on establishment and growth of Norway spruce
Authors: Johansson Karin , Örlander Göran , Nilsson Urban
Published: November 2006

Establishment of Norway spruce (Picea abies (L.) Karst.) seedlings is often restricted by competition from vegetation, drought, and damage by pine weevils. In this study, effects of mulching on these factors were investigated. Norway spruce seedlings were planted on fresh and 1-year-old clearcuts treated with mulch on three sites in southern Sweden. Mulch was made of slash from the old stand and applied on whole blocks at three different depths: 0, 10, and 20 cm. Both insecticide-treated and untreated seedlings were planted. By reducing the competing vegetation and improving soil moisture and mineralization, mulching created a favorable growth environment. Mulching significantly improved growth in terms of height, diameter, and volume of the seedlings. Growth continued to increase over time in mulched treatments, probably as an effect of increased nutrient availability. The 20 cm mulch layer generated the greatest increase in growth throughout the 10-year experimental period. Soil moisture was preserved under the isolating mulch layer and during periods of drought soil water potential was significantly higher in mulched treatments. After 2 years, percent cover of competing vegetation was 50%–60% without mulch and 10%–20% with a mulch depth of 20 cm. Insecticide-treated seedlings achieved a survival rate close to 100% in all mulching treatments, whereas survival among untreated seedlings was only 40% on some clearcuts. Mulching alone did not affect survival or abundance of pine weevils.
Twelfth-year response of Douglas-fir to area of weed control and herbaceous versus woody weed control treatments
Authors: Rose Robin , Rosner Lee S , Ketchum J Scott
Published: November 2006

Coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. menziesii) response to eight weed control treatments was measured 12 years after planting at two Oregon sites. Treatments included four areas of weed control around individual trees (0.375, 1.49, 3.35, and 5.95 m2), no weed control (check), total vegetation control, control of herbaceous competition only, or control of woody competition only. Douglas-fir growth and woody-species invasion differed between the Coast Range site (Summit) and the Cascade Range foothills site (Marcola). Woody species reinvasion was more intense at Summit, with Douglas-fir cumulative mortality in the check treatment reaching 23% in year 12. Woody-only control improved Douglas-fir growth at Summit but had no significant effect on growth at Marcola. Total vegetation control had a profound effect on stem volume growth 12 years after planting. At Summit, total vegetation control resulted in a 355% increase in volume per hectare relative to the check. At Marcola the increase was only 63%. At Summit, growth increased with each increase in area of weed control, whereas at Marcola growth increased with increasing area of weed control up to 3.35 m2 of control. Results suggest that much of the gain in volume growth attributable to weed control may be lost if weed-control treatments are not highly efficacious. The differential response to woody control indicates that its benefit at a given site is strongly related to the abundance of competitive hardwood species, which may be predicted from the preharvest stand structure and vegetation community.
Evaluation of funnel traps for estimating tree mortality and associated population phase of spruce beetle in Utah
Authors: Hansen E Matthew , Bentz Barbara J , Munson A Steven , Vandygriff James C , Turner David L
Published: November 2006

Although funnel traps are routinely used to manage bark beetles, little is known regarding the relationship between trap captures and tree mortality near the trap. We conducted a 4 year study in Utah to examine the correlation between funnel-trap captures of spruce beetle (Dendroctonus rufipennis Kirby) and mortality of Engelmann spruce (Picea engelmannii Parry ex Engelm.) within a 10 ha block of the trap. Using recursive partitioning tree analyses, rules were developed for predicting spruce mortality and associated levels of beetle population phase (endemic or epidemic), in the current year and subsequent year, for a given level of trap captures. Although model predictions of infested-stem counts had large variances, our results suggest that funnel-trap captures can be reliably used to estimate relative levels of tree mortality, expressed as spruce beetle population phase. Classification-tree analyses indicate that captures of ~842 spruce beetles during a season (late May to mid-August) from a single funnel trap represent a threshold between endemic (<2 mass-attacked stems/ha) and epidemic conditions (≥2 mass-attacked stems/ha) for either the current or the subsequent year relative to deployment of the funnel trap. Likewise, a lack of infested hosts within 10 m of a funnel trap, also known as spillover, was associated with endemic conditions, whereas trees attacked near the trap correlated with epidemic conditions.
The applicability of national forest inventories for estimating forest damage outbreaks – Experiences from a Gremmeniella outbreak in Sweden
Authors: Wulff Sören , Hansson Per , Witzell Jesper
Published: November 2006

The design of the Swedish National Forest Inventory as well as the National Forest Damage Inventory is a sparse sample of systematically allocated plots. In this study data were combined from these two independent inventories to estimate geographical distribution, area extension, and disease development of a Gremmeniella abietina (Lagerb.) Morelet epidemic. For the combined data the standard error for estimated total area of affected Scots pine (Pinus sylvestris L.) and lodgepole pine (Pinus contorta Dougl. ex Loud. var.latifolia Engelm.) forests was about 11%. Assessments of the proportion of pine trees with fresh shoot blight infection shows that changes larger than 1% are significantly (p < 0.05) estimated. By testing in pairwise cross inventory, it was shown that the accuracy of the assessment of total shoot blight symptoms was fairly good in 2001–2002, with a κ statistic of 0.59–0.61. Severely damaged trees were identified with an agreement of κ = 0.81. The total area of pine forest both slightly and severely affected by G. abietina during 2001–2003 was estimated to be 484 000 ha. Three geographically separate damage centres were distinguished. Thus, despite a relatively sparse sample plot density, the national forest inventories have good potential for estimating the geographical distribution, areal extent, and dispersal of extensive damage outbreak. Results are dependent on the inventories being carried out with an accurate identification of target objects.
Long-term thinning effects on the forest floor and the foliar nutrient status of Norway spruce stands in the Belgian Ardennes
Authors: Jonard Mathieu , Misson Laurent , Ponette Quentin
Published: November 2006

The long-term impact (30 years) of three contrasting thinning programs (unthinned, moderately thinned, and heavily thinned) on selected forest-floor properties and on the foliar nutrient status of Norway spruce (Picea abies (L.) Karst.) stands (46, 50, and 67 years old) was evaluated at three sites on acid soils in the Belgian Ardennes. Sampling involved needles (current-year, 1-year-old, and recently fallen) and soil organic layers (OL, OF, OH, OA). For all samples, dry mass and element concentrations (C, N, P, Ca, Mg, K, Na, Mn, Al, Fe) were determined. Linear mixed models were used to analyze these data and showed that forest-floor mass was negatively affected by thinning (p = 0.0003) and that the N concentration in the forest floor increased with thinning intensity (p = 0.0008), while its Mn concentration decreased (p < 0.0001). The N, P, and K concentrations in the current-year needles were decreased by thinning (p < 0.05), while the Ca, Mg, and Na concentrations were not affected. We hypothesize that thinning negatively affected N, P, and K nutrition by removing the nutrients contained in the thinned trees and by decreasing the forest-floor thickness, thus reducing its nutrient contents and its ability to support root growth.
Applications of modeling to vegetation management
Authors: Mason Euan G , Dzierzon Helge
Published: November 2006

A review of modeling applied to vegetation management shows that these models range in resolution from simple yield equations to complex representations of processes affecting growth and competition for light, water, and nutrients. The latter models inform scientists and managers about mechanisms involved, while the former are more likely to be applied by managers to estimate effects of competition. Six generic model forms were identified. Models may be further categorized by whether they focus on weed population dynamics or on processes directly affecting growth of crop plants. There is scope for these aspects of vegetation modeling to be combined. Extremely complex models are scientifically satisfying as repositories of knowledge, but they tend to be excessively parametarized and recursive. Models with many parameters are difficult to fit to specific situations because they are ambiguous; the same overall estimates of growth can be achieved in a variety of ways. In addition, their recursive nature leads to compounded errors. Simple growth and yield models, by contrast, are usually very efficient and accurate at estimating local estimates of growth, but they are inadequately sensitive to the variety of site and site management practices that vegetation managers wish to represent. A new kind of hybrid model is proposed that combines the efficiency of forest mensurational techniques with sufficient complexity to represent the results of scientific studies associated with vegetation management for use by managers.
Towards a nationwide growth and yield model for radiata pine plantations in New Zealand
Authors: Dzierzon Helge , Mason Euan G
Published: November 2006

A study was designed to evaluate a forest stand modelling approach for management use that can be applied across a wide range of site types and climatic regions. Radiata pine (Pinus radiata D. Don) plantations dominate New Zealand's forestry sector; thus, this species was the subject of the study. A major goal of the study was to compare different modelling approaches, which combine simplicity and site sensitivity. Therefore, two general modelling approaches were investigated: a site-stratified and a physiological hybrid approach. Both approaches were implemented by using difference equations. The investigation revealed more consistently improved fits of stratified models, although the fitting process showed potential bias of parameter estimates. On the other hand, the hybrid approach resulted in promising results, especially for stand basal area. The introduction of climate and site variables showed less improvement for mean top height than for basal area. The application of the model on regional scales resulted in an improved prediction in a region with plenty of growth limitations, but less precise results in a region where growth was limited primarily by light and temperature. In the whole, results of the hybrid approach will encourage further studies that incorporate more sophisticated approaches for depicting physiological processes.
Calcium addition at the Hubbard Brook Experimental Forest reduced winter injury to red spruce in a high-injury year
Authors: Hawley Gary J , Schaberg Paul G , Eagar Christopher , Borer Catherine H
Published: November 2006

Laboratory experiments have verified that acid-deposition-induced calcium (Ca) leaching reduces the foliar cold tolerance of red spruce (Picea rubens Sarg.) current-year foliage, increasing the risk of winter injury and crown deterioration. However, to date no studies have shown that ambient losses in soil Ca have resulted in increased winter injury in the field. In 2003, a year of severe region-wide winter injury to red spruce, we measured the nutrition and winter injury of current-year foliage and bud mortality for red spruce on two watersheds at the Hubbard Brook Experimental Forest in Thornton, New Hampshire: (1) a reference watershed that has undergone considerable Ca loss attributed to acid-deposition-induced leaching and (2) a watershed that was fertilized with CaSiO3in 1999 to replace lost Ca. For all crown classes combined, winter injury was significantly greater (P = 0.05) for red spruce on the reference watershed than for spruce on the Ca-addition watershed. Differences in foliar injury were particularly evident for dominant and codominant trees. For these crown classes, red spruce on the reference watershed lost about 75% of their current-year foliage to winter injury, about three times more than foliar losses for the Ca-addition watershed (P = 0.01). Patterns of bud mortality followed that of foliar injury. The only difference in foliar cation nutrition detected was a significantly greater concentration of Ca in red spruce foliage from the Ca-addition watershed relative to spruce from the reference watershed (P = 0.001). Differences in Ca concentration, foliar winter injury, and bud mortality that occurred coincident with watershed Ca treatment provide the first evidence that ambient Ca depletion is associated with elevated winter injury of red spruce trees.
ON THE DYNAMICAL FLUCTUATION OF SINGLE-EVENT TRANSVERSE MOMENTUM DISTRIBUTION
Authors: XU MINGMEI , LIU LIANSHOU
Published: November 2006

Assuming that the single-event transverse momentum distribution fluctuates event by event according to a distribution functional, we derive analytical expressions for both the variance of event-wise mean transverse momentum and the two-particle transverse momentum correlation. The relation between these two is discussed. An evaluation of statistical fluctuation is given. An exponential form for the single-event transverse momentum distribution is taken as an example to demonstrate our method for extracting event-by-event dynamical fluctuation of single-event transverse momentum distribution from experimental data.
ULTRASOFT QUARK DAMPING IN HOT QCD
Authors: ABADA A. , DAIRA-AIFA N. , BOUAKAZ K.
Published: November 2006

We determine the quark damping rates in the context of next-to-leading order hard-thermal-loop summed perturbation of high-temperature QCD where weak coupling is assumed. The quarks are ultrasoft. Three types of divergent behavior are encountered: infrared, light-cone and at specific points determined by the gluon energies. The infrared divergence persists and is logarithmic whereas the two others are circumvented.
NONCOMMUTATIVITY FROM THE SYMPLECTIC POINT OF VIEW
Authors: ABREU E. M. C. , NEVES C. , OLIVEIRA W.
Published: November 2006

The great deal in noncommutative (NC) field theories started when it was noted that NC spaces naturally arise in string theory with a constant background magnetic field in the presence of D-branes. In this work we explore how NC geometry can be introduced into a commutative field theory besides the usual introduction of the Moyal product. We propose a nonperturbative systematic new way to introduce NC geometry into commutative systems, based mainly on the symplectic approach. Further, as example, this formalism describes precisely how to obtain a Lagrangian description for the NC version of some systems reproducing well-known theories.
SPECTROSCOPY OF LIGHT HADRONS ON ANISOTROPIC LATTICES
Authors: LEE FRANK X.
Published: November 2006

The mass spectrum of spin-1/2 baryons in both parity channels is computed using the methods of lattice QCD in the quenched approximation. An anisotropic action with anisotropy as/at = 3 is employed, using tree-level coefficients with tadpole improvement. Clear splittings from the nucleon ground state are observed with smeared operators and 500 configurations. Methods for extracting the first excited states are investigated. Using the quark mass dependence of the masses, qualitative comparisons are made with previous calculations and experiment.
GENE EXPRESSION DATA ANALYSIS IN SUBTYPES OF OVARIAN CANCER USING COVARIANCE ANALYSIS
Authors: OLMAN VICTOR , HICKS CHINDO , WANG PENG , XU YING
Published: November 2006

Many studies have used microarray technology to identify the molecular signatures of human cancer, yet the critical features of these often unmanageably large set of signatures remain elusive. We have investigated co-expression pattern in four subtypes of ovarian cancer from 104 cancer patients using covariance analysis, treating each subtype of ovarian cancer as a distinct disease entity. We sought gene pairs that were transcriptionally co-expressed in one or multiple subtypes of ovarian cancer, establishing a high confidence network of 87 genes interconnected by significantly high co-expression links that were observed in at least two subtypes of ovarian cancer. We have shown that certain groups of co-expressed gene pairs are cancer subtype specific, through demonstrating significant differences in co-expression patterns of gene pairs between subtypes of ovarian cancer. In addition, we identified a set of 24 genes that classified patients into specific cancer subtypes with a misclassification error rate of less than 5%. Our findings illustrate how large public microarray gene expression datasets could be exploited for identification of cancer subtype specific molecular signatures, and how to classify cancer patients into specific subtypes of cancer using gene expression profiles.
RECOGNITION OF TRANSMEMBRANE SEGMENTS IN PROTEINS: REVIEW AND CONSISTENCY-BASED BENCHMARKING OF INTERNET SERVERS
Authors: SADOVSKAYA NATALIYA S. , SUTORMIN ROMAN A. , GELFAND MIKHAIL S.
Published: November 2006

Membrane proteins perform a number of crucial functions as transporters, receptors, and components of enzyme complexes. Identification of membrane proteins and prediction of their topology is thus an important part of genome annotation. We present here an overview of transmembrane segments in protein sequences, summarize data from large-scale genome studies, and report results of benchmarking of several popular internet servers.
RNALL: AN EFFICIENT ALGORITHM FOR PREDICTING RNA LOCAL SECONDARY STRUCTURAL LANDSCAPE IN GENOMES
Authors: WAN XIU-FENG , LIN GUOHUI , XU DONG
Published: November 2006

Background: The information of RNA local secondary structures (LSSs) can help retrieve biologically important motifs and study functions of RNA molecules. Most of the current RNA secondary structure prediction tools are not suitable for RNA LSS prediction on the genome scale due to high computational complexity.

Methods: We developed a new computer package Rnall based on a dynamic programming technique, which scans an RNA sequence with a sliding window and extracts all RNA LSSs with sizes no larger than the window size using the nearest neighbor thermodynamic parameters. The worst case running time of Rnall is O(W3L), where W is the window size and L is the query sequence length. In practice we observed a running time of O(W2L). We further introduced the concept of energy landscape for illustrating RNA LSS, which may facilitate RNA motif mining on the genomic scale.

Results: Rnall shows better prediction accuracy than two other prediction tools Lfold and Quickfold. Rnall is also applied to scan for RNA LSSs in three genomes, and the prediction maps well with known RNA motifs.

Conclusions: Rnall is designed for RNA LSS prediction and together with the energy landscape, it has unique features that could be used for RNA structural motif mining. Rnall is freely available for download at or .
Delivery of Health Services to Migrant and Seasonal Farmworkers
Authors: Arcury Thomas A. , Quandt Sara A.
Published: November 2006

Farmworkers are low-paid, uninsured employees in an extremely hazardous industry, and they provide an essential service for U.S. society. This review evaluates the delivery of health services to farmworkers. It describes the farmworker population in the United States, noting characteristics (e.g., migratory and immigration status) that limit their access to and utilization of health services. It describes the health services needs of this population, including occupational health, mental health, oral health, and chronic disease treatment. Cultural, structural, legal, financial, and geographic barriers to health services utilization are described. Existing research on health services utilization among farmworkers is discussed. Programs that have been developed to address the barriers to health services utilization among farmworkers are reviewed. Finally, research needed to improve knowledge of farmworker health services utilization is suggested. These research needs include formal evaluations of existing programs and basic research to characterize the health services utilization patterns of farmworkers.
Beryllium: A Modern Industrial Hazard
Authors: Kreiss Kathleen , Day Gregory A. , Schuler Christine R.
Published: November 2006

Beryllium exposure can cause a granulomatous lung disease in workers who develop a lymphocyte-mediated sensitization to the metal. Workers in diverse industries are at risk because beryllium's properties are critical to nuclear, aerospace, telecommunications, electronic, metal alloy, biomedical, and semiconductor industries. The occupational air concentration standard's failure to protect beryllium workers is driving many scientific and occupational health advances. These developments include study of bioavailability of different physicochemical forms of beryllium, medical surveillance to show effectiveness of skin protection in preventing sensitization in high-risk processes, gene-environment interaction, transgenic mice for use in experimental research, and risk-based management of industrial exposures in the absence of effective exposure-response information. Beryllium sensitization and disease prevention are paradigms for much broader public health action in both occupational and general population settings.
Community Factors in the Development of Antibiotic Resistance
Authors: Larson Elaine
Published: November 2006

The global impact of antibiotic resistance is potentially devastating, threatening to set back progress against certain infectious diseases to the preantibiotic era. Although most antibiotic-resistant bacteria originally emerged in hospitals, drug-resistant strains are becoming more common in the community. Factors that facilitate the development of resistance within the community can be categorized as behavioral or environmental/policy. Behavioral factors include inappropriate use of antibiotics and ineffective infection control and hygiene practices. Environmental/policy factors include the continued use of antibiotics in agriculture and the lack of new drug development. A multifaceted approach that includes behavioral strategies in the community and the political will to make difficult regulatory decisions will help to minimize the problem of antimicrobial resistance globally.
Expression and function of periostin-like factor in vascular smooth muscle cells
Authors: Litvin Judith , Chen Xing , Keleman Sheri , Zhu Shimei , Autieri Michael
Published: November 2006

In injured blood vessels activated vascular smooth muscle cells (VSMCs) migrate from the media to the intima, proliferate and synthesize matrix proteins. This results in occlusion of the lumen and detrimental clinical manifestations. We have identified a novel isoform of the periostin family of proteins referred to as periostin-like factor (PLF). PLF expression in VSMCs was increased following treatment with mitogenic compounds, suggesting that PLF plays a role in VSMC activation. Correspondingly, proliferation of the cells was significantly reduced with anti-PLF antibody treatment. PLF expression increased VSMC migration, an essential cellular process leading to vascular restenosis after injury. PLF protein was localized to neointimal VSMC of rat and swine balloon angioplasty injured arteries, as well as in human arteries with transplant restenosis, supporting the hypothesis that PLF is involved in VSMC activation and vascular proliferative diseases. Taken together, these data suggest a role for PLF in the regulation of vascular proliferative disease.
Carrageenan induces interleukin-8 production through distinct Bcl10 pathway in normal human colonic epithelial cells
Authors: Borthakur Alip , Bhattacharyya Sumit , Dudeja Pradeep K. , Tobacman Joanne K.
Published: November 2006

Carrageenan is a high molecular weight sulfated polygalactan used to improve the texture of commercial food products. Its use increased markedly during the last half century, although carrageenan is known to induce inflammation in rheumatological models and in intestinal models of colitis. We performed studies to determine its direct effects on human intestinal cells, including normal human intestinal epithelial cells from colonic surgeries, the normal intestinal epithelial cell line NCM460, and normal rat ileal epithelial cells. Cells were treated with high molecular weight λ-carrageenan at a concentration of 1 μg/ml for 1–96 h. IL-8, IL-8 promoter activity, total and nuclear NF-κB, IκBα, phospho-IκBα, and Bcl10 were assessed by immunohistochemistry, Western blot, ELISA, and cDNA microarray. Increased Bcl10, nuclear and cytoplasmic NF-κB, IL-8 promoter activation, and IL-8 secretion were detected following carrageenan exposure. Knockdown of Bcl10 by siRNA markedly reduced the increase in IL-8 that followed carrageenan exposure in the NCM460 cells. These results show, for the first time, that exposure of human intestinal epithelial cells to carrageenan triggers a distinct inflammatory pathway via activation of Bcl10 with NF-κB activation and upregulation of IL-8 secretion. Since Bcl10 contains a caspase-recruitment domain, similar to that found in NOD2/CARD15 and associated with genetic predisposition to Crohn's disease, the study findings may represent a link between genetic and environmental etiologies of inflammatory bowel disease. Because of the high use of carrageenan as a food additive in the diet, the findings may have clinical significance.
Long-term docosahexaenoic acid therapy in a congenic murine model of cystic fibrosis
Authors: Beharry Satti , Ackerley Cameron , Corey Mary , Kent Geraldine , Heng Yew-Meng , Christensen Hilary , Luk Catherine , Yantiss Rhonda K. , Nasser Imad A. , Zaman Munir , Freedman Steven D. , Durie Peter R.
Published: November 2006

We used a congenic C57Bl/6J cystic fibrosis transmembrane conductance regulator ( Cftr)−/− mouse model, which develops cystic fibrosis (CF)-like pathology in all organs, to evaluate the short- and long-term therapeutic effects of dietary docosahexaenoic acid (DHA). Thirty-day-old Cftr−/− mice and wild-type littermates were randomized to receive a liquid diet with or without DHA (40 mg/day). Animals were killed for histological and lipid analysis after 7, 30, and 60 days of therapy. DHA had no significant therapeutic or harmful effect on the lung, pancreas, or ileum of the Cftr−/− mice or their wild-type littermates. In contrast, dietary DHA resulted in highly significant amelioration of the severity of liver disease in the Cftr−/− mice, primarily a reduction in the degree of peri-portal inflammation. Additionally, these detailed measurements confirm our previous findings that Cftr−/− mice have significant alterations in the pancreas (except external acinar diameter), ileum, liver, lung, and salivary (except sublingual) glands at all ages compared with their age-matched wild-type littermates. In conclusion, inhibition of cytokines and/or eicosanoid metabolism and release of endogenous inhibitors of inflammation by DHA may account for the anti-inflammatory effects in the liver of this congenic murine model of CF. The potential therapeutic benefits of DHA in severe CF-associated liver disease remain to be explored.
Ts65Dn, a Mouse Model of Down Syndrome, Exhibits Increased GABAB-Induced Potassium Current
Authors: Best Tyler K. , Siarey Richard J. , Galdzicki Zygmunt
Published: November 2006

Down syndrome (DS) is the most common nonheritable cause of mental retardation. DS is the result of the presence of an extra chromosome 21 and its phenotype may be a consequence of overexpressed genes from that chromosome. One such gene is Kcnj6/Girk2, which encodes the G-protein-coupled inward rectifying potassium channel subunit 2 (GIRK2). We have recently shown that the DS mouse model, Ts65Dn, overexpresses GIRK2 throughout the brain and in particular the hippocampus. Here we report that this overexpression leads to a significant increase (∼2-fold) in GABAB-mediated GIRK current in primary cultured hippocampal neurons. The dose response curves for peak and steady-state GIRK current density is significantly shifted left toward lower concentrations of baclofen in Ts65Dn neurons compared with diploid controls, consistent with increased functional expression of GIRK channels. Stationary fluctuation analysis of baclofen-induced GIRK current from Ts65Dn neurons indicated no significant change in single-channel conductance compared with diploid. However, significant increases in GIRK channel density was found in Ts65Dn neurons. In normalized baclofen-induced GIRK current and GIRK current kinetics no difference was found between diploid and Ts65Dn neurons, which suggests unimpaired mechanisms of interaction between GIRK channel and GABABreceptor. These results indicate that increased expression of GIRK2 containing channels have functional consequences that likely affect the balance between excitatory and inhibitory neuronal transmission.
Trabeculectomy with Mitomycin C for Treatment of Neovascular Glaucoma in Diabetic Patients
Authors: Kiuchi Yoshiaki , Sugimoto Reiko , Nakae Kazuto , Saito Yoshihiro , Ito Shigeo
Published: November 2006

Background: To assess the efficacy and to determine the risk factors of trabeculectomy with mitomycin C (MMC) in eyes with neovascular glaucoma (NVG) secondary to diabetic retinopathy. Methods: Kaplan-Meier survival analysis of the surgical outcome was performed on 35 eyes with NVG. Age, extent of peripheral anterior synechia, surgical history (cataract, glaucoma, vitrectomy), and concurrent retinal cryotherapy were evaluated to determine factors influencing the surgical outcome. The main criterion for success was a postoperative intraocular pressure (IOP) of ≤21 mm Hg. Results: The cumulative probability of success was 67.0% at 1 year and 61.8% after 2 to 3 years. The surgical outcome was significantly better in patients without a previous vitrectomy (p = 0.03). Extensive preoperative peripheral anterior synechia was also a risk factor for surgical failure (p = 0.013). Conclusions: Trabeculectomy with MMC can effectively reduce the elevated IOP associated with NVG. The extent of peripheral anterior synechia and a history of vitrectomy are significant negative predictors of surgical outcome.
Amniotic Membrane Corrects Surgically Induced Astigmatism
Authors: Zhou Xingtao , Rho Sae Heun , Yoo Kyung Won , Ahn Hee Bae , Kim Tae Hyun , Yoo Young Hyun , Kim Jae Chan , Park Woo Chan
Published: November 2006

Human amniotic membrane (AM) has been widely used for the reconstruction of ocular surface. We conducted this study to investigate whether AM shows efficacy in maintaining the correction of astigmatism or not. We performed photoastigmatic refractive keratectomy (PARK) on rabbits and grafted AM on the cornea. The effect of AM on the degree of astigmatism was evaluated by topography and cycloplegic refraction. As will be shown, AM did not show any efficacy in maintaining the correction of astigmatism. On the contrary, AM not only eliminated PARK-induced astigmatism but prevented surgically induced astigmatism. We suggest that AM could be a useful tool for controlling the astigmatism induced by laser refractive surgery. Further clinical study is still left to be elucidated.
Rickets with Dorfman-Chanarin Syndrome
Authors: Taskin Erdal , Akarsu Saadet , Aygun A. Denizmen , Ozlu Ferda , Kilic Mehmet
Published: November 2006

Background: Dorfman-Chanarin syndrome is a rare, autosomal recessive, inherited, lipid storage disease. It is characterized by nonbullous congenital ichthyosiform erythroderma, leukocyte vacuoles and variable involvement of the liver, muscles and central nervous system, due to errors of triacylglycerol metabolism. To date only 32 cases of this syndrome have been described worldwide. Aims: To report the case of a boy with Dorfman-Chanarin syndrome with rickets. Case Report: A boy of Turkish origin was born of a nonconsanguineous marriage after an uncomplicated perinatal period. On examination the patient had failure to thrive, diffuse erythroderma and ichthyosis and clinical features suggesting rickets. A light-microscopic examination of peripheral smear revealed vacuolated leukocytes typical of Jordans’ anomaly. Lipid analysis showed an increase in triacylglycerol and very low density lipoprotein. A radiographic study of the wrist revealed rickets. Conclusion: The clinical progression in these patients ranges from mild to fatal. We believe that patients with ichthyosis should be evaluated bearing in mind the possibility of Dorfman-Chanarin syndrome. This may increase the number of reported Dorfman-Chanarin syndrome cases, and the pathogenesis and progression of the disease will become clearer.